Citrus Sinensis ID: 008442

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-----
Protein Sequence
MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLPESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKDSSGERAPTEQAQSHQQTGNAGTSASKESSIETSKQSRGRGDSVQLKGKNTFAVPRNVRPLGFPAIKPKTEEGEDLKPKSNDEFRKMFIKKD
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHcccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHccccccHHHHcHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccHHHHHcccccccHHHHHHHHcccccccEEEEEEccccccccEEEEEEEccHHHHHHHHHHcccEEccEEEEEEEcccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHcccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHccHHHHHHcccHHHHcccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHcccEEEEEEEEccccccccEEEEEEEccHHHHHHHHHHcccEEcccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccccccccccccHHHHHHHHHccc
Coil and Loop (DISEMBL)
MCNARAHLEEQisrqdlsdsEKFQQYMIYLKYeqssgdpgrVQLLYERaitdfpvssdlWLDYTQYLDKTLKVGNVVRDVYSratkncpwvgELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCyskrftgtgseDICHAWLRFEreygtledfdhsvqKVTPRLEELRLFRsqqeskslpesadqkEHSVKKtgrekrksdsnisyeqspakrqkhapqkpkkvhdkEKRQVQNLAeenegretkqtveeqpkkqpikdavpgrtkgftDECTAFLSNINLKATYEDLRRFFsdvggvssirilhdkftgksrglayvdfIDDEHLAAAVAKNKQMFLGKKlsiarsnpkqrkdssgerapteqaqshqqtgnagtsaskessietskqsrgrgdsvqlkgkntfavprnvrplgfpaikpkteegedlkpksnDEFRKMFIKKD
Flexible Loop (DISEMBL)
mcnarahleeqisrqdlsdsEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYsratkncpwvgeLWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKrftgtgseDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSqqeskslpesadqkehsvkktgrekrksdsnisyeqspakrqkhapqkpkkvhdkekrqvqnlaeenegretkqtveeqpkkqpikdavpgrtkGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMflgkklsiarsnpkqrkdssgerapteqaqshqqtgnagtsaskessietskqsrgrgdsvqlkgkntfavprnvrplgfpaikpkteegedlkpksndefrkmfikkd
Low Complexity Region (SEG)
MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVrsllslersraseeeISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLPESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKDSSGERAPTEQAQSHQQTGNAGTSASKESSIETSKQSRGRGDSVQLKGKNTFAVPRNVRPLGFPAIKPKTEEGEDLKPKSNDEFRKMFIKKD
Disordered region (IsUnstruct)
**********************FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER******EISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV**********************************************************************************************************GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLG**********************************************************************************************************
Disordered Region (DISOPRED)
*CNARAHLEEQI********EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLPESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDK******************************************DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKL**********************************************************************************************FRKMFIKK*
Disordered Region (DISEMBL)
****************LSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFR**************************************************************************************KDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIA*****************************************************LKGKNTFAVPRNVRPLGFPAIKPKTEEGEDLKPKSNDEFRKMFIKKD
Disordered Region (DISPRO)
MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESK*******************************************************************************************TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNP******************************************************TFAVPR*******************************FI***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLPESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVxxxxxxxxxxxxxxxxxxxxxQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKDSSGERAPTEQAQSHQQTGNAGTSASKESSIETSKQSRGRGDSVQLKGKNTFAVPRNVRPLGFPAIKPKTEEGEDLKPKSNDEFRKMFIKKD
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	565	2.2.26 [Sep-21-2011]
Q15020	963	Squamous cell carcinoma a	yes	no	0.784	0.460	0.271	4e-43
Q5REG1	981	Squamous cell carcinoma a	yes	no	0.784	0.451	0.271	1e-42
Q9JLI8	962	Squamous cell carcinoma a	yes	no	0.773	0.454	0.272	5e-42
Q9W4D2	941	RNA-binding protein 4F OS	yes	no	0.771	0.463	0.211	2e-11
Q9USY2	1014	Uncharacterized RNA-bindi	yes	no	0.681	0.379	0.227	1e-09
Q9DDY9	296	Polyadenylate-binding pro	N/A	no	0.132	0.253	0.333	3e-08
Q4PB37	781	Pre-mRNA-splicing factor	N/A	no	0.421	0.304	0.257	3e-08
Q6TY21	218	Embryonic polyadenylate-b	N/A	no	0.132	0.344	0.333	4e-08
Q7ZXB8	295	Polyadenylate-binding pro	N/A	no	0.132	0.254	0.333	5e-08
Q804A5	218	Embryonic polyadenylate-b	N/A	no	0.132	0.344	0.32	1e-07

>sp|Q15020|SART3_HUMAN Squamous cell carcinoma antigen recognized by T-cells 3 OS=Homo sapiens GN=SART3 PE=1 SV=1

 Score =  176 bits (447), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 130/479 (27%), Positives = 229/479 (47%), Gaps = 36/479 (7%)

Query: 18  SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVV 77
           +++ +  +Y  Y+ +E   GDP R+QL++ERA+ +  +  DLW+ Y+QYLD+ LKV ++V
Sbjct: 305 AEAPRLAEYQAYIDFEMKIGDPARIQLIFERALVENCLVPDLWIRYSQYLDRQLKVKDLV 364

Query: 78  RDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTR 137
             V++RA +NCPW   LW R LL++ER     + IS  FEK+L   F    +Y++++   
Sbjct: 365 LSVHNRAIRNCPWTVALWSRYLLAMERHGVDHQVISVTFEKALNAGFIQATDYVEIWQAY 424

Query: 138 IDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQM-----KNTDGLLRLYAYWAHLE 192
           +D LRRR+ F  +    L+   +R  F RA +YL +++     ++ D    +   WA +E
Sbjct: 425 LDYLRRRVDFKQDSSKELEE--LRAAFTRALEYLKQEVEERFNESGDPSCVIMQNWARIE 482

Query: 193 QSMGKDMVSARGVWERLLKISGA-MLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGT 251
             +  +M  AR +W+ ++    A     W  Y ++E         R    R  + + T  
Sbjct: 483 ARLCNNMQKARELWDSIMTRGNAKYANMWLEYYNLERAHGDTQHCRKALHR--AVQCTSD 540

Query: 252 GSEDICHAWLRFEREYGTLEDFDHSVQKVTPRL---EELRLFRSQQESKSL---PESADQ 305
             E +C   L  ER  G+LED+D +VQK   RL    E R+  +++E+  +    E A+Q
Sbjct: 541 YPEHVCEVLLTMERTEGSLEDWDIAVQKTETRLARVNEQRMKAAEKEAALVQQEEEKAEQ 600

Query: 306 KEHSVKKT----------GREKRKSDSNISY------EQSPAKRQKHAPQKPKKVHDKEK 349
           ++ +  +           G EKR +D +         E+ P+KR++     P     +  
Sbjct: 601 RKRARAEKKALKKKKKIRGPEKRGADEDDEKEWGDDEEEQPSKRRRVENSIPAAGETQNV 660

Query: 350 RQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFT-DECTAFLSNINLKATYED- 407
                 A +    + +   +++ K   +K  +P      + D  T F+SN+       D 
Sbjct: 661 EVAAGPAGKCAAVDVEPPSKQKEKAASLKRDMPKVLHDSSKDSITVFVSNLPYSMQEPDT 720

Query: 408 -LRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIA 465
            LR  F   G V  IR +     G  RG  YV+F +++    A+  +++   G+ + ++
Sbjct: 721 KLRPLFEACGEVVQIRPIFSN-RGDFRGYCYVEFKEEKSALQALEMDRKSVEGRPMFVS 778

Regulates Tat transactivation activity through direct interaction. May be a cellular factor for HIV-1 gene expression and viral replication.
Homo sapiens (taxid: 9606)

>sp|Q5REG1|SART3_PONAB Squamous cell carcinoma antigen recognized by T-cells 3 OS=Pongo abelii GN=SART3 PE=2 SV=1

 Score =  175 bits (443), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 130/479 (27%), Positives = 229/479 (47%), Gaps = 36/479 (7%)

Query: 18  SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVV 77
           +++ +  +Y  Y+ +E   GDP R+QL++ERA+ +  +  DLW+ Y+QYLD+ LKV ++V
Sbjct: 323 AEAPRLAEYQAYIDFEMKIGDPARIQLIFERALVENCLVPDLWIRYSQYLDRQLKVKDLV 382

Query: 78  RDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTR 137
             V++RA +NCPW   LW R LL++ER     + IS  FEK+L   F    +Y++++   
Sbjct: 383 LSVHNRAIRNCPWTVALWSRYLLAMERHGVDHQVISVTFEKALNAGFIQATDYVEIWQAY 442

Query: 138 IDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQM-----KNTDGLLRLYAYWAHLE 192
           +D LRRR+ F  +    L+   +R  F RA +YL +++     ++ D    +   WA +E
Sbjct: 443 LDYLRRRVDFKQDSSKELEE--LRAAFTRALEYLKQEVEERFNESGDPSCVIMQNWARIE 500

Query: 193 QSMGKDMVSARGVWERLLKISGA-MLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGT 251
             +  +M  AR +W+ ++    A     W  Y ++E         R    R  + + T  
Sbjct: 501 ARLCNNMQKARELWDSIMTRGNAKYANMWLEYYNLERAHGDTQHCRKALHR--AVQCTSD 558

Query: 252 GSEDICHAWLRFEREYGTLEDFDHSVQKVTPRL---EELRLFRSQQESKSL---PESADQ 305
             E +C   L  ER  G+LED+D +VQK   RL    E R+  +++E+  +    E A+Q
Sbjct: 559 YPEHVCEVLLTMERTEGSLEDWDIAVQKTETRLARVNEQRMKAAEKEAALVQQEEEKAEQ 618

Query: 306 KEHSVKKT----------GREKRKSDSNISY------EQSPAKRQKHAPQKPKKVHDKEK 349
           ++ +  +           G EKR +D +         E+ P+KR++     P     +  
Sbjct: 619 RKRARAEKKALKKKKKIRGPEKRGADEDDEKEWGDDEEEQPSKRRRVENSIPAAGETQNV 678

Query: 350 RQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFT-DECTAFLSNINLKATYED- 407
                 A +    + +   +++ K   +K  +P      + D  T F+SN+       D 
Sbjct: 679 EVAPGPAGKCAAVDVEPPSKQKEKAASLKRDMPKVLHDSSKDSITVFVSNLPYSMQEPDA 738

Query: 408 -LRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIA 465
            LR  F   G V  IR +     G  RG  YV+F +++    A+  +++   G+ + ++
Sbjct: 739 KLRPLFEACGEVVQIRPIFSN-RGDFRGYRYVEFKEEKSALQALEMDRKSVEGRPMFVS 796

Pongo abelii (taxid: 9601)

>sp|Q9JLI8|SART3_MOUSE Squamous cell carcinoma antigen recognized by T-cells 3 OS=Mus musculus GN=Sart3 PE=2 SV=1

 Score =  172 bits (437), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 132/484 (27%), Positives = 226/484 (46%), Gaps = 47/484 (9%)

Query: 18  SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVV 77
           +++ +  +Y  Y+ +E   GDP R+QL++ERA+ +  +  DLW+ Y+QYLD+ LKV ++V
Sbjct: 306 AEAPRLAEYQAYIDFEMKIGDPARIQLIFERALVENCLVPDLWIRYSQYLDRQLKVKDLV 365

Query: 78  RDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTR 137
             V+SRA +NCPW   LW R LL++ER     + IS  FE +L   F    +Y++++   
Sbjct: 366 LSVHSRAVRNCPWTVALWSRYLLAMERHGLDHQTISATFENALSAGFIQATDYVEIWQVY 425

Query: 138 IDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQM-----KNTDGLLRLYAYWAHLE 192
           +D LRRR+ F  +    L+   +R  F RA +YL +++     ++ D    +   WA +E
Sbjct: 426 LDYLRRRVDFRQDSSKELEE--LRSMFTRALEYLQQEVEERFSESGDPSCLIMQSWARVE 483

Query: 193 QSMGKDMVSARGVWERLLKISGA-MLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGT 251
             +  +M  AR +W+ ++    A     W  Y ++E         R    R  + + T  
Sbjct: 484 ARLCNNMQKARELWDSIMTRGNAKYANMWLEYYNLERAHGDTQHCRKALHR--AVQCTSD 541

Query: 252 GSEDICHAWLRFEREYGTLEDFDHSVQKVTPRL---EELRLFRSQQESKSLPESADQKEH 308
             E +C   L  ER  GTLED+D ++QK   RL    E R+  +++E+ +L +  ++K  
Sbjct: 542 YPEHVCEVLLTMERTEGTLEDWDLAIQKTETRLARVNEQRMKAAEKEA-ALVQQEEEKAE 600

Query: 309 SVKKTGREK---------RKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEEN 359
             KK   EK         R +D     E    +  +   ++P K     +R+ +N     
Sbjct: 601 QRKKVRAEKKALKKKKKTRGADKRREDEDEENEWGEEEEEQPSK-----RRRTENSLASG 655

Query: 360 EGRETKQTVEEQPKKQPIKDAVPGRTK----------------GFTDECTAFLSNI--NL 401
           E    K+  E   K   I    P + K                   D  T F+SN+  ++
Sbjct: 656 EASAMKEETELSGKCLTIDVGPPSKQKEKAASLKRDMPKVAHDSSKDSVTVFVSNLPYSI 715

Query: 402 KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKK 461
           +     LR  F   G V  IR +     G  RG  YV+F +++    A+  ++++  G+ 
Sbjct: 716 EEPEVKLRPLFEVCGEVVQIRPIFSN-RGDFRGYCYVEFGEEKSAQQALELDRKIVEGRP 774

Query: 462 LSIA 465
           + ++
Sbjct: 775 MFVS 778

Mus musculus (taxid: 10090)

>sp|Q9W4D2|RNP4F_DROME RNA-binding protein 4F OS=Drosophila melanogaster GN=Rnp4F PE=1 SV=1

 Score = 70.9 bits (172), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 111/524 (21%), Positives = 208/524 (39%), Gaps = 88/524 (16%)

Query: 5   RAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYT 64
           + HL+E     D S+  K   Y +             ++ ++ER++  FP+   LWL Y 
Sbjct: 321 KQHLDETTRGWDWSEQHKAHVYDVETLSLDDDLKNAVIRFIFERSVAKFPIVDVLWLSYI 380

Query: 65  QYLD------------------------KTLKVG---NVVRDVYSRATKNCPWVGELWVR 97
           +++                         K L  G   N   D+ +R  ++ P V +L  R
Sbjct: 381 EFIQFEGVTVPENEDENEVTAEMVAKRAKRLGKGFLRNTELDLANRGVRSHPSV-QLNHR 439

Query: 98  SLLSLERS----RASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEG 153
            L  +ERS       +EEI  + ++ +     T E +LD    RI    R    S E + 
Sbjct: 440 FLDLMERSDFELAEVDEEIRLILQRIVTDMDMTVELHLDYLAYRI----RNTNASDEQQ- 494

Query: 154 VLDYSLIRETFQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI 212
               + +R  F  A + L+    +  D    +   WA +E +      + R +W +++  
Sbjct: 495 ---VASLRAAFNHAWEELTVLYGDQADTRYEVLQLWAQVEYTQLGSPDNGREIWRQIMGY 551

Query: 213 SGAMLEA--WQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTL 270
            G+ +    W ++  ME E +  +  R + ++  S+     G   +   + R+ER YGT 
Sbjct: 552 PGSSIRGLLWLNFAQMESEYNGGHGTRDVLRKALSQPVLENGLM-VQEFFRRYERCYGTY 610

Query: 271 EDFDHSVQKVTPRLEELRLFRSQQESKSLPESADQKEHSVKKTGREKRKSDSNISYEQSP 330
                                   ES +  ++ D     VK   R K  S S    +Q  
Sbjct: 611 ------------------------ESIAACQALDLPVEYVKPRSRIKPNSQSAYPRQQKL 646

Query: 331 AKRQKHAPQKPKKVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAV--PGRTKGF 388
             RQ+      + ++ +++R+  +  ++ + ++ K  +++  + +P   A   P + KG 
Sbjct: 647 KPRQQQQQTNREPLNREQRRRQAHEQQQQQQQQQKHGIKKS-RTEPSGGATSPPSKVKGP 705

Query: 389 TDE---------------CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
            +                   F+ N++   + E+L   FS  G +  +R++H K   + +
Sbjct: 706 ANAEAKESNFKYSPNMEINKIFVRNLHPACSKEELHELFSPFGTIKDVRLVH-KLNKQFK 764

Query: 434 GLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNPKQRKDSS 476
           G+AYV+F        AVA ++  +F G  +S+A SNP  R  S+
Sbjct: 765 GIAYVEFEKPGEAQRAVAGRDGCLFKGMNISVAISNPPPRGTSA 808

May be involved in gene regulation during development. Binds RNA.

Drosophila melanogaster (taxid: 7227)

>sp|Q9USY2|YOW4_SCHPO Uncharacterized RNA-binding protein C1861.04c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC1861.04c PE=4 SV=1

 Score = 65.5 bits (158), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 104/458 (22%), Positives = 181/458 (39%), Gaps = 73/458 (15%)

Query: 18  SDSEKFQQYMIYLKYE--QSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGN 75
           S +   + YM  +  E  +S+ +   +  LYERAI  +P+  +LWL YT +L K     +
Sbjct: 265 SANHSLEAYMDLINDESRRSTAELQYITTLYERAIVLYPLIPELWLQYTAWLSKVDFSSS 324

Query: 76  VVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS----TFEEYL 131
               V  RAT+NC W+G +W   L  +  S AS    S V E+   C  S     F+E +
Sbjct: 325 QASSVAERATRNCSWIGRIWSIKLTYMTLSGAS---TSAVCEEKDRCLNSNLLVNFDEVI 381

Query: 132 DLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNT-DGLLRLYAYWAH 190
           D F     G  +  L+    E       ++    +  DYL +  K + D  +R+     +
Sbjct: 382 DFF----SGFLKACLYLSSNEDK-PQEFLKHQIHKVEDYLRKNHKGSKDARMRIELSKIY 436

Query: 191 LEQSMGKDMVSARGVWERLLKISGAMLEAWQS-YISM---EIELDHINEARSIYKRCYSK 246
           L   +  D  S    W  +          W S YIS      EL      +S+YK     
Sbjct: 437 LYSEIS-DFESVEKCWSDMFHDFQNQALYWISRYISTMKYNPELAAETLKKSLYK----- 490

Query: 247 RFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLPESADQK 306
                   ++    L F+  Y ++ D ++     T  L ++   +     + L   A++ 
Sbjct: 491 --------NVDQPQLLFQF-YQSIMDLNNDCFTNTSHLYDVLNAQRISFKRQLDSFAEET 541

Query: 307 EHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEENEGRETKQ 366
           + +V+ T                          +P KV      Q  + A  ++ R+  Q
Sbjct: 542 KQTVENT--------------------------EPLKV-----PQADDTAALSKKRKPGQ 570

Query: 367 TVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHD 426
             +   K +PI+     R +   +E T  ++N+    +  +L+ FF D G +  I IL D
Sbjct: 571 EGDVFKKSKPIEQ---HRNR---EELTVLVTNLPSDISENELKIFFKDCGNIIRIFILED 624

Query: 427 KFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSI 464
               K   +A ++F +   + AA  ++ +   G ++S+
Sbjct: 625 --NQKDVKVAQIEFSETSEVLAAKTRDLKSIRGHEISV 660

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

>sp|Q9DDY9|PAB2A_XENLA Polyadenylate-binding protein 2-A OS=Xenopus laevis GN=pabpn1-a PE=2 SV=1

 Score = 60.5 bits (145), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 46/75 (61%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           D  + ++ N++  AT E+L   F   G V+ + IL DKFTG  +G AY++F D E +  +
Sbjct: 161 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFTGHPKGFAYIEFCDKESVRTS 220

Query: 450 VAKNKQMFLGKKLSI 464
           +A ++ +F G+++ +
Sbjct: 221 LALDESLFRGRQIKV 235

Involved in the 3'-end formation of mRNA precursors (pre-mRNA) by the addition of a poly(A) tail of 200-250 nt to the upstream cleavage product. Stimulates poly(A) polymerase (PAPOLA) conferring processivity on the poly(A) tail elongation reaction and controls also the poly(A) tail length. Increases the affinity of poly(A) polymerase for RNA. Binds to poly(A) and to poly(G) with high affinity. May protect the poly(A) tail from degradation.

Xenopus laevis (taxid: 8355)

>sp|Q4PB37|CLF1_USTMA Pre-mRNA-splicing factor CLF1 OS=Ustilago maydis (strain 521 / FGSC 9021) GN=CLF1 PE=3 SV=1

 Score = 60.5 bits (145), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 73/284 (25%), Positives = 126/284 (44%), Gaps = 46/284 (16%)

Query: 5   RAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYT 64
           R+  E+++ R  L+ S     ++ Y  +E S G+  R + +YERA+   P    LWL YT
Sbjct: 56  RSEFEDRLRRNGLNMS----TWIKYASWEASQGEMDRCRSIYERALDVEPHHLPLWLRYT 111

Query: 65  QYLDKTLKVGNV--VRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLC 122
           +   + LK+ NV   R++Y RA    P + +LW +  + LE    +      VFE+ +  
Sbjct: 112 E---QELKMRNVQHARNLYDRAVSILPRIDQLWYK-YVHLEELLGNIPGTRQVFERWMKW 167

Query: 123 AFS--TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG 180
                 +  Y++L + R D L R                        +  + E+      
Sbjct: 168 EPEEKAWHAYINLEV-RYDELDR------------------------ASAIWERCVTCHP 202

Query: 181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG----AMLEA---WQSYISMEIELDHI 233
           + + +  WA  E+  G ++  AR V++  L   G    AM +A   + ++  ME  L   
Sbjct: 203 VPKQWIRWAKFEEDRG-NLEKARIVFQMALDYIGEDEDAMEKAQSVFTAFAKMETRLKEY 261

Query: 234 NEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSV 277
             AR IYK    +R   + SE I  ++ RFE+++GT+   + +V
Sbjct: 262 ERARVIYKYAL-ERLPRSKSEGIYSSYTRFEKQFGTMNSVEDTV 304

Involved in pre-mRNA splicing and cell cycle progression. Required for the spliceosome assembly and initiation of the DNA replication.

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

>sp|Q6TY21|EPA2B_XENLA Embryonic polyadenylate-binding protein 2-B OS=Xenopus laevis GN=Pabpn1l-b PE=1 SV=1

 Score = 60.5 bits (145), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 47/75 (62%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           D+ + ++ N++  +T +DL   FS  G ++ I IL DKF+G  +G AY++F +   + AA
Sbjct: 91  DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA 150

Query: 450 VAKNKQMFLGKKLSI 464
           VA ++ +F G+ + +
Sbjct: 151 VAMDETVFRGRTIKV 165

Binds the poly(A) tail of mRNA. Unable to interact with the cap-binding complex and is therefore unlikely to be involved in translation initiation.

Xenopus laevis (taxid: 8355)

>sp|Q7ZXB8|PAB2B_XENLA Polyadenylate-binding protein 2-B OS=Xenopus laevis GN=pabpn1-b PE=2 SV=1

 Score = 60.1 bits (144), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 46/75 (61%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           D  + ++ N++  AT E+L   F   G V+ + IL DKFTG  +G AY++F D E +  +
Sbjct: 160 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFTGHPKGFAYIEFSDKESVRTS 219

Query: 450 VAKNKQMFLGKKLSI 464
           +A ++ +F G+++ +
Sbjct: 220 LALDESLFRGRQIKV 234

Involved in the 3'-end formation of mRNA precursors (pre-mRNA) by the addition of a poly(A) tail of 200-250 nt to the upstream cleavage product. Stimulates poly(A) polymerase (PAPOLA) conferring processivity on the poly(A) tail elongation reaction and controls also the poly(A) tail length. Increases the affinity of poly(A) polymerase for RNA. Binds to poly(A) and to poly(G) with high affinity. May protect the poly(A) tail from degradation.

Xenopus laevis (taxid: 8355)

>sp|Q804A5|EPA2A_XENLA Embryonic polyadenylate-binding protein 2-A OS=Xenopus laevis GN=Pabpn1l-a PE=1 SV=1

 Score = 58.5 bits (140), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 45/75 (60%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           D+ + ++ N++   T +DL   FS  G ++ I IL DKF+G  +G AY++F +   + AA
Sbjct: 91  DKRSVYVGNVDYGGTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA 150

Query: 450 VAKNKQMFLGKKLSI 464
           V  ++ +F G+ + +
Sbjct: 151 VTMDETVFRGRTIKV 165

Binds the poly(A) tail of mRNA. Unable to interact with the cap-binding complex and is therefore unlikely to be involved in translation initiation.

Xenopus laevis (taxid: 8355)

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	565
255573806	852	Squamous cell carcinoma antigen recogniz	0.989	0.656	0.682	0.0
297739447	819	unnamed protein product [Vitis vinifera]	0.975	0.672	0.656	0.0
359486200	838	PREDICTED: squamous cell carcinoma antig	0.989	0.667	0.649	0.0
356541840	837	PREDICTED: squamous cell carcinoma antig	0.976	0.659	0.613	0.0
356560763	847	PREDICTED: squamous cell carcinoma antig	0.976	0.651	0.608	0.0
449450119	800	PREDICTED: squamous cell carcinoma antig	0.969	0.685	0.602	0.0
224129810	843	predicted protein [Populus trichocarpa]	0.950	0.637	0.612	0.0
30686462	816	protein embryo defective 140 [Arabidopsi	0.948	0.656	0.574	0.0
18700131	816	AT4g24270/T22A6_100 [Arabidopsis thalian	0.948	0.656	0.572	0.0
30686466	817	protein embryo defective 140 [Arabidopsi	0.948	0.656	0.573	0.0

>gi|255573806|ref|XP_002527822.1| Squamous cell carcinoma antigen recognized by T-cells, putative [Ricinus communis] gi|223532746|gb|EEF34525.1| Squamous cell carcinoma antigen recognized by T-cells, putative [Ricinus communis]

 Score =  785 bits (2028), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 387/567 (68%), Positives = 461/567 (81%), Gaps = 8/567 (1%)

Query: 1   MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLW 60
           M N RA  EEQI +QD+S+ EKFQ +M YL +E+++GDP RVQ+LYERAIT+FPVSSD+W
Sbjct: 289 MYNTRAQHEEQIYKQDISEQEKFQNFMNYLNFEKTAGDPARVQVLYERAITEFPVSSDIW 348

Query: 61  LDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSL 120
           LDYT YLDKTLKVGN+V+D Y RAT+NC WVGELWVR LLSLERSRA E+EISTVFE+SL
Sbjct: 349 LDYTCYLDKTLKVGNIVKDAYFRATRNCSWVGELWVRYLLSLERSRAHEKEISTVFEESL 408

Query: 121 LCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG 180
            C FST EEYLDLFLTR+DGLRRRILF  E EGVL+YSLI+ET Q ASDYLS Q+KNT+G
Sbjct: 409 QCLFSTAEEYLDLFLTRVDGLRRRILFGSEAEGVLNYSLIKETMQHASDYLSPQLKNTEG 468

Query: 181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIY 240
           LLRL+AYWA LE ++GKD+V+ARGVWE LLKISG+MLE WQ YI+ME EL HINEARSIY
Sbjct: 469 LLRLHAYWARLELNLGKDLVAARGVWESLLKISGSMLEVWQGYITMETELGHINEARSIY 528

Query: 241 KRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLP 300
           KRCYSKRFTGTGSEDICH+WLRFERE+G LEDFDH+VQKVTPRLEEL+L+R QQESK+  
Sbjct: 529 KRCYSKRFTGTGSEDICHSWLRFEREFGALEDFDHAVQKVTPRLEELQLYRMQQESKAFV 588

Query: 301 ESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEENE 360
            SADQKE+ +K+  REKRK     + EQSPAKR+K  PQ  +K ++K K Q QNLAE  +
Sbjct: 589 ASADQKENPIKRNVREKRKGGPEYTDEQSPAKRKKQTPQ-TQKGYEKSKDQPQNLAEVTK 647

Query: 361 GRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSS 420
            +  ++T  +Q K+Q  KD   GR KG+TD+CTAFLSN++LKA YEDLR+FFSDVGGV S
Sbjct: 648 PK-VEKTDSKQEKQQ--KDYDSGRNKGYTDQCTAFLSNLHLKANYEDLRKFFSDVGGVVS 704

Query: 421 IRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRK----DSS 476
           IRIL DK+TGKSRGLAYVDF DDEHLAAA+AKNKQM LGK+LSIARSNPKQ K    D S
Sbjct: 705 IRILLDKYTGKSRGLAYVDFSDDEHLAAAIAKNKQMLLGKRLSIARSNPKQNKKGGRDFS 764

Query: 477 GERAPTEQAQSHQQTGNAGTSASKESSIETSKQSRGRGDSVQLKGKNTFAVPRNVRPLGF 536
            ++  T+Q+  ++++ +  ++ + + S      +R   D++QLKGKNTF VPRNV+PLG+
Sbjct: 765 KQQTHTDQSAKNEESASYMSTETSKGSRAPQSANRKLDDNIQLKGKNTFLVPRNVKPLGW 824

Query: 537 PAIKPKTEEGEDLKPKSNDEFRKMFIK 563
            A KPKT E  D KPKSNDEFRKMFIK
Sbjct: 825 DANKPKTVEEGDEKPKSNDEFRKMFIK 851

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297739447|emb|CBI29629.3| unnamed protein product [Vitis vinifera]

 Score =  727 bits (1876), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 373/568 (65%), Positives = 442/568 (77%), Gaps = 17/568 (2%)

Query: 1   MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLW 60
           M +ARAHLEEQI RQD+SDSE+ QQ++ YL +EQSSGDP RVQ+LYERAIT+FPVS DLW
Sbjct: 263 MYDARAHLEEQIVRQDISDSERHQQFLNYLNFEQSSGDPARVQILYERAITEFPVSRDLW 322

Query: 61  LDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSL 120
           LDYTQYLDKTLKV NVVRDVYSRA KNCPWVGELWV+ LLSLER+RASE EISTVF+KSL
Sbjct: 323 LDYTQYLDKTLKVANVVRDVYSRAVKNCPWVGELWVQYLLSLERARASEREISTVFDKSL 382

Query: 121 LCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG 180
            C FS F EYL+LFLTR+DGLRRRI   G+ E VL+Y+LIR+ FQ ASDYLS  +K TD 
Sbjct: 383 QCTFSRFGEYLNLFLTRVDGLRRRISLPGQ-EEVLEYALIRDAFQYASDYLSPHLKCTDD 441

Query: 181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIY 240
           L+RL+AYWA LE ++ KD+V+ARGVWE LLK SG+M  AWQ YI+ME+E  HINEARSIY
Sbjct: 442 LVRLHAYWARLELNLNKDLVAARGVWESLLKNSGSMFGAWQGYIAMELEAGHINEARSIY 501

Query: 241 KRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLP 300
           KRCYSKRF GTGSEDICH+WLRFERE+GTLED +H+V+KVTPRL EL+LF+  QESKS  
Sbjct: 502 KRCYSKRFAGTGSEDICHSWLRFEREFGTLEDLEHAVRKVTPRLAELQLFK-LQESKSTA 560

Query: 301 ESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEENE 360
            S DQ E+  KK  REKRKS S+ + EQ PAKRQK   Q PKKV  K + +++N+   NE
Sbjct: 561 ASTDQIENPHKKNAREKRKSTSSRTDEQPPAKRQKDTAQNPKKVDGKGRIELENVVASNE 620

Query: 361 GRETKQTVEEQP---KKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGG 417
            +E K   +++P    K+ +K     + K + D+CTAF+SN++L+A YE LR FFSDVGG
Sbjct: 621 EQELKAK-DDKPDDMNKRQMKGPSHEKNK-YLDQCTAFISNLDLEANYEHLRDFFSDVGG 678

Query: 418 VSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKDSSG 477
           V++IRIL DKFTGKSRGLAYVDF DD HLAAAVAKNK+M  GK+LSIARS+PKQ+   +G
Sbjct: 679 VTAIRILKDKFTGKSRGLAYVDFSDDAHLAAAVAKNKKMLRGKRLSIARSDPKQKGKGAG 738

Query: 478 ERAPTEQAQSHQQTGNAGTSASKESS-IETSKQSRG-RGDSVQLKGKNTFAVPRNVRPLG 535
                    S+ QTG  G S SKES  I +SK  +  R D+ QLKG+NTFAVPRNVRPLG
Sbjct: 739 --------HSNDQTGTVGESDSKESGQISSSKAPQARRDDNFQLKGRNTFAVPRNVRPLG 790

Query: 536 FPAIKPKTEEGEDLKPKSNDEFRKMFIK 563
           +   K KTEE  D  PKSNDEFRKM +K
Sbjct: 791 WIDKKKKTEEETDEMPKSNDEFRKMLLK 818

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359486200|ref|XP_002268805.2| PREDICTED: squamous cell carcinoma antigen recognized by T-cells 3-like [Vitis vinifera]

 Score =  724 bits (1869), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 376/579 (64%), Positives = 445/579 (76%), Gaps = 20/579 (3%)

Query: 1   MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLW 60
           M +ARAHLEEQI RQD+SDSE+ QQ++ YL +EQSSGDP RVQ+LYERAIT+FPVS DLW
Sbjct: 263 MYDARAHLEEQIVRQDISDSERHQQFLNYLNFEQSSGDPARVQILYERAITEFPVSRDLW 322

Query: 61  LDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSL 120
           LDYTQYLDKTLKV NVVRDVYSRA KNCPWVGELWV+ LLSLER+RASE EISTVF+KSL
Sbjct: 323 LDYTQYLDKTLKVANVVRDVYSRAVKNCPWVGELWVQYLLSLERARASEREISTVFDKSL 382

Query: 121 LCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG 180
            C FS F EYL+LFLTR+DGLRRRI   G+ E VL+Y+LIR+ FQ ASDYLS  +K TD 
Sbjct: 383 QCTFSRFGEYLNLFLTRVDGLRRRISLPGQ-EEVLEYALIRDAFQYASDYLSPHLKCTDD 441

Query: 181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIY 240
           L+RL+AYWA LE ++ KD+V+ARGVWE LLK SG+M  AWQ YI+ME+E  HINEARSIY
Sbjct: 442 LVRLHAYWARLELNLNKDLVAARGVWESLLKNSGSMFGAWQGYIAMELEAGHINEARSIY 501

Query: 241 KRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLP 300
           KRCYSKRF GTGSEDICH+WLRFERE+GTLED +H+V+KVTPRL EL+LF+  QESKS  
Sbjct: 502 KRCYSKRFAGTGSEDICHSWLRFEREFGTLEDLEHAVRKVTPRLAELQLFK-LQESKSTA 560

Query: 301 ESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEENE 360
            S DQ E+  KK  REKRKS S+ + EQ PAKRQK   Q PKKV  K + +++N+   NE
Sbjct: 561 ASTDQIENPHKKNAREKRKSTSSRTDEQPPAKRQKDTAQNPKKVDGKGRIELENVVASNE 620

Query: 361 GRETKQTVEEQP---KKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGG 417
            +E K   +++P    K+ +K     + K + D+CTAF+SN++L+A YE LR FFSDVGG
Sbjct: 621 EQELKAK-DDKPDDMNKRQMKGPSHEKNK-YLDQCTAFISNLDLEANYEHLRDFFSDVGG 678

Query: 418 VSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQ--RKDS 475
           V++IRIL DKFTGKSRGLAYVDF DD HLAAAVAKNK+M  GK+LSIARS+PKQ  +K S
Sbjct: 679 VTAIRILKDKFTGKSRGLAYVDFSDDAHLAAAVAKNKKMLRGKRLSIARSDPKQKGKKGS 738

Query: 476 SGERAPTEQ---------AQSHQQTGNAGTSASKESS-IETSKQSRG-RGDSVQLKGKNT 524
           +     T Q           S+ QTG  G S SKES  I +SK  +  R D+ QLKG+NT
Sbjct: 739 AYRSNHTRQVMITGSKGAGHSNDQTGTVGESDSKESGQISSSKAPQARRDDNFQLKGRNT 798

Query: 525 FAVPRNVRPLGFPAIKPKTEEGEDLKPKSNDEFRKMFIK 563
           FAVPRNVRPLG+   K KTEE  D  PKSNDEFRKM +K
Sbjct: 799 FAVPRNVRPLGWIDKKKKTEEETDEMPKSNDEFRKMLLK 837

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356541840|ref|XP_003539380.1| PREDICTED: squamous cell carcinoma antigen recognized by T-cells 3-like [Glycine max]

 Score =  702 bits (1811), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 352/574 (61%), Positives = 442/574 (77%), Gaps = 22/574 (3%)

Query: 1   MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLW 60
           M NAR HLEEQI   ++SDSE+ Q YM YLK+EQSSG P R+Q+LYERAITDFP++ DLW
Sbjct: 275 MYNARFHLEEQILSPNISDSERLQHYMNYLKFEQSSGMPARIQVLYERAITDFPITPDLW 334

Query: 61  LDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSL 120
           LD T+ LD TLKVGN+V +VYSRATKNCPWVGELWVR +LSLER  ASE+++S +FEKSL
Sbjct: 335 LDCTRNLDNTLKVGNIVSNVYSRATKNCPWVGELWVRYMLSLERGHASEKDLSEIFEKSL 394

Query: 121 LCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG 180
           LC FST +EYLDLFLTR+DGLRRR+  S E +  L+Y +IRETFQRASDYLS  +KNT+G
Sbjct: 395 LCTFSTLDEYLDLFLTRVDGLRRRMASSSEED--LEYKIIRETFQRASDYLSPYLKNTEG 452

Query: 181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIY 240
           LL L+AYWA LE  +GKD+ +ARGVWE  LK+ G+MLE+W  YI+ME+EL HINEARSIY
Sbjct: 453 LLHLHAYWARLETKLGKDITAARGVWENCLKLCGSMLESWTGYIAMEVELGHINEARSIY 512

Query: 241 KRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLP 300
           KRCYSKRF+GTGSEDIC +WLRFERE+G LEDFDH++ KVTPR++EL+LFR QQESK   
Sbjct: 513 KRCYSKRFSGTGSEDICQSWLRFEREFGKLEDFDHALHKVTPRMDELKLFRMQQESK--- 569

Query: 301 ESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEEN- 359
            SA++ E + K+  REKRK  S+I+ EQSP+KR +     PKK  ++ K  VQN+++   
Sbjct: 570 -SAEESEKNTKRNAREKRKLGSDITEEQSPSKRFRDVGN-PKKAPEENKYHVQNISQVTK 627

Query: 360 -EGRETKQT-VEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGG 417
            EG   K T +++ P +Q        + +G++D+CTAFLSN++  A YE +R FFSDVGG
Sbjct: 628 VEGVNWKNTKIDDNPSEQQFSHE---KNRGYSDQCTAFLSNLHPTANYEHIRNFFSDVGG 684

Query: 418 VSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQ-RKDSS 476
           + +IRILHDKFTGKSRGLAYVDF+D+EHLAAA+AKN+   +GKKLSIARS+PK+  ++SS
Sbjct: 685 IVAIRILHDKFTGKSRGLAYVDFLDEEHLAAAIAKNRLKLIGKKLSIARSDPKRGGRESS 744

Query: 477 GERAPTEQA-----QSHQQTGNAGTSASKESSIETSK-QSRGRG-DSVQLKGKNTFAVPR 529
             +  TE A      S + +G+  T  + +  ++  K  SR  G D++QLKGKNTFAVPR
Sbjct: 745 NPKTLTEHADATNHSSQKASGSKETDDTYKGDVKDVKFSSRKPGNDNIQLKGKNTFAVPR 804

Query: 530 NVRPLGFPAIKPKTEEGEDLKPKSNDEFRKMFIK 563
           NVRPLGF   KPK EEG D KPKSN+EFRK+FI+
Sbjct: 805 NVRPLGFTTNKPKAEEG-DEKPKSNEEFRKIFIR 837

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356560763|ref|XP_003548657.1| PREDICTED: squamous cell carcinoma antigen recognized by T-cells 3-like [Glycine max]

 Score =  693 bits (1788), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 349/574 (60%), Positives = 436/574 (75%), Gaps = 22/574 (3%)

Query: 1   MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLW 60
           M NAR HLEEQI   ++SDSE+ Q YM YLK+EQSSG P R+Q+LYERAITDFP++ DLW
Sbjct: 285 MYNARFHLEEQILSPNVSDSERLQHYMNYLKFEQSSGTPARIQVLYERAITDFPITPDLW 344

Query: 61  LDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSL 120
           LDYT  LD TLKVGN+V +VYSRATKNCPWVGELWVR +LSLER  ASE+++S +FEKSL
Sbjct: 345 LDYTCNLDNTLKVGNIVNNVYSRATKNCPWVGELWVRCMLSLERGHASEKDLSEIFEKSL 404

Query: 121 LCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG 180
            C FST +EYLDLFLTR+DGLRRR+  S E +  L+Y +IRETFQRASDYLS  +KNT+G
Sbjct: 405 QCTFSTLDEYLDLFLTRVDGLRRRMASSNEED--LEYKIIRETFQRASDYLSPYLKNTEG 462

Query: 181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIY 240
           LL L+AYWA LE  +GKD+ +ARGVWE  LKI G+MLE+W  YI+ME+EL HINEARSIY
Sbjct: 463 LLHLHAYWARLETKLGKDITAARGVWENCLKICGSMLESWTGYIAMEVELGHINEARSIY 522

Query: 241 KRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLP 300
           KRCYSKRF+GTGSEDIC +WLRFERE+G LEDFDH++ KVTPRLEEL+LFR QQESK   
Sbjct: 523 KRCYSKRFSGTGSEDICQSWLRFEREFGKLEDFDHALHKVTPRLEELKLFRIQQESK--- 579

Query: 301 ESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEEN- 359
            +A++ E + K+  REKRK  S+I+ EQ P KR +     PKK  ++ K Q+QN ++   
Sbjct: 580 -TAEESEKNPKRNAREKRKLGSDITEEQYPTKRFRDVGN-PKKAPEENKYQLQNTSQVTK 637

Query: 360 -EGRETKQT-VEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGG 417
            EG   K T +++ P +Q        + + ++D+CT F+SN++  A YE +R FF D GG
Sbjct: 638 VEGANWKNTKIDDNPSEQQFNHE---KNRAYSDQCTVFISNLHPTANYEHIRNFFGDDGG 694

Query: 418 VSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQ-RKDSS 476
           + +IRILHDKFTGKSRGLAYVDF+D+EHLAAA+AKN+Q  +GKKLSIARS+PK+  K+SS
Sbjct: 695 IVAIRILHDKFTGKSRGLAYVDFLDEEHLAAAIAKNRQKLIGKKLSIARSDPKRGGKESS 754

Query: 477 GERAPTEQAQSHQQTGNAG-----TSASKESSIETSK-QSRGRG-DSVQLKGKNTFAVPR 529
             +  TE A++   +   G     T  + +  ++ +K  SR  G D++QLKGKNTFAVPR
Sbjct: 755 NPKTWTEHARATNHSSQKGFVSKETDDTHKGDVKDAKFSSRKPGNDNIQLKGKNTFAVPR 814

Query: 530 NVRPLGFPAIKPKTEEGEDLKPKSNDEFRKMFIK 563
           NV+PLGF A K K EEG D KPKSN+EFRKMFI+
Sbjct: 815 NVKPLGFTANKLKAEEG-DEKPKSNEEFRKMFIR 847

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449450119|ref|XP_004142811.1| PREDICTED: squamous cell carcinoma antigen recognized by T-cells 3-like [Cucumis sativus]

 Score =  690 bits (1781), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 339/563 (60%), Positives = 428/563 (76%), Gaps = 15/563 (2%)

Query: 1   MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLW 60
           M NAR  LE+QIS+QDL+D+E+  QY+IYLK+EQS+GDP RVQ+L+ERAI DFPVS DLW
Sbjct: 252 MYNARVQLEDQISKQDLTDTERLHQYIIYLKFEQSAGDPARVQVLFERAIADFPVSVDLW 311

Query: 61  LDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSL 120
           LDYT Y+DKTLKVGN+VR+VYSRAT+NCPW+G+LWVR LL+LERS ASE EI++VF KSL
Sbjct: 312 LDYTCYMDKTLKVGNIVRNVYSRATRNCPWIGDLWVRYLLALERSHASEGEIASVFGKSL 371

Query: 121 LCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG 180
            C+FST +EYLDLFLTRIDGLRRRI    ++E  L+YSLIRETFQRASDYLS  +KN++ 
Sbjct: 372 QCSFSTLDEYLDLFLTRIDGLRRRISSGVQLEDALEYSLIRETFQRASDYLSPHLKNSEV 431

Query: 181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIY 240
           L+RLYAYWA LE +MGK++ SARGVWE LLKI G++  AW+ YI+ME+EL+HIN ARSIY
Sbjct: 432 LVRLYAYWARLEINMGKNLDSARGVWESLLKICGSLSAAWEGYIAMEVELNHINNARSIY 491

Query: 241 KRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLP 300
           KRCYSKRF G+GSEDICH+WLRFERE+G+LEDFDH+V+KV PRLEEL+ ++ Q       
Sbjct: 492 KRCYSKRFPGSGSEDICHSWLRFEREFGSLEDFDHAVRKVNPRLEELKSYKLQ------- 544

Query: 301 ESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEENE 360
              D  E+ VK+  R KRK   +    +SPAK+ K +   PKKV +K K Q++N+ ++  
Sbjct: 545 --IDDSENPVKQNDRSKRKLGGDAPNVESPAKKLKDSAHGPKKVTEKGKAQLENVDDQTG 602

Query: 361 GRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSS 420
               +    +    Q + D++  + K + D+CTAF+SN+NLK TY+ LR FF DVGGV +
Sbjct: 603 DIRGRVKKLDDISDQQMNDSIQEKGKVYNDQCTAFISNLNLKVTYDHLRDFFQDVGGVVA 662

Query: 421 IRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKDSSGERA 480
           IRILHDKFTGKSRGLAYVDF DD HL A VAKNKQ+ LGKK+SIARS+PK  K   G   
Sbjct: 663 IRILHDKFTGKSRGLAYVDFSDDAHLEAGVAKNKQLLLGKKISIARSDPK--KGGHG--- 717

Query: 481 PTEQAQSHQQTGNAGTSASKESSIETSKQSRGRGDSVQLKGKNTFAVPRNVRPLGFPAIK 540
            T++A + ++  +  +  S + + + S   R  G+SV LKGKNTFAVPRNVR LG+   K
Sbjct: 718 -TDKAGAGKRFESRSSKESHKGNEQPSGVRRHGGNSVDLKGKNTFAVPRNVRALGWTTDK 776

Query: 541 PKTEEGEDLKPKSNDEFRKMFIK 563
           PKT E +D KPK+NDEFRK++ K
Sbjct: 777 PKTLEQDDEKPKTNDEFRKLYFK 799

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224129810|ref|XP_002328808.1| predicted protein [Populus trichocarpa] gi|222839106|gb|EEE77457.1| predicted protein [Populus trichocarpa]

 Score =  680 bits (1755), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 364/594 (61%), Positives = 433/594 (72%), Gaps = 57/594 (9%)

Query: 3   NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLD 62
           NARA  EEQIS Q++SD+EK Q +M YLK+E+S GDP RVQ+LYERA+ DFP+S DLWLD
Sbjct: 275 NARAQHEEQISMQNISDTEKIQNFMNYLKFEKSVGDPARVQVLYERAMADFPISIDLWLD 334

Query: 63  YTQYLDKTLK---------VGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEIS 113
           YT+YLD+TLK         VGNV+RDVYSRATKNCPW+GELWV+ +LSLER RA E+EIS
Sbjct: 335 YTRYLDRTLKIIYTLSLFQVGNVLRDVYSRATKNCPWIGELWVQYMLSLERGRAPEKEIS 394

Query: 114 TVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSE 173
           +VFEKSL C FST EEYLDLFLTR+ GLRRRI   GEV GVLDYSLIRETFQ ASDYLS 
Sbjct: 395 SVFEKSLQCTFSTIEEYLDLFLTRVHGLRRRIECGGEVNGVLDYSLIRETFQHASDYLSP 454

Query: 174 QMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI------------SGAMLEAWQ 221
            +KNTDGLLRLYAYWA LE ++GKD+V+AR VWE LLKI            +G+ LEAWQ
Sbjct: 455 HLKNTDGLLRLYAYWARLEMNLGKDLVAARRVWESLLKIRHTIYSIHLVLPNGSTLEAWQ 514

Query: 222 SYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT 281
            +I+ME E  HI+EARSIYKRC+SKRF GTGSEDICH+WLRFE E+GTLE FDH++QKVT
Sbjct: 515 GFIAMETESGHISEARSIYKRCFSKRFPGTGSEDICHSWLRFEEEFGTLEAFDHAIQKVT 574

Query: 282 PRLEELRLFRSQQESKSLPESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKP 341
           PRLEEL+L+R QQE+K+   S DQ E S KK  REKRK  S  + ++SPAKRQK   Q  
Sbjct: 575 PRLEELKLYRIQQETKA---STDQSEVSGKKIAREKRKGGSTATDKESPAKRQKQTAQTQ 631

Query: 342 KKVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINL 401
           KK ++ +K Q+Q   E NE +E K  +E+        D+ P       DE     S++  
Sbjct: 632 KKGYE-DKDQLQKY-EVNEAQEAKIDLEK-------TDSAP-------DEKQMKGSDV-- 673

Query: 402 KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKK 461
            A  ED+R+FFSDVGGV+SIRILHD+ TGKSRGLAYVDF+DDEHLAAA+ KNKQ+  GK+
Sbjct: 674 -ANSEDIRKFFSDVGGVASIRILHDRNTGKSRGLAYVDFVDDEHLAAAITKNKQLLFGKR 732

Query: 462 LSIARSNPKQ-RKDSSGERAPTEQAQSHQQTGNAGTSASKESSIETSKQSRGR------- 513
           LSIARS+PKQ R+D  G R P EQA +  +  +   SASKE  ++T   S  +       
Sbjct: 733 LSIARSDPKQNRRD--GRRVPREQAFASDRRRHNWESASKE-YVDTHNASGSQEAPQTAT 789

Query: 514 ---GDSVQLKGKNTFAVPRNVRPLGFPAIKPKTEEGEDLKPKSNDEFRKMFIKK 564
               D++Q KGKN FAVPRNVR LG  A K KT E  D KPKSNDEFRKMFIK+
Sbjct: 790 LKSDDNIQFKGKNIFAVPRNVRTLGLSANKSKTVEEGDEKPKSNDEFRKMFIKE 843

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30686462|ref|NP_849551.1| protein embryo defective 140 [Arabidopsis thaliana] gi|332659481|gb|AEE84881.1| protein embryo defective 140 [Arabidopsis thaliana]

 Score =  644 bits (1660), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 329/573 (57%), Positives = 414/573 (72%), Gaps = 37/573 (6%)

Query: 1   MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLW 60
           M + RAHLEE IS+QDLSD+EKFQ++M Y+K+E++SGDP RVQ +YERA+ ++PVSSDLW
Sbjct: 272 MYSERAHLEENISKQDLSDTEKFQEFMNYIKFEKTSGDPTRVQAIYERAVAEYPVSSDLW 331

Query: 61  LDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSL 120
           +DYT YLDKTLKVG  +   YSRAT++CPW G+LW R LL+LER  ASE+EI  VFEKSL
Sbjct: 332 IDYTVYLDKTLKVGKAITHAYSRATRSCPWTGDLWARYLLALERGSASEKEIYDVFEKSL 391

Query: 121 LCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG 180
            C FS+FEEYLDL+LTR+DGLRRR+L +  +E  LDYSLIRETFQ+ASDYL+  M+NTD 
Sbjct: 392 QCTFSSFEEYLDLYLTRVDGLRRRMLSTRMLEA-LDYSLIRETFQQASDYLTPHMQNTDS 450

Query: 181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIY 240
           LL L+ YWA+LE ++GKD+  ARGVW+  LK SG ML AW +YI ME+ L HI EARSIY
Sbjct: 451 LLHLHTYWANLELNIGKDLAGARGVWDSFLKKSGGMLAAWHAYIDMEVHLGHIKEARSIY 510

Query: 241 KRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLP 300
           +RCY+++F GTGSEDIC  WLRFERE+G LE FD +VQKV PRLEEL+L R QQES  + 
Sbjct: 511 RRCYTRKFDGTGSEDICKGWLRFEREHGDLEHFDLAVQKVMPRLEELQLMRLQQESTPVK 570

Query: 301 ESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEENE 360
            SA  KEHS      +KRK++ N+  E+S AKRQK   +K +K  D   +     A +N 
Sbjct: 571 PSAGLKEHS-----SQKRKAEQNVE-EESLAKRQK---RKSQKEVDLGGQSATVPATKNV 621

Query: 361 GRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSS 420
             E  +T +    K+  +DA P + K + DECTAF+SN+++KA  ED+R+FF D GGV S
Sbjct: 622 KAENGKTADSD--KEETEDAKPLKPKVYRDECTAFISNLSVKAQEEDIRKFFGDDGGVDS 679

Query: 421 IRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKDSSGERA 480
           IRILH K TGK RGLAY DF+DDEHLAAA+AKN++MF GKK+SIARSNPK+ K     R 
Sbjct: 680 IRILHHKDTGKPRGLAYADFVDDEHLAAAIAKNRKMFFGKKISIARSNPKKGKKEFTRR- 738

Query: 481 PTEQAQSHQQTGNAGTSASKESSI--ETSKQSRG-------RGDSVQLKGKNTFAVPRNV 531
                      GN G+  SK+ S+  E +K   G       +G+ V+++GKNTFAVPRNV
Sbjct: 739 -----------GNDGSGNSKDPSLISEKAKAPLGGETEGERKGNEVEVRGKNTFAVPRNV 787

Query: 532 RPLGFPAIKPKTEEGEDLKPKSNDEFRKMFIKK 564
           +PLG+   KP  +E     PKSNDEFR MF+KK
Sbjct: 788 KPLGYTTPKPSADE----TPKSNDEFRNMFLKK 816

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18700131|gb|AAL77677.1| AT4g24270/T22A6_100 [Arabidopsis thaliana]

 Score =  642 bits (1655), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 328/573 (57%), Positives = 413/573 (72%), Gaps = 37/573 (6%)

Query: 1   MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLW 60
           M + RAHLEE IS+QDLSD+EKFQ++M Y+K+E++SGDP RVQ +YERA+ ++PVSSDLW
Sbjct: 272 MYSERAHLEENISKQDLSDTEKFQEFMNYIKFEKTSGDPTRVQAIYERAVAEYPVSSDLW 331

Query: 61  LDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSL 120
           +DYT YLDKTLKVG  +   YSRAT++CPW G+LW R LL+LER  ASE+EI  VFEKSL
Sbjct: 332 IDYTVYLDKTLKVGKAITHAYSRATRSCPWTGDLWARYLLALERGSASEKEIYDVFEKSL 391

Query: 121 LCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG 180
            C FS+FEEYLDL+LTR+DGLRRR+L +  +E  LDYSLIRETFQ+ASDYL+  M+NTD 
Sbjct: 392 QCTFSSFEEYLDLYLTRVDGLRRRMLSTRMLEA-LDYSLIRETFQQASDYLTPHMQNTDS 450

Query: 181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIY 240
           LL L+ YWA+LE ++GKD+  ARGVW+  LK SG ML AW +YI ME+ L HI EARSIY
Sbjct: 451 LLHLHTYWANLELNIGKDLAGARGVWDSFLKKSGGMLAAWHAYIDMEVHLGHIKEARSIY 510

Query: 241 KRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLP 300
           +RCY+++F GTGSEDIC  WLRFERE+G LE FD +VQKV PRLEEL+L R QQES  + 
Sbjct: 511 RRCYTRKFDGTGSEDICKGWLRFEREHGDLEHFDLAVQKVMPRLEELQLMRLQQESTPVK 570

Query: 301 ESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEENE 360
            SA  KEHS      +KRK++ N+  E+S AKRQK   +K +K  D   +     A +N 
Sbjct: 571 PSAGLKEHS-----SQKRKAEQNVE-EESLAKRQK---RKSQKEVDLGGQSATVPATKNV 621

Query: 361 GRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSS 420
             E  +T +    K+  +D  P + K + DECTAF+SN+++KA  ED+R+FF D GGV S
Sbjct: 622 KAENGKTADSD--KEETEDVKPLKPKVYRDECTAFISNLSVKAQEEDIRKFFGDDGGVDS 679

Query: 421 IRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKDSSGERA 480
           IRILH K TGK RGLAY DF+DDEHLAAA+AKN++MF GKK+SIARSNPK+ K     R 
Sbjct: 680 IRILHHKDTGKPRGLAYADFVDDEHLAAAIAKNRKMFFGKKISIARSNPKKGKKEFTRR- 738

Query: 481 PTEQAQSHQQTGNAGTSASKESSI--ETSKQSRG-------RGDSVQLKGKNTFAVPRNV 531
                      GN G+  SK+ S+  E +K   G       +G+ V+++GKNTFAVPRNV
Sbjct: 739 -----------GNDGSGNSKDPSLISEKAKAPLGGETEGERKGNEVEVRGKNTFAVPRNV 787

Query: 532 RPLGFPAIKPKTEEGEDLKPKSNDEFRKMFIKK 564
           +PLG+   KP  +E     PKSNDEFR MF+KK
Sbjct: 788 KPLGYTTPKPSADE----TPKSNDEFRNMFLKK 816

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30686466|ref|NP_194158.3| protein embryo defective 140 [Arabidopsis thaliana] gi|332659482|gb|AEE84882.1| protein embryo defective 140 [Arabidopsis thaliana]

 Score =  640 bits (1651), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 329/574 (57%), Positives = 414/574 (72%), Gaps = 38/574 (6%)

Query: 1   MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLW 60
           M + RAHLEE IS+QDLSD+EKFQ++M Y+K+E++SGDP RVQ +YERA+ ++PVSSDLW
Sbjct: 272 MYSERAHLEENISKQDLSDTEKFQEFMNYIKFEKTSGDPTRVQAIYERAVAEYPVSSDLW 331

Query: 61  LDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSL 120
           +DYT YLDKTLKVG  +   YSRAT++CPW G+LW R LL+LER  ASE+EI  VFEKSL
Sbjct: 332 IDYTVYLDKTLKVGKAITHAYSRATRSCPWTGDLWARYLLALERGSASEKEIYDVFEKSL 391

Query: 121 LCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG 180
            C FS+FEEYLDL+LTR+DGLRRR+L +  +E  LDYSLIRETFQ+ASDYL+  M+NTD 
Sbjct: 392 QCTFSSFEEYLDLYLTRVDGLRRRMLSTRMLEA-LDYSLIRETFQQASDYLTPHMQNTDS 450

Query: 181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIY 240
           LL L+ YWA+LE ++GKD+  ARGVW+  LK SG ML AW +YI ME+ L HI EARSIY
Sbjct: 451 LLHLHTYWANLELNIGKDLAGARGVWDSFLKKSGGMLAAWHAYIDMEVHLGHIKEARSIY 510

Query: 241 KRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLP 300
           +RCY+++F GTGSEDIC  WLRFERE+G LE FD +VQKV PRLEEL+L R QQES  + 
Sbjct: 511 RRCYTRKFDGTGSEDICKGWLRFEREHGDLEHFDLAVQKVMPRLEELQLMRLQQESTPVK 570

Query: 301 ESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEENE 360
            SA  KEHS      +KRK++ N+  E+S AKRQK   +K +K  D   +     A +N 
Sbjct: 571 PSAGLKEHS-----SQKRKAEQNVE-EESLAKRQK---RKSQKEVDLGGQSATVPATKNV 621

Query: 361 GRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSS 420
             E  +T +    K+  +DA P + K + DECTAF+SN+++KA  ED+R+FF D GGV S
Sbjct: 622 KAENGKTADSD--KEETEDAKPLKPKVYRDECTAFISNLSVKAQEEDIRKFFGDDGGVDS 679

Query: 421 IRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKDSSGERA 480
           IRILH K TGK RGLAY DF+DDEHLAAA+AKN++MF GKK+SIARSNPK+ K     R 
Sbjct: 680 IRILHHKDTGKPRGLAYADFVDDEHLAAAIAKNRKMFFGKKISIARSNPKKGKKEFTRR- 738

Query: 481 PTEQAQSHQQTGNA-GTSASKESSI--ETSKQSRG-------RGDSVQLKGKNTFAVPRN 530
                      GN  G+  SK+ S+  E +K   G       +G+ V+++GKNTFAVPRN
Sbjct: 739 -----------GNVDGSGNSKDPSLISEKAKAPLGGETEGERKGNEVEVRGKNTFAVPRN 787

Query: 531 VRPLGFPAIKPKTEEGEDLKPKSNDEFRKMFIKK 564
           V+PLG+   KP  +E     PKSNDEFR MF+KK
Sbjct: 788 VKPLGYTTPKPSADE----TPKSNDEFRNMFLKK 817

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	565
TAIR|locus:2135892	817	EMB140 "EMBRYO DEFECTIVE 140"	0.939	0.649	0.554	1.7e-155
ZFIN|ZDB-GENE-040724-10	952	sart3 "squamous cell carcinoma	0.584	0.346	0.301	1.1e-47
UNIPROTKB|F1N0I9	655	SART3 "Uncharacterized protein	0.672	0.580	0.265	2.2e-47
UNIPROTKB|F1RGA7	959	SART3 "Uncharacterized protein	0.582	0.343	0.298	2.2e-47
UNIPROTKB|E1BWJ0	731	SART3 "Uncharacterized protein	0.768	0.593	0.284	4.7e-47
RGD|1311646	960	Sart3 "squamous cell carcinoma	0.633	0.372	0.280	9.7e-47
UNIPROTKB|E2QXZ2	1082	SART3 "Uncharacterized protein	0.594	0.310	0.290	9.9e-47
MGI|MGI:1858230	962	Sart3 "squamous cell carcinoma	0.644	0.378	0.272	1.6e-46
UNIPROTKB|Q15020	963	SART3 "Squamous cell carcinoma	0.594	0.348	0.282	5.7e-44
UNIPROTKB|F1NUL7	857	SART3 "Uncharacterized protein	0.571	0.376	0.295	4.7e-39

TAIR|locus:2135892 EMB140 "EMBRYO DEFECTIVE 140" [Arabidopsis thaliana (taxid:3702)]

 Score = 1516 (538.7 bits), Expect = 1.7e-155, P = 1.7e-155
 Identities = 302/545 (55%), Positives = 384/545 (70%)

Query:     1 MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLW 60
             M + RAHLEE IS+QDLSD+EKFQ++M Y+K+E++SGDP RVQ +YERA+ ++PVSSDLW
Sbjct:   272 MYSERAHLEENISKQDLSDTEKFQEFMNYIKFEKTSGDPTRVQAIYERAVAEYPVSSDLW 331

Query:    61 LDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVXXXXXXXXXXXXXXXISTVFEKSL 120
             +DYT YLDKTLKVG  +   YSRAT++CPW G+LW                I  VFEKSL
Sbjct:   332 IDYTVYLDKTLKVGKAITHAYSRATRSCPWTGDLWARYLLALERGSASEKEIYDVFEKSL 391

Query:   121 LCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG 180
              C FS+FEEYLDL+LTR+DGLRRR+L +  +E  LDYSLIRETFQ+ASDYL+  M+NTD 
Sbjct:   392 QCTFSSFEEYLDLYLTRVDGLRRRMLSTRMLEA-LDYSLIRETFQQASDYLTPHMQNTDS 450

Query:   181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIY 240
             LL L+ YWA+LE ++GKD+  ARGVW+  LK SG ML AW +YI ME+ L HI EARSIY
Sbjct:   451 LLHLHTYWANLELNIGKDLAGARGVWDSFLKKSGGMLAAWHAYIDMEVHLGHIKEARSIY 510

Query:   241 KRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLP 300
             +RCY+++F GTGSEDIC  WLRFERE+G LE FD +VQKV PRLEEL+L R QQES  + 
Sbjct:   511 RRCYTRKFDGTGSEDICKGWLRFEREHGDLEHFDLAVQKVMPRLEELQLMRLQQESTPVK 570

Query:   301 ESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEENE 360
              SA  KEHS      +KRK++ N+  E+S AKRQK   QK  +V D   +     A +N 
Sbjct:   571 PSAGLKEHS-----SQKRKAEQNVE-EESLAKRQKRKSQK--EV-DLGGQSATVPATKNV 621

Query:   361 GRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSS 420
               E  +T +    K+  +DA P + K + DECTAF+SN+++KA  ED+R+FF D GGV S
Sbjct:   622 KAENGKTADSD--KEETEDAKPLKPKVYRDECTAFISNLSVKAQEEDIRKFFGDDGGVDS 679

Query:   421 IRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKDSSGERA 480
             IRILH K TGK RGLAY DF+DDEHLAAA+AKN++MF GKK+SIARSNPK+ K     R 
Sbjct:   680 IRILHHKDTGKPRGLAYADFVDDEHLAAAIAKNRKMFFGKKISIARSNPKKGKKEFTRRG 739

Query:   481 PTEQAQSHQQTGNAGTSASKESSIETSKQSRGRGDSVQLKGKNTFAVPRNVRPLGFPAIK 540
               + + + +        A      ET  +   +G+ V+++GKNTFAVPRNV+PLG+   K
Sbjct:   740 NVDGSGNSKDPSLISEKAKAPLGGET--EGERKGNEVEVRGKNTFAVPRNVKPLGYTTPK 797

Query:   541 PKTEE 545
             P  +E
Sbjct:   798 PSADE 802

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0006396 "RNA processing" evidence=IEA

GO:0009793 "embryo development ending in seed dormancy" evidence=NAS

GO:0009560 "embryo sac egg cell differentiation" evidence=RCA

ZFIN|ZDB-GENE-040724-10 sart3 "squamous cell carcinoma antigen recognised by T cells 3" [Danio rerio (taxid:7955)]

 Score = 400 (145.9 bits), Expect = 1.1e-47, Sum P(2) = 1.1e-47
 Identities = 107/355 (30%), Positives = 168/355 (47%)

Query:    17 LSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNV 76
             +S+  K  +Y  Y+ +E   GDP RVQ+++ RA+ +  +  DLW+ YT YLD+ LK+ ++
Sbjct:   285 VSEPPKLAEYQSYIDFEIKEGDPARVQIIFGRALAENCLVPDLWIKYTTYLDRQLKIKDL 344

Query:    77 VRDVYSRATKNCPWVGELWVXXXXXXXXXXXXXXXISTVFEKSLLCAFSTFEEYLDLFLT 136
             V   + RA +NCPW   LW                +  VFEK+L   F    +Y++++ +
Sbjct:   345 VLSAHERAVRNCPWTMGLWKSYLLALERHGADHQTVKDVFEKALNAGFIQATDYVEIWQS 404

Query:   137 RIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMK---NTDGLLR--LYAYWAHL 191
              +D LRRR+ FS E    LD   +R  F R+ +YL + ++   +  G L   L   WA +
Sbjct:   405 YLDYLRRRVDFSKEWSRELDE--LRAAFSRSLEYLKQDVEERFSESGDLSCTLMQIWARI 462

Query:   192 EQSMGKDMVSARGVWERLL-KISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTG 250
             E    K+M  AR +W+ ++ K +      W  Y ++E         R    R    + T 
Sbjct:   463 EALHCKNMQKARELWDSIMTKGNAKYANMWLEYYNLERSYGDAAHCRKALHRAV--QCTS 520

Query:   251 TGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLPESADQKEHSV 310
                E +C   L FER  G+LED+D +VQK   +L  +   R++   K   E+   ++   
Sbjct:   521 DYPEHVCDVLLNFERVEGSLEDWDAAVQKTETKLNRVCEQRARVAEK---EALHARQEEE 577

Query:   311 KKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEENEGRETK 365
             K   R K K+D          K QK   QK  +  DK K +  +  EE  G E +
Sbjct:   578 KAEQRRKVKADK---------KAQKKG-QKANRTGDKRKAEDDD--EEEWGEEAE 620

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0000245 "spliceosomal complex assembly" evidence=IMP

GO:0031017 "exocrine pancreas development" evidence=IMP

GO:0030098 "lymphocyte differentiation" evidence=IMP

GO:0048538 "thymus development" evidence=IMP

UNIPROTKB|F1N0I9 SART3 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 406 (148.0 bits), Expect = 2.2e-47, Sum P(2) = 2.2e-47
 Identities = 106/399 (26%), Positives = 185/399 (46%)

Query:    18 SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVV 77
             +++ +  +Y  Y+ +E   GDP R+QL++ERA+ +  +  DLW+ Y+QYLD+ LKV ++V
Sbjct:     3 AEAPRLAEYQAYIDFEMKIGDPARIQLIFERALVENCLVPDLWIRYSQYLDRQLKVKDLV 62

Query:    78 RDVYSRATKNCPWVGELWVXXXXXXXXXXXXXXXISTVFEKSLLCAFSTFEEYLDLFLTR 137
                +SRA +NCPW   LW                IS  FEK+L   F    +Y++++   
Sbjct:    63 LSAHSRAVRNCPWTVALWSRYLLALERHGVEHRVISVTFEKALSAGFIQATDYVEIWQAY 122

Query:   138 IDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNT-----DGLLRLYAYWAHLE 192
             +D LRRR+ F  +    L+   +R  F RA +YL ++++       D    +   WA +E
Sbjct:   123 LDYLRRRVDFKQDSSKELEE--LRSAFARALEYLKQEVEERFSESGDPSCLIMQNWARIE 180

Query:   193 QSMGKDMVSARGVWERLLKISGAML-EAWQSYISMEIELDHINEARSIYKRCYSKRFTGT 251
               +  +M  AR +W+ ++    A     W  Y ++E         R    R    + T  
Sbjct:   181 ARLCNNMQKARELWDSIMTRGNAKFANMWLEYYNLERAHGDTQHCRKALHRAV--QCTSD 238

Query:   252 GSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLPESADQKEHSVK 311
               E +C   L  ER  GTLED+D +VQK   RL  +    ++Q  K+  + A   +   +
Sbjct:   239 YPEHVCEVLLTMERTEGTLEDWDIAVQKTETRLARV----NEQRIKAAEKEAALAQQEEE 294

Query:   312 KTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEE-NEGRETKQTVEE 370
             K  + KR      + ++   K++     K +   D EK    +  E+ ++ R  + +V  
Sbjct:   295 KVEQRKRARAEKKALKK---KKKTRGADKHRADEDDEKEWGDDEEEQPSKRRRVENSVPP 351

Query:   371 QPKKQPIKDA-VPGRTKGFTDECTAFLSNINLKATYEDL 408
               + +P  +A + G +     E  + L  + + A   D+
Sbjct:   352 AGEAEPGSEADLSGSSAPAATESPSELKEVRVGARRRDV 390

GO:0043231 "intracellular membrane-bounded organelle" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1RGA7 SART3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 412 (150.1 bits), Expect = 2.2e-47, Sum P(2) = 2.2e-47
 Identities = 106/355 (29%), Positives = 176/355 (49%)

Query:    18 SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVV 77
             +++ +  +Y  Y+ +E   GDP R+QL++ERA+ +  +  DLW+ Y+QYLD+ LKV ++V
Sbjct:   306 AEAPRLAEYQAYIDFEMKIGDPARIQLIFERALVENCLVPDLWIRYSQYLDRQLKVKDLV 365

Query:    78 RDVYSRATKNCPWVGELWVXXXXXXXXXXXXXXXISTVFEKSLLCAFSTFEEYLDLFLTR 137
               V+SRA +NCPW   LW                IS  FEK+L   F    +Y++++   
Sbjct:   366 LSVHSRAVRNCPWTVALWSRYLLAMERHGVDHRGISVTFEKALSAGFIQATDYVEIWQAY 425

Query:   138 IDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMK---NTDG--LLRLYAYWAHLE 192
             +D LRRR+ F  +    L+   +R  F RA +YL ++++   N  G     +   WA +E
Sbjct:   426 LDYLRRRVDFKQDSSKELEE--LRSAFARALEYLKQEVEERFNESGDPSCLIMQNWARIE 483

Query:   193 QSMGKDMVSARGVWERLL-KISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGT 251
               +  +M  AR +W+ ++ K +      W  Y ++E         R    R    + T  
Sbjct:   484 ARLCNNMQKARELWDSIMTKGNAKYANMWLEYYNLERAHGDTQHCRKALHRAV--QCTSD 541

Query:   252 GSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLPESADQKEHSVK 311
               E +C   L  ER  GTLED+D +VQK   RL  +    ++Q  K     A +KE ++ 
Sbjct:   542 YPEHVCEVLLTMERTEGTLEDWDIAVQKTETRLARV----NEQRIK-----AAEKEAALA 592

Query:   312 KTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEENEGRETKQ 366
             +  +E+ K++     ++  A+ +K A +K KK    EK  V    E+  G E ++
Sbjct:   593 Q--QEEEKAE-----QRKRARAEKKALKKKKKTRGAEKNMVDEDDEKEWGDEEEE 640

GO:0043231 "intracellular membrane-bounded organelle" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E1BWJ0 SART3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 495 (179.3 bits), Expect = 4.7e-47, P = 4.7e-47
 Identities = 130/457 (28%), Positives = 223/457 (48%)

Query:    18 SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVV 77
             +++ K  +Y  Y+ +E  +GDP R+QL+YERA+ +  +  DLW  Y QYLD+ LKV  +V
Sbjct:   269 AETPKLAEYQAYIDFEMKAGDPARIQLIYERALAENCLVPDLWARYNQYLDRQLKVKELV 328

Query:    78 RDVYSRATKNCPWVGELWVXXXXXXXXXXXXXXXISTVFEKSLLCAFSTFEEYLDLFLTR 137
                + RA +NCPW   LW+               IS +FEK+L   F    +Y++++   
Sbjct:   329 LSAHDRAVRNCPWTVGLWIQYLLAMERHGVDHCIISDMFEKALNAGFIQATDYVEIWQAY 388

Query:   138 IDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMG- 196
             +D LRRR+ F+ +    L+   +R  F RA +YL ++++       L    +H +  +G 
Sbjct:   389 LDYLRRRVDFTQDSSKELEE--LRSAFARAVEYLKQEVEELQTCRYLGQQASHGDLEIGG 446

Query:   197 -KDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGS-- 253
               ++V A   +  LL      L  +Q+YI  E++       + IY++   +    T    
Sbjct:   447 AAEVVGACSFY--LLGAETPKLAEYQAYIDFEMKAGDPARIQLIYEKALHRAVQCTSDYP 504

Query:   254 EDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESK--SLPESADQKEHSVK 311
             E +C   L  ER  GTLED+D +VQK   RL  +   R++   K   L E   +K+ + K
Sbjct:   505 EHVCEVLLTLERIEGTLEDWDAAVQKTENRLARVNEQRAKLRRKPSKLSEGGGKKKQTEK 564

Query:   312 KTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEENEGRETKQTVEEQ 371
                 EK  + +    E++  ++Q  A +K  K   K +   +  A++++  E  Q  EE 
Sbjct:   565 NRAAEKEAALARQEEEKAEQRKQSRAEKKASKKAKKNRIGEKRKADDDDEGEWGQEEEED 624

Query:   372 PKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYED--LRRFFSDVGGVSSIR-ILHDKF 428
             P +Q   D+         D  T F+SN++   T  +  L+  F   G VS +R +  +K 
Sbjct:   625 PLRQREHDS--------KDNITVFVSNLSYNMTDPEVKLKELFESCGEVSQVRPVFSNK- 675

Query:   429 TGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIA 465
              G  RG  YV+F D++    A+  ++++  G+ + ++
Sbjct:   676 -GTFRGYCYVEFKDEKSALQALGMDRKVVEGRPMFVS 711

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

RGD|1311646 Sart3 "squamous cell carcinoma antigen recognized by T-cells 3" [Rattus norvegicus (taxid:10116)]

 Score = 408 (148.7 bits), Expect = 9.7e-47, Sum P(2) = 9.7e-47
 Identities = 107/382 (28%), Positives = 179/382 (46%)

Query:    18 SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVV 77
             +++ +  +Y  Y+ +E   GDP R+QL++ERA+ +  +  DLW+ Y+QYLD+ LKV ++V
Sbjct:   304 AEAPRLAEYQAYIDFEMKVGDPARIQLIFERALVENCLVPDLWIRYSQYLDRQLKVKDLV 363

Query:    78 RDVYSRATKNCPWVGELWVXXXXXXXXXXXXXXXISTVFEKSLLCAFSTFEEYLDLFLTR 137
               V+SRA +NCPW   LW                IS  FE +L   F    +Y++++   
Sbjct:   364 LSVHSRAVRNCPWTVALWSRYLLAMERHGLDHQMISATFENALSAGFIQATDYVEIWQVY 423

Query:   138 IDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNT-----DGLLRLYAYWAHLE 192
             +D LRRR+ F  +    L+   +R  F RA +YL ++++       D    +   WA +E
Sbjct:   424 LDYLRRRVDFRQDSSKELEE--LRSMFTRALEYLQQEVEERFSESGDPSCLIMQSWARVE 481

Query:   193 QSMGKDMVSARGVWERLLKISGAML-EAWQSYISMEIELDHINEARSIYKRCYSKRFTGT 251
               +  +M  AR +W+ ++    A     W  Y ++E         R    R    + T  
Sbjct:   482 ARLCNNMQKARELWDSIMTRGNAKYANMWLEYYNLERAHGDTQHCRKALHRAV--QCTSD 539

Query:   252 GSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLPESADQKEHSVK 311
               E +C   L  ER  GTLED+D ++QK   RL  +    ++Q  K     A +KE ++ 
Sbjct:   540 YPEHVCEVLLTMERTEGTLEDWDLAIQKTETRLARV----NEQRMK-----AAEKEAALV 590

Query:   312 KTGREKRKSDSNISYEQSPAKRQK-HAPQKPKKVHDKEKRQVQNLAEENEGRETKQTVEE 370
             +   EK +    +  E+   K++K     K K   D ++R+     EE E + +K+   E
Sbjct:   591 QQEEEKAEQRKKVRAEKKALKKKKTRGADKRKAGEDDDEREC---GEEEEEQPSKRRRME 647

Query:   371 QPKKQPIKDAVPGRTKGFTDEC 392
                   +  A    TK  + +C
Sbjct:   648 NSLASGVASAKEEETK-LSGKC 668

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0006396 "RNA processing" evidence=IEA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IEA;ISO

UNIPROTKB|E2QXZ2 SART3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 413 (150.4 bits), Expect = 9.9e-47, Sum P(2) = 9.9e-47
 Identities = 105/362 (29%), Positives = 181/362 (50%)

Query:    18 SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVV 77
             +++ +  +Y  Y+ +E   GDP RVQL++ERA+ +  +  DLW+ Y+QYLD+ LKV ++V
Sbjct:   424 AEAPRLAEYQAYIDFEMKIGDPARVQLIFERALVENCLVPDLWIRYSQYLDRQLKVKDLV 483

Query:    78 RDVYSRATKNCPWVGELWVXXXXXXXXXXXXXXXISTVFEKSLLCAFSTFEEYLDLFLTR 137
               V++RA +NCPW   LW                IS  FEK+L   F    +Y++++   
Sbjct:   484 LSVHNRAVRNCPWTVALWTRYLLAMERHGVDHRVISVTFEKALSAGFIQATDYVEIWQAY 543

Query:   138 IDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMK---NTDG--LLRLYAYWAHLE 192
             +D LRRR+ F  +    L+   +R  F RA +YL ++++   N  G     +   WA +E
Sbjct:   544 LDYLRRRVDFKQDSSKELEE--LRSAFTRALEYLKQEVEERFNESGDPSCMIMQNWARIE 601

Query:   193 QSMGKDMVSARGVWERLL-KISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGT 251
               +  +M  AR +W+ ++ K +      W  Y ++E         R    R    + T  
Sbjct:   602 ARLCNNMQKARELWDSIMTKGNAKYANMWLEYYNLERAHGDTQHCRKALHRAV--QCTSD 659

Query:   252 GSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLPESADQKEHSVK 311
               E +C   L  ER  GTLED+D +VQK   RL  +    ++Q  K     A +KE ++ 
Sbjct:   660 YPEHVCEVLLTMERTEGTLEDWDIAVQKTETRLARV----NEQRIK-----AAEKEAALA 710

Query:   312 KTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEENEGRETKQTVEEQ 371
             +  +E+ K++     ++  A+ +K A +K KK    +KR+ +   E+  G + ++   ++
Sbjct:   711 Q--QEEEKAE-----QRKRARAEKKALKKKKKTRGADKRKAEEDDEKEWGDDEEEQPSKR 763

Query:   372 PK 373
              K
Sbjct:   764 RK 765

GO:0006396 "RNA processing" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:1858230 Sart3 "squamous cell carcinoma antigen recognized by T cells 3" [Mus musculus (taxid:10090)]

 Score = 406 (148.0 bits), Expect = 1.6e-46, Sum P(2) = 1.6e-46
 Identities = 104/382 (27%), Positives = 176/382 (46%)

Query:    18 SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVV 77
             +++ +  +Y  Y+ +E   GDP R+QL++ERA+ +  +  DLW+ Y+QYLD+ LKV ++V
Sbjct:   306 AEAPRLAEYQAYIDFEMKIGDPARIQLIFERALVENCLVPDLWIRYSQYLDRQLKVKDLV 365

Query:    78 RDVYSRATKNCPWVGELWVXXXXXXXXXXXXXXXISTVFEKSLLCAFSTFEEYLDLFLTR 137
               V+SRA +NCPW   LW                IS  FE +L   F    +Y++++   
Sbjct:   366 LSVHSRAVRNCPWTVALWSRYLLAMERHGLDHQTISATFENALSAGFIQATDYVEIWQVY 425

Query:   138 IDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNT-----DGLLRLYAYWAHLE 192
             +D LRRR+ F  +    L+   +R  F RA +YL ++++       D    +   WA +E
Sbjct:   426 LDYLRRRVDFRQDSSKELEE--LRSMFTRALEYLQQEVEERFSESGDPSCLIMQSWARVE 483

Query:   193 QSMGKDMVSARGVWERLLKISGAML-EAWQSYISMEIELDHINEARSIYKRCYSKRFTGT 251
               +  +M  AR +W+ ++    A     W  Y ++E         R    R    + T  
Sbjct:   484 ARLCNNMQKARELWDSIMTRGNAKYANMWLEYYNLERAHGDTQHCRKALHRAV--QCTSD 541

Query:   252 GSEDICHAWLRFEREYGTLEDFDHSVQKVTPRL---EELRLFRSQQESKSLPESADQKEH 308
               E +C   L  ER  GTLED+D ++QK   RL    E R+  +++E+ +L +  ++K  
Sbjct:   542 YPEHVCEVLLTMERTEGTLEDWDLAIQKTETRLARVNEQRMKAAEKEA-ALVQQEEEKAE 600

Query:   309 SVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKE----KRQVQNLAEENEGRET 364
               KK   EK+          +  +R+    +      ++E    +R+ +N     E    
Sbjct:   601 QRKKVRAEKKALKKKKKTRGADKRREDEDEENEWGEEEEEQPSKRRRTENSLASGEASAM 660

Query:   365 KQTVEEQPKKQPIKDAVPGRTK 386
             K+  E   K   I    P + K
Sbjct:   661 KEETELSGKCLTIDVGPPSKQK 682

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q15020 SART3 "Squamous cell carcinoma antigen recognized by T-cells 3" [Homo sapiens (taxid:9606)]

 Score = 399 (145.5 bits), Expect = 5.7e-44, Sum P(2) = 5.7e-44
 Identities = 99/351 (28%), Positives = 171/351 (48%)

Query:    18 SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVV 77
             +++ +  +Y  Y+ +E   GDP R+QL++ERA+ +  +  DLW+ Y+QYLD+ LKV ++V
Sbjct:   305 AEAPRLAEYQAYIDFEMKIGDPARIQLIFERALVENCLVPDLWIRYSQYLDRQLKVKDLV 364

Query:    78 RDVYSRATKNCPWVGELWVXXXXXXXXXXXXXXXISTVFEKSLLCAFSTFEEYLDLFLTR 137
               V++RA +NCPW   LW                IS  FEK+L   F    +Y++++   
Sbjct:   365 LSVHNRAIRNCPWTVALWSRYLLAMERHGVDHQVISVTFEKALNAGFIQATDYVEIWQAY 424

Query:   138 IDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMK---NTDG--LLRLYAYWAHLE 192
             +D LRRR+ F  +    L+   +R  F RA +YL ++++   N  G     +   WA +E
Sbjct:   425 LDYLRRRVDFKQDSSKELEE--LRAAFTRALEYLKQEVEERFNESGDPSCVIMQNWARIE 482

Query:   193 QSMGKDMVSARGVWERLLKISGAML-EAWQSYISMEIELDHINEARSIYKRCYSKRFTGT 251
               +  +M  AR +W+ ++    A     W  Y ++E         R    R    + T  
Sbjct:   483 ARLCNNMQKARELWDSIMTRGNAKYANMWLEYYNLERAHGDTQHCRKALHRAV--QCTSD 540

Query:   252 GSEDICHAWLRFEREYGTLEDFDHSVQKVTPRL---EELRLFRSQQESKSLPESADQKEH 308
               E +C   L  ER  G+LED+D +VQK   RL    E R+  +++E+  + +  ++ E 
Sbjct:   541 YPEHVCEVLLTMERTEGSLEDWDIAVQKTETRLARVNEQRMKAAEKEAALVQQEEEKAEQ 600

Query:   309 SVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEEN 359
               +K  R ++K+       + P KR      + +   D+E++  +    EN
Sbjct:   601 --RKRARAEKKALKKKKKIRGPEKRGADEDDEKEWGDDEEEQPSKRRRVEN 649

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IDA

UNIPROTKB|F1NUL7 SART3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 368 (134.6 bits), Expect = 4.7e-39, Sum P(2) = 4.7e-39
 Identities = 102/345 (29%), Positives = 162/345 (46%)

Query:    18 SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVV 77
             +++ K  +Y  Y+ +E  +GDP R+QL+YERA+ +  +  DLW  Y QYLD+ LKV  +V
Sbjct:   243 AETPKLAEYQAYIDFEMKAGDPARIQLIYERALAENCLVPDLWARYNQYLDRQLKVKELV 302

Query:    78 RDVYSRATKNCPWVGELWVXXXXXXXXXXXXXXXISTVFEKSLLCAFSTFEEYLDLFLTR 137
                + RA +NCPW   LW+               IS +FEK+L   F    +Y++++   
Sbjct:   303 LSAHDRAVRNCPWTVGLWIQYLLAMERHGVDHCIISDMFEKALNAGFIQATDYVEIWQAY 362

Query:   138 IDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNT-----DGLLRLYAYWAH-L 191
             +D LRRR+ F+ +    L+   +R  F RA +YL ++++       D    +   WA  +
Sbjct:   363 LDYLRRRVDFTQDSSKELEE--LRSAFARAVEYLKQEVEERFSESGDPSCTIMQNWAREI 420

Query:   192 EQSMGKDMVSARGVWERLLKISGAMLEA--WQSYISMEIELDHINEARSIYKRCYSKRFT 249
                  KD +    +W  LL   G   +A   + Y ++E         R    R    + T
Sbjct:   421 WLDWLKDEIKMASLWYDLLS-QGMPKDANMGREYYNLERAHGDTQHCRKALHRAV--QCT 477

Query:   250 GTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRL---EELRLFRSQQESKSLPESADQK 306
                 E +C   L  ER  GTLED+D +VQK   RL    E R    ++ SK   E+   +
Sbjct:   478 SDYPEHVCEVLLTLERIEGTLEDWDAAVQKTENRLARVNEQRAKLRRKPSKLNKENMSFQ 537

Query:   307 EHSVKKTGREKRKSDSN-ISYEQSPAKRQKHAPQKPKK-VHDKEK 349
              HS  +   ++ K D + +  E+      +  P+KP    + KEK
Sbjct:   538 FHSSAEQPSKRHKGDGDGLLLEEE----MESGPEKPDHPTNQKEK 578

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0043231 "intracellular membrane-bounded organelle" 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.00860083 hypothetical protein (844 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	565
smart00360	73	smart00360, RRM, RNA recognition motif	2e-15
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-14
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-13
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	3e-13
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-13
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-12
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-12
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-12
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-12
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	1e-11
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	5e-11
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	7e-11
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	8e-11
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	3e-10
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	5e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	5e-10
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	7e-10
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	9e-10
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-09
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	6e-09
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	8e-09
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	1e-08
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-08
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-08
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-08
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	5e-08
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	5e-08
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	6e-08
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	7e-08
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	7e-08
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	8e-08
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	9e-08
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	9e-08
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-07
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-07
cd12536	85	cd12536, RRM1_RBM39, RNA recognition motif 1 in ve	1e-07
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-07
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	3e-07
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	3e-07
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	3e-07
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	4e-07
cd12537	85	cd12537, RRM1_RBM23, RNA recognition motif 1 in ve	1e-06
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-06
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	1e-06
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	2e-06
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-06
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	3e-06
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	3e-06
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	5e-06
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	5e-06
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	7e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	8e-06
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	9e-06
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-05
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	2e-05
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	2e-05
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	2e-05
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	3e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	3e-05
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	4e-05
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	4e-05
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	4e-05
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	4e-05
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	5e-05
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	5e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	7e-05
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	1e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	1e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-04
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-04
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	1e-04
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	2e-04
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-04
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-04
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	2e-04
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	3e-04
cd12396	85	cd12396, RRM1_Nop13p_fungi, RNA recognition motif	3e-04
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	3e-04
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	3e-04
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	3e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	3e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	4e-04
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	4e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	4e-04
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	5e-04
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	5e-04
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	5e-04
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	6e-04
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	6e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	7e-04
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	7e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	8e-04
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	8e-04
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	8e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	8e-04
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	9e-04
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	0.001
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	0.001
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	0.001
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	0.001
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	0.001
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	0.001
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	0.001
cd12657	76	cd12657, RRM1_hnRNPM, RNA recognition motif 1 in v	0.002
smart00386	33	smart00386, HAT, HAT (Half-A-TPR) repeats	0.002
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	0.002
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	0.002
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	0.003
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	0.003
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	0.003
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	0.003
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.004
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	0.004
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	0.004
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	0.004
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	0.004

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

 Score = 71.1 bits (175), Expect = 2e-15
 Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T F+ N+    T E+LR  FS  G V S+R++ DK TGKS+G A+V+F  +E    A+  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 453 -NKQMFLGKKLSI 464
            N +   G+ L +
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 73.1 bits (178), Expect = 4e-14
 Identities = 55/277 (19%), Positives = 103/277 (37%), Gaps = 17/277 (6%)

Query: 295 ESKSLPESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQN 354
           ES  L E   ++E+   +    K  +    S +           +K     ++++   + 
Sbjct: 22  ESGKLTELLLKEEYGGLEEANSKELNLEVNSRKIESEISPP--SKKRLLSSERKEENERE 79

Query: 355 LAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSD 414
           + E+N+G        E+   +  +     +     +  T F+ N+    T EDLR  F  
Sbjct: 80  MEEQNDGERGYTKEFEEELFRSSESPKSRQKS-KEENNTLFVGNLPYDVTEEDLRELFKK 138

Query: 415 VGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV-AKNKQMFLGKKL--SIARSNPKQ 471
            G V  +R++ D+ TGKSRG A+V+F  +E    A+   N +   G+ L    A+   + 
Sbjct: 139 FGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQP 198

Query: 472 RKDSSG-------ERAPTEQAQSHQQTGN----AGTSASKESSIETSKQSRGRGDSVQLK 520
           R + S        ++    +A   +++ N         + E  +    +SRG      L 
Sbjct: 199 RSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLP 258

Query: 521 GKNTFAVPRNVRPLGFPAIKPKTEEGEDLKPKSNDEF 557
                 +P++   +G  A K   E       K     
Sbjct: 259 PSKDGKIPKSRSFVGNEASKDALESNSRGNKKKILGR 295

Length = 306

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

 Score = 65.3 bits (160), Expect = 2e-13
 Identities = 26/72 (36%), Positives = 43/72 (59%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T F+  ++LK    DL  FFS  G V  +RI+ D+ + +S+G+AYV+F D+E +  A+  
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGL 60

Query: 453 NKQMFLGKKLSI 464
             Q  LG+ + +
Sbjct: 61  TGQRLLGQPIMV 72

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

 Score = 64.6 bits (158), Expect = 3e-13
 Identities = 24/70 (34%), Positives = 43/70 (61%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+ N++   T E+L+  F   G ++ I IL DKFTG+ +G AY++F+D   +  A+  N+
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNE 62

Query: 455 QMFLGKKLSI 464
             F G+++ +
Sbjct: 63  SEFRGRQIKV 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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 64.6 bits (158), Expect = 3e-13
 Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
             ++ N+    T EDL+  F   G V+S R++ D+ TG+SRG  +V+    E   AA+ K
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 453 -NKQMFLGKKLSIARSNP 469
            N   F G+ L++  + P
Sbjct: 61  LNGTDFGGRTLTVNEARP 78

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

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

 Score = 63.0 bits (154), Expect = 1e-12
 Identities = 28/69 (40%), Positives = 42/69 (60%), Gaps = 2/69 (2%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV-AKN 453
           F+ N+    T EDL+  FS  G + SIRI+ D  TG+S+G A+V+F D+E    A+ A N
Sbjct: 2   FVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 454 KQMFLGKKL 462
            +   G++L
Sbjct: 61  GKELGGREL 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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 62.3 bits (152), Expect = 2e-12
 Identities = 28/71 (39%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+ N+    T EDLR  FS  G + S+RI+ DK  GKS+G A+V+F   E    A+   N
Sbjct: 2   FVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEALN 60

Query: 454 KQMFLGKKLSI 464
            +   G+KL +
Sbjct: 61  GKELDGRKLKV 71

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

 Score = 68.8 bits (168), Expect = 2e-12
 Identities = 43/186 (23%), Positives = 80/186 (43%), Gaps = 20/186 (10%)

Query: 291 RSQQESKSLPESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKR 350
           R +   ++    +D+     ++  R + +S      +    +R +   + P + +     
Sbjct: 5   RERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPRGD 64

Query: 351 QVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRR 410
           +     +   GR TK+ + E  +                D+ T F+  + LKA   DL  
Sbjct: 65  RSYRRDDRRSGRNTKEPLTEAER----------------DDRTVFVLQLALKARERDLYE 108

Query: 411 FFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGK----KLSIAR 466
           FFS VG V  ++ + D+ + +S+G+AYV+F D E +  A+A   QM LG+    + S A 
Sbjct: 109 FFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAE 168

Query: 467 SNPKQR 472
            N   +
Sbjct: 169 KNRAAK 174

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

 Score = 61.5 bits (150), Expect = 4e-12
 Identities = 28/71 (39%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+ NI   AT E L   FS+VG V S R++ D+ TGK +G  + +F D E  A+A+   N
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 454 KQMFLGKKLSI 464
              F G+ L +
Sbjct: 62  GYEFNGRALRV 72

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

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

 Score = 60.1 bits (146), Expect = 1e-11
 Identities = 25/73 (34%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T ++ N+    T +D+R FF     ++S+R+  DK TG+ +G  +VDF D+E L AA+  
Sbjct: 1   TVYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALKL 59

Query: 453 NKQMFLGKKLSIA 465
           +  +  G+ + IA
Sbjct: 60  DGTVLCGRPIRIA 72

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|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 58.5 bits (142), Expect = 5e-11
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 394 AFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEH-LAAAVAK 452
            F+ N+    T E+LR  F   G +S + +  DK T +S+G A+V F+  EH + A    
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 453 NKQMFLGKKLSI 464
           +  +F G+ L +
Sbjct: 62  DGSIFQGRLLHV 73

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

 Score = 57.9 bits (141), Expect = 7e-11
 Identities = 23/72 (31%), Positives = 39/72 (54%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           + F+ N+      E+LR+ F D G V ++RI+ D+ TG  +G  YV F   + +A A+  
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL 60

Query: 453 NKQMFLGKKLSI 464
           N     G+K+ +
Sbjct: 61  NGIKLKGRKIRV 72

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

 Score = 57.8 bits (140), Expect = 8e-11
 Identities = 26/76 (34%), Positives = 45/76 (59%), Gaps = 2/76 (2%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+S +    T E+L + F   G V S+R++ ++ +GK +GLAYV++ ++   + AV K +
Sbjct: 6   FVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVLKMD 64

Query: 454 KQMFLGKKLSIARSNP 469
                 K +S+A SNP
Sbjct: 65  GTEIKEKTISVAISNP 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|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 56.2 bits (136), Expect = 3e-10
 Identities = 25/70 (35%), Positives = 41/70 (58%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+ N+    T EDL   F + G   S+R+L DK TGKS+G A+V+F   E +  A+  + 
Sbjct: 4   FVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLHH 63

Query: 455 QMFLGKKLSI 464
            +  G+K+++
Sbjct: 64  TLLKGRKINV 73

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

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

 Score = 55.6 bits (134), Expect = 5e-10
 Identities = 24/70 (34%), Positives = 44/70 (62%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           ++ N++  AT E+L   F   G V+ + IL DKF+G  +G AY++F D E +  A+A ++
Sbjct: 3   YVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALDE 62

Query: 455 QMFLGKKLSI 464
            +F G+++ +
Sbjct: 63  SLFRGRQIKV 72

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 55.2 bits (134), Expect = 5e-10
 Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 2/67 (2%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           ++ N+    T EDLR FFS  G V  +R++ +K   + RG A+V+F   E   AA+ K  
Sbjct: 2   YVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKLN 59

Query: 455 QMFLGKK 461
            + L  +
Sbjct: 60  GLVLDGR 66

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

>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 = 55.4 bits (134), Expect = 7e-10
 Identities = 30/78 (38%), Positives = 44/78 (56%), Gaps = 5/78 (6%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
            T ++SN+    T  DL + FS  G V  + I+ DK T KS+G+A++ F+D E     V 
Sbjct: 2   STVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVK 61

Query: 452 --KNKQMFLGKKL--SIA 465
              NK++F G+ L  SIA
Sbjct: 62  ALNNKELF-GRTLKCSIA 78

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

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

 Score = 54.6 bits (132), Expect = 9e-10
 Identities = 23/78 (29%), Positives = 43/78 (55%), Gaps = 1/78 (1%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T F+ N++  A  +DL  FF + G V  +RI  D   G+S+G  +V+F  +E    A+ K
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDD-DGRSKGFGHVEFATEEGAQKALEK 59

Query: 453 NKQMFLGKKLSIARSNPK 470
           + +  LG+++ +  +  +
Sbjct: 60  SGEELLGREIRVDLATER 77

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

>gnl|CDD|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 = 54.9 bits (133), Expect = 1e-09
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+S ++ + T ++L   FS  G V  + ++ D  TG+SRG  +V F   E   AA+   N
Sbjct: 5   FVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDLN 64

Query: 454 KQMFLGKKLSIARS 467
            +   G+ + + ++
Sbjct: 65  GKELEGRVIKVEKA 78

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

>gnl|CDD|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 = 52.2 bits (126), Expect = 6e-09
 Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 2/66 (3%)

Query: 396 LSNINLKATYEDLRRFFSDVG-GVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           L  +   AT ED+R FFS +      I I++D   G+  G AYV+F   E    A+ K+ 
Sbjct: 4   LRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDD-GRPTGEAYVEFASPEDARRALRKHN 62

Query: 455 QMFLGK 460
               G+
Sbjct: 63  NKMGGR 68

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

 Score = 52.4 bits (126), Expect = 8e-09
 Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFID-DEHLAAAVAKN 453
           F+ N+      +DL + FS  G +S + +  DK +GKS+G AYV F+D ++ + A    +
Sbjct: 6   FVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKELD 65

Query: 454 KQMFLGKKLSI 464
            ++F G+ + I
Sbjct: 66  GKVFQGRLIHI 76

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

 Score = 51.4 bits (123), Expect = 1e-08
 Identities = 23/72 (31%), Positives = 44/72 (61%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           + ++ N++  +T E+L   FS  G ++ + IL DKF+G  +G AY++F   + + AAVA 
Sbjct: 1   SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVAL 60

Query: 453 NKQMFLGKKLSI 464
           ++  F G+ + +
Sbjct: 61  DESSFRGRVIKV 72

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

 Score = 51.9 bits (125), Expect = 2e-08
 Identities = 22/57 (38%), Positives = 34/57 (59%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           T F++ +N   T   LRR F + G +  IR++ DK TGK RG A+++F  +  + AA
Sbjct: 3   TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAA 59

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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 21/72 (29%), Positives = 47/72 (65%), Gaps = 1/72 (1%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T F+SN++     ++LR+ FS  G ++ +R++ + + GKS+G AYV+F ++E +  A+  
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKN-YKGKSKGYAYVEFENEESVQEALKL 59

Query: 453 NKQMFLGKKLSI 464
           ++++  G+ + +
Sbjct: 60  DRELIKGRPMFV 71

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

 Score = 50.8 bits (122), Expect = 2e-08
 Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV-AKN 453
           F+ N++  A  + +   F + G +SS+R+  D  +G+ +G  YV+F   E   AA+ A  
Sbjct: 2   FVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDALG 61

Query: 454 KQMFLGK 460
               LG+
Sbjct: 62  GTDLLGR 68

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

 Score = 50.0 bits (120), Expect = 5e-08
 Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 404 TYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV-AKNKQMFLGKKL 462
           T E+LR  F  +G + S +I+ D+ TG+S G  +VD++D+     A+   N      K+L
Sbjct: 13  TQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRL 72

Query: 463 SIA 465
            ++
Sbjct: 73  KVS 75

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

 Score = 49.6 bits (119), Expect = 5e-08
 Identities = 23/73 (31%), Positives = 36/73 (49%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
             F+ N+      ++L+ +FS  G V S  +  DK TG S+G  +V F   + L  A+ K
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 453 NKQMFLGKKLSIA 465
            K +  G KL + 
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|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 50.0 bits (120), Expect = 6e-08
 Identities = 27/78 (34%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
             F+  I    T E+LR FFS  G V  ++I+ D+  G S+G  +V F   E     +A 
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILAM 62

Query: 453 NKQMFLGKKLSIARSNPK 470
               F GKKL+I  +  K
Sbjct: 63  GNLNFRGKKLNIGPAIRK 80

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

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

 Score = 49.6 bits (119), Expect = 7e-08
 Identities = 25/68 (36%), Positives = 36/68 (52%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  +    T EDLR +FS  G V S+ I+ DK TGK RG A+V F D + +   V +  
Sbjct: 3   FVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQKY 62

Query: 455 QMFLGKKL 462
               G ++
Sbjct: 63  HTINGHRV 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|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 49.5 bits (119), Expect = 7e-08
 Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 6/76 (7%)

Query: 396 LSNINLKATYEDLRRFFSDVGG--VSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKN 453
           L  ++L  T ED+ +  S +    +  +R++ DK TG SRG A+V+F   E     +   
Sbjct: 7   LRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDAL 66

Query: 454 KQMF----LGKKLSIA 465
             +      G+ + ++
Sbjct: 67  NNLDPFVIDGRVVRVS 82

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

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

 Score = 49.1 bits (118), Expect = 8e-08
 Identities = 25/79 (31%), Positives = 34/79 (43%), Gaps = 2/79 (2%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
            T +++N        D+R  F   G + SIR    +F  K+R   YV F   E  AAAVA
Sbjct: 1   STLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRF-NKTRRFCYVQFTSPESAAAAVA 59

Query: 452 KNKQMFLGK-KLSIARSNP 469
                     KL +  S+P
Sbjct: 60  LLNGKLGEGYKLVVKISDP 78

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

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

 Score = 49.3 bits (118), Expect = 9e-08
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           TAF+ N+       DL   F D+  V S+R++ DK T K +G  YV+F D E L  A+  
Sbjct: 3   TAFVGNLPFNTVQGDLDAIFKDLS-VKSVRLVRDKETDKFKGFCYVEFEDVESLKEALEY 61

Query: 453 NKQMFLGKKLSI 464
           +  +F  + L +
Sbjct: 62  DGALFDDRSLRV 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|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 49.1 bits (117), Expect = 9e-08
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV---A 451
           F+ N+  +   E L R F   GG+  +RI+ D  T   +G AYV F D+  +  A+    
Sbjct: 3   FVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLNE 62

Query: 452 KNKQMFLGKKLSIAR 466
           K     L ++L ++R
Sbjct: 63  KKFPPMLPRELRVSR 77

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

 Score = 49.1 bits (118), Expect = 1e-07
 Identities = 30/82 (36%), Positives = 44/82 (53%), Gaps = 6/82 (7%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEH----LA 447
            T F+ N+   AT E+L+  FS  G V   RI+ DK TG S+G A+V F   E     L 
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 448 AA-VAKNKQMFL-GKKLSIARS 467
           AA  A++  + L G++L +  +
Sbjct: 61  AADNAEDSGLSLDGRRLIVTLA 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|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 49.1 bits (118), Expect = 1e-07
 Identities = 21/56 (37%), Positives = 31/56 (55%)

Query: 397 SNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           +N++  A  +DLR  F   G +S + +  DK TG+SRG A+V F   E    A+ K
Sbjct: 5   TNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

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|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)

 Score = 49.3 bits (117), Expect = 1e-07
 Identities = 24/81 (29%), Positives = 43/81 (53%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T F   +  +    DL  FFS VG V  +R++ D+ + +S+G+AYV+F+D   +  A+  
Sbjct: 3   TVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAIGL 62

Query: 453 NKQMFLGKKLSIARSNPKQRK 473
             Q  LG  + +  S  ++ +
Sbjct: 63  TGQRVLGVPIIVQASQAEKNR 83

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

 Score = 48.7 bits (116), Expect = 2e-07
 Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T F+ N+    T EDL  FFSDV  +    ++ D  TG+SRG  +V F   E    A+AK
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 453 -NKQMFLGKKLSI 464
              +   G+ L +
Sbjct: 61  LKNKKLHGRILRL 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|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 47.7 bits (114), Expect = 3e-07
 Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 398 NINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV-AKNKQM 456
           N+  + T +DLRR F   G V  + I  D++T +SRG A+V F D      A+ A + + 
Sbjct: 5   NLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKE 64

Query: 457 FLGKKLSIA 465
             G++L + 
Sbjct: 65  LDGRELRVQ 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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 47.8 bits (114), Expect = 3e-07
 Identities = 21/62 (33%), Positives = 30/62 (48%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T F+ N++     E L+  F   G V   R++ D+ TG+SRG  YVDF   E    A+  
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 453 NK 454
             
Sbjct: 61  MD 62

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

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 22/60 (36%), Positives = 35/60 (58%), Gaps = 3/60 (5%)

Query: 406 EDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK--NKQMFLGKKLS 463
            +LR++FS  G V+ +R+   K TGKS+G A+V+F   E +A  VA+  N  +   + L 
Sbjct: 14  PELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPE-VAKIVAETMNNYLLFERLLK 72

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

 Score = 47.5 bits (114), Expect = 3e-07
 Identities = 17/43 (39%), Positives = 23/43 (53%)

Query: 398 NINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDF 440
           +++   T   L   FS  G V SIR+  D  T +S G AYV+F
Sbjct: 6   DLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNF 48

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

 Score = 47.6 bits (114), Expect = 4e-07
 Identities = 19/68 (27%), Positives = 35/68 (51%)

Query: 391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV 450
             T F+  ++L+ T E LR  FS  G +  +R++ D  TG S+G A+V++  +     A 
Sbjct: 3   YLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAY 62

Query: 451 AKNKQMFL 458
               ++ +
Sbjct: 63  RDAHKLVI 70

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|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

 Score = 46.6 bits (110), Expect = 1e-06
 Identities = 24/83 (28%), Positives = 44/83 (53%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T F   +  +    DL  FFS VG V  +RI+ D+ + +S+G+AYV+F + + +  A+  
Sbjct: 3   TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGL 62

Query: 453 NKQMFLGKKLSIARSNPKQRKDS 475
             Q  LG  + +  S  ++ + +
Sbjct: 63  TGQRLLGVPIIVQASQAEKNRLA 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|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T F+ N+    T E L  FFS+VG +    ++ DK + K RG  YV F  +E    A+ +
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 453 -NKQMFLGKKLSI 464
             K  F G+K+ +
Sbjct: 61  KKKTKFGGRKIHV 73

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|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 = 45.9 bits (109), Expect = 1e-06
 Identities = 21/50 (42%), Positives = 33/50 (66%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDE 444
           F+ NI  +AT E L+  FS+VG V S R+++D+ TGK +G  + ++ D E
Sbjct: 2   FVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQE 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|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRI-LHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
           TA+L N+    T ED++ FF  +  VSS+R+       G+ RG  Y +F D + L  A++
Sbjct: 3   TAYLGNLPYDVTEEDIKEFFRGLN-VSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALS 61

Query: 452 KNKQMFLGKKLSI 464
            N +    +++ +
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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 21/71 (29%), Positives = 33/71 (46%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
              F+  +    T + LR++FS  G +    ++ D+ TGKSRG  +V F D E    A  
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 452 KNKQMFLGKKL 462
               +  G+K 
Sbjct: 61  DPNPIIDGRKA 71

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

 Score = 45.2 bits (107), Expect = 3e-06
 Identities = 17/61 (27%), Positives = 30/61 (49%)

Query: 391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV 450
            C  F+  +NLK +   LRR F+  G ++   ++ D  T +SRG  ++ F   +    A+
Sbjct: 2   LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61

Query: 451 A 451
            
Sbjct: 62  E 62

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

 Score = 45.1 bits (107), Expect = 3e-06
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+ N+    T EDL + FS  G +S + +  DK T K +G A+V ++  EH   A A+ +
Sbjct: 6   FIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAELD 65

Query: 454 KQMFLGKKLSI 464
             +F G+ L +
Sbjct: 66  GTVFQGRLLHL 76

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|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 = 44.1 bits (105), Expect = 5e-06
 Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 8/60 (13%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
            T ++ N+    T E+L+R FS  G +  +R+  DK      G A+V F  D H AAA A
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRF--DTHEAAATA 52

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

 Score = 44.9 bits (106), Expect = 5e-06
 Identities = 20/62 (32%), Positives = 28/62 (45%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T F+ N+   AT E L   FS  G V     + DK TG+++G  +V F D     A +  
Sbjct: 3   TLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKN 62

Query: 453 NK 454
             
Sbjct: 63  AP 64

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

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 44.2 bits (105), Expect = 7e-06
 Identities = 21/88 (23%), Positives = 34/88 (38%), Gaps = 17/88 (19%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRI----LHDKFTGKSRGL------------ 435
            T F+ N+ L    +DL++ F   G + S+R     + +K   K                
Sbjct: 1   RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60

Query: 436 -AYVDFIDDEHLAAAVAKNKQMFLGKKL 462
            AYV F ++E    A+  N   F G  +
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|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 43.8 bits (104), Expect = 8e-06
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRI---LHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
           ++ N++ K   +DLR  FS  G V SIRI     +K    + G A+V F D      A+ 
Sbjct: 4   YVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQ 63

Query: 452 KNKQMFLGKKLSIAR 466
            N     G+K+S++ 
Sbjct: 64  LNGTELGGRKISVSL 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|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 = 43.4 bits (103), Expect = 9e-06
 Identities = 26/76 (34%), Positives = 37/76 (48%), Gaps = 7/76 (9%)

Query: 395 FLSNINLKATYEDLRRFFSDVG--GVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           ++ N+    T EDL    ++ G   V SI+    K  GKS+G AYV+F  +   AAA  K
Sbjct: 2   YVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEA--AAAAVK 59

Query: 453 ---NKQMFLGKKLSIA 465
                + F GKK  + 
Sbjct: 60  EKLEGREFNGKKCVVT 75

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

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 396 LSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NK 454
           +SN++   T EDL   F  VG V  ++I +D+ +G+S G A V F   E    A+ + N 
Sbjct: 5   VSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQFNG 63

Query: 455 QMFLGKKLSIA 465
            +  G+ + + 
Sbjct: 64  VLLDGQPMQVE 74

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

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

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T ++ N++   T + L  FFS  G V  +R+  D+   +    A+V+F +   +  A+  
Sbjct: 6   TIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDE--TQPTRYAFVEFAEQTSVINALKL 63

Query: 453 NKQMFLGKKLSIARSN 468
           N  MF G+ L +  SN
Sbjct: 64  NGAMFGGRPLKVNHSN 79

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

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

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 18/64 (28%), Positives = 33/64 (51%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
           C  F+  ++ + T E LR +F   G V    ++ D  T +SRG  +V F+D   +   +A
Sbjct: 1   CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

Query: 452 KNKQ 455
           +++ 
Sbjct: 61  QSRH 64

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

 Score = 42.2 bits (99), Expect = 2e-05
 Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  +N + T + LR +F   G V+   ++ D  TG+SRG  ++ F         V K +
Sbjct: 2   FIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTF-KKPKSVNEVMKKE 60

Query: 455 QMFLGKKLSIARSNPK 470
            +  GK +   R+ P+
Sbjct: 61  HILDGKIIDPKRAIPR 76

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

>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 16/38 (42%), Positives = 24/38 (63%)

Query: 403 ATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDF 440
            T +DLR  F+  G +  I ++ DK T +S+G+AYV 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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 42.2 bits (99), Expect = 3e-05
 Identities = 19/65 (29%), Positives = 30/65 (46%)

Query: 407 DLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIAR 466
           DL   FS  G V    ++ DK TGK RG  +V F + +    A         G ++ + +
Sbjct: 15  DLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVKFHPINGHRVEVKK 74

Query: 467 SNPKQ 471
           + PK+
Sbjct: 75  AVPKE 79

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

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

 Score = 42.1 bits (99), Expect = 4e-05
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 2/74 (2%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+  I+ K    DLR+FFS  G V  ++I++D+  G S+G  +V F   E     + + N
Sbjct: 6   FVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKILQEAN 64

Query: 454 KQMFLGKKLSIARS 467
           +  F  KKL+I ++
Sbjct: 65  RLCFRDKKLNIGQA 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|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 42.0 bits (99), Expect = 4e-05
 Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 1/67 (1%)

Query: 404 TYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLG-KKL 462
           T E+ R  F  VG V + +I+ DK TG S G  +VD+   E    A+     + L  K++
Sbjct: 13  TDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRI 72

Query: 463 SIARSNP 469
            +A + P
Sbjct: 73  KVAYARP 79

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

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

 Score = 41.4 bits (98), Expect = 4e-05
 Identities = 20/57 (35%), Positives = 29/57 (50%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
           F+  ++   T E LR +FS  G V    I+ D  TG+SRG  +V F D   +   +A
Sbjct: 2   FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLA 58

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|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 = 41.4 bits (98), Expect = 4e-05
 Identities = 21/55 (38%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 398 NINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           N+  +AT ++LR  FS  G V S+R L  KF G  RG A+V+F+  +    A+  
Sbjct: 7   NVPFEATKKELRELFSPFGQVKSVR-LPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

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

 Score = 41.5 bits (98), Expect = 5e-05
 Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 2/57 (3%)

Query: 398 NINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
            ++L  T  DLR  FS  G +  +++++D+ TG+SRG  +V F   E   A  AK +
Sbjct: 6   GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVED--AKEAKER 60

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

 Score = 41.6 bits (98), Expect = 5e-05
 Identities = 19/75 (25%), Positives = 39/75 (52%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  +    T  DLR++FS  G V+ + +++D    + RG  ++ F  ++ +   V ++ 
Sbjct: 6   FVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNEHF 65

Query: 455 QMFLGKKLSIARSNP 469
               GKK+ + R+ P
Sbjct: 66  HDINGKKVEVKRAEP 80

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

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

 Score = 44.9 bits (106), Expect = 7e-05
 Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 11/80 (13%)

Query: 404 TYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-------KNKQM 456
           T E++R  F+ +G + S +++ DK TG+S G  +V+++  E    AV        +NK +
Sbjct: 16  TQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTI 75

Query: 457 FLGKKLSIARSNPKQRKDSS 476
               K+S AR +    K ++
Sbjct: 76  ----KVSYARPSSDSIKGAN 91

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

 Score = 41.0 bits (96), Expect = 1e-04
 Identities = 27/81 (33%), Positives = 45/81 (55%), Gaps = 5/81 (6%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T F+  I+++    ++R FF+  G V  ++I+ D+ TG S+G  +V F DD  +   V +
Sbjct: 7   TVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKIV-E 64

Query: 453 NKQMFLGKKLSIARSNPKQRK 473
           ++  F GKKL +    P  RK
Sbjct: 65  SQINFHGKKLKLG---PAIRK 82

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

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

 Score = 40.5 bits (95), Expect = 1e-04
 Identities = 19/48 (39%), Positives = 26/48 (54%)

Query: 403 ATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV 450
            T EDLR  F + G +  + I+ DK TG+S+G  YV F      A A+
Sbjct: 12  YTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 44.8 bits (106), Expect = 1e-04
 Identities = 31/96 (32%), Positives = 51/96 (53%), Gaps = 8/96 (8%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           ++ N++   T E LR  FS+ G ++S +++ D+  G SRG  +V F + E    AV + +
Sbjct: 289 YVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTEMH 347

Query: 454 KQMFLGKKLSIARSNPKQRKDSSGERAPTEQAQSHQ 489
            +M  GK L +A +   QRK+   +R    Q Q  Q
Sbjct: 348 GRMLGGKPLYVALA---QRKE---QRRAHLQDQFMQ 377

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

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           ++ N++   T +DLR  F   G +  +++  D  TG+S+G  ++ F D E    A+ +  
Sbjct: 2   YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61

Query: 455 QMFL-GKKLSI 464
              L G+ + +
Sbjct: 62  GFELAGRPIKV 72

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|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 = 39.9 bits (94), Expect = 1e-04
 Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 404 TYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV-AKNKQMFLGKKL 462
           T +DL + F+  G V S ++  DK TG+S+   +V + + E   AA+ A N     GK+L
Sbjct: 11  TDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRL 70

Query: 463 SI 464
            +
Sbjct: 71  KV 72

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

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

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 23/76 (30%), Positives = 36/76 (47%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  ++ + T E LRR+FS  G V    I+ DK T +SRG  +V F D   +   +A   
Sbjct: 3   FVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGGP 62

Query: 455 QMFLGKKLSIARSNPK 470
               G+ +      P+
Sbjct: 63  HTLDGRTIDPKPCTPR 78

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

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 18/57 (31%), Positives = 31/57 (54%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
           F+ +++ +   E LR  F+  G +S  R++ D  TGKS+G  +V F+  E    A+ 
Sbjct: 3   FVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQ 59

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

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           ++ N+      E L+  F   G ++S +++ D   GKS+G  +V+F + E    AV + N
Sbjct: 5   YVKNLGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVEELN 63

Query: 454 KQMFLGKKLSIARSNPK 470
            +   GKKL + R+  K
Sbjct: 64  GKEVNGKKLYVGRAQKK 80

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

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

 Score = 39.8 bits (93), Expect = 2e-04
 Identities = 19/60 (31%), Positives = 36/60 (60%), Gaps = 1/60 (1%)

Query: 406 EDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLA-AAVAKNKQMFLGKKLSI 464
           ++L+++FS  G V ++R+   K TG S+   ++ F++ E  A AA + N  + +GK L +
Sbjct: 14  KELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSMNNYLLMGKVLQV 73

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

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

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           + ++ N+      +DLRR F   G +  + I  D +T + RG AYV F D      A+  
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 453 -NKQMFLGKKLSIA 465
            ++  FLG+++ I 
Sbjct: 62  LDRTRFLGREIEIQ 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|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 22/60 (36%), Positives = 35/60 (58%), Gaps = 2/60 (3%)

Query: 399 INLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDF--IDDEHLAAAVAKNKQM 456
           ++L  T  DLR  FS  G ++ + +++D+ TG+SRG A+V F  IDD   A   A   ++
Sbjct: 7   LSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMEL 66

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

 Score = 39.6 bits (92), Expect = 3e-04
 Identities = 20/77 (25%), Positives = 35/77 (45%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  I        LR +F   G + +I ++ D+ +GK RG A+V F D + +   V +  
Sbjct: 4   FVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKY 63

Query: 455 QMFLGKKLSIARSNPKQ 471
               G    + ++  KQ
Sbjct: 64  HTINGHNCEVKKALSKQ 80

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

>gnl|CDD|240842 cd12396, RRM1_Nop13p_fungi, RNA recognition motif 1 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 39.8 bits (93), Expect = 3e-04
 Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 11/78 (14%)

Query: 398 NINLKATYEDLRRFFSDVGGV----SSIRILH-------DKFTGKSRGLAYVDFIDDEHL 446
           N++   T E LR+FF    G       I  +H        K   +++G AYVDF   E  
Sbjct: 5   NLSFTTTKEMLRQFFVSKSGDRITDEQITRVHMPDSKAKRKGVKQNKGFAYVDFTSQEAT 64

Query: 447 AAAVAKNKQMFLGKKLSI 464
            AA+A ++++  G+KL I
Sbjct: 65  KAAIALSEKILNGRKLLI 82

This subfamily corresponds to the RRM1 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 = 85

>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 = 39.3 bits (92), Expect = 3e-04
 Identities = 18/72 (25%), Positives = 34/72 (47%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  +    T E+ + +FS  G V   +++ D  TG+SRG  +V F  +  +    +   
Sbjct: 3   FVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAGM 62

Query: 455 QMFLGKKLSIAR 466
               GK++ + R
Sbjct: 63  LELGGKQVEVKR 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|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 39.3 bits (91), Expect = 3e-04
 Identities = 19/77 (24%), Positives = 35/77 (45%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  I        LR +F + G + +I I+ D+ +GK RG  +V F D + +   V +  
Sbjct: 4   FVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQKY 63

Query: 455 QMFLGKKLSIARSNPKQ 471
               G    + ++  +Q
Sbjct: 64  HTINGHNAEVRKALSRQ 80

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

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

 Score = 39.3 bits (91), Expect = 3e-04
 Identities = 19/67 (28%), Positives = 36/67 (53%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+ +++ + T ED++  F+  G +S  R++ D  TGKS+G  +V F +      A+    
Sbjct: 5   FVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMG 64

Query: 455 QMFLGKK 461
             +LG +
Sbjct: 65  GQWLGGR 71

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

 Score = 39.1 bits (92), Expect = 3e-04
 Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 9/81 (11%)

Query: 392 CTAFLSNI--NLKATYED-LRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAA 448
           C  F+  I  +L   +ED L   F   G +  +R++ D F+G +RG A+V + + E    
Sbjct: 2   CEVFVGKIPRDL---FEDELVPLFEKAGPIYELRLMMD-FSGLNRGYAFVTYTNKEAAQR 57

Query: 449 AVAK--NKQMFLGKKLSIARS 467
           AV +  N ++  GK+L +  S
Sbjct: 58  AVKQLHNYEIRPGKRLGVCIS 78

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

 Score = 39.1 bits (91), Expect = 4e-04
 Identities = 18/57 (31%), Positives = 33/57 (57%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
           +++N+  + T ++LR+ F   G +    +L DK TG  RG+A+V +   E   AA++
Sbjct: 4   YVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

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

 Score = 39.5 bits (93), Expect = 4e-04
 Identities = 18/71 (25%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFID-DEHLAAAVAKN 453
           F++ ++ +A  ED+   F++ G + ++ +  D+ TG  +G A +++    E  AA    N
Sbjct: 10  FVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGLN 69

Query: 454 KQMFLGKKLSI 464
            +  LG+ +S+
Sbjct: 70  GKELLGQTISV 80

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

>gnl|CDD|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 = 38.9 bits (91), Expect = 4e-04
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T  +  I+   + +DL+ FFS+ G V+ +R+  D     S   A+V+F D E   +A+  
Sbjct: 2   TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGD--RQHSARFAFVEFADAESALSALNL 59

Query: 453 NKQMFLGKKLSIARS 467
           +  +  G  L ++ S
Sbjct: 60  SGTLLGGHPLRVSPS 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|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 38.6 bits (90), Expect = 5e-04
 Identities = 17/67 (25%), Positives = 32/67 (47%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+ +++ + T   L   FS     S  R++ D  +G+SRG  +V F   +    A+ +  
Sbjct: 3   FVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEMN 62

Query: 455 QMFLGKK 461
             +LG +
Sbjct: 63  GKWLGSR 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|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 38.5 bits (90), Expect = 5e-04
 Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 402 KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKK 461
           K T +DL+ +FS  G +  +++  D  TG+S+G  +V F D E     V   + M  G+ 
Sbjct: 10  KTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYE-DQVKVLSQRHMIDGRW 68

Query: 462 LSIARSNPK 470
             +   N K
Sbjct: 69  CDVKIPNSK 77

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

>gnl|CDD|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 = 38.6 bits (90), Expect = 5e-04
 Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 2/66 (3%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
            T ++S+I+ + T E L   FS+ G V   R+  D         A+++F D+E   AA++
Sbjct: 3   RTVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGD--PNSVLRFAFIEFTDEEGARAALS 60

Query: 452 KNKQMF 457
            +  M 
Sbjct: 61  LSGTML 66

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

 Score = 38.5 bits (90), Expect = 6e-04
 Identities = 16/74 (21%), Positives = 34/74 (45%), Gaps = 3/74 (4%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           D+ + F+  ++   T E+L   FS  G +  + ++       +   A++ F  ++  A A
Sbjct: 2   DKYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKR--ANHTNAFAFIKFEREQAAARA 59

Query: 450 V-AKNKQMFLGKKL 462
           V ++N  M   K +
Sbjct: 60  VESENHSMLKNKTM 73

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|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 = 38.3 bits (90), Expect = 6e-04
 Identities = 18/46 (39%), Positives = 28/46 (60%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDF 440
           F+  +   AT ED+R  F + G +  + I+ DK TG+S+G A+V F
Sbjct: 3   FVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKF 48

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

 Score = 38.6 bits (89), Expect = 7e-04
 Identities = 16/47 (34%), Positives = 28/47 (59%)

Query: 404 TYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV 450
           T E+ R  F  +G + S +++ DK TG+S G  +V++ID +    A+
Sbjct: 15  TQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 38.2 bits (89), Expect = 7e-04
 Identities = 20/68 (29%), Positives = 34/68 (50%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  ++ + T E LR +FS  G +    ++ D  T +SRG  +V F D   +   +A+  
Sbjct: 2   FIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGP 61

Query: 455 QMFLGKKL 462
               GKK+
Sbjct: 62  HELDGKKI 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|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 37.8 bits (88), Expect = 8e-04
 Identities = 17/50 (34%), Positives = 32/50 (64%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDE 444
           F+ N++ + T ++LR  F  VG +  +R++  + +GK +G A+VDF + E
Sbjct: 2   FVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIE 51

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

 Score = 38.0 bits (89), Expect = 8e-04
 Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 398 NINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NKQM 456
           N+  K T  DL++ FS  G V  + I   K  GK +G A+V F        A+   N + 
Sbjct: 6   NLPFKCTEADLKKLFSPFGFVWEVTIPR-KPDGKKKGFAFVQFTSKADAEKAIKGVNGKK 64

Query: 457 FLGKKLSI 464
             G+ +++
Sbjct: 65  IKGRPVAV 72

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|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 38.1 bits (89), Expect = 8e-04
 Identities = 14/43 (32%), Positives = 24/43 (55%)

Query: 408 LRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV 450
           L   FS  G ++ + I  D+ TG S+G AY++F   + +  A+
Sbjct: 20  LTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKAL 62

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

 Score = 37.9 bits (89), Expect = 8e-04
 Identities = 17/46 (36%), Positives = 23/46 (50%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDF 440
           F+  ++   T  DL   FS  G VS + I+  K  G  RG AY+D 
Sbjct: 3   FVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDL 48

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

 Score = 38.2 bits (89), Expect = 9e-04
 Identities = 16/47 (34%), Positives = 30/47 (63%)

Query: 404 TYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV 450
           T +++R  FS +G + S +++ DK TG+S G  +V+++D E    A+
Sbjct: 14  TQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60

This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

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

 Score = 37.8 bits (87), Expect = 0.001
 Identities = 18/67 (26%), Positives = 37/67 (55%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+ +++ + T +D++  F+  G +S  R++ D  TGKS+G  +V F +      A+ +  
Sbjct: 5   FVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMG 64

Query: 455 QMFLGKK 461
             +LG +
Sbjct: 65  GQWLGGR 71

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

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 20/58 (34%), Positives = 28/58 (48%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           F+  +N   T EDL   FS  G + S  ++ DK TG S   A+++F   E    A  K
Sbjct: 7   FVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFK 64

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 10/72 (13%)

Query: 395 FLSNIN-LKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK- 452
           F+ N+N  K + EDL   FS  G +  I  LH       +G  +V F ++E   AAVA  
Sbjct: 4   FVGNLNTDKVSKEDLEEIFSKYGKILGIS-LH-------KGYGFVQFDNEEDARAAVAGE 55

Query: 453 NKQMFLGKKLSI 464
           N +   G+KL I
Sbjct: 56  NGREIAGQKLDI 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|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 37.8 bits (87), Expect = 0.001
 Identities = 16/47 (34%), Positives = 29/47 (61%)

Query: 404 TYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV 450
           T E+L+  F  +G + S +++ DK TG+S G  +V++ID +    A+
Sbjct: 17  TQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 63

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 19/70 (27%), Positives = 30/70 (42%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           D    F+ N+    T ++L+ FF + G V  +RI      G+     +V F D E +   
Sbjct: 2   DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKI 61

Query: 450 VAKNKQMFLG 459
           +A     F G
Sbjct: 62  LANKPIYFRG 71

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 14/38 (36%), Positives = 24/38 (63%)

Query: 408 LRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEH 445
           +   F++ G V+S++I+ +K TGKS G  +V+F   E 
Sbjct: 16  IYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEA 53

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

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSI-RILHDKF--TGKSRGLAYVDFIDDEHLAAAVA 451
           ++ N++ + T   L + FS  G +     + H      G+ RG  +V F   E    A+ 
Sbjct: 3   WIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALK 62

Query: 452 K-NKQMFLGKKLSI 464
             N +  LGKKL +
Sbjct: 63  SLNGKTALGKKLVV 76

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|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 3/73 (4%)

Query: 394 AFLSNINLKATYEDLRRFFSD-VGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           AF+SNI     ++ L+    + VG V+ + +L D   GKSRG A V+F  +E +  AV  
Sbjct: 2   AFISNIPFDVKWQSLKDLVKEKVGEVTYVELLMDA-EGKSRGCAVVEFKMEESMKKAVEV 60

Query: 453 -NKQMFLGKKLSI 464
            NK +  G+ L +
Sbjct: 61  LNKHVLNGRPLKV 73

This subgroup corresponds to the RRM1 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>gnl|CDD|214642 smart00386, HAT, HAT (Half-A-TPR) repeats

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 14/31 (45%), Positives = 20/31 (64%)

Query: 37 GDPGRVQLLYERAITDFPVSSDLWLDYTQYL 67
          GD  R + +YERA+  FP S +LWL Y ++ 
Sbjct: 1  GDIERARKIYERALEKFPKSVELWLKYAEFE 31

Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs. Length = 33

>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
            T  + N+    T   +R+FF D G +  ++I+  +  G     A ++F  ++   AA+ 
Sbjct: 1   LTVKVKNLPKDTTENKIRQFFKDCGEIREVKIVESE-GGLV---AVIEFETEDEALAALT 56

Query: 452 KNKQMFLGKKLSIAR 466
           K+ +   G ++S++R
Sbjct: 57  KDHKRLGGNEISVSR 71

This subfamily corresponds to the RRM1 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 = 71

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

 Score = 40.8 bits (95), Expect = 0.002
 Identities = 29/109 (26%), Positives = 51/109 (46%), Gaps = 2/109 (1%)

Query: 365 KQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRIL 424
           KQT   Q ++   +     R +     C  ++ +I+ +   + +RR F   G + SI + 
Sbjct: 81  KQTKAHQQQQLENQQRQQQRQQALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMS 140

Query: 425 HDKFTGKSRGLAYVDF-IDDEHLAAAVAKNKQMFLGKKLSIAR-SNPKQ 471
            D  TGK +G A+V++ + +    A    N QM  G+ + + R SN  Q
Sbjct: 141 WDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQ 189

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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 36.6 bits (84), Expect = 0.003
 Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 1/80 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+ N++ +A    L + F   G V++++++ D  T K +G  +V   + +  A A+A   
Sbjct: 5   FVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLN 64

Query: 455 QMFLGKK-LSIARSNPKQRK 473
              LG + L ++    KQ K
Sbjct: 65  GYRLGDRVLQVSFKTSKQHK 84

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|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGV-SSIRILHDKFTGKSRGLAYVDF 440
           T  L  + L  T ED+R      G     +R++  K TG SRG A+V+F
Sbjct: 4   TIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEF 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|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 36.5 bits (84), Expect = 0.003
 Identities = 16/46 (34%), Positives = 28/46 (60%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDF 440
           ++S +    T ++L + FS  G + + RIL D+ TG SRG+ ++ F
Sbjct: 4   YVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRF 49

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

 Score = 36.1 bits (83), Expect = 0.003
 Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 5/70 (7%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T F++N++ K  ++ L+  FS  G V    IL DK  GKSRG+  V F  ++ + A  A 
Sbjct: 2   TVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDK-DGKSRGIGTVTF--EQPIEAVQAI 58

Query: 453 NKQMFLGKKL 462
           +  MF G+ L
Sbjct: 59  S--MFNGQLL 66

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

 Score = 39.8 bits (93), Expect = 0.004
 Identities = 28/100 (28%), Positives = 49/100 (49%), Gaps = 9/100 (9%)

Query: 385 TKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDE 444
            K FT+    ++ N++     + LR  F+  G ++S  ++ D  +G+SRG A+V+F   E
Sbjct: 175 LKKFTN---LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHE 230

Query: 445 HLAAAV-----AKNKQMFLGKKLSIARSNPKQRKDSSGER 479
             A AV      K      GKKL + R+  +  +++   R
Sbjct: 231 DAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRR 270

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

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 14/50 (28%), Positives = 28/50 (56%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDE 444
           F+  +++  T ED++++F   G V    ++ DK T + RG  +V F  ++
Sbjct: 3   FVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52

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

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 25/68 (36%), Positives = 35/68 (51%), Gaps = 5/68 (7%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F++N++ K  ++ L+  F   G V    I  DK  GKSRG+  V F   EH   AV +  
Sbjct: 2   FVANLDYKVGWKKLKEVFKLAGKVVRADIKEDK-EGKSRGMGVVQF---EHPIEAV-QAI 56

Query: 455 QMFLGKKL 462
            MF G+ L
Sbjct: 57  SMFNGQML 64

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

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 2/61 (3%)

Query: 406 EDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NKQMFLGKKLSI 464
           E LR  FS  G ++S +++ D+  G+S+G  +V F   E    AV + N ++  GK L +
Sbjct: 16  ERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYV 74

Query: 465 A 465
           A
Sbjct: 75  A 75

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

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 20/73 (27%), Positives = 36/73 (49%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  ++   T +DL+ +FS  G V    +  D  TG+SRG  +V F + E +   + + +
Sbjct: 2   FIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKE 61

Query: 455 QMFLGKKLSIARS 467
               GK +   R+
Sbjct: 62  HKLNGKVIDPKRA 74

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	565
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	100.0
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.97
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.96
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.91
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	99.88
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.88
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.87
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.86
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.85
KOG1258	577	consensus mRNA processing protein [RNA processing	99.83
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.8
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.76
KOG2396	568	consensus HAT (Half-A-TPR) repeat-containing prote	99.71
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	99.67
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	99.65
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.61
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.56
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.56
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.54
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	99.54
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	99.54
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.53
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.53
KOG1258	577	consensus mRNA processing protein [RNA processing	99.53
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.52
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	99.52
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.51
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.51
KOG0122	270	consensus Translation initiation factor 3, subunit	99.51
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.5
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.49
PLN03120	260	nucleic acid binding protein; Provisional	99.48
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	99.48
PLN03121	243	nucleic acid binding protein; Provisional	99.43
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.43
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.43
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.43
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.41
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.41
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.4
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.4
PLN03213	759	repressor of silencing 3; Provisional	99.39
KOG2396	568	consensus HAT (Half-A-TPR) repeat-containing prote	99.36
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.35
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.33
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.33
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.33
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.31
smart00362	72	RRM_2 RNA recognition motif.	99.28
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.27
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.27
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.27
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.26
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.26
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.26
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.26
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.25
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.24
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.23
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.22
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.22
smart00360	71	RRM RNA recognition motif.	99.22
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.2
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.19
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.19
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.18
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.17
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.16
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.15
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.15
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.14
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.1
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.1
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.1
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.1
smart00361	70	RRM_1 RNA recognition motif.	99.08
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.07
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.07
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.04
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.03
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.03
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.0
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	98.98
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.96
PRK11788	389	tetratricopeptide repeat protein; Provisional	98.96
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.96
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.95
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.95
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.93
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	98.91
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.91
PF08424	321	NRDE-2: NRDE-2, necessary for RNA interference; In	98.91
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	98.88
PRK11788	389	tetratricopeptide repeat protein; Provisional	98.87
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.86
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.86
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.86
PRK11189	296	lipoprotein NlpI; Provisional	98.85
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.84
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.83
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.83
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.82
PRK12370	553	invasion protein regulator; Provisional	98.82
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	98.82
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	98.81
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.8
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.79
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.79
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.78
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.74
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.72
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.7
PRK12370	553	invasion protein regulator; Provisional	98.69
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.68
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.67
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.67
PRK11189	296	lipoprotein NlpI; Provisional	98.65
COG5191	435	Uncharacterized conserved protein, contains HAT (H	98.62
KOG0547	606	consensus Translocase of outer mitochondrial membr	98.62
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.61
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.6
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.6
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.59
PF08424	321	NRDE-2: NRDE-2, necessary for RNA interference; In	98.59
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.58
PF05391	21	Lsm_interact: Lsm interaction motif; InterPro: IPR	98.57
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.56
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.55
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.54
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.5
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	98.47
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	98.47
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.46
PF08311	126	Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro	98.45
PLN03218	1060	maturation of RBCL 1; Provisional	98.44
KOG0547	606	consensus Translocase of outer mitochondrial membr	98.43
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.39
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.38
PLN03218	1060	maturation of RBCL 1; Provisional	98.38
PRK14574	822	hmsH outer membrane protein; Provisional	98.37
KOG0226	290	consensus RNA-binding proteins [General function p	98.37
KOG1125	579	consensus TPR repeat-containing protein [General f	98.35
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.33
KOG2076	895	consensus RNA polymerase III transcription factor	98.32
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.31
COG5191	435	Uncharacterized conserved protein, contains HAT (H	98.31
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.29
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.28
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.28
KOG1129	478	consensus TPR repeat-containing protein [General f	98.27
PLN02789	320	farnesyltranstransferase	98.27
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.25
KOG2076	895	consensus RNA polymerase III transcription factor	98.25
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.12
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	98.09
KOG4210	285	consensus Nuclear localization sequence binding pr	98.08
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.08
smart00777	125	Mad3_BUB1_I Mad3/BUB1 hoMad3/BUB1 homology region	98.07
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.07
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	98.04
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.01
KOG1125	579	consensus TPR repeat-containing protein [General f	98.01
PLN03077	857	Protein ECB2; Provisional	98.0
KOG3060	289	consensus Uncharacterized conserved protein [Funct	97.96
KOG1126	638	consensus DNA-binding cell division cycle control	97.95
PLN02789	320	farnesyltranstransferase	97.95
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	97.93
KOG0151	877	consensus Predicted splicing regulator, contains R	97.93
PRK15359	144	type III secretion system chaperone protein SscB;	97.92
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	97.91
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.91
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.87
PRK10370	198	formate-dependent nitrite reductase complex subuni	97.86
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	97.86
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.86
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	97.84
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	97.83
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.81
smart00386	33	HAT HAT (Half-A-TPR) repeats. Present in several R	97.79
PRK14720	906	transcript cleavage factor/unknown domain fusion p	97.78
PF08311	126	Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro	97.78
KOG1126	638	consensus DNA-binding cell division cycle control	97.77
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	97.75
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	97.72
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.72
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	97.71
KOG3060	289	consensus Uncharacterized conserved protein [Funct	97.7
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	97.68
PF02184	32	HAT: HAT (Half-A-TPR) repeat; InterPro: IPR003107	97.62
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	97.61
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	97.54
PRK14574	822	hmsH outer membrane protein; Provisional	97.53
PLN03077	857	Protein ECB2; Provisional	97.51
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	97.5
PRK15359	144	type III secretion system chaperone protein SscB;	97.49
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.48
smart00386	33	HAT HAT (Half-A-TPR) repeats. Present in several R	97.46
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.44
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.42
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	97.31
PRK14720	906	transcript cleavage factor/unknown domain fusion p	97.3
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.29
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.27
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.22
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.19
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	97.18
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.17
KOG1128	777	consensus Uncharacterized conserved protein, conta	97.15
PF02184	32	HAT: HAT (Half-A-TPR) repeat; InterPro: IPR003107	97.14
PF13428	44	TPR_14: Tetratricopeptide repeat	97.1
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.06
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.06
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	97.04
KOG2003	840	consensus TPR repeat-containing protein [General f	97.01
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.0
KOG2003	840	consensus TPR repeat-containing protein [General f	96.97
smart00777	125	Mad3_BUB1_I Mad3/BUB1 hoMad3/BUB1 homology region	96.96
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.93
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	96.92
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	96.91
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	96.88
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	96.87
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.86
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	96.85
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	96.85
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	96.85
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.82
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.81
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.8
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	96.73
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	96.69
PF13428	44	TPR_14: Tetratricopeptide repeat	96.63
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.61
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	96.59
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.56
KOG1548	382	consensus Transcription elongation factor TAT-SF1	96.54
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	96.53
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.51
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	96.47
KOG3152	278	consensus TBP-binding protein, activator of basal	96.43
PF13371	73	TPR_9: Tetratricopeptide repeat	96.43
PF13371	73	TPR_9: Tetratricopeptide repeat	96.36
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.34
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	96.31
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	96.25
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	96.23
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	96.22
KOG1128	777	consensus Uncharacterized conserved protein, conta	96.22
KOG2314	698	consensus Translation initiation factor 3, subunit	96.19
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	96.13
KOG1129	478	consensus TPR repeat-containing protein [General f	96.12
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.03
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	95.98
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	95.97
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	95.86
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	95.79
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	95.74
COG4783	484	Putative Zn-dependent protease, contains TPR repea	95.74
KOG3785	557	consensus Uncharacterized conserved protein [Funct	95.74
COG4783	484	Putative Zn-dependent protease, contains TPR repea	95.73
PRK11906	458	transcriptional regulator; Provisional	95.73
KOG0553	304	consensus TPR repeat-containing protein [General f	95.71
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	95.68
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	95.63
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	95.56
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	95.55
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	95.52
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	95.43
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	95.4
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	95.39
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	95.34
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	95.29
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	95.24
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	95.18
KOG0553	304	consensus TPR repeat-containing protein [General f	95.18
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	95.17
PRK10803	263	tol-pal system protein YbgF; Provisional	95.05
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.89
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	94.82
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	94.75
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	94.6
PF13431	34	TPR_17: Tetratricopeptide repeat	94.58
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	94.54
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	94.47
PF12688	120	TPR_5: Tetratrico peptide repeat	94.44
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	94.35
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	94.35
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	94.26
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	94.07
PRK11906	458	transcriptional regulator; Provisional	94.01
PF03704	146	BTAD: Bacterial transcriptional activator domain;	93.83
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	93.81
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	93.75
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	93.68
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	93.58
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	93.41
PRK10803	263	tol-pal system protein YbgF; Provisional	93.36
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	93.3
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	92.97
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	92.9
KOG1996	378	consensus mRNA splicing factor [RNA processing and	92.86
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	92.78
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	92.75
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	92.73
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	92.69
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	92.26
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	92.25
PF13431	34	TPR_17: Tetratricopeptide repeat	92.01
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	91.37
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	90.94
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	90.45
PF13512	142	TPR_18: Tetratricopeptide repeat	90.32
PF03704	146	BTAD: Bacterial transcriptional activator domain;	89.91
KOG2068	327	consensus MOT2 transcription factor [Transcription	89.43
PF13512	142	TPR_18: Tetratricopeptide repeat	89.23
KOG2376	652	consensus Signal recognition particle, subunit Srp	89.13
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	89.02
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	89.0
KOG3824	472	consensus Huntingtin interacting protein HYPE [Gen	88.82
PF12688	120	TPR_5: Tetratrico peptide repeat	88.33
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	88.03
KOG4210	285	consensus Nuclear localization sequence binding pr	88.01
PF06552	186	TOM20_plant: Plant specific mitochondrial import r	87.98
PRK15331	165	chaperone protein SicA; Provisional	87.18
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	87.03
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	86.42
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	86.2
KOG4555	175	consensus TPR repeat-containing protein [Function	85.82
KOG4234	271	consensus TPR repeat-containing protein [General f	85.72
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	85.34
PF06552	186	TOM20_plant: Plant specific mitochondrial import r	84.86
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	84.62
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	84.57
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	84.54
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	84.47
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	83.99
KOG1166	974	consensus Mitotic checkpoint serine/threonine prot	83.94
PRK15331	165	chaperone protein SicA; Provisional	83.18
KOG2591	684	consensus c-Mpl binding protein, contains La domai	83.11
KOG4555	175	consensus TPR repeat-containing protein [Function	82.88
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	82.62
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	82.59
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	82.52
PF15297	353	CKAP2_C: Cytoskeleton-associated protein 2 C-termi	81.77
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	80.6
PF15297	353	CKAP2_C: Cytoskeleton-associated protein 2 C-termi	80.56
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	80.07

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=6.5e-46  Score=378.20  Aligned_cols=430  Identities=32%  Similarity=0.504  Sum_probs=308.1

Q ss_pred             hHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHH
Q 008442            5 RAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRA   84 (565)
Q Consensus         5 R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erA   84 (565)
                      +..||..++..+.    ....|+.||+||++.|++.+++.+|||++..+|.+.++|+.|..|+....+.+.....++-||
T Consensus       298 ~~~~e~~~q~~~~----~~q~~~~yidfe~~~G~p~ri~l~~eR~~~E~~~~~~~wi~y~~~~d~eLkv~~~~~~~~~ra  373 (881)
T KOG0128|consen  298 LFKFERLVQKEPI----KDQEWMSYIDFEKKSGDPVRIQLIEERAVAEMVLDRALWIGYGVYLDTELKVPQRGVSVHPRA  373 (881)
T ss_pred             HHHHHHHhhhhHH----HHHHHHHHHHHHHhcCCchHHHHHHHHHHHhccccHHHHhhhhhhcccccccccccccccchh
Confidence            3445555555554    889999999999999999999999999999999999999999999999888888899999999


Q ss_pred             HHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHH
Q 008442           85 TKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETF  164 (565)
Q Consensus        85 l~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~  164 (565)
                      +++|||...||.+|+..|++.......|...|++++...+.       ++   .+++.++....+.+. ..+++.++.+|
T Consensus       374 ~R~cp~tgdL~~rallAleR~re~~~vI~~~l~~~ls~~~~-------l~---~~~~~~rr~~~~~~~-s~~~s~lr~~F  442 (881)
T KOG0128|consen  374 VRSCPWTGDLWKRALLALERNREEITVIVQNLEKDLSMTVE-------LH---NDYLAYRRRCTNIID-SQDYSSLRAAF  442 (881)
T ss_pred             hcCCchHHHHHHHHHHHHHhcCcchhhHHHHHHHHHHHHHH-------HH---HHHHHHHHhhcccch-hhhHHHHHHHH
Confidence            99999999999999999999888888898999998864322       22   233333333333322 25788999999


Q ss_pred             HHHHHHHHhhhcC-CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHH-HHHHHHHHHHHcCChHHHHHHHHH
Q 008442          165 QRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLE-AWQSYISMEIELDHINEARSIYKR  242 (565)
Q Consensus       165 ~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~-lw~~yi~~e~~~~~~~~aR~i~~~  242 (565)
                      ..|..+|...... .++.+.+.+.|+++|..+.++++.||.||+..+......+. .|+.|+++|..+|+...||.++.+
T Consensus       443 ~~A~~eLt~~~~~~~Dt~~~~~q~wA~~E~sl~~nmd~~R~iWn~imty~~~~iag~Wle~~~lE~~~g~~~~~R~~~R~  522 (881)
T KOG0128|consen  443 NHAWEELTELYGDQLDTRTEVLQLWAQVEASLLKNMDKAREIWNFIMTYGGGSIAGKWLEAINLEREYGDGPSARKVLRK  522 (881)
T ss_pred             HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHhhchhhhhHhhhccccCCcchHHHHHHHHHhHHHHhCCchhHHHHHHH
Confidence            9999999999987 89999999999999999999999999999999998555555 999999999999999999999999


Q ss_pred             HHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhhHHHHHHHHHHHhhhccCCcchhhhhhhccccccccccCCC
Q 008442          243 CYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLPESADQKEHSVKKTGREKRKSDS  322 (565)
Q Consensus       243 al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~krk~~~  322 (565)
                      |+......+....+++.|..||+++|+++++..+..+.+++.......++++++....+.+...+     .....++...
T Consensus       523 ay~~~~~~~~~~ev~~~~~r~Ere~gtl~~~~~~~~~~~pr~~~~~~~~~e~~s~~v~p~~~~ke-----~~~~~~k~~~  597 (881)
T KOG0128|consen  523 AYSQVVDPEDALEVLEFFRRFEREYGTLESFDLCPEKVLPRVYEAPLERREKESTNVYPEQQKKE-----IQRRQFKGEG  597 (881)
T ss_pred             HHhcCcCchhHHHHHHHHHHHHhccccHHHHhhhHHhhcchhhhhhhhhhhhcccCCCcchhhHH-----hhHHHhhccc
Confidence            98754433335679999999999999999999999999998887666555544433222111111     0011111111


Q ss_pred             CccccCCcccccccCCCC----CCCCCch-hhhhhccccccccCCCcccccccCCCCCC-cccCCCCCCCCCCCCCeEEE
Q 008442          323 NISYEQSPAKRQKHAPQK----PKKVHDK-EKRQVQNLAEENEGRETKQTVEEQPKKQP-IKDAVPGRTKGFTDECTAFL  396 (565)
Q Consensus       323 ~~~~~~~~~k~~~~~~~~----~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~V  396 (565)
                      .......+.++.+...++    ....+.. .+..++     +.+..+......++..+. ..+.....+...++.+++||
T Consensus       598 ~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~p-----a~~~~a~~~~av~~ad~~~~~~~~kvs~n~~R~~~~~fv  672 (881)
T KOG0128|consen  598 NVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATVP-----AGGALANRSAAVGLADAEEKEENFKVSPNEIRDLIKIFV  672 (881)
T ss_pred             ccccccCccccccccccchhhhhhccccchhhcccc-----cccccCCccccCCCCCchhhhhccCcCchHHHHHHHHHH
Confidence            111111111111110000    0000000 000000     000000000000010000 11122223444577789999


Q ss_pred             cCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCC
Q 008442          397 SNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLG  459 (565)
Q Consensus       397 ~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g  459 (565)
                      +||+..+.+.+|...|..+|.+..+++.....+++.||+|||+|..++.+.+||.++...+-|
T Consensus       673 snl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  673 SNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             hhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            999999999999999999999888877755668999999999999999999999976555555

>KOG1915 consensus Cell cycle control protein (crooked neck) [Cell cycle control, cell division, chromosome partitioning]

Probab=99.97  E-value=8.2e-29  Score=238.45  Aligned_cols=243  Identities=23%  Similarity=0.395  Sum_probs=211.2

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ..|+.||..|.++..    ++..|+.|+.||..++++.+++.+|||||.....+..||+.|+++..+ ++...+++.|++
T Consensus        57 RkRkefEd~irrnR~----~~~~WikYaqwEesq~e~~RARSv~ERALdvd~r~itLWlkYae~Emk-nk~vNhARNv~d  131 (677)
T KOG1915|consen   57 RKRKEFEDQIRRNRL----NMQVWIKYAQWEESQKEIQRARSVFERALDVDYRNITLWLKYAEFEMK-NKQVNHARNVWD  131 (677)
T ss_pred             HHHHHHHHHHHHHHH----HHHHHHHHHHHHHhHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHh-hhhHhHHHHHHH
Confidence            479999999999988    899999999999999999999999999999999999999999997654 447788999999


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc--cHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHH
Q 008442           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLI  160 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~--~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~  160 (565)
                      ||+..+|...+||..|+. +|...+++.-+++||+|-+...++  .|..|+.+.+.|.                 +++.+
T Consensus       132 RAvt~lPRVdqlWyKY~y-mEE~LgNi~gaRqiferW~~w~P~eqaW~sfI~fElRyk-----------------eiera  193 (677)
T KOG1915|consen  132 RAVTILPRVDQLWYKYIY-MEEMLGNIAGARQIFERWMEWEPDEQAWLSFIKFELRYK-----------------EIERA  193 (677)
T ss_pred             HHHHhcchHHHHHHHHHH-HHHHhcccHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhh-----------------HHHHH
Confidence            999999999999999997 777789999999999999987765  3444555544443                 56677


Q ss_pred             HHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchH---HHHHHHHHHHHHcCChHHHH
Q 008442          161 RETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAML---EAWQSYISMEIELDHINEAR  237 (565)
Q Consensus       161 ~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~---~lw~~yi~~e~~~~~~~~aR  237 (565)
                      |.+|++..-        +++...-|+.|++||.++| ++..||.+|++|+..+++..   .+..+|+.||..+..+++||
T Consensus       194 R~IYerfV~--------~HP~v~~wikyarFE~k~g-~~~~aR~VyerAie~~~~d~~~e~lfvaFA~fEe~qkE~ERar  264 (677)
T KOG1915|consen  194 RSIYERFVL--------VHPKVSNWIKYARFEEKHG-NVALARSVYERAIEFLGDDEEAEILFVAFAEFEERQKEYERAR  264 (677)
T ss_pred             HHHHHHHhe--------ecccHHHHHHHHHHHHhcC-cHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            777775433        3466788999999999999 99999999999999977653   48999999999999999999


Q ss_pred             HHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHH
Q 008442          238 SIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQ  278 (565)
Q Consensus       238 ~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~  278 (565)
                      -||+-||. ..+.+..+.|+..|+.||..||+...++.++.
T Consensus       265 ~iykyAld-~~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv  304 (677)
T KOG1915|consen  265 FIYKYALD-HIPKGRAEELYKKYTAFEKQFGDKEGIEDAIV  304 (677)
T ss_pred             HHHHHHHH-hcCcccHHHHHHHHHHHHHHhcchhhhHHHHh
Confidence            99999998 45777778999999999999999999887763

>KOG1915 consensus Cell cycle control protein (crooked neck) [Cell cycle control, cell division, chromosome partitioning]

Probab=99.96  E-value=9.8e-28  Score=231.05  Aligned_cols=252  Identities=22%  Similarity=0.438  Sum_probs=207.4

Q ss_pred             chhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHH---------HHHHHHHHHHHhcc
Q 008442            2 CNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSD---------LWLDYTQYLDKTLK   72 (565)
Q Consensus         2 ~~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~---------lW~~Y~~~l~~~~~   72 (565)
                      .+.|..||..|..+|+    +++.|..|+.++...|+.++|+.+|||||...|...+         ||+.|+-|.+-..+
T Consensus       305 ~KRk~qYE~~v~~np~----nYDsWfdylrL~e~~g~~~~Ire~yErAIanvpp~~ekr~W~RYIYLWinYalyeEle~e  380 (677)
T KOG1915|consen  305 GKRKFQYEKEVSKNPY----NYDSWFDYLRLEESVGDKDRIRETYERAIANVPPASEKRYWRRYIYLWINYALYEELEAE  380 (677)
T ss_pred             hhhhhHHHHHHHhCCC----CchHHHHHHHHHHhcCCHHHHHHHHHHHHccCCchhHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4678999999999999    9999999999999999999999999999999886543         99999999998888


Q ss_pred             hhhHHHHHHHHHHHcCCCC----HHHHHHHHHHHHHhcCCHHHHHHHHHHHH-hcccc-cHHHHHHHHHHHHHHHHHHhh
Q 008442           73 VGNVVRDVYSRATKNCPWV----GELWVRSLLSLERSRASEEEISTVFEKSL-LCAFS-TFEEYLDLFLTRIDGLRRRIL  146 (565)
Q Consensus        73 ~~~~~~~v~erAl~~~p~~----~~lW~~yi~~le~~~~~~~~~~~if~ral-~~~~~-~~~~~~~~~~~~~~~~~r~~~  146 (565)
                      +.+..++||+.+|..+|+.    ..||+.|+. +|..+.++..++.++-.|+ .||.+ .+..||.+.+...        
T Consensus       381 d~ertr~vyq~~l~lIPHkkFtFaKiWlmyA~-feIRq~~l~~ARkiLG~AIG~cPK~KlFk~YIelElqL~--------  451 (677)
T KOG1915|consen  381 DVERTRQVYQACLDLIPHKKFTFAKIWLMYAQ-FEIRQLNLTGARKILGNAIGKCPKDKLFKGYIELELQLR--------  451 (677)
T ss_pred             hHHHHHHHHHHHHhhcCcccchHHHHHHHHHH-HHHHHcccHHHHHHHHHHhccCCchhHHHHHHHHHHHHh--------
Confidence            9999999999999999974    589999998 6666788999999999999 47755 4566666655432        


Q ss_pred             ccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccc--hHHHHHHHH
Q 008442          147 FSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA--MLEAWQSYI  224 (565)
Q Consensus       147 ~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~--~~~lw~~yi  224 (565)
                               +++++|.+|+       .++...|..|..|..|+.||..+| +.++||.||+-|+..+.-  ..-+|..||
T Consensus       452 ---------efDRcRkLYE-------kfle~~Pe~c~~W~kyaElE~~Lg-dtdRaRaifelAi~qp~ldmpellwkaYI  514 (677)
T KOG1915|consen  452 ---------EFDRCRKLYE-------KFLEFSPENCYAWSKYAELETSLG-DTDRARAIFELAISQPALDMPELLWKAYI  514 (677)
T ss_pred             ---------hHHHHHHHHH-------HHHhcChHhhHHHHHHHHHHHHhh-hHHHHHHHHHHHhcCcccccHHHHHHHhh
Confidence                     3444555555       444445677889999999999999 999999999999988533  356999999


Q ss_pred             HHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHH-----HhC-----------CHHHHHHHHHHHhhHHHHH
Q 008442          225 SMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFER-----EYG-----------TLEDFDHSVQKVTPRLEEL  287 (565)
Q Consensus       225 ~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~-----~~G-----------~~~~~~~~~~k~~~~~~~~  287 (565)
                      +||...|.+++||+||++.|..    .....+|..+..||.     ..|           +...++.++++++..+++.
T Consensus       515 dFEi~~~E~ekaR~LYerlL~r----t~h~kvWisFA~fe~s~~~~~~~~~~~~~e~~~~~~~~AR~iferAn~~~k~~  589 (677)
T KOG1915|consen  515 DFEIEEGEFEKARALYERLLDR----TQHVKVWISFAKFEASASEGQEDEDLAELEITDENIKRARKIFERANTYLKES  589 (677)
T ss_pred             hhhhhcchHHHHHHHHHHHHHh----cccchHHHhHHHHhccccccccccchhhhhcchhHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999974    223459999999998     334           4445666777777666543

>KOG0495 consensus HAT repeat protein [RNA processing and modification]

Probab=99.91  E-value=3.4e-22  Score=199.73  Aligned_cols=248  Identities=19%  Similarity=0.239  Sum_probs=214.9

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (565)
                      +|.+|-.+|+.+|.    +..+|..-+-||+.+|..+....++++|+..||.++.||++|++--+.. ++...++.|+.+
T Consensus       535 arAVya~alqvfp~----k~slWlra~~~ek~hgt~Esl~Allqkav~~~pkae~lwlM~ake~w~a-gdv~~ar~il~~  609 (913)
T KOG0495|consen  535 ARAVYAHALQVFPC----KKSLWLRAAMFEKSHGTRESLEALLQKAVEQCPKAEILWLMYAKEKWKA-GDVPAARVILDQ  609 (913)
T ss_pred             HHHHHHHHHhhccc----hhHHHHHHHHHHHhcCcHHHHHHHHHHHHHhCCcchhHHHHHHHHHHhc-CCcHHHHHHHHH
Confidence            78999999999987    7889999999999999999999999999999999999999999865554 477779999999


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHH
Q 008442           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRET  163 (565)
Q Consensus        84 Al~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~  163 (565)
                      |+...|++.+||...+. +|..+..++++|.+|.+|......     -.+|..+.                 .++...+.
T Consensus       610 af~~~pnseeiwlaavK-le~en~e~eraR~llakar~~sgT-----eRv~mKs~-----------------~~er~ld~  666 (913)
T KOG0495|consen  610 AFEANPNSEEIWLAAVK-LEFENDELERARDLLAKARSISGT-----ERVWMKSA-----------------NLERYLDN  666 (913)
T ss_pred             HHHhCCCcHHHHHHHHH-HhhccccHHHHHHHHHHHhccCCc-----chhhHHHh-----------------HHHHHhhh
Confidence            99999999999999998 888888999999999999864332     14455444                 33344566


Q ss_pred             HHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHH
Q 008442          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRC  243 (565)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~a  243 (565)
                      +++|+.+++..+...+.++.||+...++|...+ +++.||..|..+++.+|++.-+|+..+++|...|++.+||.|++++
T Consensus       667 ~eeA~rllEe~lk~fp~f~Kl~lmlGQi~e~~~-~ie~aR~aY~~G~k~cP~~ipLWllLakleEk~~~~~rAR~ildra  745 (913)
T KOG0495|consen  667 VEEALRLLEEALKSFPDFHKLWLMLGQIEEQME-NIEMAREAYLQGTKKCPNSIPLWLLLAKLEEKDGQLVRARSILDRA  745 (913)
T ss_pred             HHHHHHHHHHHHHhCCchHHHHHHHhHHHHHHH-HHHHHHHHHHhccccCCCCchHHHHHHHHHHHhcchhhHHHHHHHH
Confidence            777777777777778889999999999999988 9999999999999999999999999999999999999999999999


Q ss_pred             HhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhhH
Q 008442          244 YSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPR  283 (565)
Q Consensus       244 l~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~~  283 (565)
                      ..+   .+....+|..-+++|.+.|+.+.++.++.++++.
T Consensus       746 rlk---NPk~~~lwle~Ir~ElR~gn~~~a~~lmakALQe  782 (913)
T KOG0495|consen  746 RLK---NPKNALLWLESIRMELRAGNKEQAELLMAKALQE  782 (913)
T ss_pred             Hhc---CCCcchhHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            753   3455689999999999999999999887776543

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=99.88  E-value=2e-20  Score=183.90  Aligned_cols=275  Identities=18%  Similarity=0.251  Sum_probs=198.1

Q ss_pred             chhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchh----hHH
Q 008442            2 CNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVG----NVV   77 (565)
Q Consensus         2 ~~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~----~~~   77 (565)
                      -+.|..||+.+...|.    ...+|+.||+.|....+++.+..+|.|||... .+.+||..|+.|+.+.....    +.+
T Consensus        36 ~~~R~~YEq~~~~FP~----s~r~W~~yi~~El~skdfe~VEkLF~RCLvkv-LnlDLW~lYl~YVR~~~~~~~~~r~~m  110 (656)
T KOG1914|consen   36 DKVRETYEQLVNVFPS----SPRAWKLYIERELASKDFESVEKLFSRCLVKV-LNLDLWKLYLSYVRETKGKLFGYREKM  110 (656)
T ss_pred             HHHHHHHHHHhccCCC----CcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH-hhHhHHHHHHHHHHHHccCcchHHHHH
Confidence            3689999999999998    78899999999999999999999999999876 77999999999998876443    346


Q ss_pred             HHHHHHHHHcCC---CCHHHHHHHHHHHHH--------hcCCHHHHHHHHHHHHhcccc----cHHHHHHHHH-------
Q 008442           78 RDVYSRATKNCP---WVGELWVRSLLSLER--------SRASEEEISTVFEKSLLCAFS----TFEEYLDLFL-------  135 (565)
Q Consensus        78 ~~v~erAl~~~p---~~~~lW~~yi~~le~--------~~~~~~~~~~if~ral~~~~~----~~~~~~~~~~-------  135 (565)
                      ...|+-|+..|.   .+..||..|+.+|+.        .+..++.+|.+|+||+..|..    .|.+|..+..       
T Consensus       111 ~qAy~f~l~kig~di~s~siW~eYi~FL~~vea~gk~ee~QRI~~vRriYqral~tPm~nlEkLW~DY~~fE~~IN~~ta  190 (656)
T KOG1914|consen  111 VQAYDFALEKIGMDIKSYSIWDEYINFLEGVEAVGKYEENQRITAVRRIYQRALVTPMHNLEKLWKDYEAFEQEINIITA  190 (656)
T ss_pred             HHHHHHHHHHhccCcccchhHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHhcCccccHHHHHHHHHHHHHHHHHHHH
Confidence            678999999885   678899999998874        224688899999999987654    2333332222       


Q ss_pred             ---------------------------------------------------HHHHHHHH-------------Hhhccc--
Q 008442          136 ---------------------------------------------------TRIDGLRR-------------RILFSG--  149 (565)
Q Consensus       136 ---------------------------------------------------~~~~~~~r-------------~~~~~~--  149 (565)
                                                                         .++.+.+.             |+.+.-  
T Consensus       191 rK~i~e~s~~Ym~AR~~~qel~~lt~GL~r~~~~vp~~~T~~e~~qv~~W~n~I~wEksNpL~t~~~~~~~~Rv~yayeQ  270 (656)
T KOG1914|consen  191 RKFIGERSPEYMNARRVYQELQNLTRGLNRNAPAVPPKGTKDEIQQVELWKNWIKWEKSNPLRTLDGTMLTRRVMYAYEQ  270 (656)
T ss_pred             HHHHHhhCHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHHHHHHHHhcCCcccccccHHHHHHHHHHHH
Confidence                                                               11111110             000000  


Q ss_pred             c----------c-------hhhhh--------------HHHHHHHHHHHHHHH---------------------------
Q 008442          150 E----------V-------EGVLD--------------YSLIRETFQRASDYL---------------------------  171 (565)
Q Consensus       150 ~----------~-------e~~~~--------------~~~~~~~~~~a~~~l---------------------------  171 (565)
                      .          +       ....+              ...+..+|+.+++.+                           
T Consensus       271 ~ll~l~~~peiWy~~s~yl~~~s~l~~~~~d~~~a~~~t~e~~~~yEr~I~~l~~~~~~Ly~~~a~~eE~~~~~n~~~~~  350 (656)
T KOG1914|consen  271 CLLYLGYHPEIWYDYSMYLIEISDLLTEKGDVPDAKSLTDEAASIYERAIEGLLKENKLLYFALADYEESRYDDNKEKKV  350 (656)
T ss_pred             HHHHHhcCHHHHHHHHHHHHHhhHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHhcccchhhhh
Confidence            0          0       00000              111223333322211                           


Q ss_pred             ---------------------------------------HhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH
Q 008442          172 ---------------------------------------SEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI  212 (565)
Q Consensus       172 ---------------------------------------~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~  212 (565)
                                                             ..+-+.....+.++..-|-+|....+|..-|-.||+-+|+.
T Consensus       351 ~~~~~~ll~~~~~~~tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cskD~~~AfrIFeLGLkk  430 (656)
T KOG1914|consen  351 HEIYNKLLKIEDIDLTLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCSKDKETAFRIFELGLKK  430 (656)
T ss_pred             HHHHHHHHhhhccCCceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhcCChhHHHHHHHHHHHh
Confidence                                                   11111111123344455667877888999999999999999


Q ss_pred             ccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          213 SGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       213 ~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      +++...+-+.|++|....++-.++|.+|++++....+.+....||+.|++||-.+||++++.++.++-.
T Consensus       431 f~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~  499 (656)
T KOG1914|consen  431 FGDSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRF  499 (656)
T ss_pred             cCCChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHH
Confidence            999999999999999999999999999999998645556667899999999999999999987665543

>KOG2047 consensus mRNA splicing factor [RNA processing and modification]

Probab=99.88  E-value=6.9e-21  Score=190.24  Aligned_cols=257  Identities=18%  Similarity=0.264  Sum_probs=158.3

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCC-------------------CHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPV-------------------SSDLWLDY   63 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~-------------------~~~lW~~Y   63 (565)
                      .+|.+||.++..+...-.+...+|..|++.|..+.+.+.+..+.++|+.. |.                   +..+|..|
T Consensus       405 ~aRvifeka~~V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~v-P~~~~~~~yd~~~pvQ~rlhrSlkiWs~y  483 (835)
T KOG2047|consen  405 DARVIFEKATKVPYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRATHV-PTNPELEYYDNSEPVQARLHRSLKIWSMY  483 (835)
T ss_pred             HHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcC-CCchhhhhhcCCCcHHHHHHHhHHHHHHH
Confidence            47888888887764322334567888888888877777888888777643 22                   23488888


Q ss_pred             HHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-cccccHHHHHHHHHHHHHHHH
Q 008442           64 TQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLL-CAFSTFEEYLDLFLTRIDGLR  142 (565)
Q Consensus        64 ~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~-~~~~~~~~~~~~~~~~~~~~~  142 (565)
                      +++++..+ ..+..+.||+|.+..-=-.+++-+.|..+||. +..+++..++|+|.+. +.++   ...++|.+|+.-.-
T Consensus       484 ~DleEs~g-tfestk~vYdriidLriaTPqii~NyAmfLEe-h~yfeesFk~YErgI~LFk~p---~v~diW~tYLtkfi  558 (835)
T KOG2047|consen  484 ADLEESLG-TFESTKAVYDRIIDLRIATPQIIINYAMFLEE-HKYFEESFKAYERGISLFKWP---NVYDIWNTYLTKFI  558 (835)
T ss_pred             HHHHHHhc-cHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-hHHHHHHHHHHHcCCccCCCc---cHHHHHHHHHHHHH
Confidence            88765443 44555555555554332344555555554444 3444555555555543 1211   22233333322111


Q ss_pred             HHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCC-------------------------
Q 008442          143 RRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGK-------------------------  197 (565)
Q Consensus       143 r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~-------------------------  197 (565)
                      .+.  ++     ...+.+|..|++|++.+..     ...-.+++.|++||+++|-                         
T Consensus       559 ~ry--gg-----~klEraRdLFEqaL~~Cpp-----~~aKtiyLlYA~lEEe~GLar~amsiyerat~~v~~a~~l~myn  626 (835)
T KOG2047|consen  559 KRY--GG-----TKLERARDLFEQALDGCPP-----EHAKTIYLLYAKLEEEHGLARHAMSIYERATSAVKEAQRLDMYN  626 (835)
T ss_pred             HHh--cC-----CCHHHHHHHHHHHHhcCCH-----HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            111  11     1233445555544442210     0012344455555544330                         


Q ss_pred             ----------ChHHHHHHHHHHHHHccch--HHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHH
Q 008442          198 ----------DMVSARGVWERLLKISGAM--LEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFER  265 (565)
Q Consensus       198 ----------~~~~ar~i~e~~l~~~~~~--~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~  265 (565)
                                .+...|.||+++|+..|++  .++.+.|++||...|.+++||.||..+-+ .++......+|+.|-.||-
T Consensus       627 i~I~kaae~yGv~~TR~iYekaIe~Lp~~~~r~mclrFAdlEtklGEidRARaIya~~sq-~~dPr~~~~fW~twk~FEv  705 (835)
T KOG2047|consen  627 IYIKKAAEIYGVPRTREIYEKAIESLPDSKAREMCLRFADLETKLGEIDRARAIYAHGSQ-ICDPRVTTEFWDTWKEFEV  705 (835)
T ss_pred             HHHHHHHHHhCCcccHHHHHHHHHhCChHHHHHHHHHHHHHhhhhhhHHHHHHHHHhhhh-cCCCcCChHHHHHHHHHHH
Confidence                      2447889999999997765  57999999999999999999999999977 4566667799999999999


Q ss_pred             HhCCHHHHHHHHH
Q 008442          266 EYGTLEDFDHSVQ  278 (565)
Q Consensus       266 ~~G~~~~~~~~~~  278 (565)
                      +|||.+++++.+.
T Consensus       706 rHGnedT~keMLR  718 (835)
T KOG2047|consen  706 RHGNEDTYKEMLR  718 (835)
T ss_pred             hcCCHHHHHHHHH
Confidence            9999999998763

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=99.87  E-value=3.2e-20  Score=199.11  Aligned_cols=254  Identities=19%  Similarity=0.329  Sum_probs=193.9

Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcC-CCCH----HHHHHHHHHHHHhcchhhHHHHHH
Q 008442            7 HLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDF-PVSS----DLWLDYTQYLDKTLKVGNVVRDVY   81 (565)
Q Consensus         7 ~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~-p~~~----~lW~~Y~~~l~~~~~~~~~~~~v~   81 (565)
                      -||..+...|.    ..-.|++|+.|-.+.++++.++.++||||... +.-.    .+|+.|++++...+ ..+.+.++|
T Consensus      1446 DferlvrssPN----SSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG-~eesl~kVF 1520 (1710)
T KOG1070|consen 1446 DFERLVRSSPN----SSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYG-TEESLKKVF 1520 (1710)
T ss_pred             HHHHHHhcCCC----cchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhC-cHHHHHHHH
Confidence            46666666665    55678888888888888888888888888863 3222    38888888765555 556688888


Q ss_pred             HHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHH
Q 008442           82 SRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIR  161 (565)
Q Consensus        82 erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~  161 (565)
                      +||++.|- ...++...+.+++. ...++.+.++|++.++.    +.....+|..|.+++-++-          +.+.++
T Consensus      1521 eRAcqycd-~~~V~~~L~~iy~k-~ek~~~A~ell~~m~KK----F~q~~~vW~~y~~fLl~~n----------e~~aa~ 1584 (1710)
T KOG1070|consen 1521 ERACQYCD-AYTVHLKLLGIYEK-SEKNDEADELLRLMLKK----FGQTRKVWIMYADFLLRQN----------EAEAAR 1584 (1710)
T ss_pred             HHHHHhcc-hHHHHHHHHHHHHH-hhcchhHHHHHHHHHHH----hcchhhHHHHHHHHHhccc----------HHHHHH
Confidence            88888873 23455555555555 34456677777777642    2234567777776664332          335677


Q ss_pred             HHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHH
Q 008442          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYK  241 (565)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~  241 (565)
                      .++.+|+.++..     ..+..++..+|+||.++| |.+++|.+|+-.+..+|...++|.-||+.|+.+|+.+.+|.+|+
T Consensus      1585 ~lL~rAL~~lPk-----~eHv~~IskfAqLEFk~G-DaeRGRtlfEgll~ayPKRtDlW~VYid~eik~~~~~~vR~lfe 1658 (1710)
T KOG1070|consen 1585 ELLKRALKSLPK-----QEHVEFISKFAQLEFKYG-DAERGRTLFEGLLSAYPKRTDLWSVYIDMEIKHGDIKYVRDLFE 1658 (1710)
T ss_pred             HHHHHHHhhcch-----hhhHHHHHHHHHHHhhcC-CchhhHHHHHHHHhhCccchhHHHHHHHHHHccCCHHHHHHHHH
Confidence            888888887754     236788999999999999 99999999999999999999999999999999999999999999


Q ss_pred             HHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhhHHHHH
Q 008442          242 RCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEEL  287 (565)
Q Consensus       242 ~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~~~~~~  287 (565)
                      |++...+......-++..|++||..+||.+.++.+-.+|..+.+..
T Consensus      1659 Rvi~l~l~~kkmKfffKkwLeyEk~~Gde~~vE~VKarA~EYv~s~ 1704 (1710)
T KOG1070|consen 1659 RVIELKLSIKKMKFFFKKWLEYEKSHGDEKNVEYVKARAKEYVESI 1704 (1710)
T ss_pred             HHHhcCCChhHhHHHHHHHHHHHHhcCchhhHHHHHHHHHHHHHHh
Confidence            9998655555556799999999999999999998877777666543

>KOG0495 consensus HAT repeat protein [RNA processing and modification]

Probab=99.86  E-value=2e-19  Score=180.15  Aligned_cols=220  Identities=20%  Similarity=0.275  Sum_probs=176.5

Q ss_pred             chhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHH
Q 008442            2 CNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVY   81 (565)
Q Consensus         2 ~~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~   81 (565)
                      |..|..++..|++.....|....+|+.|+.--...|+...++.++.+|+..+|++.+||+.-++.+.. +...++++.+|
T Consensus       563 hgt~Esl~Allqkav~~~pkae~lwlM~ake~w~agdv~~ar~il~~af~~~pnseeiwlaavKle~e-n~e~eraR~ll  641 (913)
T KOG0495|consen  563 HGTRESLEALLQKAVEQCPKAEILWLMYAKEKWKAGDVPAARVILDQAFEANPNSEEIWLAAVKLEFE-NDELERARDLL  641 (913)
T ss_pred             cCcHHHHHHHHHHHHHhCCcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHhhc-cccHHHHHHHH
Confidence            44566666666655444444677999999988899999999999999999999999999999986554 44788999999


Q ss_pred             HHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHH
Q 008442           82 SRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIR  161 (565)
Q Consensus        82 erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~  161 (565)
                      .+|...-| ...+|..|+. +|+..+.++++..++++||+..+.    +-.+|+.......          ...+++..|
T Consensus       642 akar~~sg-TeRv~mKs~~-~er~ld~~eeA~rllEe~lk~fp~----f~Kl~lmlGQi~e----------~~~~ie~aR  705 (913)
T KOG0495|consen  642 AKARSISG-TERVWMKSAN-LERYLDNVEEALRLLEEALKSFPD----FHKLWLMLGQIEE----------QMENIEMAR  705 (913)
T ss_pred             HHHhccCC-cchhhHHHhH-HHHHhhhHHHHHHHHHHHHHhCCc----hHHHHHHHhHHHH----------HHHHHHHHH
Confidence            99998655 5789999998 899999999999999999985443    3344443332211          111334445


Q ss_pred             HHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHH
Q 008442          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYK  241 (565)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~  241 (565)
                      .+|.       ..+..++.+..||+..+++|+..+ ++.+||.|++++...+|.+..+|+..|.+|.+.|+.+.|+.+..
T Consensus       706 ~aY~-------~G~k~cP~~ipLWllLakleEk~~-~~~rAR~ildrarlkNPk~~~lwle~Ir~ElR~gn~~~a~~lma  777 (913)
T KOG0495|consen  706 EAYL-------QGTKKCPNSIPLWLLLAKLEEKDG-QLVRARSILDRARLKNPKNALLWLESIRMELRAGNKEQAELLMA  777 (913)
T ss_pred             HHHH-------hccccCCCCchHHHHHHHHHHHhc-chhhHHHHHHHHHhcCCCcchhHHHHHHHHHHcCCHHHHHHHHH
Confidence            5544       445556778889999999999999 99999999999999999999999999999999999999999999


Q ss_pred             HHHhc
Q 008442          242 RCYSK  246 (565)
Q Consensus       242 ~al~~  246 (565)
                      +||+.
T Consensus       778 kALQe  782 (913)
T KOG0495|consen  778 KALQE  782 (913)
T ss_pred             HHHHh
Confidence            99983

>KOG2047 consensus mRNA splicing factor [RNA processing and modification]

Probab=99.85  E-value=1.5e-19  Score=180.72  Aligned_cols=255  Identities=18%  Similarity=0.291  Sum_probs=185.7

Q ss_pred             HHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcch-------hhHHH
Q 008442            6 AHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKV-------GNVVR   78 (565)
Q Consensus         6 ~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~-------~~~~~   78 (565)
                      ..||+.|.++|.    ++..|+.||++-.. ....++..+|||||+..|.++.||..|+++-..+.+.       .+.+.
T Consensus        14 vpfEeEilRnp~----svk~W~RYIe~k~~-sp~k~~~~lYERal~~lp~sykiW~~YL~~R~~~vk~~~~T~~~~~~vn   88 (835)
T KOG2047|consen   14 VPFEEEILRNPF----SVKCWLRYIEHKAG-SPDKQRNLLYERALKELPGSYKIWYDYLKARRAQVKHLCPTDPAYESVN   88 (835)
T ss_pred             cchHHHHHcCch----hHHHHHHHHHHHcc-CChHHHHHHHHHHHHHCCCchHHHHHHHHHHHHHhhccCCCChHHHHHH
Confidence            479999999999    89999999998654 3446788999999999999999999999876654432       34578


Q ss_pred             HHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc-----cHHHHHHHHHH------HHHHHHHHhh-
Q 008442           79 DVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS-----TFEEYLDLFLT------RIDGLRRRIL-  146 (565)
Q Consensus        79 ~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~-----~~~~~~~~~~~------~~~~~~r~~~-  146 (565)
                      ..|+||+.....++.||+.|+.++-. ++.+..+|.+|.+||...+.     .|..|+.+...      -+...||... 
T Consensus        89 ~c~er~lv~mHkmpRIwl~Ylq~l~~-Q~~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rvyrRYLk~  167 (835)
T KOG2047|consen   89 NCFERCLVFMHKMPRIWLDYLQFLIK-QGLITRTRRTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRVYRRYLKV  167 (835)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHh-cchHHHHHHHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHHHHHHHhc
Confidence            89999999777778999999996644 78899999999999975432     34444433221      1112222222 


Q ss_pred             ccccchhhhhHHHHHHHHHHHHHHHHhhhc-------CCchhHHHHHHHHHHHHHcCCCh--HHHHHHHHHHHHHccchH
Q 008442          147 FSGEVEGVLDYSLIRETFQRASDYLSEQMK-------NTDGLLRLYAYWAHLEQSMGKDM--VSARGVWERLLKISGAML  217 (565)
Q Consensus       147 ~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~-------~~~~~~~l~~~~a~~e~~~~~~~--~~ar~i~e~~l~~~~~~~  217 (565)
                      .....+.++++-...+.+..+.+.+...+.       .....+++|....++-..+-+-+  -....|+..++..+++++
T Consensus       168 ~P~~~eeyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~  247 (835)
T KOG2047|consen  168 APEAREEYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQL  247 (835)
T ss_pred             CHHHHHHHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHH
Confidence            223344444444444445555544443332       24556778888877776543111  145678999999999886


Q ss_pred             -HHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHH
Q 008442          218 -EAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFERE  266 (565)
Q Consensus       218 -~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~  266 (565)
                       .+|...++|+.+.|.+++||.+|+.+|.......+-..|++.|..||+.
T Consensus       248 g~Lw~SLAdYYIr~g~~ekarDvyeeai~~v~tvrDFt~ifd~Ya~FEE~  297 (835)
T KOG2047|consen  248 GFLWCSLADYYIRSGLFEKARDVYEEAIQTVMTVRDFTQIFDAYAQFEES  297 (835)
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHhheehhhHHHHHHHHHHHHHH
Confidence             5999999999999999999999999998766666677899999999976

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=99.83  E-value=1.9e-18  Score=173.81  Aligned_cols=273  Identities=20%  Similarity=0.332  Sum_probs=207.1

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ..|..|-..|...|.    ....|..|+++|.+.|..+.+..+|||+|...|.+.++|+.|+.|+.....+++.++..|+
T Consensus        63 ~~r~~y~~fL~kyPl----~~gyW~kfA~~E~klg~~~~s~~Vfergv~aip~SvdlW~~Y~~f~~n~~~d~~~lr~~fe  138 (577)
T KOG1258|consen   63 ALREVYDIFLSKYPL----CYGYWKKFADYEYKLGNAENSVKVFERGVQAIPLSVDLWLSYLAFLKNNNGDPETLRDLFE  138 (577)
T ss_pred             HHHHHHHHHHhhCcc----HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhccCCCHHHHHHHHH
Confidence            468899999999998    8899999999999999999999999999999999999999999999887778888999999


Q ss_pred             HHHHcCCC---CHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHH-------------HHhh
Q 008442           83 RATKNCPW---VGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLR-------------RRIL  146 (565)
Q Consensus        83 rAl~~~p~---~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~-------------r~~~  146 (565)
                      ||+..++.   +..||-.||. +|..+.+...+-.||+|.|..|.-.+..+...|...++...             +...
T Consensus       139 ~A~~~vG~dF~S~~lWdkyie-~en~qks~k~v~~iyeRileiP~~~~~~~f~~f~~~l~~~~~~~l~~~d~~~~l~~~~  217 (577)
T KOG1258|consen  139 RAKSYVGLDFLSDPLWDKYIE-FENGQKSWKRVANIYERILEIPLHQLNRHFDRFKQLLNQNEEKILLSIDELIQLRSDV  217 (577)
T ss_pred             HHHHhcccchhccHHHHHHHH-HHhccccHHHHHHHHHHHHhhhhhHhHHHHHHHHHHHhcCChhhhcCHHHHHHHhhhH
Confidence            99999974   6789999999 45557888999999999998765433333333333222100             0000


Q ss_pred             cc--------ccch---h----------hhh---------HHHHHHHHHHHHHHHHhh-------------hcC-CchhH
Q 008442          147 FS--------GEVE---G----------VLD---------YSLIRETFQRASDYLSEQ-------------MKN-TDGLL  182 (565)
Q Consensus       147 ~~--------~~~e---~----------~~~---------~~~~~~~~~~a~~~l~~~-------------~~~-~~~~~  182 (565)
                      ..        ...+   .          ..+         ...-+.+|+.....+...             .+. ....+
T Consensus       218 ~~~~~~~~~~~~~e~~~~~v~~~~~~s~~l~~~~~~l~~~~~~~~~~~~~s~~~~~kr~~fE~~IkrpYfhvkpl~~aql  297 (577)
T KOG1258|consen  218 AERSKITHSQEPLEELEIGVKDSTDPSKSLTEEKTILKRIVSIHEKVYQKSEEEEEKRWGFEEGIKRPYFHVKPLDQAQL  297 (577)
T ss_pred             HhhhhcccccChhHHHHHHHhhccCccchhhHHHHHHHHHHHHHHHHHHhhHhHHHHHHhhhhhccccccccCcccHHHH
Confidence            00        0000   0          000         011122333222222111             111 23346


Q ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHH
Q 008442          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLR  262 (565)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~  262 (565)
                      .-|.+|..++...| +.+.+.-+|++++-.+....++|+.|+.|....|+.+-|..++.++....  ....+.|-..|..
T Consensus       298 ~nw~~yLdf~i~~g-~~~~~~~l~ercli~cA~Y~efWiky~~~m~~~~~~~~~~~~~~~~~~i~--~k~~~~i~L~~a~  374 (577)
T KOG1258|consen  298 KNWRYYLDFEITLG-DFSRVFILFERCLIPCALYDEFWIKYARWMESSGDVSLANNVLARACKIH--VKKTPIIHLLEAR  374 (577)
T ss_pred             HHHHHHhhhhhhcc-cHHHHHHHHHHHHhHHhhhHHHHHHHHHHHHHcCchhHHHHHHHhhhhhc--CCCCcHHHHHHHH
Confidence            67999999999999 99999999999999999999999999999999999999999999998643  3345578888999


Q ss_pred             HHHHhCCHHHHHHHHHHHhhH
Q 008442          263 FEREYGTLEDFDHSVQKVTPR  283 (565)
Q Consensus       263 fE~~~G~~~~~~~~~~k~~~~  283 (565)
                      ||+..||..+++.+++++...
T Consensus       375 f~e~~~n~~~A~~~lq~i~~e  395 (577)
T KOG1258|consen  375 FEESNGNFDDAKVILQRIESE  395 (577)
T ss_pred             HHHhhccHHHHHHHHHHHHhh
Confidence            999999999999999887644

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

Probab=99.80  E-value=1.8e-18  Score=149.40  Aligned_cols=84  Identities=23%  Similarity=0.456  Sum_probs=78.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||+++++++|+++|.+||.|.++.|+.++.+++++|||||+|.++++|+.|+. +++..|+|++|.|.++
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            446799999999999999999999999999999999999899999999999999999999997 8999999999999998


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .++..
T Consensus       112 ~~~~~  116 (144)
T PLN03134        112 NDRPS  116 (144)
T ss_pred             CcCCC
Confidence            76543

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=99.76  E-value=6.1e-17  Score=174.25  Aligned_cols=211  Identities=19%  Similarity=0.271  Sum_probs=173.2

Q ss_pred             HHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcC-CCC----HHHHHHHHHHHHHhcCCHHHHHHHHH
Q 008442           43 QLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNC-PWV----GELWVRSLLSLERSRASEEEISTVFE  117 (565)
Q Consensus        43 ~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~-p~~----~~lW~~yi~~le~~~~~~~~~~~if~  117 (565)
                      .+=|+|.|...|++.-+|+.|+.|...-. +.+.+|++++|||..+ +.-    ..||+.|+. ||...++.+.+.++|+
T Consensus      1444 aeDferlvrssPNSSi~WI~YMaf~Lels-EiekAR~iaerAL~tIN~REeeEKLNiWiA~lN-lEn~yG~eesl~kVFe 1521 (1710)
T KOG1070|consen 1444 AEDFERLVRSSPNSSILWIRYMAFHLELS-EIEKARKIAERALKTINFREEEEKLNIWIAYLN-LENAYGTEESLKKVFE 1521 (1710)
T ss_pred             HHHHHHHHhcCCCcchHHHHHHHHHhhhh-hhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHh-HHHhhCcHHHHHHHHH
Confidence            46799999999999999999999876544 7888999999999977 322    259999998 8888889999999999


Q ss_pred             HHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCC
Q 008442          118 KSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGK  197 (565)
Q Consensus       118 ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~  197 (565)
                      ||.+..     +-+.++++.+..+                 ..-+-|..|.+++...++.....+.+|..|+++..+.. 
T Consensus      1522 RAcqyc-----d~~~V~~~L~~iy-----------------~k~ek~~~A~ell~~m~KKF~q~~~vW~~y~~fLl~~n- 1578 (1710)
T KOG1070|consen 1522 RACQYC-----DAYTVHLKLLGIY-----------------EKSEKNDEADELLRLMLKKFGQTRKVWIMYADFLLRQN- 1578 (1710)
T ss_pred             HHHHhc-----chHHHHHHHHHHH-----------------HHhhcchhHHHHHHHHHHHhcchhhHHHHHHHHHhccc-
Confidence            998732     2233444433222                 12244566667776666666667889999999999988 


Q ss_pred             ChHHHHHHHHHHHHHccc--hHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHH
Q 008442          198 DMVSARGVWERLLKISGA--MLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDH  275 (565)
Q Consensus       198 ~~~~ar~i~e~~l~~~~~--~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~  275 (565)
                      +-+.||.++.+||+..|.  +.++.-.++++|..+|+.+++|.+|+-.+.   ..+.-.++|..|++.|..+|+.+.++.
T Consensus      1579 e~~aa~~lL~rAL~~lPk~eHv~~IskfAqLEFk~GDaeRGRtlfEgll~---ayPKRtDlW~VYid~eik~~~~~~vR~ 1655 (1710)
T KOG1070|consen 1579 EAEAARELLKRALKSLPKQEHVEFISKFAQLEFKYGDAERGRTLFEGLLS---AYPKRTDLWSVYIDMEIKHGDIKYVRD 1655 (1710)
T ss_pred             HHHHHHHHHHHHHhhcchhhhHHHHHHHHHHHhhcCCchhhHHHHHHHHh---hCccchhHHHHHHHHHHccCCHHHHHH
Confidence            889999999999999887  789999999999999999999999999987   223356899999999999999999999


Q ss_pred             HHHHHh
Q 008442          276 SVQKVT  281 (565)
Q Consensus       276 ~~~k~~  281 (565)
                      ++++++
T Consensus      1656 lfeRvi 1661 (1710)
T KOG1070|consen 1656 LFERVI 1661 (1710)
T ss_pred             HHHHHH
Confidence            999986

>KOG2396 consensus HAT (Half-A-TPR) repeat-containing protein [General function prediction only]

Probab=99.71  E-value=4e-15  Score=145.97  Aligned_cols=272  Identities=17%  Similarity=0.264  Sum_probs=184.1

Q ss_pred             HHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHH
Q 008442            6 AHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRAT   85 (565)
Q Consensus         6 ~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl   85 (565)
                      ..|..++.+++.    +...|..||.|.++.+.+.++..+|..+|..+|++++||+.-+.|+..-+-+.+.++++|.|+|
T Consensus        92 ~lyr~at~rf~~----D~~lW~~yi~f~kk~~~~~~v~ki~~~~l~~Hp~~~dLWI~aA~wefe~n~ni~saRalflrgL  167 (568)
T KOG2396|consen   92 FLYRRATNRFNG----DVKLWLSYIAFCKKKKTYGEVKKIFAAMLAKHPNNPDLWIYAAKWEFEINLNIESARALFLRGL  167 (568)
T ss_pred             HHHHHHHHhcCC----CHHHHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCchhHHhhhhhHHhhccchHHHHHHHHHHh
Confidence            357788888876    8899999999999999999999999999999999999999999999887777889999999999


Q ss_pred             HcCCCCHHHHHHHHHHHHHhc--------------CC----------------------------H--------------
Q 008442           86 KNCPWVGELWVRSLLSLERSR--------------AS----------------------------E--------------  109 (565)
Q Consensus        86 ~~~p~~~~lW~~yi~~le~~~--------------~~----------------------------~--------------  109 (565)
                      +.+|.++.||..|++......              .+                            .              
T Consensus       168 R~npdsp~Lw~eyfrmEL~~~~Kl~~rr~~~g~~~~~~~~eie~ge~~~~~~~~s~~~~~~~~k~~e~~~~~~~d~~kel  247 (568)
T KOG2396|consen  168 RFNPDSPKLWKEYFRMELMYAEKLRNRREELGLDSSDKDEEIERGELAWINYANSVDIIKGAVKSVELSVAEKFDFLKEL  247 (568)
T ss_pred             hcCCCChHHHHHHHHHHHHHHHHHHHHHHHhccccchhHHHHHHHHHHHHhhccchhhhhcchhhcchHHHHHHHHHHHH
Confidence            999999999999986211000              00                            0              


Q ss_pred             ---------------------------------------------------HHHHHHHHHHHhcccc--cHHHHHHHHHH
Q 008442          110 ---------------------------------------------------EEISTVFEKSLLCAFS--TFEEYLDLFLT  136 (565)
Q Consensus       110 ---------------------------------------------------~~~~~if~ral~~~~~--~~~~~~~~~~~  136 (565)
                                                                         +..-.+|+.+++..+.  .|..||.+++.
T Consensus       248 ~k~i~d~~~~~~~~np~~~~~laqr~l~i~~~tdl~~~~~~~~~~~~~~k~s~~~~v~ee~v~~l~t~sm~e~YI~~~lE  327 (568)
T KOG2396|consen  248 QKNIIDDLQSKAPDNPLLWDDLAQRELEILSQTDLQHTDNQAKAVEVGSKESRCCAVYEEAVKTLPTESMWECYITFCLE  327 (568)
T ss_pred             HHHHHHHHhccCCCCCccHHHHHHHHHHHHHHhhccchhhhhhchhcchhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence                                                               0011233333332222  34556666666


Q ss_pred             HHHHHHHHh------hcccc----------chhh-------------------hh--------------HHH-------H
Q 008442          137 RIDGLRRRI------LFSGE----------VEGV-------------------LD--------------YSL-------I  160 (565)
Q Consensus       137 ~~~~~~r~~------~~~~~----------~e~~-------------------~~--------------~~~-------~  160 (565)
                      .++.++-..      ++.+.          .+.+                   +.              +..       .
T Consensus       328 ~~~~~r~~~I~h~~~~~~~~~~~~~l~~~~~~~ys~~~l~~~t~~~~r~~a~~l~~e~f~~s~k~~~~kl~~~~~s~sD~  407 (568)
T KOG2396|consen  328 RFTFLRGKRILHTMCVFRKAHELKLLSECLYKQYSVLLLCLNTLNEAREVAVKLTTELFRDSGKMWQLKLQVLIESKSDF  407 (568)
T ss_pred             HHHhhhhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHhccchHhHHHHHhhHHHhcchHHHHHHHHHHHHhhcchh
Confidence            555444211      11100          0000                   00              000       0


Q ss_pred             HHHHHHHHHHHHhhhc-------------------------------CCchhHHHHHHHHHHHHHcCCChHHHHHHHHHH
Q 008442          161 RETFQRASDYLSEQMK-------------------------------NTDGLLRLYAYWAHLEQSMGKDMVSARGVWERL  209 (565)
Q Consensus       161 ~~~~~~a~~~l~~~~~-------------------------------~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~  209 (565)
                      .-.|......+...+.                               ..+....|-..|.++..+.+ ....||++|.+.
T Consensus       408 q~~f~~l~n~~r~~~~s~~~~~w~s~~~~dsl~~~~~~~Ii~a~~s~~~~~~~tl~s~~l~~~~e~~-~~~~ark~y~~l  486 (568)
T KOG2396|consen  408 QMLFEELFNHLRKQVCSELLISWASASEGDSLQEDTLDLIISALLSVIGADSVTLKSKYLDWAYESG-GYKKARKVYKSL  486 (568)
T ss_pred             HHHHHHHHHHHHHHhcchhHHHHHHHhhccchhHHHHHHHHHHHHHhcCCceeehhHHHHHHHHHhc-chHHHHHHHHHH
Confidence            0011111111111100                               01111122234566666666 788999999999


Q ss_pred             HHHccchHHHHHHHHHHHHHcC--ChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhhHHH
Q 008442          210 LKISGAMLEAWQSYISMEIELD--HINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLE  285 (565)
Q Consensus       210 l~~~~~~~~lw~~yi~~e~~~~--~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~~~~  285 (565)
                      ....|.+..+....|+||...-  ++.++|.+|++|+. .|.  ...++|..|+.||+.+|..+++..+..+++..++
T Consensus       487 ~~lpp~sl~l~r~miq~e~~~~sc~l~~~r~~yd~a~~-~fg--~d~~lw~~y~~~e~~~g~~en~~~~~~ra~ktl~  561 (568)
T KOG2396|consen  487 QELPPFSLDLFRKMIQFEKEQESCNLANIREYYDRALR-EFG--ADSDLWMDYMKEELPLGRPENCGQIYWRAMKTLQ  561 (568)
T ss_pred             HhCCCccHHHHHHHHHHHhhHhhcCchHHHHHHHHHHH-HhC--CChHHHHHHHHhhccCCCcccccHHHHHHHHhhC
Confidence            9999999999999999997542  59999999999987 455  4559999999999999999999988888876664

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=99.67  E-value=8.3e-16  Score=149.61  Aligned_cols=102  Identities=28%  Similarity=0.474  Sum_probs=85.7

Q ss_pred             hHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCC-cHHHHHH
Q 008442          181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTG-SEDICHA  259 (565)
Q Consensus       181 ~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~-~~~i~~~  259 (565)
                      ...+|..+|.+|..++++.+.|+.||+.+++.++.+..+|+.|++|+...++.++||.+|++++.. ++... ...||..
T Consensus        34 ~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~f~~~~~~~~~Y~~~l~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~  112 (280)
T PF05843_consen   34 TYHVYVAYALMEYYCNKDPKRARKIFERGLKKFPSDPDFWLEYLDFLIKLNDINNARALFERAISS-LPKEKQSKKIWKK  112 (280)
T ss_dssp             -THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHH
Confidence            345788999999998879989999999999999999999999999999999999999999999984 44444 5679999


Q ss_pred             HHHHHHHhCCHHHHHHHHHHHhhH
Q 008442          260 WLRFEREYGTLEDFDHSVQKVTPR  283 (565)
Q Consensus       260 ~~~fE~~~G~~~~~~~~~~k~~~~  283 (565)
                      |++||..||+++++.++..++...
T Consensus       113 ~i~fE~~~Gdl~~v~~v~~R~~~~  136 (280)
T PF05843_consen  113 FIEFESKYGDLESVRKVEKRAEEL  136 (280)
T ss_dssp             HHHHHHHHS-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHH
Confidence            999999999999999877666543

The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=99.65  E-value=6.1e-14  Score=135.61  Aligned_cols=269  Identities=15%  Similarity=0.192  Sum_probs=196.8

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchh-----hHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVG-----NVV   77 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~-----~~~   77 (565)
                      +.|+.||+.+.-.|.    -..+|..|+.-|....++..+..+|-|||... .+.+||..|+.|+.+.....     ..+
T Consensus        60 ~~re~yeq~~~pfp~----~~~aw~ly~s~ELA~~df~svE~lf~rCL~k~-l~ldLW~lYl~YIRr~n~~~tGq~r~~i  134 (660)
T COG5107          60 AEREMYEQLSSPFPI----MEHAWRLYMSGELARKDFRSVESLFGRCLKKS-LNLDLWMLYLEYIRRVNNLITGQKRFKI  134 (660)
T ss_pred             HHHHHHHHhcCCCcc----ccHHHHHHhcchhhhhhHHHHHHHHHHHHhhh-ccHhHHHHHHHHHHhhCcccccchhhhh
Confidence            579999999998888    56799999999998889999999999999876 77999999999998866332     347


Q ss_pred             HHHHHHHHHcC---CCCHHHHHHHHHHHHH--------hcCCHHHHHHHHHHHHhccccc---HHHHHHHHHHHHHHHHH
Q 008442           78 RDVYSRATKNC---PWVGELWVRSLLSLER--------SRASEEEISTVFEKSLLCAFST---FEEYLDLFLTRIDGLRR  143 (565)
Q Consensus        78 ~~v~erAl~~~---p~~~~lW~~yi~~le~--------~~~~~~~~~~if~ral~~~~~~---~~~~~~~~~~~~~~~~r  143 (565)
                      .++||-.+...   |.+..+|..|..++|.        .+..++.+|.+|.|||..|+..   .|.-...|...++-+..
T Consensus       135 ~~ayefv~~~~~~e~~s~~~W~ey~~fle~~~~~~kwEeQqrid~iR~~Y~ral~tP~~nleklW~dy~~fE~e~N~~Ta  214 (660)
T COG5107         135 YEAYEFVLGCAIFEPQSENYWDEYGLFLEYIEELGKWEEQQRIDKIRNGYMRALQTPMGNLEKLWKDYENFELELNKITA  214 (660)
T ss_pred             HHHHHHHHhcccccccccchHHHHHHHHHhccccccHHHHHHHHHHHHHHHHHHcCccccHHHHHHHHHHHHHHHHHHHH
Confidence            78888888722   7888999999998875        2346788999999999988763   23223334444444433


Q ss_pred             HhhccccchhhhhHHHHHHHHHHHHHHHHhhhc------------CCchhHHHHHHHHHHHHHcC----CChH--HHHHH
Q 008442          144 RILFSGEVEGVLDYSLIRETFQRASDYLSEQMK------------NTDGLLRLYAYWAHLEQSMG----KDMV--SARGV  205 (565)
Q Consensus       144 ~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~------------~~~~~~~l~~~~a~~e~~~~----~~~~--~ar~i  205 (565)
                      +...++..   ..+..+|..+++..... ..+.            .......-|..|+++|...+    +++-  +..-+
T Consensus       215 rKfvge~s---p~ym~ar~~yqe~~nlt-~Gl~v~~~~~~Rt~nK~~r~s~S~WlNwIkwE~en~l~L~~~~~~qRi~y~  290 (660)
T COG5107         215 RKFVGETS---PIYMSARQRYQEIQNLT-RGLSVKNPINLRTANKAARTSDSNWLNWIKWEMENGLKLGGRPHEQRIHYI  290 (660)
T ss_pred             HHHhcccC---HHHHHHHHHHHHHHHHh-ccccccCchhhhhhccccccccchhhhHhhHhhcCCcccCCCcHHHHHHHH
Confidence            33322221   24555666666543322 1111            11123345899999997632    2332  34458


Q ss_pred             HHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhhHHH
Q 008442          206 WERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLE  285 (565)
Q Consensus       206 ~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~~~~  285 (565)
                      |+.++..++-..++|..|..+....++-++|.....+++. .+    | .+-..+.+.+....+.+.+..++++|...+.
T Consensus       291 ~~q~~~y~~~~~evw~dys~Y~~~isd~q~al~tv~rg~~-~s----p-sL~~~lse~yel~nd~e~v~~~fdk~~q~L~  364 (660)
T COG5107         291 HNQILDYFYYAEEVWFDYSEYLIGISDKQKALKTVERGIE-MS----P-SLTMFLSEYYELVNDEEAVYGCFDKCTQDLK  364 (660)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHhhccHHHHHHHHHHhccc-CC----C-chheeHHHHHhhcccHHHHhhhHHHHHHHHH
Confidence            9999999999999999999999999999999999999976 21    2 3666677778888889999999999987775


Q ss_pred             H
Q 008442          286 E  286 (565)
Q Consensus       286 ~  286 (565)
                      .
T Consensus       365 r  365 (660)
T COG5107         365 R  365 (660)
T ss_pred             H
Confidence            3

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.61  E-value=1e-14  Score=144.41  Aligned_cols=83  Identities=25%  Similarity=0.456  Sum_probs=76.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCC--eEEEEee
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLG--KKLSIAR  466 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g--~~l~v~~  466 (565)
                      ...+|||+|||.++++++|+++|++||.|..++|+.++.+|+++|||||+|.+.++|++||. +|+..+.|  ++|.|.+
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            35689999999999999999999999999999999998899999999999999999999998 89998866  6899999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +.....
T Consensus       272 a~~~~~  277 (346)
T TIGR01659       272 AEEHGK  277 (346)
T ss_pred             CCcccc
Confidence            876543

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).

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.56  E-value=4.5e-14  Score=128.97  Aligned_cols=87  Identities=25%  Similarity=0.442  Sum_probs=79.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ..=+||||+-|++++++..|+..|+.||.|+.|+||.|+.||+++|||||+|+++-+..+|-+ .+|..|+|+.|.|.+-
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            445899999999999999999999999999999999999999999999999999999999998 7999999999999987


Q ss_pred             CCCCCCCC
Q 008442          468 NPKQRKDS  475 (565)
Q Consensus       468 ~~~~~~~~  475 (565)
                      .....+..
T Consensus       179 RgRTvkgW  186 (335)
T KOG0113|consen  179 RGRTVKGW  186 (335)
T ss_pred             cccccccc
Confidence            66554443

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.56  E-value=2.8e-14  Score=120.93  Aligned_cols=78  Identities=14%  Similarity=0.278  Sum_probs=69.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      +..++|||+|||.++.+.+|+.+|.+||.|..|.+...+   ...+||||+|+++-+|+.||. .+|..++|.+|+|+++
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            456899999999999999999999999999999985532   345899999999999999998 7999999999999996


Q ss_pred             CC
Q 008442          468 NP  469 (565)
Q Consensus       468 ~~  469 (565)
                      ..
T Consensus        81 rg   82 (241)
T KOG0105|consen   81 RG   82 (241)
T ss_pred             cC
Confidence            54

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.54  E-value=1.5e-14  Score=115.15  Aligned_cols=79  Identities=19%  Similarity=0.413  Sum_probs=75.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      +..+|||||||++.++|+.|.++|+.||.|+.|-+-.|+.+-.+.|||||+|.+.++|..|+. +++..++.++|.|.+.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            456999999999999999999999999999999999999888899999999999999999999 8999999999999884

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=99.54  E-value=1.5e-12  Score=135.13  Aligned_cols=429  Identities=19%  Similarity=0.184  Sum_probs=229.7

Q ss_pred             HHHHHHHhcCCCCChHhHHHHHHHHHHHHh-cCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHH
Q 008442            6 AHLEEQISRQDLSDSEKFQQYMIYLKYEQS-SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRA   84 (565)
Q Consensus         6 ~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~-~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erA   84 (565)
                      ..||.++...+.    +...|+.|.-+.-. .+-+.++..+|-|++..||...+||..|+--++++......+...++++
T Consensus       333 l~~eR~~~E~~~----~~~~wi~y~~~~d~eLkv~~~~~~~~~ra~R~cp~tgdL~~rallAleR~re~~~vI~~~l~~~  408 (881)
T KOG0128|consen  333 LIEERAVAEMVL----DRALWIGYGVYLDTELKVPQRGVSVHPRAVRSCPWTGDLWKRALLALERNREEITVIVQNLEKD  408 (881)
T ss_pred             HHHHHHHHhccc----cHHHHhhhhhhcccccccccccccccchhhcCCchHHHHHHHHHHHHHhcCcchhhHHHHHHHH
Confidence            467888888776    67789998887543 2345678889999999999999999999977777776777788888888


Q ss_pred             HHcCCCCHHHHHHHHHHHHHhc-----CCHHHHHHHHHHHHhcccccHHHHHHH-HHHHHHHHHHHhhccccchhhhhHH
Q 008442           85 TKNCPWVGELWVRSLLSLERSR-----ASEEEISTVFEKSLLCAFSTFEEYLDL-FLTRIDGLRRRILFSGEVEGVLDYS  158 (565)
Q Consensus        85 l~~~p~~~~lW~~yi~~le~~~-----~~~~~~~~if~ral~~~~~~~~~~~~~-~~~~~~~~~r~~~~~~~~e~~~~~~  158 (565)
                      +...   ..++..|+.++-+..     ...+.++..|..|.....    .+... |-+.+.++.       .+   ..++
T Consensus       409 ls~~---~~l~~~~~~~rr~~~~~~~s~~~s~lr~~F~~A~~eLt----~~~~~~~Dt~~~~~q-------~w---A~~E  471 (881)
T KOG0128|consen  409 LSMT---VELHNDYLAYRRRCTNIIDSQDYSSLRAAFNHAWEELT----ELYGDQLDTRTEVLQ-------LW---AQVE  471 (881)
T ss_pred             HHHH---HHHHHHHHHHHHhhcccchhhhHHHHHHHHHHHHHHHH----HHhhhhhhhHHHHHH-------HH---HHHH
Confidence            8742   246677766444432     235667788888763110    11111 111111110       00   0000


Q ss_pred             -HHHHHHHHHHHHHHhhhcCCchhHH-HHHHHHHHHHHcCCChHHHHHHHHHHHHH--ccc-hHHHHHHHHHHHHHcCCh
Q 008442          159 -LIRETFQRASDYLSEQMKNTDGLLR-LYAYWAHLEQSMGKDMVSARGVWERLLKI--SGA-MLEAWQSYISMEIELDHI  233 (565)
Q Consensus       159 -~~~~~~~~a~~~l~~~~~~~~~~~~-l~~~~a~~e~~~~~~~~~ar~i~e~~l~~--~~~-~~~lw~~yi~~e~~~~~~  233 (565)
                       .+....+.|+.+....+......+. .|+.|+++|..++ +...||.++.+++..  .++ ...+...|..||+..|.+
T Consensus       472 ~sl~~nmd~~R~iWn~imty~~~~iag~Wle~~~lE~~~g-~~~~~R~~~R~ay~~~~~~~~~~ev~~~~~r~Ere~gtl  550 (881)
T KOG0128|consen  472 ASLLKNMDKAREIWNFIMTYGGGSIAGKWLEAINLEREYG-DGPSARKVLRKAYSQVVDPEDALEVLEFFRRFEREYGTL  550 (881)
T ss_pred             HHHhhchhhhhHhhhccccCCcchHHHHHHHHHhHHHHhC-CchhHHHHHHHHHhcCcCchhHHHHHHHHHHHHhccccH
Confidence             0111223333333333333334444 8999999999999 999999999999987  343 467899999999999998


Q ss_pred             HHHHHHHHHHHhcccCCCCcHHHH-HHHHHHHHHhCCHHH------HHHHHHHHhhHHHHHHHHHHHhhhccCCcchhhh
Q 008442          234 NEARSIYKRCYSKRFTGTGSEDIC-HAWLRFEREYGTLED------FDHSVQKVTPRLEELRLFRSQQESKSLPESADQK  306 (565)
Q Consensus       234 ~~aR~i~~~al~~~~~~~~~~~i~-~~~~~fE~~~G~~~~------~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~  306 (565)
                      +.+-..-.+-+.+         +. ..+-.-|..--++..      ......+.....++++--+  ...++-.+ + +.
T Consensus       551 ~~~~~~~~~~~pr---------~~~~~~~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~--~g~k~h~q-~-~~  617 (881)
T KOG0128|consen  551 ESFDLCPEKVLPR---------VYEAPLERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPK--RGFKAHEQ-P-QQ  617 (881)
T ss_pred             HHHhhhHHhhcch---------hhhhhhhhhhhcccCCCcchhhHHhhHHHhhcccccccccCcc--cccccccc-c-hh
Confidence            8766554444321         11 000011111000000      0001111111111110000  00000000 0 00


Q ss_pred             hhhccccccccc------cCCCCcc-ccCCcccccccCCCC--CCCCCchhhhhhccccccccCCCc----------ccc
Q 008442          307 EHSVKKTGREKR------KSDSNIS-YEQSPAKRQKHAPQK--PKKVHDKEKRQVQNLAEENEGRET----------KQT  367 (565)
Q Consensus       307 ~~~~~~~~~~kr------k~~~~~~-~~~~~~k~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~----------~~~  367 (565)
                      +.........+.      +.-.... ......++.+.+..+  |.......+.+++|+.......+.          +..
T Consensus       618 ~~~~s~~~~~esat~pa~~~~a~~~~av~~ad~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~v  697 (881)
T KOG0128|consen  618 QKVQSKHGSAESATVPAGGALANRSAAVGLADAEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVV  697 (881)
T ss_pred             hhhhccccchhhcccccccccCCccccCCCCCchhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhH
Confidence            000000000000      0000000 000000000000000  001112234455555432111110          000


Q ss_pred             c------ccCCC-----------CCCcccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCC
Q 008442          368 V------EEQPK-----------KQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTG  430 (565)
Q Consensus       368 ~------~~~~~-----------~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g  430 (565)
                      .      ..++.           ....+-..  +....-....|||.|.|+..|.+.++.+++.+|.+.+.++++.+ .|
T Consensus       698 qi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f--~d~~~~gK~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~g  774 (881)
T KOG0128|consen  698 QIVIHKNEKRFRGKAYVEFLKPEHAGAAVAF--RDSCFFGKISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AG  774 (881)
T ss_pred             HHHHHhhccccccceeeEeecCCchhhhhhh--hhhhhhhhhhhheeCCCCCCchHHHHhhccccCCccccchhhhh-cc
Confidence            0      00000           00000000  01112336789999999999999999999999999999999987 89


Q ss_pred             CcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCCCCC
Q 008442          431 KSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNPKQR  472 (565)
Q Consensus       431 ~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~~~~  472 (565)
                      +++|.|||.|.++.++..++. .+...+.-+.+.|..++|...
T Consensus       775 kpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp~~~  817 (881)
T KOG0128|consen  775 KPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNPERD  817 (881)
T ss_pred             ccccceeccCCCcchhhhhcccchhhhhhhcCccccccCCccc
Confidence            999999999999999999987 677777777788888877433

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=99.54  E-value=1.1e-12  Score=127.06  Aligned_cols=230  Identities=18%  Similarity=0.242  Sum_probs=169.7

Q ss_pred             HHHHHHHHHHHHhcC-----C--chhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHH
Q 008442           23 FQQYMIYLKYEQSSG-----D--PGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELW   95 (565)
Q Consensus        23 ~~~W~~yi~~e~~~~-----~--~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW   95 (565)
                      ...|+.||+||...+     .  ..++.-+|+.++...|.++++|.+|..|+.... +.+.+..+.+|++..||.   |.
T Consensus       261 ~S~WlNwIkwE~en~l~L~~~~~~qRi~y~~~q~~~y~~~~~evw~dys~Y~~~is-d~q~al~tv~rg~~~sps---L~  336 (660)
T COG5107         261 DSNWLNWIKWEMENGLKLGGRPHEQRIHYIHNQILDYFYYAEEVWFDYSEYLIGIS-DKQKALKTVERGIEMSPS---LT  336 (660)
T ss_pred             cchhhhHhhHhhcCCcccCCCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhcc-HHHHHHHHHHhcccCCCc---hh
Confidence            346999999998764     2  257889999999999999999999999987544 667788888888888774   66


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcc------------------cccHHH--------HHHHHHHHHHHHHHHhhccc
Q 008442           96 VRSLLSLERSRASEEEISTVFEKSLLCA------------------FSTFEE--------YLDLFLTRIDGLRRRILFSG  149 (565)
Q Consensus        96 ~~yi~~le~~~~~~~~~~~if~ral~~~------------------~~~~~~--------~~~~~~~~~~~~~r~~~~~~  149 (565)
                      ..|....|. ..+.+.+...|++|++..                  +....+        +.-+|-+++++++|.     
T Consensus       337 ~~lse~yel-~nd~e~v~~~fdk~~q~L~r~ys~~~s~~~s~~D~N~e~~~Ell~kr~~k~t~v~C~~~N~v~r~-----  410 (660)
T COG5107         337 MFLSEYYEL-VNDEEAVYGCFDKCTQDLKRKYSMGESESASKVDNNFEYSKELLLKRINKLTFVFCVHLNYVLRK-----  410 (660)
T ss_pred             eeHHHHHhh-cccHHHHhhhHHHHHHHHHHHHhhhhhhhhccccCCccccHHHHHHHHhhhhhHHHHHHHHHHHH-----
Confidence            666664444 566788888888887521                  100011        112223333333322     


Q ss_pred             cchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHH
Q 008442          150 EVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE  229 (565)
Q Consensus       150 ~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~  229 (565)
                           ..++.+|.+|.++...-   +    ..+.++++-|-+|....+|...|-.||+-++..+|+...+-..|..|...
T Consensus       411 -----~Gl~aaR~~F~k~rk~~---~----~~h~vyi~~A~~E~~~~~d~~ta~~ifelGl~~f~d~~~y~~kyl~fLi~  478 (660)
T COG5107         411 -----RGLEAARKLFIKLRKEG---I----VGHHVYIYCAFIEYYATGDRATAYNIFELGLLKFPDSTLYKEKYLLFLIR  478 (660)
T ss_pred             -----hhHHHHHHHHHHHhccC---C----CCcceeeeHHHHHHHhcCCcchHHHHHHHHHHhCCCchHHHHHHHHHHHH
Confidence                 14556777777666531   1    12345666677777776799999999999999999999999999999999


Q ss_pred             cCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHH
Q 008442          230 LDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDH  275 (565)
Q Consensus       230 ~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~  275 (565)
                      .++-++||.+|+.++.+ ...+.-..||+.|+++|-.+|++..+-.
T Consensus       479 inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN~v~s  523 (660)
T COG5107         479 INDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLNNVYS  523 (660)
T ss_pred             hCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchHHHHh
Confidence            99999999999999884 3334456799999999999999987763

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.53  E-value=4.9e-14  Score=118.86  Aligned_cols=78  Identities=24%  Similarity=0.448  Sum_probs=70.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      -+++||||||+..+++.+|+..|..||.|.+|-|-..     +.|||||+|+++.+|..|+. |+|..|+|..|.|+.+.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            3689999999999999999999999999999988553     46999999999999999998 99999999999999986


Q ss_pred             CCCC
Q 008442          469 PKQR  472 (565)
Q Consensus       469 ~~~~  472 (565)
                      ....
T Consensus        84 G~~r   87 (195)
T KOG0107|consen   84 GRPR   87 (195)
T ss_pred             CCcc
Confidence            5544

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.53  E-value=4.7e-14  Score=143.39  Aligned_cols=83  Identities=19%  Similarity=0.316  Sum_probs=78.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ..+++|||+|||+++++++|+++|++||.|.+++|+.|+.||.++|||||+|.+.++|..|+. |||..|+|++|.|.+.
T Consensus       267 ~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~  346 (352)
T TIGR01661       267 GAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFK  346 (352)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            445689999999999999999999999999999999999899999999999999999999998 8999999999999998


Q ss_pred             CCCC
Q 008442          468 NPKQ  471 (565)
Q Consensus       468 ~~~~  471 (565)
                      .++.
T Consensus       347 ~~~~  350 (352)
T TIGR01661       347 TNKA  350 (352)
T ss_pred             cCCC
Confidence            7764

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

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=99.53  E-value=4.6e-12  Score=128.22  Aligned_cols=258  Identities=17%  Similarity=0.218  Sum_probs=184.2

Q ss_pred             hhhHHHHHHHhcCC----CCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHH
Q 008442            3 NARAHLEEQISRQD----LSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVR   78 (565)
Q Consensus         3 ~~R~~~E~~l~~~~----~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~   78 (565)
                      ..|+.||..|.+..    ..+..++..|+.|++|+...|+.+++..+|+||+..|.+..++|+.|+.|++.. +..+.+.
T Consensus       273 ~kr~~fE~~IkrpYfhvkpl~~aql~nw~~yLdf~i~~g~~~~~~~l~ercli~cA~Y~efWiky~~~m~~~-~~~~~~~  351 (577)
T KOG1258|consen  273 EKRWGFEEGIKRPYFHVKPLDQAQLKNWRYYLDFEITLGDFSRVFILFERCLIPCALYDEFWIKYARWMESS-GDVSLAN  351 (577)
T ss_pred             HHHHhhhhhccccccccCcccHHHHHHHHHHhhhhhhcccHHHHHHHHHHHHhHHhhhHHHHHHHHHHHHHc-CchhHHH
Confidence            57899999997752    236668889999999999999999999999999999999999999999999988 4777789


Q ss_pred             HHHHHHHH-cCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhH
Q 008442           79 DVYSRATK-NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDY  157 (565)
Q Consensus        79 ~v~erAl~-~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~  157 (565)
                      .++.+|.+ ++|..+.|.+.|.. ++.+.+++..++.++++..+.-++    ++.+.+.++..++|+.-....       
T Consensus       352 ~~~~~~~~i~~k~~~~i~L~~a~-f~e~~~n~~~A~~~lq~i~~e~pg----~v~~~l~~~~~e~r~~~~~~~-------  419 (577)
T KOG1258|consen  352 NVLARACKIHVKKTPIIHLLEAR-FEESNGNFDDAKVILQRIESEYPG----LVEVVLRKINWERRKGNLEDA-------  419 (577)
T ss_pred             HHHHhhhhhcCCCCcHHHHHHHH-HHHhhccHHHHHHHHHHHHhhCCc----hhhhHHHHHhHHHHhcchhhh-------
Confidence            99999998 56888889999987 666788999999999998864433    334444445444443321111       


Q ss_pred             HHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcC---ChH
Q 008442          158 SLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELD---HIN  234 (565)
Q Consensus       158 ~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~---~~~  234 (565)
                         .. .............+..-...++..++++-.....+.+.|+.++..++...|++-.+|+.+++|+..+.   +.+
T Consensus       420 ---~~-~~~l~s~~~~~~~~~~i~~~l~~~~~r~~~~i~~d~~~a~~~l~~~~~~~~~~k~~~~~~~~~~~~~~~~~e~d  495 (577)
T KOG1258|consen  420 ---NY-KNELYSSIYEGKENNGILEKLYVKFARLRYKIREDADLARIILLEANDILPDCKVLYLELIRFELIQPSGREYD  495 (577)
T ss_pred             ---hH-HHHHHHHhcccccCcchhHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhcCCccHHHHHHHHHHHHhCCcchhhh
Confidence               10 11111111111122233446777888888888889999999999999999999999999999998765   333


Q ss_pred             HHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHH
Q 008442          235 EARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSV  277 (565)
Q Consensus       235 ~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~  277 (565)
                      -.--+....+......+.+..--..|++|-.-+|+.....+..
T Consensus       496 ~~e~~~~~~~~~~~~~~~~~~~~~k~~ef~e~~g~~~~~~~~~  538 (577)
T KOG1258|consen  496 LLEPIDWKELKMLIDFDDSRSSTDKYIEFLEWFGIDHKGAQDE  538 (577)
T ss_pred             hhhhHHHHHHhhhccccccccchHHHHHHHHhccchhHhHhhc
Confidence            3333333333321122233233355999999999765554443

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.52  E-value=3.9e-14  Score=125.55  Aligned_cols=78  Identities=26%  Similarity=0.458  Sum_probs=72.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSN  468 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~  468 (565)
                      -.+||||||++.+..++|+++|++||+|.+..|+.|+.+|+|||||||+|.|.++|.+|++--.-.|+||+..+.+|-
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLAS   89 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchhh
Confidence            468999999999999999999999999999999999999999999999999999999999865567999998887763

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=99.52  E-value=4.5e-12  Score=125.65  Aligned_cols=242  Identities=17%  Similarity=0.240  Sum_probs=169.4

Q ss_pred             HHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcC
Q 008442            9 EEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNC   88 (565)
Q Consensus         9 E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~   88 (565)
                      ++.|..+|+    +.+.|...|...... .+++++..||+.+..+|.++..|..|+.-+... ++.+.+..+|.|||...
T Consensus        10 ~~rie~nP~----di~sw~~lire~qt~-~~~~~R~~YEq~~~~FP~s~r~W~~yi~~El~s-kdfe~VEkLF~RCLvkv   83 (656)
T KOG1914|consen   10 RERIEENPY----DIDSWSQLIREAQTQ-PIDKVRETYEQLVNVFPSSPRAWKLYIERELAS-KDFESVEKLFSRCLVKV   83 (656)
T ss_pred             HHHHhcCCc----cHHHHHHHHHHHccC-CHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHh-hhHHHHHHHHHHHHHHH
Confidence            677888998    999999999955444 889999999999999999999999999866544 48888999999999865


Q ss_pred             CCCHHHHHHHHHHHHHhcCCHHHHHHH----HHHHHh-cccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHH
Q 008442           89 PWVGELWVRSLLSLERSRASEEEISTV----FEKSLL-CAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRET  163 (565)
Q Consensus        89 p~~~~lW~~yi~~le~~~~~~~~~~~i----f~ral~-~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~  163 (565)
                      - +-+||..||.++.+..+.....+..    |+=++. +..+  -....+|..|+++++---..+ .++.-..+..+|.+
T Consensus        84 L-nlDLW~lYl~YVR~~~~~~~~~r~~m~qAy~f~l~kig~d--i~s~siW~eYi~FL~~vea~g-k~ee~QRI~~vRri  159 (656)
T KOG1914|consen   84 L-NLDLWKLYLSYVRETKGKLFGYREKMVQAYDFALEKIGMD--IKSYSIWDEYINFLEGVEAVG-KYEENQRITAVRRI  159 (656)
T ss_pred             h-hHhHHHHHHHHHHHHccCcchHHHHHHHHHHHHHHHhccC--cccchhHHHHHHHHHcccccc-cHHHHHHHHHHHHH
Confidence            3 3689999999887766655544444    444443 2221  012356777776665222222 22222356678899


Q ss_pred             HHHHHHHHHhhhcCCchhHHHHHHHHHHHHHc------------CCChHHHHHHHHHHHHH-------cc----------
Q 008442          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSM------------GKDMVSARGVWERLLKI-------SG----------  214 (565)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~------------~~~~~~ar~i~e~~l~~-------~~----------  214 (565)
                      |++|+..      ..+....||.-|..||...            ..++..||.++......       .+          
T Consensus       160 Yqral~t------Pm~nlEkLW~DY~~fE~~IN~~tarK~i~e~s~~Ym~AR~~~qel~~lt~GL~r~~~~vp~~~T~~e  233 (656)
T KOG1914|consen  160 YQRALVT------PMHNLEKLWKDYEAFEQEINIITARKFIGERSPEYMNARRVYQELQNLTRGLNRNAPAVPPKGTKDE  233 (656)
T ss_pred             HHHHhcC------ccccHHHHHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCChHH
Confidence            9987663      1345667899888888643            22455788887765542       11          


Q ss_pred             -chHHHHHHHHHHHHHcCC--------hHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCC
Q 008442          215 -AMLEAWQSYISMEIELDH--------INEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGT  269 (565)
Q Consensus       215 -~~~~lw~~yi~~e~~~~~--------~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~  269 (565)
                       .++++|+.||+||.+.+-        ..+..-+|+.+|.-   ....++||-.+..|-...++
T Consensus       234 ~~qv~~W~n~I~wEksNpL~t~~~~~~~~Rv~yayeQ~ll~---l~~~peiWy~~s~yl~~~s~  294 (656)
T KOG1914|consen  234 IQQVELWKNWIKWEKSNPLRTLDGTMLTRRVMYAYEQCLLY---LGYHPEIWYDYSMYLIEISD  294 (656)
T ss_pred             HHHHHHHHHHHHHHhcCCcccccccHHHHHHHHHHHHHHHH---HhcCHHHHHHHHHHHHHhhH
Confidence             146799999999987642        24556678899862   34577999999888777666

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.51  E-value=5.8e-14  Score=139.16  Aligned_cols=84  Identities=24%  Similarity=0.349  Sum_probs=78.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      .....++|||+|||+++++++|+++|+.||.|.+|+|+.|+.+++++|||||+|.++++|..||. |++..|.+++|.|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            34567999999999999999999999999999999999998899999999999999999999997 89999999999999


Q ss_pred             ecCCC
Q 008442          466 RSNPK  470 (565)
Q Consensus       466 ~a~~~  470 (565)
                      ++.|.
T Consensus       183 ~a~p~  187 (346)
T TIGR01659       183 YARPG  187 (346)
T ss_pred             ccccc
Confidence            88653

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).

>PF00076 RRM_1: RNA recognition motif

Probab=99.51  E-value=6.9e-14  Score=106.01  Aligned_cols=69  Identities=33%  Similarity=0.627  Sum_probs=65.9

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEE
Q 008442          394 AFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLS  463 (565)
Q Consensus       394 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~  463 (565)
                      |||+|||.++++++|+++|++||.|..+.+..+ .++.++|+|||+|.+.++|..|+. +++..++|++|+
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 489999999999999999999998 899999999885

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.51  E-value=6e-14  Score=124.70  Aligned_cols=82  Identities=29%  Similarity=0.434  Sum_probs=79.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .+.++|-|.|||.++++.+|+++|.+||.|..+.|.+|+.||.+||||||.|.+.++|.+||. |||.-.+.--|.|+++
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            478999999999999999999999999999999999999999999999999999999999998 8999999999999999


Q ss_pred             CCC
Q 008442          468 NPK  470 (565)
Q Consensus       468 ~~~  470 (565)
                      +|+
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            986

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.50  E-value=8.5e-14  Score=120.28  Aligned_cols=84  Identities=25%  Similarity=0.451  Sum_probs=78.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      ....-.+|-|-||.+-++.++|+.+|++||.|-+|.|+.|+.|+.++|||||-|.+..+|+.|+. |+|.+|+|+.|.|.
T Consensus         9 dv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq   88 (256)
T KOG4207|consen    9 DVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQ   88 (256)
T ss_pred             CcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeeh
Confidence            33445789999999999999999999999999999999999999999999999999999999998 89999999999999


Q ss_pred             ecCCC
Q 008442          466 RSNPK  470 (565)
Q Consensus       466 ~a~~~  470 (565)
                      .|.-.
T Consensus        89 ~aryg   93 (256)
T KOG4207|consen   89 MARYG   93 (256)
T ss_pred             hhhcC
Confidence            98643

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.49  E-value=1e-13  Score=140.88  Aligned_cols=81  Identities=23%  Similarity=0.479  Sum_probs=77.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      ..+|||+|||+++++++|+++|+.||.|.+|+|+.++.+|+++|||||+|.++++|..||. +++..|.|++|.|.++.|
T Consensus         3 ~~~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~~   82 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP   82 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc
Confidence            4799999999999999999999999999999999998899999999999999999999997 899999999999999876


Q ss_pred             CC
Q 008442          470 KQ  471 (565)
Q Consensus       470 ~~  471 (565)
                      ..
T Consensus        83 ~~   84 (352)
T TIGR01661        83 SS   84 (352)
T ss_pred             cc
Confidence            54

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

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.48  E-value=1.6e-13  Score=126.43  Aligned_cols=76  Identities=25%  Similarity=0.402  Sum_probs=70.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~~  469 (565)
                      .++|||+|||+.+++++|+++|+.||.|.+|+|+.++   .++|||||+|.++++|..||.|+|..|.|++|.|..+..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~---~~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN---ERSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC---CCCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccC
Confidence            5799999999999999999999999999999999875   257999999999999999999999999999999999764

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=99.48  E-value=7.4e-13  Score=128.94  Aligned_cols=97  Identities=15%  Similarity=0.296  Sum_probs=73.0

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Q 008442           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER  104 (565)
Q Consensus        25 ~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~  104 (565)
                      +|..|++|....+..+.++.+|++|+...+.+..+|+.|+.....+.++...++.|||++++.+|.+..+|..|+.+|..
T Consensus         3 v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~f~~~~~~~~~Y~~~l~~   82 (280)
T PF05843_consen    3 VWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEYYCNKDPKRARKIFERGLKKFPSDPDFWLEYLDFLIK   82 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
Confidence            68888888888777888888888888777777888888887666656777778888888888888888888888876654


Q ss_pred             hcCCHHHHHHHHHHHHhc
Q 008442          105 SRASEEEISTVFEKSLLC  122 (565)
Q Consensus       105 ~~~~~~~~~~if~ral~~  122 (565)
                       .++.+.+|.+|+||+..
T Consensus        83 -~~d~~~aR~lfer~i~~   99 (280)
T PF05843_consen   83 -LNDINNARALFERAISS   99 (280)
T ss_dssp             -TT-HHHHHHHHHHHCCT
T ss_pred             -hCcHHHHHHHHHHHHHh
Confidence             56677788888877753

The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.43  E-value=6.3e-13  Score=120.35  Aligned_cols=77  Identities=29%  Similarity=0.403  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecC
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSN  468 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~  468 (565)
                      .++.+|||+||++.+++++|+++|+.||.|.+|+|+.+.   ..+|||||+|.+++++..|+.|+|..|.|++|.|....
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCc
Confidence            356899999999999999999999999999999999874   45689999999999999999999999999999998864

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.43  E-value=2.2e-14  Score=121.40  Aligned_cols=83  Identities=25%  Similarity=0.453  Sum_probs=78.2

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEE
Q 008442          385 TKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLS  463 (565)
Q Consensus       385 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~  463 (565)
                      +..+.++.-|||||||++.|+.||--+|++||+|.+|.+++|+.||+|+||||+.|++.-+..-|+. +||..|.||.|+
T Consensus        29 H~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtir  108 (219)
T KOG0126|consen   29 HQEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIR  108 (219)
T ss_pred             hhhcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEE
Confidence            5567888999999999999999999999999999999999999999999999999999998888887 899999999999


Q ss_pred             Eeec
Q 008442          464 IARS  467 (565)
Q Consensus       464 v~~a  467 (565)
                      |...
T Consensus       109 VDHv  112 (219)
T KOG0126|consen  109 VDHV  112 (219)
T ss_pred             eeec
Confidence            9775

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.43  E-value=8.8e-13  Score=99.84  Aligned_cols=69  Identities=39%  Similarity=0.657  Sum_probs=63.0

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEE
Q 008442          394 AFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLS  463 (565)
Q Consensus       394 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~  463 (565)
                      |||+|||+++++++|+++|+.||.|..+.+..++. |.++|+|||+|.++++|..|+. .++..++|+.|+
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            79999999999999999999999999999999875 9999999999999999999999 577999999874

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 ....

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.43  E-value=1.6e-13  Score=119.56  Aligned_cols=95  Identities=23%  Similarity=0.389  Sum_probs=86.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...+|||||+|..++++.-|...|-+||.|.+|.++.|-.++++||||||+|...++|.+||. ||+.+|.||.|+|.++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            446899999999999999999999999999999999999999999999999999999999998 9999999999999999


Q ss_pred             CCCCCCCCCCCCCCcc
Q 008442          468 NPKQRKDSSGERAPTE  483 (565)
Q Consensus       468 ~~~~~~~~~~~~~~~~  483 (565)
                      .|.+-+..+...-|..
T Consensus        88 kP~kikegsqkPvWAD  103 (298)
T KOG0111|consen   88 KPEKIKEGSQKPVWAD  103 (298)
T ss_pred             CCccccCCCCCCcccC
Confidence            9988776665544543

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.41  E-value=2.8e-12  Score=115.64  Aligned_cols=76  Identities=25%  Similarity=0.411  Sum_probs=70.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .++|+|||||++..+++++|++.|++||.|.+|||..++      ||+||.|.+.++|..||. +|+.+|.|+.+++.+-
T Consensus       162 p~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q------GYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWG  235 (321)
T KOG0148|consen  162 PDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ------GYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWG  235 (321)
T ss_pred             CCCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc------ceEEEEecchhhHHHHHHHhcCceeCceEEEEecc
Confidence            468999999999999999999999999999999999875      899999999999999997 8999999999999986


Q ss_pred             CCC
Q 008442          468 NPK  470 (565)
Q Consensus       468 ~~~  470 (565)
                      +..
T Consensus       236 Ke~  238 (321)
T KOG0148|consen  236 KEG  238 (321)
T ss_pred             ccC
Confidence            543

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

Probab=99.41  E-value=8.8e-13  Score=137.67  Aligned_cols=84  Identities=11%  Similarity=0.235  Sum_probs=78.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      ..++|||+|||+++++++|+.+|+.||.|.+++|+.++.+|+++|||||+|.+.++|..|+. ||+..|+|+.|+|.++.
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            45799999999999999999999999999999999998889999999999999999999998 89999999999999997


Q ss_pred             CCCCC
Q 008442          469 PKQRK  473 (565)
Q Consensus       469 ~~~~~  473 (565)
                      +++..
T Consensus       283 ~pP~~  287 (612)
T TIGR01645       283 TPPDA  287 (612)
T ss_pred             CCccc
Confidence            65443

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.

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.40  E-value=6.6e-13  Score=122.92  Aligned_cols=80  Identities=21%  Similarity=0.371  Sum_probs=73.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|+|+|+|+...+.||+.+|.+||.|.+|.|+.+  ..-|||||||+|+++++|++|-. ++|..|.||+|.|..+
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            44579999999999999999999999999999999986  35589999999999999999997 8999999999999998


Q ss_pred             CCC
Q 008442          468 NPK  470 (565)
Q Consensus       468 ~~~  470 (565)
                      .++
T Consensus       172 Tar  174 (376)
T KOG0125|consen  172 TAR  174 (376)
T ss_pred             chh
Confidence            665

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

Probab=99.40  E-value=8.9e-13  Score=137.63  Aligned_cols=79  Identities=28%  Similarity=0.516  Sum_probs=75.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      ..++|||+|||+++++++|+++|..||.|.+|+|+.|+.+|+++|||||+|.++++|+.|+. +||..|+|++|.|....
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            45899999999999999999999999999999999999999999999999999999999997 89999999999998653

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.

>PLN03213 repressor of silencing 3; Provisional

Probab=99.39  E-value=1.1e-12  Score=127.45  Aligned_cols=77  Identities=21%  Similarity=0.429  Sum_probs=70.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCH--HHHHHHHH-cCCcccCCeEEEEee
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDD--EHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~--~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ...+||||||++.+++++|+.+|..||.|.+|.|++  .+|  ||||||+|.+.  .++.+||. |||..+.|+.|+|..
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            357999999999999999999999999999999994  477  89999999987  67999998 899999999999999


Q ss_pred             cCCC
Q 008442          467 SNPK  470 (565)
Q Consensus       467 a~~~  470 (565)
                      |+|.
T Consensus        85 AKP~   88 (759)
T PLN03213         85 AKEH   88 (759)
T ss_pred             ccHH
Confidence            9864

>KOG2396 consensus HAT (Half-A-TPR) repeat-containing protein [General function prediction only]

Probab=99.36  E-value=8.1e-10  Score=109.20  Aligned_cols=136  Identities=23%  Similarity=0.415  Sum_probs=112.4

Q ss_pred             chhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhc-------------C-------CchhHHHHHHHHHhcCCCCHHHHH
Q 008442            2 CNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS-------------G-------DPGRVQLLYERAITDFPVSSDLWL   61 (565)
Q Consensus         2 ~~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~-------------~-------~~~~~~~lyERal~~~p~~~~lW~   61 (565)
                      .+.|..||..|.+-..    ...-++.||++|...             +       -+.+|..+|.+|+..++.++.||.
T Consensus        34 vk~Rr~fE~kL~rr~~----~i~Dfi~YI~YE~nl~~lr~kR~Kk~~~k~S~sd~si~~rIv~lyr~at~rf~~D~~lW~  109 (568)
T KOG2396|consen   34 VKKRRDFELKLQRRTL----SIEDFINYIQYEINLEELRAKRRKKKRVKYSFSDDSIPNRIVFLYRRATNRFNGDVKLWL  109 (568)
T ss_pred             HHHHHHHHHHHccCcc----cHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHHhcCCCHHHHH
Confidence            4689999999988765    677899999998642             1       135788999999999999999999


Q ss_pred             HHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc---cHHHHHHHHHHHH
Q 008442           62 DYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS---TFEEYLDLFLTRI  138 (565)
Q Consensus        62 ~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~---~~~~~~~~~~~~~  138 (565)
                      +|+.|..+.. ....+-.||..+|...|.++.||+..+.++-..+.+++.+|.+|.++|...+.   .|.+|..+.+.+.
T Consensus       110 ~yi~f~kk~~-~~~~v~ki~~~~l~~Hp~~~dLWI~aA~wefe~n~ni~saRalflrgLR~npdsp~Lw~eyfrmEL~~~  188 (568)
T KOG2396|consen  110 SYIAFCKKKK-TYGEVKKIFAAMLAKHPNNPDLWIYAAKWEFEINLNIESARALFLRGLRFNPDSPKLWKEYFRMELMYA  188 (568)
T ss_pred             HHHHHHHHhc-chhHHHHHHHHHHHhCCCCchhHHhhhhhHHhhccchHHHHHHHHHHhhcCCCChHHHHHHHHHHHHHH
Confidence            9999988665 46678899999999999999999998875544456699999999999997654   5677777778877


Q ss_pred             HHHH
Q 008442          139 DGLR  142 (565)
Q Consensus       139 ~~~~  142 (565)
                      .-++
T Consensus       189 ~Kl~  192 (568)
T KOG2396|consen  189 EKLR  192 (568)
T ss_pred             HHHH
Confidence            7665

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=99.35  E-value=6.3e-12  Score=125.20  Aligned_cols=88  Identities=22%  Similarity=0.337  Sum_probs=74.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecC
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSN  468 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~  468 (565)
                      ....+|||+|||++++..+|+++|..||.|+..+|......++..+||||+|.+.+.++.||..+...|+|++|.|+.-.
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            45567999999999999999999999999999888664334555599999999999999999988888999999999987


Q ss_pred             CCCCCCCC
Q 008442          469 PKQRKDSS  476 (565)
Q Consensus       469 ~~~~~~~~  476 (565)
                      +.....+.
T Consensus       366 ~~~~g~~~  373 (419)
T KOG0116|consen  366 PGFRGNGN  373 (419)
T ss_pred             cccccccc
Confidence            76554443

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.33  E-value=1.1e-11  Score=129.41  Aligned_cols=74  Identities=23%  Similarity=0.399  Sum_probs=68.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccC--CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDV--GGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~--G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .++|||+|||.++++++|+++|+.|  |.|.+|.++        ++||||+|.+.++|.+|+. ||+..|+|+.|.|.++
T Consensus       233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~A  304 (578)
T TIGR01648       233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLA  304 (578)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            4789999999999999999999999  999998765        3699999999999999998 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .|+..
T Consensus       305 kp~~~  309 (578)
T TIGR01648       305 KPVDK  309 (578)
T ss_pred             cCCCc
Confidence            87643

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.

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.33  E-value=3.3e-12  Score=102.71  Aligned_cols=84  Identities=25%  Similarity=0.377  Sum_probs=79.3

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEE
Q 008442          385 TKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLS  463 (565)
Q Consensus       385 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~  463 (565)
                      |.+..++-.|||+++...+++++|...|..||+|+.|.+-.|+.||..+|||.|+|.+...|++|+. +||..|.|.+|.
T Consensus        66 PqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~  145 (170)
T KOG0130|consen   66 PQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVS  145 (170)
T ss_pred             CccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCcee
Confidence            4456778899999999999999999999999999999999999999999999999999999999998 899999999999


Q ss_pred             EeecC
Q 008442          464 IARSN  468 (565)
Q Consensus       464 v~~a~  468 (565)
                      |.++-
T Consensus       146 VDw~F  150 (170)
T KOG0130|consen  146 VDWCF  150 (170)
T ss_pred             EEEEE
Confidence            99984

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.33  E-value=1.6e-12  Score=110.48  Aligned_cols=80  Identities=23%  Similarity=0.439  Sum_probs=76.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ....|||||||+..++++-|.++|-++|+|.+++++.|+.++..+|||||+|.++++|+-|++ ||...|.|++|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            456899999999999999999999999999999999999999999999999999999999999 7988899999999998


Q ss_pred             C
Q 008442          468 N  468 (565)
Q Consensus       468 ~  468 (565)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            7

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.31  E-value=7.5e-12  Score=131.85  Aligned_cols=82  Identities=37%  Similarity=0.594  Sum_probs=77.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      ..+.++|||+|||..+++++|+++|+.||.|.+|+|+.++.+|+++|||||+|.+.++|.+||.++|..+.|++|.|..+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~  165 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSS  165 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeec
Confidence            45678999999999999999999999999999999999998999999999999999999999999999999999999876


Q ss_pred             CC
Q 008442          468 NP  469 (565)
Q Consensus       468 ~~  469 (565)
                      ..
T Consensus       166 ~~  167 (457)
T TIGR01622       166 QA  167 (457)
T ss_pred             ch
Confidence            43

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.

>smart00362 RRM_2 RNA recognition motif

Probab=99.28  E-value=2.1e-11  Score=92.38  Aligned_cols=71  Identities=35%  Similarity=0.609  Sum_probs=65.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       393 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      +|||+|||..++.++|+.+|..||.|..+.+..++  +.++|+|||+|.+.+.|..|+. +++..+.|++|.|.
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            58999999999999999999999999999998775  7789999999999999999998 79899999998873

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.27  E-value=1.4e-11  Score=110.30  Aligned_cols=84  Identities=20%  Similarity=0.455  Sum_probs=79.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .....|.|.-||.++|+++++.+|...|+|++|.+++|+.+|.+-||+||.|.++.+|++|+. +||..+..+.|+|+++
T Consensus        39 ~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyA  118 (360)
T KOG0145|consen   39 ESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYA  118 (360)
T ss_pred             cccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEec
Confidence            345679999999999999999999999999999999999999999999999999999999998 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      +|...
T Consensus       119 RPSs~  123 (360)
T KOG0145|consen  119 RPSSD  123 (360)
T ss_pred             cCChh
Confidence            99765

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.27  E-value=3.2e-11  Score=92.50  Aligned_cols=80  Identities=23%  Similarity=0.304  Sum_probs=72.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ..++-|||.|||+.+|.++..++|..||.|..|+|-..+   ..+|-|||.|++..+|..|+. |+|..++++.+.|-+.
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            446889999999999999999999999999999997644   458999999999999999998 8999999999999998


Q ss_pred             CCCC
Q 008442          468 NPKQ  471 (565)
Q Consensus       468 ~~~~  471 (565)
                      .|..
T Consensus        93 q~~~   96 (124)
T KOG0114|consen   93 QPED   96 (124)
T ss_pred             CHHH
Confidence            7654

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

Probab=99.27  E-value=1.9e-11  Score=131.97  Aligned_cols=78  Identities=26%  Similarity=0.402  Sum_probs=74.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCCC
Q 008442          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNPK  470 (565)
Q Consensus       393 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~~  470 (565)
                      +|||+|||.++++++|+++|+.||.|.+|+|++|+.|++++|||||+|.+.++|++|+. +++..|.|++|+|.++...
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~   80 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRD   80 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccc
Confidence            79999999999999999999999999999999999889999999999999999999997 8999999999999987543

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.26  E-value=1.7e-11  Score=118.17  Aligned_cols=81  Identities=27%  Similarity=0.509  Sum_probs=75.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCccc-CCeEEEEee
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMF-LGKKLSIAR  466 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~-~g~~l~v~~  466 (565)
                      ..+|-||||.||.++.|++|..+|+..|.|-++||+.|+.+|.+||||||+|.+.+.|+.||. +|+++| .|+.|.|..
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            568999999999999999999999999999999999999999999999999999999999998 899987 588888877


Q ss_pred             cCC
Q 008442          467 SNP  469 (565)
Q Consensus       467 a~~  469 (565)
                      +..
T Consensus       161 Sva  163 (506)
T KOG0117|consen  161 SVA  163 (506)
T ss_pred             eee
Confidence            643

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.26  E-value=1.6e-11  Score=128.21  Aligned_cols=79  Identities=28%  Similarity=0.501  Sum_probs=71.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccC-CeEEEEee
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFL-GKKLSIAR  466 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~-g~~l~v~~  466 (565)
                      ...++|||+|||.++++++|+++|+.||.|.+++|+.| .+|+++|||||+|.+.++|+.||. ||+..|. |+.|.|..
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~  134 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCI  134 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccc
Confidence            34699999999999999999999999999999999999 599999999999999999999998 8988874 77776665


Q ss_pred             cC
Q 008442          467 SN  468 (565)
Q Consensus       467 a~  468 (565)
                      +.
T Consensus       135 S~  136 (578)
T TIGR01648       135 SV  136 (578)
T ss_pred             cc
Confidence            53

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.

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.26  E-value=1.5e-11  Score=111.07  Aligned_cols=84  Identities=25%  Similarity=0.421  Sum_probs=78.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      +....|||+.|...++-++|++.|.+||+|.+++|++|..|++++|||||.|.+.++|+.||. |||.=|++|.|+-.+|
T Consensus        60 ~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWA  139 (321)
T KOG0148|consen   60 NQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWA  139 (321)
T ss_pred             ccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccc
Confidence            346789999999999999999999999999999999999999999999999999999999998 9999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      ..++.
T Consensus       140 TRKp~  144 (321)
T KOG0148|consen  140 TRKPS  144 (321)
T ss_pred             ccCcc
Confidence            66553

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.26  E-value=6.4e-12  Score=112.88  Aligned_cols=87  Identities=21%  Similarity=0.338  Sum_probs=81.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEE
Q 008442          386 KGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSI  464 (565)
Q Consensus       386 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v  464 (565)
                      ....++|.|||-.||.+..+.+|.++|-+||.|.+..+..|+.|+.|+|||||.|.++.++++||. |||..|+-++|+|
T Consensus       280 reGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKV  359 (371)
T KOG0146|consen  280 REGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKV  359 (371)
T ss_pred             hcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhh
Confidence            345789999999999999999999999999999999999999999999999999999999999998 9999999999999


Q ss_pred             eecCCCCC
Q 008442          465 ARSNPKQR  472 (565)
Q Consensus       465 ~~a~~~~~  472 (565)
                      ...+|+..
T Consensus       360 QLKRPkda  367 (371)
T KOG0146|consen  360 QLKRPKDA  367 (371)
T ss_pred             hhcCcccc
Confidence            99887643

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.25  E-value=3.8e-11  Score=126.52  Aligned_cols=79  Identities=22%  Similarity=0.474  Sum_probs=75.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      .++|||+|||..+++++|+.+|+.||.|..|.++.++.+|+++|||||+|.+.++|..|+. |+|..|.|++|.|.++..
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            6899999999999999999999999999999999998889999999999999999999997 899999999999999863

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.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.24  E-value=4.2e-11  Score=128.03  Aligned_cols=82  Identities=20%  Similarity=0.346  Sum_probs=77.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||..+++++|+++|..||.|..+.|+.+..+|.++|||||+|.+.++|..|+. |+|..|.|+.|.|.++
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            356899999999999999999999999999999999998899999999999999999999997 8999999999999998


Q ss_pred             CCC
Q 008442          468 NPK  470 (565)
Q Consensus       468 ~~~  470 (565)
                      ...
T Consensus       373 ~~~  375 (509)
T TIGR01642       373 CVG  375 (509)
T ss_pred             ccC
Confidence            654

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.23  E-value=8.8e-12  Score=119.57  Aligned_cols=86  Identities=29%  Similarity=0.458  Sum_probs=77.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcc-cCC--eEEEE
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQM-FLG--KKLSI  464 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~-~~g--~~l~v  464 (565)
                      .++++||||-|+..++|.+++++|++||.|++|.|.++. .|.+||||||.|.+.+.|..||+ ||+.. +.|  .+|.|
T Consensus       122 ~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVV  200 (510)
T KOG0144|consen  122 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVV  200 (510)
T ss_pred             ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEE
Confidence            457899999999999999999999999999999999997 89999999999999999999998 88754 654  59999


Q ss_pred             eecCCCCCCCC
Q 008442          465 ARSNPKQRKDS  475 (565)
Q Consensus       465 ~~a~~~~~~~~  475 (565)
                      .+|++.+.+..
T Consensus       201 kFADtqkdk~~  211 (510)
T KOG0144|consen  201 KFADTQKDKDG  211 (510)
T ss_pred             EecccCCCchH
Confidence            99999877544

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.22  E-value=2e-11  Score=122.42  Aligned_cols=82  Identities=32%  Similarity=0.552  Sum_probs=78.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCCC
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNPK  470 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~~  470 (565)
                      +.|||||+|+++++++|..+|+..|.|.+++++.|+.||+++||||++|.+.+++..|+. +||..+.|++|+|.++...
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            899999999999999999999999999999999999999999999999999999999998 8999999999999998765


Q ss_pred             CCC
Q 008442          471 QRK  473 (565)
Q Consensus       471 ~~~  473 (565)
                      +.+
T Consensus        99 ~~~  101 (435)
T KOG0108|consen   99 KNA  101 (435)
T ss_pred             chh
Confidence            543

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

Probab=99.22  E-value=3.8e-11  Score=129.59  Aligned_cols=80  Identities=31%  Similarity=0.520  Sum_probs=75.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      ...+|||+|||..+++++|+++|+.||.|.++.++.+. +|.++|||||+|.+.++|.+|+. +|+..++|++|.|.++.
T Consensus       284 ~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~-~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~  362 (562)
T TIGR01628       284 QGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQ  362 (562)
T ss_pred             CCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECC-CCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEecc
Confidence            45789999999999999999999999999999999994 89999999999999999999997 89999999999999987


Q ss_pred             CC
Q 008442          469 PK  470 (565)
Q Consensus       469 ~~  470 (565)
                      ++
T Consensus       363 ~k  364 (562)
T TIGR01628       363 RK  364 (562)
T ss_pred             Cc
Confidence            64

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>smart00360 RRM RNA recognition motif

Probab=99.22  E-value=5.6e-11  Score=89.72  Aligned_cols=70  Identities=36%  Similarity=0.609  Sum_probs=65.2

Q ss_pred             EcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          396 LSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       396 V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      |+|||..+++++|+.+|..||.|..+.+..++.++.++|+|||+|.+.++|..|+. +++..+.|++|.|.
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            68999999999999999999999999999887778999999999999999999998 78899999998873

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.20  E-value=7.5e-11  Score=113.86  Aligned_cols=75  Identities=23%  Similarity=0.426  Sum_probs=69.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      -.-|||+||+.++|++.|+++|..||.|..|..++|        ||||.|.+.++|.+|++ +|++.|+|..|.|.+|+|
T Consensus       259 VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP  330 (506)
T KOG0117|consen  259 VKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKP  330 (506)
T ss_pred             eeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCC
Confidence            468999999999999999999999999999887754        99999999999999998 899999999999999998


Q ss_pred             CCCC
Q 008442          470 KQRK  473 (565)
Q Consensus       470 ~~~~  473 (565)
                      ...+
T Consensus       331 ~~k~  334 (506)
T KOG0117|consen  331 VDKK  334 (506)
T ss_pred             hhhh
Confidence            7553

>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70)

Probab=99.19  E-value=7.9e-09  Score=113.05  Aligned_cols=239  Identities=13%  Similarity=0.090  Sum_probs=151.3

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++-..|+.+|.... ..+.....|.....+....|+++.+...|+++|...|.+...|+.++..+. ..++.+.+...|+
T Consensus       312 ~A~~~~~~al~~~~-~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~P~~~~~~~~la~~~~-~~g~~~eA~~~~~  389 (615)
T TIGR00990       312 EAARAFEKALDLGK-LGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELDPRVTQSYIKRASMNL-ELGDPDKAEEDFD  389 (615)
T ss_pred             HHHHHHHHHHhcCC-CChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHH-HCCCHHHHHHHHH
Confidence            34567788876542 123355667777777777888888888888888888888888887776544 3446677888888


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHH---------HHHHHHh-hccccch
Q 008442           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRI---------DGLRRRI-LFSGEVE  152 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~---------~~~~r~~-~~~~~~e  152 (565)
                      +|+...|....+|..... +....++.+++...|++++...+.....++.+-..+.         ..+++.+ ......+
T Consensus       390 ~al~~~p~~~~~~~~lg~-~~~~~g~~~~A~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~P~~~~  468 (615)
T TIGR00990       390 KALKLNSEDPDIYYHRAQ-LHFIKGEFAQAGKDYQKSIDLDPDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNFPEAPD  468 (615)
T ss_pred             HHHHhCCCCHHHHHHHHH-HHHHcCCHHHHHHHHHHHHHcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChH
Confidence            888888888888877665 4444677888888888888765543333322211111         1111110 1111111


Q ss_pred             hhh---hHHHHHHHHHHHHHHHHhhhcCCch----h---HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHH
Q 008442          153 GVL---DYSLIRETFQRASDYLSEQMKNTDG----L---LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQS  222 (565)
Q Consensus       153 ~~~---~~~~~~~~~~~a~~~l~~~~~~~~~----~---~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~  222 (565)
                      .+.   ..-.....|++|+..+...+...+.    .   ..++.....+....+ ++++|..+|++++...|++...|..
T Consensus       469 ~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~-~~~eA~~~~~kAl~l~p~~~~a~~~  547 (615)
T TIGR00990       469 VYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQ-DFIEAENLCEKALIIDPECDIAVAT  547 (615)
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhh-hHHHHHHHHHHHHhcCCCcHHHHHH
Confidence            100   1111112345555555544432211    1   112222222333345 9999999999999999998889999


Q ss_pred             HHHHHHHcCChHHHHHHHHHHHh
Q 008442          223 YISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       223 yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      .+......|+++.|..+|++++.
T Consensus       548 la~~~~~~g~~~eAi~~~e~A~~  570 (615)
T TIGR00990       548 MAQLLLQQGDVDEALKLFERAAE  570 (615)
T ss_pred             HHHHHHHccCHHHHHHHHHHHHH
Confidence            99999999999999999999986

>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70)

Probab=99.19  E-value=2.9e-08  Score=108.60  Aligned_cols=186  Identities=9%  Similarity=0.035  Sum_probs=118.6

Q ss_pred             cCCchhHHHHHHHHHhcC---CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHH
Q 008442           36 SGDPGRVQLLYERAITDF---PVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEI  112 (565)
Q Consensus        36 ~~~~~~~~~lyERal~~~---p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~  112 (565)
                      .+.++.+..+|++++...   |.....|.....+.. ..++.+.+...|++|+...|.....|......+ ...++.+++
T Consensus       307 ~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~-~~g~~~eA~~~~~kal~l~P~~~~~~~~la~~~-~~~g~~~eA  384 (615)
T TIGR00990       307 DESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKC-LKGKHLEALADLSKSIELDPRVTQSYIKRASMN-LELGDPDKA  384 (615)
T ss_pred             hhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHH-HHCCCHHHH
Confidence            456788999999999864   555566766665444 455788899999999999999888888776633 346889999


Q ss_pred             HHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHH
Q 008442          113 STVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLE  192 (565)
Q Consensus       113 ~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e  192 (565)
                      ...|++++...+.....+..+-..+..        .      .++..+...|+++       +...+.....+...+.+.
T Consensus       385 ~~~~~~al~~~p~~~~~~~~lg~~~~~--------~------g~~~~A~~~~~ka-------l~l~P~~~~~~~~la~~~  443 (615)
T TIGR00990       385 EEDFDKALKLNSEDPDIYYHRAQLHFI--------K------GEFAQAGKDYQKS-------IDLDPDFIFSHIQLGVTQ  443 (615)
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHH--------c------CCHHHHHHHHHHH-------HHcCccCHHHHHHHHHHH
Confidence            999999998765543333322222110        0      0222223333333       222233334455555555


Q ss_pred             HHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          193 QSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       193 ~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ...+ +++.|...|++++..+|+...+|..+.......|+++.|.+.|++++.
T Consensus       444 ~~~g-~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~  495 (615)
T TIGR00990       444 YKEG-SIASSMATFRRCKKNFPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIE  495 (615)
T ss_pred             HHCC-CHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHHHh
Confidence            5656 666666666666666666666666666666666666666666666665

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.18  E-value=6.3e-11  Score=116.97  Aligned_cols=86  Identities=27%  Similarity=0.425  Sum_probs=77.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcC------C-cccCC
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKN------K-QMFLG  459 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~------~-~~~~g  459 (565)
                      ....+.||||.|||+++++++|.+.|++||.|..+.++.++.||.++|.|||.|.++..++.||.+-      | ..|+|
T Consensus       288 n~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~G  367 (678)
T KOG0127|consen  288 NITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDG  367 (678)
T ss_pred             cccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEec
Confidence            4456799999999999999999999999999999999999999999999999999999999999732      3 55899


Q ss_pred             eEEEEeecCCCCC
Q 008442          460 KKLSIARSNPKQR  472 (565)
Q Consensus       460 ~~l~v~~a~~~~~  472 (565)
                      |.|.|..+.++..
T Consensus       368 R~Lkv~~Av~Rke  380 (678)
T KOG0127|consen  368 RLLKVTLAVTRKE  380 (678)
T ss_pred             cEEeeeeccchHH
Confidence            9999999977643

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.17  E-value=2e-11  Score=114.36  Aligned_cols=75  Identities=29%  Similarity=0.563  Sum_probs=73.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      |+||||.+.+.+.++.|+..|.+||.|++|.+..|+.|++++|||||+|+-++.|+-|++ |||.+++||.|+|..
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr  189 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  189 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC
Confidence            899999999999999999999999999999999999999999999999999999999998 899999999999975

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.16  E-value=2.5e-10  Score=109.60  Aligned_cols=77  Identities=31%  Similarity=0.563  Sum_probs=71.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhc-cCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFS-DVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~-~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      .+.+||+|+|+++.+++|+.+|. +.|+|..|.+..|. +|++||||.|+|++++.+++|++ ||.+.+.||+|.|+...
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            35699999999999999999995 67999999999996 99999999999999999999998 89999999999998753

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.15  E-value=1.2e-10  Score=114.48  Aligned_cols=79  Identities=35%  Similarity=0.636  Sum_probs=75.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      .++|||+|||.++++++|..+|..||.|..+.++.++.+|.++|||||+|.+++++..|+. +++..+.|++|.|..+.+
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            6999999999999999999999999999999999998899999999999999999999998 799999999999999654

>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=99.15  E-value=2.8e-10  Score=86.67  Aligned_cols=73  Identities=40%  Similarity=0.615  Sum_probs=66.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       393 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      +|+|+|||..+++++|+++|..||.|..+.+..++ .+.++|+|||+|.+.++|..|+. +++..+.|+++.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~-~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDK-DTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            58999999999999999999999999999999876 44778999999999999999998 788889999998863

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).

>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein

Probab=99.14  E-value=3.8e-08  Score=112.63  Aligned_cols=267  Identities=13%  Similarity=0.057  Sum_probs=136.3

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (565)
                      +...|+.++...|.    ....+...+......|+.+.+..++++.+...|.+..+|..++.... ..++.+.+..+|++
T Consensus       416 A~~~~~~a~~~~~~----~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~A~~~~~~  490 (899)
T TIGR02917       416 AIADLETAAQLDPE----LGRADLLLILSYLRSGQFDKALAAAKKLEKKQPDNASLHNLLGAIYL-GKGDLAKAREAFEK  490 (899)
T ss_pred             HHHHHHHHHhhCCc----chhhHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCCcHHHHHHHHHHH-hCCCHHHHHHHHHH
Confidence            44555555555443    22333333444444555555555555555555555555555544333 22344555555555


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHH---------HHHHHh-hccccchh
Q 008442           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRID---------GLRRRI-LFSGEVEG  153 (565)
Q Consensus        84 Al~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~---------~~~r~~-~~~~~~e~  153 (565)
                      ++...|.....|..... +....+..+++..+|++++...+.....+..+...+..         ++.+.. ........
T Consensus       491 a~~~~~~~~~~~~~la~-~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~  569 (899)
T TIGR02917       491 ALSIEPDFFPAAANLAR-IDIQEGNPDDAIQRFEKVLTIDPKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNPQEIEP  569 (899)
T ss_pred             HHhhCCCcHHHHHHHHH-HHHHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchhH
Confidence            55555555555544443 22224455555555555554332222111111111100         000000 00000000


Q ss_pred             h---hhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHc
Q 008442          154 V---LDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIEL  230 (565)
Q Consensus       154 ~---~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~  230 (565)
                      .   .........+.+++.++.......+....+|..++......+ +++.|..+|++++...|.+...|..++.+....
T Consensus       570 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~  648 (899)
T TIGR02917       570 ALALAQYYLGKGQLKKALAILNEAADAAPDSPEAWLMLGRAQLAAG-DLNKAVSSFKKLLALQPDSALALLLLADAYAVM  648 (899)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHc
Confidence            0   000001122344555554444434444566777777777777 888888888888887777777888888888788


Q ss_pred             CChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHH
Q 008442          231 DHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (565)
Q Consensus       231 ~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~  280 (565)
                      |+++.|..+|++++..   .+.....|..........|+.+.+...+...
T Consensus       649 ~~~~~A~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~  695 (899)
T TIGR02917       649 KNYAKAITSLKRALEL---KPDNTEAQIGLAQLLLAAKRTESAKKIAKSL  695 (899)
T ss_pred             CCHHHHHHHHHHHHhc---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            8888888888888762   1223355555666666667766666555443

This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.10  E-value=1.9e-10  Score=113.63  Aligned_cols=81  Identities=26%  Similarity=0.411  Sum_probs=75.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      .-+|+|.|||+.+...+|+.+|+.||.|..|.|++.+ .|+-+|||||.|....+|..|+. +|+..|+||+|.|.+|-+
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVD  195 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecc
Confidence            5689999999999999999999999999999999876 67777999999999999999998 899999999999999987


Q ss_pred             CCC
Q 008442          470 KQR  472 (565)
Q Consensus       470 ~~~  472 (565)
                      +..
T Consensus       196 Kd~  198 (678)
T KOG0127|consen  196 KDT  198 (678)
T ss_pred             ccc
Confidence            654

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.10  E-value=1.4e-07  Score=103.45  Aligned_cols=270  Identities=10%  Similarity=-0.006  Sum_probs=180.1

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      .+...|+.++...|.    +...|..........|+.+.+...|++++...|.+..+|...+..+. ..+..+.+..+|+
T Consensus        94 ~A~~~l~~~l~~~P~----~~~a~~~la~~l~~~g~~~~Ai~~l~~Al~l~P~~~~a~~~la~~l~-~~g~~~eA~~~~~  168 (656)
T PRK15174         94 AVLQVVNKLLAVNVC----QPEDVLLVASVLLKSKQYATVADLAEQAWLAFSGNSQIFALHLRTLV-LMDKELQAISLAR  168 (656)
T ss_pred             HHHHHHHHHHHhCCC----ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH-HCCChHHHHHHHH
Confidence            467789999998887    78889999888889999999999999999999999999999888654 4457778999999


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccc-ccHHHHHHHHHHH---------HHHHHHHh-hccccc
Q 008442           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAF-STFEEYLDLFLTR---------IDGLRRRI-LFSGEV  151 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~-~~~~~~~~~~~~~---------~~~~~r~~-~~~~~~  151 (565)
                      +++...|.....|...+. + ...+..+++..++.+++...+ ........+...+         ...+++-. ...+..
T Consensus       169 ~~~~~~P~~~~a~~~~~~-l-~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~p~~~  246 (656)
T PRK15174        169 TQAQEVPPRGDMIATCLS-F-LNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARGLDGA  246 (656)
T ss_pred             HHHHhCCCCHHHHHHHHH-H-HHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCH
Confidence            999988988887755433 3 346888899999999887532 2111111100000         00111000 000100


Q ss_pred             hhhhhHHH---HHHHHH----HHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHH
Q 008442          152 EGVLDYSL---IRETFQ----RASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYI  224 (565)
Q Consensus       152 e~~~~~~~---~~~~~~----~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi  224 (565)
                      ........   ....+.    +|...+...+...+.....+..++.+....+ +++.|...|++++...|++..+|..++
T Consensus       247 ~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~g-~~~eA~~~l~~al~l~P~~~~a~~~La  325 (656)
T PRK15174        247 ALRRSLGLAYYQSGRSREAKLQAAEHWRHALQFNSDNVRIVTLYADALIRTG-QNEKAIPLLQQSLATHPDLPYVRAMYA  325 (656)
T ss_pred             HHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence            00000000   001122    3556666655555556677888888888888 888999999999988888888888888


Q ss_pred             HHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhhH
Q 008442          225 SMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPR  283 (565)
Q Consensus       225 ~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~~  283 (565)
                      ......|+++.|...|++++..  ..+.+ ..+..........|+.+.+...+++++..
T Consensus       326 ~~l~~~G~~~eA~~~l~~al~~--~P~~~-~~~~~~a~al~~~G~~deA~~~l~~al~~  381 (656)
T PRK15174        326 RALRQVGQYTAASDEFVQLARE--KGVTS-KWNRYAAAALLQAGKTSEAESVFEHYIQA  381 (656)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHh--Cccch-HHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            8888889999999999988863  11111 22222223345678888777777766533

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.10  E-value=1.2e-07  Score=103.92  Aligned_cols=268  Identities=12%  Similarity=0.020  Sum_probs=192.2

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      .+...++..+...|.    +...+...+-.....|+++.+...|++++...|.+...|...+..+.. .++.+.+...|+
T Consensus        60 ~A~~l~~~~l~~~p~----~~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~P~~~~a~~~la~~l~~-~g~~~~Ai~~l~  134 (656)
T PRK15174         60 VGLTLLSDRVLTAKN----GRDLLRRWVISPLASSQPDAVLQVVNKLLAVNVCQPEDVLLVASVLLK-SKQYATVADLAE  134 (656)
T ss_pred             hhHHHhHHHHHhCCC----chhHHHHHhhhHhhcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHH-cCCHHHHHHHHH
Confidence            467788999999887    777787777777788999999999999999999999999998876554 447788999999


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHH--HHHH------HHHHHHHhhccccchh-
Q 008442           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDL--FLTR------IDGLRRRILFSGEVEG-  153 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~--~~~~------~~~~~r~~~~~~~~e~-  153 (565)
                      +|+...|....+|..... +....+..+++...+.+++...+.....+..+  ....      ...++ +.+....... 
T Consensus       135 ~Al~l~P~~~~a~~~la~-~l~~~g~~~eA~~~~~~~~~~~P~~~~a~~~~~~l~~~g~~~eA~~~~~-~~l~~~~~~~~  212 (656)
T PRK15174        135 QAWLAFSGNSQIFALHLR-TLVLMDKELQAISLARTQAQEVPPRGDMIATCLSFLNKSRLPEDHDLAR-ALLPFFALERQ  212 (656)
T ss_pred             HHHHhCCCcHHHHHHHHH-HHHHCCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHcCCHHHHHHHHH-HHHhcCCCcch
Confidence            999999999999998776 44557888999999998876544322222111  1110      00111 1111100000 


Q ss_pred             -hh----hHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHH----HHHHHHHHHHHccchHHHHHHHH
Q 008442          154 -VL----DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVS----ARGVWERLLKISGAMLEAWQSYI  224 (565)
Q Consensus       154 -~~----~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~----ar~i~e~~l~~~~~~~~lw~~yi  224 (565)
                       ..    ..-.-..-+..|+..+...+...+....++..++.+....+ +.+.    |...|++++...|++..+|..++
T Consensus       213 ~~~~~l~~~l~~~g~~~eA~~~~~~al~~~p~~~~~~~~Lg~~l~~~G-~~~eA~~~A~~~~~~Al~l~P~~~~a~~~lg  291 (656)
T PRK15174        213 ESAGLAVDTLCAVGKYQEAIQTGESALARGLDGAALRRSLGLAYYQSG-RSREAKLQAAEHWRHALQFNSDNVRIVTLYA  291 (656)
T ss_pred             hHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcC-CchhhHHHHHHHHHHHHhhCCCCHHHHHHHH
Confidence             00    00001123566777776666655556677778888888888 6664    89999999999999999999999


Q ss_pred             HHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          225 SMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       225 ~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      ......|+++.|...|++++..  . +....++..+...-...|..+.+...+.+++
T Consensus       292 ~~l~~~g~~~eA~~~l~~al~l--~-P~~~~a~~~La~~l~~~G~~~eA~~~l~~al  345 (656)
T PRK15174        292 DALIRTGQNEKAIPLLQQSLAT--H-PDLPYVRAMYARALRQVGQYTAASDEFVQLA  345 (656)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHh--C-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            9999999999999999999973  2 2344556555666666788887777766654

>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein

Probab=99.10  E-value=8.4e-08  Score=109.78  Aligned_cols=269  Identities=13%  Similarity=-0.028  Sum_probs=176.7

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...++..+...|.    +...|...+......|+.+.+..+|++++...|.+...|..++..... .+..+.+..+|+
T Consensus       449 ~A~~~~~~~~~~~~~----~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~-~g~~~~A~~~~~  523 (899)
T TIGR02917       449 KALAAAKKLEKKQPD----NASLHNLLGAIYLGKGDLAKAREAFEKALSIEPDFFPAAANLARIDIQ-EGNPDDAIQRFE  523 (899)
T ss_pred             HHHHHHHHHHHhCCC----CcHHHHHHHHHHHhCCCHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHH-CCCHHHHHHHHH
Confidence            355667777776665    566788888888888888889999999998888888888888775443 446777888999


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHH---------HHHHHHhh-ccccch
Q 008442           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRI---------DGLRRRIL-FSGEVE  152 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~---------~~~~r~~~-~~~~~e  152 (565)
                      +++...|.....|..+...+.. .+..+++...|++++...+.....++.+-..+.         ..+++... .....+
T Consensus       524 ~~~~~~~~~~~~~~~l~~~~~~-~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~  602 (899)
T TIGR02917       524 KVLTIDPKNLRAILALAGLYLR-TGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAADAAPDSPE  602 (899)
T ss_pred             HHHHhCcCcHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHhCccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHH
Confidence            9998888888888777764444 677888888888887655443332222211111         01111100 000001


Q ss_pred             hhh---hHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHH
Q 008442          153 GVL---DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE  229 (565)
Q Consensus       153 ~~~---~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~  229 (565)
                      .+.   .......-+++|+..+...+...+.....+..++.+....+ +.++|..+|++++...|++...|..++.+...
T Consensus       603 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~  681 (899)
T TIGR02917       603 AWLMLGRAQLAAGDLNKAVSSFKKLLALQPDSALALLLLADAYAVMK-NYAKAITSLKRALELKPDNTEAQIGLAQLLLA  681 (899)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcC-CHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHH
Confidence            000   00011123455666665555444444556677778787778 99999999999999999989999999999999


Q ss_pred             cCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          230 LDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       230 ~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      .|+++.|..+++.+....   +....++......-...|+.+.+...+.+++
T Consensus       682 ~~~~~~A~~~~~~~~~~~---~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~  730 (899)
T TIGR02917       682 AKRTESAKKIAKSLQKQH---PKAALGFELEGDLYLRQKDYPAAIQAYRKAL  730 (899)
T ss_pred             cCCHHHHHHHHHHHHhhC---cCChHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            999999999999987632   2223444444444445677776666665543

This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.

>smart00361 RRM_1 RNA recognition motif

Probab=99.08  E-value=4.7e-10  Score=84.42  Aligned_cols=61  Identities=33%  Similarity=0.471  Sum_probs=54.5

Q ss_pred             HHHHHHHhc----cCCCeeEEE-EeecCCC--CCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          405 YEDLRRFFS----DVGGVSSIR-ILHDKFT--GKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       405 ~~~l~~~f~----~~G~i~~~~-~~~~~~~--g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      +++|+++|+    .||.|.++. ++.++.+  |.++|||||+|.+.++|..|+. |||..+.|+.|.+.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            578999998    999999995 7776656  8999999999999999999998 89999999998763

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.07  E-value=3.2e-10  Score=109.06  Aligned_cols=85  Identities=24%  Similarity=0.466  Sum_probs=75.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-c-CCcccCC--eEEEE
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-K-NKQMFLG--KKLSI  464 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~-~~~~~~g--~~l~v  464 (565)
                      .+.-++|||.+|..++|.||+.+|++||.|.+|-|++|+.||.++|||||.|.+.++|.+|+. + |.+.|-|  .+|.|
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            556789999999999999999999999999999999999999999999999999999999997 7 5667765  47889


Q ss_pred             eecCCCCCC
Q 008442          465 ARSNPKQRK  473 (565)
Q Consensus       465 ~~a~~~~~~  473 (565)
                      .+++..+.+
T Consensus       112 k~Ad~E~er  120 (510)
T KOG0144|consen  112 KYADGERER  120 (510)
T ss_pred             cccchhhhc
Confidence            888765443

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.07  E-value=6.3e-10  Score=117.10  Aligned_cols=77  Identities=19%  Similarity=0.342  Sum_probs=70.8

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          389 TDECTAFLSNINL-KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       389 ~~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ..+++|||+|||+ .+++++|+++|+.||.|.+|.|+.++     +|||||+|.+.++|..|+. ||+..|.|++|.|.+
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~  347 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCP  347 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            4578999999998 69999999999999999999998763     5999999999999999998 899999999999999


Q ss_pred             cCCC
Q 008442          467 SNPK  470 (565)
Q Consensus       467 a~~~  470 (565)
                      +...
T Consensus       348 s~~~  351 (481)
T TIGR01649       348 SKQQ  351 (481)
T ss_pred             cccc
Confidence            8654

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).

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.04  E-value=2.2e-07  Score=108.70  Aligned_cols=266  Identities=13%  Similarity=0.085  Sum_probs=180.5

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHH--------------
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLD--------------   68 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~--------------   68 (565)
                      ++...|+.++...|.    +...|..........|+++.+...|+++|...|.+...|...+....              
T Consensus       369 eA~~~~~~Al~~~P~----~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~~~~a~~~L~~l~~~~~~~~A~~~l~~l  444 (1157)
T PRK11447        369 QAERLYQQARQVDNT----DSYAVLGLGDVAMARKDYAAAERYYQQALRMDPGNTNAVRGLANLYRQQSPEKALAFIASL  444 (1157)
T ss_pred             HHHHHHHHHHHhCCC----CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCHHHHHHHHHhC
Confidence            366778888888876    67788888888889999999999999999999999887765443211              


Q ss_pred             ---------------------------HhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 008442           69 ---------------------------KTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLL  121 (565)
Q Consensus        69 ---------------------------~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~  121 (565)
                                                 ...+..+.+..+|++|+...|.+..+|......+ ...+..+++..+|++++.
T Consensus       445 ~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~P~~~~~~~~LA~~~-~~~G~~~~A~~~l~~al~  523 (1157)
T PRK11447        445 SASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALDPGSVWLTYRLAQDL-RQAGQRSQADALMRRLAQ  523 (1157)
T ss_pred             CHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH-HHcCCHHHHHHHHHHHHH
Confidence                                       0123556788999999999999888877766634 447889999999999997


Q ss_pred             cccccHHHHHH--HHHH-------HHHHHHHHhhcc---ccchh---------h---hhHHHHHHHHHHHHHHHHhhhcC
Q 008442          122 CAFSTFEEYLD--LFLT-------RIDGLRRRILFS---GEVEG---------V---LDYSLIRETFQRASDYLSEQMKN  177 (565)
Q Consensus       122 ~~~~~~~~~~~--~~~~-------~~~~~~r~~~~~---~~~e~---------~---~~~~~~~~~~~~a~~~l~~~~~~  177 (565)
                      ..+.....+..  ++..       -...+.+ +...   ..+..         .   .+.-.....+++|+.++..    
T Consensus       524 ~~P~~~~~~~a~al~l~~~~~~~~Al~~l~~-l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~~----  598 (1157)
T PRK11447        524 QKPNDPEQVYAYGLYLSGSDRDRAALAHLNT-LPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLRQ----  598 (1157)
T ss_pred             cCCCCHHHHHHHHHHHHhCCCHHHHHHHHHh-CCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHHh----
Confidence            55443322221  1110       0001100 0000   00000         0   0000011224556666653    


Q ss_pred             CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHH
Q 008442          178 TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDIC  257 (565)
Q Consensus       178 ~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~  257 (565)
                      .+....++..++.+....+ ++++|..+|++++...|++...|+..+.+....|+++.|+++|++++..  . +....++
T Consensus       599 ~p~~~~~~~~La~~~~~~g-~~~~A~~~y~~al~~~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~--~-p~~~~~~  674 (1157)
T PRK11447        599 QPPSTRIDLTLADWAQQRG-DYAAARAAYQRVLTREPGNADARLGLIEVDIAQGDLAAARAQLAKLPAT--A-NDSLNTQ  674 (1157)
T ss_pred             CCCCchHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--C-CCChHHH
Confidence            2334456677888888888 9999999999999999999999999999999999999999999998762  2 2233444


Q ss_pred             HHHHHHHHHhCCHHHHHHHHHHHhh
Q 008442          258 HAWLRFEREYGTLEDFDHSVQKVTP  282 (565)
Q Consensus       258 ~~~~~fE~~~G~~~~~~~~~~k~~~  282 (565)
                      ......-...|+.+.+...+++++.
T Consensus       675 ~~la~~~~~~g~~~eA~~~~~~al~  699 (1157)
T PRK11447        675 RRVALAWAALGDTAAAQRTFNRLIP  699 (1157)
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHhh
Confidence            4444444567888888888777764

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.03  E-value=8.5e-10  Score=116.09  Aligned_cols=74  Identities=22%  Similarity=0.224  Sum_probs=67.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-c--CCcccCCeEEEEeec
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-K--NKQMFLGKKLSIARS  467 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~--~~~~~~g~~l~v~~a  467 (565)
                      .++|||+|||+++++++|+++|++||.|.+|.++.+      +|||||+|.+.++|..|+. +  ++..|.|++|.|.++
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            479999999999999999999999999999998853      4899999999999999997 3  778899999999998


Q ss_pred             CCC
Q 008442          468 NPK  470 (565)
Q Consensus       468 ~~~  470 (565)
                      .++
T Consensus        76 ~~~   78 (481)
T TIGR01649        76 TSQ   78 (481)
T ss_pred             CCc
Confidence            643

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).

>KOG4626 consensus O-linked N-acetylglucosamine transferase OGT [Carbohydrate transport and metabolism; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=99.03  E-value=3.5e-08  Score=99.88  Aligned_cols=246  Identities=16%  Similarity=0.128  Sum_probs=123.1

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (565)
                      +-..||++++-.|.    -.++|....+..+..+-++++...|+||+..-|++....-..+. +....+..+.+...|+|
T Consensus       237 aiq~y~eAvkldP~----f~dAYiNLGnV~ke~~~~d~Avs~Y~rAl~lrpn~A~a~gNla~-iYyeqG~ldlAI~~Ykr  311 (966)
T KOG4626|consen  237 AIQHYEEAVKLDPN----FLDAYINLGNVYKEARIFDRAVSCYLRALNLRPNHAVAHGNLAC-IYYEQGLLDLAIDTYKR  311 (966)
T ss_pred             HHHHHHHhhcCCCc----chHHHhhHHHHHHHHhcchHHHHHHHHHHhcCCcchhhccceEE-EEeccccHHHHHHHHHH
Confidence            34455555555543    44555555555555555556666666666665555443333221 11122345566666777


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHH----------HHHHHhhccccchh
Q 008442           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRID----------GLRRRILFSGEVEG  153 (565)
Q Consensus        84 Al~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~----------~~~r~~~~~~~~e~  153 (565)
                      ||..-|+.+.-+......|.. .+++.++...|.+||...+........+-..+.+          |+.....+....+.
T Consensus       312 al~~~P~F~~Ay~NlanALkd-~G~V~ea~~cYnkaL~l~p~hadam~NLgni~~E~~~~e~A~~ly~~al~v~p~~aaa  390 (966)
T KOG4626|consen  312 ALELQPNFPDAYNNLANALKD-KGSVTEAVDCYNKALRLCPNHADAMNNLGNIYREQGKIEEATRLYLKALEVFPEFAAA  390 (966)
T ss_pred             HHhcCCCchHHHhHHHHHHHh-ccchHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhccchHHHHHHHHHHhhChhhhhh
Confidence            776666666666555543432 4666777777777775332211111111111110          00000001111010


Q ss_pred             hhhH---HHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHc
Q 008442          154 VLDY---SLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIEL  230 (565)
Q Consensus       154 ~~~~---~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~  230 (565)
                      ..+.   -.-+..+.+|+..+...+...+....-+......+...+ +++.|...|+++|..+|...+..-..+...+..
T Consensus       391 ~nNLa~i~kqqgnl~~Ai~~YkealrI~P~fAda~~NmGnt~ke~g-~v~~A~q~y~rAI~~nPt~AeAhsNLasi~kDs  469 (966)
T KOG4626|consen  391 HNNLASIYKQQGNLDDAIMCYKEALRIKPTFADALSNMGNTYKEMG-DVSAAIQCYTRAIQINPTFAEAHSNLASIYKDS  469 (966)
T ss_pred             hhhHHHHHHhcccHHHHHHHHHHHHhcCchHHHHHHhcchHHHHhh-hHHHHHHHHHHHHhcCcHHHHHHhhHHHHhhcc
Confidence            0111   111233444555554444444443344444444455555 677777777777777777777777777777777


Q ss_pred             CChHHHHHHHHHHHhcccCCCCcHHHHH
Q 008442          231 DHINEARSIYKRCYSKRFTGTGSEDICH  258 (565)
Q Consensus       231 ~~~~~aR~i~~~al~~~~~~~~~~~i~~  258 (565)
                      |++..|..-|+.||.  +..|-|+.-+.
T Consensus       470 Gni~~AI~sY~~aLk--lkPDfpdA~cN  495 (966)
T KOG4626|consen  470 GNIPEAIQSYRTALK--LKPDFPDAYCN  495 (966)
T ss_pred             CCcHHHHHHHHHHHc--cCCCCchhhhH
Confidence            777777777777764  23444544444

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.00  E-value=4.2e-10  Score=111.91  Aligned_cols=77  Identities=21%  Similarity=0.472  Sum_probs=72.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       393 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      +||||||++++++++|+.+|++||.|..|.++.|..||.++|||||+|.+.++|..|+. +||..|-|+.|+|....-
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~  357 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTE  357 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeee
Confidence            39999999999999999999999999999999998899999999999999999999987 899999999999877643

>KOG4626 consensus O-linked N-acetylglucosamine transferase OGT [Carbohydrate transport and metabolism; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=98.98  E-value=6.5e-08  Score=98.00  Aligned_cols=262  Identities=14%  Similarity=0.122  Sum_probs=157.7

Q ss_pred             HHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCC
Q 008442           10 EQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCP   89 (565)
Q Consensus        10 ~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p   89 (565)
                      .++..+|.    -.+.+..|.+..+..|..+.+..+|+.+|...|...+.|+..+.-+...+ +.+.+...|..||+..|
T Consensus       107 ~a~r~~~q----~ae~ysn~aN~~kerg~~~~al~~y~~aiel~p~fida~inla~al~~~~-~~~~a~~~~~~alqlnP  181 (966)
T KOG4626|consen  107 LAIRKNPQ----GAEAYSNLANILKERGQLQDALALYRAAIELKPKFIDAYINLAAALVTQG-DLELAVQCFFEALQLNP  181 (966)
T ss_pred             hhhhccch----HHHHHHHHHHHHHHhchHHHHHHHHHHHHhcCchhhHHHhhHHHHHHhcC-CCcccHHHHHHHHhcCc
Confidence            34445544    56788889999899999999999999999999999999999988766554 56678899999999888


Q ss_pred             CCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc--c--------HHHHHHHHHHHHHHHHHHhhccccchhhhhHHH
Q 008442           90 WVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS--T--------FEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSL  159 (565)
Q Consensus        90 ~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~--~--------~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~  159 (565)
                      ......... -.|.+..+.++++...|.+|+...+.  .        +...-++|+..-.|.+...+...-.+.+++...
T Consensus       182 ~l~ca~s~l-gnLlka~Grl~ea~~cYlkAi~~qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkldP~f~dAYiNLGn  260 (966)
T KOG4626|consen  182 DLYCARSDL-GNLLKAEGRLEEAKACYLKAIETQPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKLDPNFLDAYINLGN  260 (966)
T ss_pred             chhhhhcch-hHHHHhhcccchhHHHHHHHHhhCCceeeeehhcchHHhhcchHHHHHHHHHHhhcCCCcchHHHhhHHH
Confidence            543333222 23455567777788888888764321  1        111224555544444444444443333333322


Q ss_pred             HH---HHHHHHHH----------------------------------HHHhhhcCCchhHHHHHHHHHHHHHcCCChHHH
Q 008442          160 IR---ETFQRASD----------------------------------YLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSA  202 (565)
Q Consensus       160 ~~---~~~~~a~~----------------------------------~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~a  202 (565)
                      +.   ..|.+|+.                                  .+++.+...+....-+...+.-....| ++.+|
T Consensus       261 V~ke~~~~d~Avs~Y~rAl~lrpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~P~F~~Ay~NlanALkd~G-~V~ea  339 (966)
T KOG4626|consen  261 VYKEARIFDRAVSCYLRALNLRPNHAVAHGNLACIYYEQGLLDLAIDTYKRALELQPNFPDAYNNLANALKDKG-SVTEA  339 (966)
T ss_pred             HHHHHhcchHHHHHHHHHHhcCCcchhhccceEEEEeccccHHHHHHHHHHHHhcCCCchHHHhHHHHHHHhcc-chHHH
Confidence            22   22333333                                  333333333333333334444444455 66677


Q ss_pred             HHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          203 RGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       203 r~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      ..+|.++|..+|++.+.-.......++.|.++.|..+|.+++.- ++  .-..-+.-....-...|+++++-.+.+.++
T Consensus       340 ~~cYnkaL~l~p~hadam~NLgni~~E~~~~e~A~~ly~~al~v-~p--~~aaa~nNLa~i~kqqgnl~~Ai~~Ykeal  415 (966)
T KOG4626|consen  340 VDCYNKALRLCPNHADAMNNLGNIYREQGKIEEATRLYLKALEV-FP--EFAAAHNNLASIYKQQGNLDDAIMCYKEAL  415 (966)
T ss_pred             HHHHHHHHHhCCccHHHHHHHHHHHHHhccchHHHHHHHHHHhh-Ch--hhhhhhhhHHHHHHhcccHHHHHHHHHHHH
Confidence            77777777777777766666777777777777777777777652 11  111223333344455566666555555444

>PF13893 RRM_5: RNA recognition motif

Probab=98.96  E-value=2.7e-09  Score=76.45  Aligned_cols=55  Identities=35%  Similarity=0.624  Sum_probs=49.0

Q ss_pred             HHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          408 LRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       408 l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      |..+|++||.|.++.+..+.     +|+|||+|.+.++|..|+. +|+..+.|++|.|.+|
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            67899999999999987643     5899999999999999998 8999999999999875

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=98.96  E-value=1.3e-06  Score=90.23  Aligned_cols=86  Identities=7%  Similarity=-0.036  Sum_probs=51.8

Q ss_pred             hcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCH----HHHHHHHHHHHHhcCCHH
Q 008442           35 SSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVG----ELWVRSLLSLERSRASEE  110 (565)
Q Consensus        35 ~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~----~lW~~yi~~le~~~~~~~  110 (565)
                      ..++++.+...|++++...|.+..+|...+..+.. .+..+.+..++++++..-+...    ..|......+ ...+..+
T Consensus        47 ~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~-~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~-~~~g~~~  124 (389)
T PRK11788         47 LNEQPDKAIDLFIEMLKVDPETVELHLALGNLFRR-RGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDY-LKAGLLD  124 (389)
T ss_pred             hcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHH-cCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHH-HHCCCHH
Confidence            45667777777777777777777777776665443 3355667777777776422221    2333333322 2346677


Q ss_pred             HHHHHHHHHHhc
Q 008442          111 EISTVFEKSLLC  122 (565)
Q Consensus       111 ~~~~if~ral~~  122 (565)
                      .+..+|++++..
T Consensus       125 ~A~~~~~~~l~~  136 (389)
T PRK11788        125 RAEELFLQLVDE  136 (389)
T ss_pred             HHHHHHHHHHcC
Confidence            777777777764

>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B

Probab=98.96  E-value=6.5e-09  Score=102.07  Aligned_cols=236  Identities=14%  Similarity=0.070  Sum_probs=75.3

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~  101 (565)
                      +...|..+.+.....++.+.+...|++.+...+.++.....++.++  ..++++.+..+++++.+.. .++.+|..++..
T Consensus        43 ~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~~~~~~~~~l~~l~--~~~~~~~A~~~~~~~~~~~-~~~~~l~~~l~~  119 (280)
T PF13429_consen   43 DPEYWRLLADLAWSLGDYDEAIEAYEKLLASDKANPQDYERLIQLL--QDGDPEEALKLAEKAYERD-GDPRYLLSALQL  119 (280)
T ss_dssp             ------------------------------------------------------------------------------H-
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccc--ccccccccccccccccccc-cccchhhHHHHH
Confidence            5677888888777777888888888888887777777777777652  3345666777777777654 345666666664


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchh
Q 008442          102 LERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGL  181 (565)
Q Consensus       102 le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~  181 (565)
                      + ...+..+++..+++++.....  ......+|..+..+..+.          .+.......|++++..       .|..
T Consensus       120 ~-~~~~~~~~~~~~l~~~~~~~~--~~~~~~~~~~~a~~~~~~----------G~~~~A~~~~~~al~~-------~P~~  179 (280)
T PF13429_consen  120 Y-YRLGDYDEAEELLEKLEELPA--APDSARFWLALAEIYEQL----------GDPDKALRDYRKALEL-------DPDD  179 (280)
T ss_dssp             H-HHTT-HHHHHHHHHHHHH-T-----T-HHHHHHHHHHHHHC----------CHHHHHHHHHHHHHHH--------TT-
T ss_pred             H-HHHhHHHHHHHHHHHHHhccC--CCCCHHHHHHHHHHHHHc----------CCHHHHHHHHHHHHHc-------CCCC
Confidence            3 335677777777777664221  111122222222221100          1233334444444443       2333


Q ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHH
Q 008442          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWL  261 (565)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~  261 (565)
                      ..++..++.+....+ +.++++.++.......|++..+|..++......|+.+.|..+|++++..  . +....+...|.
T Consensus       180 ~~~~~~l~~~li~~~-~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~--~-p~d~~~~~~~a  255 (280)
T PF13429_consen  180 PDARNALAWLLIDMG-DYDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEALEYLEKALKL--N-PDDPLWLLAYA  255 (280)
T ss_dssp             HHHHHHHHHHHCTTC-HHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHH--S-TT-HHHHHHHH
T ss_pred             HHHHHHHHHHHHHCC-ChHHHHHHHHHHHHHCcCHHHHHHHHHHHhccccccccccccccccccc--c-ccccccccccc
Confidence            445555666666666 6777777777777776666777777777777778888888888887752  2 22335556677


Q ss_pred             HHHHHhCCHHHHHHHHHHHhhHH
Q 008442          262 RFEREYGTLEDFDHSVQKVTPRL  284 (565)
Q Consensus       262 ~fE~~~G~~~~~~~~~~k~~~~~  284 (565)
                      +.-...|..+.+..+..++...+
T Consensus       256 ~~l~~~g~~~~A~~~~~~~~~~l  278 (280)
T PF13429_consen  256 DALEQAGRKDEALRLRRQALRLL  278 (280)
T ss_dssp             HHHT-------------------
T ss_pred             ccccccccccccccccccccccc
Confidence            77777777777776666665544

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.95  E-value=1.9e-09  Score=100.96  Aligned_cols=80  Identities=25%  Similarity=0.385  Sum_probs=75.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      ..-|||.-|.+-+++++|.-+|+.||.|.+|.|++|+.||.+-.||||+|.+.+++++|.- |+...|++++|.|.++.+
T Consensus       239 eNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQS  318 (479)
T KOG0415|consen  239 ENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQS  318 (479)
T ss_pred             cceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhhh
Confidence            5789999999999999999999999999999999999999999999999999999999985 899999999999999865


Q ss_pred             C
Q 008442          470 K  470 (565)
Q Consensus       470 ~  470 (565)
                      -
T Consensus       319 V  319 (479)
T KOG0415|consen  319 V  319 (479)
T ss_pred             h
Confidence            4

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=98.95  E-value=1.3e-09  Score=93.01  Aligned_cols=83  Identities=22%  Similarity=0.345  Sum_probs=75.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeE-EEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSS-IRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~-~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ..+.++||+||.+.+++..|...|+.||.+.+ -.++++..||.++|||||.|.+.+.+.+|+. +||..++.+++.|.+
T Consensus        94 ~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~y  173 (203)
T KOG0131|consen   94 DVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSY  173 (203)
T ss_pred             cccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEE
Confidence            44589999999999999999999999998765 4788888899999999999999999999998 899999999999999


Q ss_pred             cCCCC
Q 008442          467 SNPKQ  471 (565)
Q Consensus       467 a~~~~  471 (565)
                      +..+.
T Consensus       174 a~k~~  178 (203)
T KOG0131|consen  174 AFKKD  178 (203)
T ss_pred             EEecC
Confidence            86553

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.93  E-value=2.3e-09  Score=93.66  Aligned_cols=82  Identities=23%  Similarity=0.379  Sum_probs=73.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccC-CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDV-GGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~-G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ....-+||..+|..+.+..+..+|.++ |.+..+++-+++.||.|+|||||+|++++.|.-|.+ ||+..|.|+.|.|.+
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~v  126 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHV  126 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEE
Confidence            334568999999999999999999998 678888888888899999999999999999999987 999999999999988


Q ss_pred             cCCC
Q 008442          467 SNPK  470 (565)
Q Consensus       467 a~~~  470 (565)
                      -.|.
T Consensus       127 mppe  130 (214)
T KOG4208|consen  127 MPPE  130 (214)
T ss_pred             eCch
Confidence            7765

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=98.91  E-value=8.5e-09  Score=92.71  Aligned_cols=81  Identities=21%  Similarity=0.334  Sum_probs=75.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ..+--|||-||.+++++.-|=++|.+||.|..|.|++|..|.+.+|||||.+.+-++|..||. +||..++++.|.|++.
T Consensus       276 ~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFK  355 (360)
T KOG0145|consen  276 GGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFK  355 (360)
T ss_pred             CCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEe
Confidence            446789999999999999999999999999999999999889999999999999999999997 8999999999999885


Q ss_pred             CC
Q 008442          468 NP  469 (565)
Q Consensus       468 ~~  469 (565)
                      ..
T Consensus       356 tn  357 (360)
T KOG0145|consen  356 TN  357 (360)
T ss_pred             cC
Confidence            43

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.91  E-value=1.6e-09  Score=104.28  Aligned_cols=83  Identities=25%  Similarity=0.496  Sum_probs=78.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecCC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~~  469 (565)
                      +.++|||++|+++++++.|+..|.+||.|.++.++.|+.+++++||+||+|.+++.+.+++....+.|+|+.|.+..+.|
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~   84 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVS   84 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccC
Confidence            67999999999999999999999999999999999999999999999999999999998888888899999999999987


Q ss_pred             CCC
Q 008442          470 KQR  472 (565)
Q Consensus       470 ~~~  472 (565)
                      +..
T Consensus        85 r~~   87 (311)
T KOG4205|consen   85 RED   87 (311)
T ss_pred             ccc
Confidence            764

>PF08424 NRDE-2: NRDE-2, necessary for RNA interference; InterPro: IPR013633 This is domain is found in eukaryotic proteins of unknown function

Probab=98.91  E-value=1.3e-07  Score=94.00  Aligned_cols=114  Identities=18%  Similarity=0.247  Sum_probs=87.8

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCC------------chhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGD------------PGRVQLLYERAITDFPVSSDLWLDYTQYLDKT   70 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~------------~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~   70 (565)
                      +....|+..|..+|.    +.+.|+.|++|....-.            .++-..+|||||..+|.+..||+.|++...+.
T Consensus         3 ~r~~el~~~v~~~P~----di~~Wl~li~~Qd~~~~~~~~~~~~~~a~~E~klsilerAL~~np~~~~L~l~~l~~~~~~   78 (321)
T PF08424_consen    3 KRTAELNRRVRENPH----DIEAWLELIEFQDELFRLQSSSKAERRALAERKLSILERALKHNPDSERLLLGYLEEGEKV   78 (321)
T ss_pred             hHHHHHHHHHHhCcc----cHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHh
Confidence            456678888888887    88999999998665321            13456789999999999999999999866544


Q ss_pred             cchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhc--CCHHHHHHHHHHHHh
Q 008442           71 LKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSR--ASEEEISTVFEKSLL  121 (565)
Q Consensus        71 ~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~--~~~~~~~~if~ral~  121 (565)
                      - +.+.+...+++++...|.+..||..||.+.....  -.++.++.+|.+||.
T Consensus        79 ~-~~~~l~~~we~~l~~~~~~~~LW~~yL~~~q~~~~~f~v~~~~~~y~~~l~  130 (321)
T PF08424_consen   79 W-DSEKLAKKWEELLFKNPGSPELWREYLDFRQSNFASFTVSDVRDVYEKCLR  130 (321)
T ss_pred             C-CHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHhccCcHHHHHHHHHHHHH
Confidence            3 6667888899999999999999999998665532  346677777777774

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=98.88  E-value=1.5e-06  Score=101.85  Aligned_cols=245  Identities=10%  Similarity=0.010  Sum_probs=131.0

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHH--HHHHHHHH-----------HHHh
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSD--LWLDYTQY-----------LDKT   70 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~--lW~~Y~~~-----------l~~~   70 (565)
                      +...|+.+|...|.    +..+|..........|+.+.+...|++++...|.+..  .|..++.-           ....
T Consensus       288 A~~~l~~aL~~~P~----~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g~~~~~  363 (1157)
T PRK11447        288 AIPELQQAVRANPK----DSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQGDAALK  363 (1157)
T ss_pred             HHHHHHHHHHhCCC----CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHHHHHHH
Confidence            34445555555544    4555555555555556666666666666666555432  23222110           0112


Q ss_pred             cchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhcccc
Q 008442           71 LKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGE  150 (565)
Q Consensus        71 ~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~  150 (565)
                      .+..+.+...|++|+...|.....|..... +....+..+++...|++++...+.....+..+...+.            
T Consensus       364 ~g~~~eA~~~~~~Al~~~P~~~~a~~~Lg~-~~~~~g~~~eA~~~y~~aL~~~p~~~~a~~~L~~l~~------------  430 (1157)
T PRK11447        364 ANNLAQAERLYQQARQVDNTDSYAVLGLGD-VAMARKDYAAAERYYQQALRMDPGNTNAVRGLANLYR------------  430 (1157)
T ss_pred             CCCHHHHHHHHHHHHHhCCCCHHHHHHHHH-HHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH------------
Confidence            234455666666666666655555444333 2233455666666666666543332221111111110            


Q ss_pred             chhhhhHHHHHHHHHHHHHHHHhhhcCCch---------hHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHH
Q 008442          151 VEGVLDYSLIRETFQRASDYLSEQMKNTDG---------LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQ  221 (565)
Q Consensus       151 ~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~---------~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~  221 (565)
                                ...+++|+.++.........         ....+...+......+ +.+.|..+|+++++..|++..++.
T Consensus       431 ----------~~~~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g-~~~eA~~~~~~Al~~~P~~~~~~~  499 (1157)
T PRK11447        431 ----------QQSPEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQG-KWAQAAELQRQRLALDPGSVWLTY  499 (1157)
T ss_pred             ----------hcCHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCHHHHH
Confidence                      01112233332211110000         0112334566666677 999999999999999999999999


Q ss_pred             HHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHH
Q 008442          222 SYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQK  279 (565)
Q Consensus       222 ~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k  279 (565)
                      ..+......|+++.|..+|++++..  ..+.+ ..+.....+....|..+.+...+.+
T Consensus       500 ~LA~~~~~~G~~~~A~~~l~~al~~--~P~~~-~~~~a~al~l~~~~~~~~Al~~l~~  554 (1157)
T PRK11447        500 RLAQDLRQAGQRSQADALMRRLAQQ--KPNDP-EQVYAYGLYLSGSDRDRAALAHLNT  554 (1157)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHc--CCCCH-HHHHHHHHHHHhCCCHHHHHHHHHh
Confidence            9999999999999999999999863  22333 3333334444455665555544443

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=98.87  E-value=1.8e-06  Score=89.07  Aligned_cols=252  Identities=11%  Similarity=0.052  Sum_probs=168.3

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCH----HHHHHHHHHHHHhcchhhHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS----DLWLDYTQYLDKTLKVGNVVR   78 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~----~lW~~Y~~~l~~~~~~~~~~~   78 (565)
                      .+...|+.++...|.    +...|...+......|+++.+..+|++++...+...    ..|...+.... ..++.+.+.
T Consensus        53 ~A~~~~~~al~~~p~----~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~-~~g~~~~A~  127 (389)
T PRK11788         53 KAIDLFIEMLKVDPE----TVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYL-KAGLLDRAE  127 (389)
T ss_pred             HHHHHHHHHHhcCcc----cHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHH-HCCCHHHHH
Confidence            356788888888776    788899999999999999999999999988643332    35565555433 445778899


Q ss_pred             HHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHH-HHHHHHHHHHHHHHHHhhccccchhhhhH
Q 008442           79 DVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFE-EYLDLFLTRIDGLRRRILFSGEVEGVLDY  157 (565)
Q Consensus        79 ~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~-~~~~~~~~~~~~~~r~~~~~~~~e~~~~~  157 (565)
                      .+|++++...|.....+...+..+ ...+..+++..+|++++...+.... ....++.........    .      .++
T Consensus       128 ~~~~~~l~~~~~~~~~~~~la~~~-~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~----~------~~~  196 (389)
T PRK11788        128 ELFLQLVDEGDFAEGALQQLLEIY-QQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALA----R------GDL  196 (389)
T ss_pred             HHHHHHHcCCcchHHHHHHHHHHH-HHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHh----C------CCH
Confidence            999999998887777777776633 4468889999999998875433211 111122222111100    0      133


Q ss_pred             HHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccch-HHHHHHHHHHHHHcCChHHH
Q 008442          158 SLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM-LEAWQSYISMEIELDHINEA  236 (565)
Q Consensus       158 ~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~-~~lw~~yi~~e~~~~~~~~a  236 (565)
                      ..+...|.+++..       .+.....+..++.++...+ ++++|..+|++++...|.. ..+|...+..+...|+++.|
T Consensus       197 ~~A~~~~~~al~~-------~p~~~~~~~~la~~~~~~g-~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A  268 (389)
T PRK11788        197 DAARALLKKALAA-------DPQCVRASILLGDLALAQG-DYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEG  268 (389)
T ss_pred             HHHHHHHHHHHhH-------CcCCHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHH
Confidence            3444455544442       2223445566677777777 8888888888888876654 45667777777788888888


Q ss_pred             HHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhh
Q 008442          237 RSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTP  282 (565)
Q Consensus       237 R~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~  282 (565)
                      ..++++++..  . +.+ .++..+...-...|+.+.+...+.+++.
T Consensus       269 ~~~l~~~~~~--~-p~~-~~~~~la~~~~~~g~~~~A~~~l~~~l~  310 (389)
T PRK11788        269 LEFLRRALEE--Y-PGA-DLLLALAQLLEEQEGPEAAQALLREQLR  310 (389)
T ss_pred             HHHHHHHHHh--C-CCc-hHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            8888888763  1 122 3345666667777888877777776653

>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B

Probab=98.86  E-value=1.3e-08  Score=99.94  Aligned_cols=230  Identities=15%  Similarity=0.157  Sum_probs=86.6

Q ss_pred             HHHHHHHHHHHhcCCchhHHHHHHHHHhcC--CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHH
Q 008442           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDF--PVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (565)
Q Consensus        24 ~~W~~yi~~e~~~~~~~~~~~lyERal~~~--p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~  101 (565)
                      ...+.++......|+++.+..++.+++...  |.+.++|..++...+ ..++.+.+..+|++.+..-+.+......++..
T Consensus         9 ~~~l~~A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~-~~~~~~~A~~ay~~l~~~~~~~~~~~~~l~~l   87 (280)
T PF13429_consen    9 EEALRLARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAW-SLGDYDEAIEAYEKLLASDKANPQDYERLIQL   87 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccc-cccccccccccccccccccccccccccccccc
Confidence            345577888888999999999998877665  899999999987544 45577889999999998777777777777764


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcccc--cHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCc
Q 008442          102 LERSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTD  179 (565)
Q Consensus       102 le~~~~~~~~~~~if~ral~~~~~--~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~  179 (565)
                        ...++.+++..+++++......  .+..++.++...                 .++..+...+..+..     ....+
T Consensus        88 --~~~~~~~~A~~~~~~~~~~~~~~~~l~~~l~~~~~~-----------------~~~~~~~~~l~~~~~-----~~~~~  143 (280)
T PF13429_consen   88 --LQDGDPEEALKLAEKAYERDGDPRYLLSALQLYYRL-----------------GDYDEAEELLEKLEE-----LPAAP  143 (280)
T ss_dssp             --------------------------------H-HHHT-----------------T-HHHHHHHHHHHHH------T---
T ss_pred             --cccccccccccccccccccccccchhhHHHHHHHHH-----------------hHHHHHHHHHHHHHh-----ccCCC
Confidence              3456677888888887754322  111111211110                 144445555554432     11123


Q ss_pred             hhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHH
Q 008442          180 GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHA  259 (565)
Q Consensus       180 ~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~  259 (565)
                      ....+|..++.++...| +.++|..+|++++...|++..++..++.+....|+.+.++.+++......   +....+|..
T Consensus       144 ~~~~~~~~~a~~~~~~G-~~~~A~~~~~~al~~~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~---~~~~~~~~~  219 (280)
T PF13429_consen  144 DSARFWLALAEIYEQLG-DPDKALRDYRKALELDPDDPDARNALAWLLIDMGDYDEAREALKRLLKAA---PDDPDLWDA  219 (280)
T ss_dssp             T-HHHHHHHHHHHHHCC-HHHHHHHHHHHHHHH-TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH----HTSCCHCHH
T ss_pred             CCHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC---cCHHHHHHH
Confidence            45678999999999999 99999999999999999999999999999999999999999999987631   122357777


Q ss_pred             HHHHHHHhCCHHHHHHHHHHHhh
Q 008442          260 WLRFEREYGTLEDFDHSVQKVTP  282 (565)
Q Consensus       260 ~~~fE~~~G~~~~~~~~~~k~~~  282 (565)
                      +.......|+.+.+...+.++..
T Consensus       220 la~~~~~lg~~~~Al~~~~~~~~  242 (280)
T PF13429_consen  220 LAAAYLQLGRYEEALEYLEKALK  242 (280)
T ss_dssp             HHHHHHHHT-HHHHHHHHHHHHH
T ss_pred             HHHHhcccccccccccccccccc
Confidence            77777777888888877777654

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.86  E-value=1.3e-06  Score=82.31  Aligned_cols=196  Identities=15%  Similarity=0.090  Sum_probs=124.3

Q ss_pred             HHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHH
Q 008442           23 FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSL  102 (565)
Q Consensus        23 ~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~l  102 (565)
                      ...|..........|+.+.+...|++++...|.+...|...+.... ..++.+.+...|++++...|....+|..+...+
T Consensus        31 ~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~-~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  109 (234)
T TIGR02521        31 AKIRVQLALGYLEQGDLEVAKENLDKALEHDPDDYLAYLALALYYQ-QLGELEKAEDSFRRALTLNPNNGDVLNNYGTFL  109 (234)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHH-HcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHH
Confidence            4567777777778899999999999999999999999888876554 345778899999999999998888888776633


Q ss_pred             HHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhH
Q 008442          103 ERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLL  182 (565)
Q Consensus       103 e~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~  182 (565)
                       ...+..+++...|++++..+...                                                     ...
T Consensus       110 -~~~g~~~~A~~~~~~~~~~~~~~-----------------------------------------------------~~~  135 (234)
T TIGR02521       110 -CQQGKYEQAMQQFEQAIEDPLYP-----------------------------------------------------QPA  135 (234)
T ss_pred             -HHcccHHHHHHHHHHHHhccccc-----------------------------------------------------cch
Confidence             44677888888888877532100                                                     000


Q ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHH
Q 008442          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLR  262 (565)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~  262 (565)
                      ..+..++......+ +++.|...|++++...|.....|..++.+....|+++.|..++++++..  ... ....+.....
T Consensus       136 ~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--~~~-~~~~~~~~~~  211 (234)
T TIGR02521       136 RSLENAGLCALKAG-DFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKDARAYLERYQQT--YNQ-TAESLWLGIR  211 (234)
T ss_pred             HHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCC-CHHHHHHHHH
Confidence            11112223333444 5556666666666655555555555555555566666666666666542  111 2223334444


Q ss_pred             HHHHhCCHHHHHHHH
Q 008442          263 FEREYGTLEDFDHSV  277 (565)
Q Consensus       263 fE~~~G~~~~~~~~~  277 (565)
                      .....|+.+.+....
T Consensus       212 ~~~~~~~~~~a~~~~  226 (234)
T TIGR02521       212 IARALGDVAAAQRYG  226 (234)
T ss_pred             HHHHHhhHHHHHHHH
Confidence            555555555555443

Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=98.86  E-value=3.4e-09  Score=97.04  Aligned_cols=71  Identities=23%  Similarity=0.385  Sum_probs=66.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCCC
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNPK  470 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~~  470 (565)
                      .+|||||||..+++.+|+.+|++||.|.+|.|+.+        ||||..++...+..||. |++..|+|..|.|+-++.+
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            46899999999999999999999999999999864        99999999999999998 9999999999999988766

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.85  E-value=2.9e-06  Score=83.79  Aligned_cols=210  Identities=16%  Similarity=0.178  Sum_probs=141.7

Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHH
Q 008442            7 HLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATK   86 (565)
Q Consensus         7 ~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~   86 (565)
                      .+...|...+...+.....|..........|+...+...|++++...|.++..|......+. ..++.+.+...|++|+.
T Consensus        48 ~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~~~-~~g~~~~A~~~~~~Al~  126 (296)
T PRK11189         48 RLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALRPDMADAYNYLGIYLT-QAGNFDAAYEAFDSVLE  126 (296)
T ss_pred             HHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH-HCCCHHHHHHHHHHHHH
Confidence            34455555554334456778888777788899999999999999999999999999887655 44578889999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHH
Q 008442           87 NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQR  166 (565)
Q Consensus        87 ~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~  166 (565)
                      ..|.....|......+ ...+..+++...|++++...+...  +..+|......       .      .+...+...|.+
T Consensus       127 l~P~~~~a~~~lg~~l-~~~g~~~eA~~~~~~al~~~P~~~--~~~~~~~l~~~-------~------~~~~~A~~~l~~  190 (296)
T PRK11189        127 LDPTYNYAYLNRGIAL-YYGGRYELAQDDLLAFYQDDPNDP--YRALWLYLAES-------K------LDPKQAKENLKQ  190 (296)
T ss_pred             hCCCCHHHHHHHHHHH-HHCCCHHHHHHHHHHHHHhCCCCH--HHHHHHHHHHc-------c------CCHHHHHHHHHH
Confidence            9999888887766533 457899999999999998665533  22333321100       0      123333344433


Q ss_pred             HHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHH-------HHccchHHHHHHHHHHHHHcCChHHHHHH
Q 008442          167 ASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLL-------KISGAMLEAWQSYISMEIELDHINEARSI  239 (565)
Q Consensus       167 a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l-------~~~~~~~~lw~~yi~~e~~~~~~~~aR~i  239 (565)
                      +....      .+.   .|. |......++ ++..+ ..++.++       +..++..+.|..........|+++.|+..
T Consensus       191 ~~~~~------~~~---~~~-~~~~~~~lg-~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~  258 (296)
T PRK11189        191 RYEKL------DKE---QWG-WNIVEFYLG-KISEE-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAAL  258 (296)
T ss_pred             HHhhC------Ccc---ccH-HHHHHHHcc-CCCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH
Confidence            22211      111   121 223333345 44333 3444444       33455667899999999999999999999


Q ss_pred             HHHHHh
Q 008442          240 YKRCYS  245 (565)
Q Consensus       240 ~~~al~  245 (565)
                      |++++.
T Consensus       259 ~~~Al~  264 (296)
T PRK11189        259 FKLALA  264 (296)
T ss_pred             HHHHHH
Confidence            999997

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.84  E-value=7.6e-09  Score=103.40  Aligned_cols=78  Identities=26%  Similarity=0.458  Sum_probs=71.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCCC
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNPK  470 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~~  470 (565)
                      ..|||.||+++++..+|..+|+.||.|.+|.+.++. .| ++|| ||+|.++++|.+|+. +||..+.|++|.|....++
T Consensus        77 ~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~  153 (369)
T KOG0123|consen   77 SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERK  153 (369)
T ss_pred             ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccch
Confidence            349999999999999999999999999999999996 67 9999 999999999999998 7999999999999887665


Q ss_pred             CC
Q 008442          471 QR  472 (565)
Q Consensus       471 ~~  472 (565)
                      ..
T Consensus       154 ~e  155 (369)
T KOG0123|consen  154 EE  155 (369)
T ss_pred             hh
Confidence            43

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.83  E-value=1.3e-08  Score=95.70  Aligned_cols=80  Identities=31%  Similarity=0.408  Sum_probs=71.2

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH--cCCcccCCeE
Q 008442          384 RTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA--KNKQMFLGKK  461 (565)
Q Consensus       384 ~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~--~~~~~~~g~~  461 (565)
                      .++.+..-.||||++|-..+++.+|+..|.+||+|++|+++..+      |+|||+|.+.++|+.|..  .+...|+|++
T Consensus       221 epPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G~R  294 (377)
T KOG0153|consen  221 EPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVINGFR  294 (377)
T ss_pred             CCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecceE
Confidence            34556667899999999999999999999999999999997653      699999999999999886  4877899999


Q ss_pred             EEEeecCC
Q 008442          462 LSIARSNP  469 (565)
Q Consensus       462 l~v~~a~~  469 (565)
                      |.|.++.|
T Consensus       295 l~i~Wg~~  302 (377)
T KOG0153|consen  295 LKIKWGRP  302 (377)
T ss_pred             EEEEeCCC
Confidence            99999888

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.83  E-value=1.1e-08  Score=91.26  Aligned_cols=80  Identities=30%  Similarity=0.462  Sum_probs=72.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHH----HhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEE
Q 008442          390 DECTAFLSNINLKATYEDLRR----FFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSI  464 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~----~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v  464 (565)
                      .+.||||.||+..+..++|+.    +|++||.|.+|....   +.+.||-|||.|.+.+.|..|+. |+|..+.|++++|
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mri   84 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRI   84 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhhe
Confidence            345999999999999999888    999999999988754   78899999999999999999998 8999999999999


Q ss_pred             eecCCCCC
Q 008442          465 ARSNPKQR  472 (565)
Q Consensus       465 ~~a~~~~~  472 (565)
                      .+|..+..
T Consensus        85 qyA~s~sd   92 (221)
T KOG4206|consen   85 QYAKSDSD   92 (221)
T ss_pred             ecccCccc
Confidence            99976643

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.82  E-value=2.9e-08  Score=91.65  Aligned_cols=81  Identities=22%  Similarity=0.340  Sum_probs=74.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      ..+|+|.|||+.+++.||+++|..||.+..+-|..++ +|.+.|.|-|.|...++|.+|+. +++..++|++|.+....+
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            4789999999999999999999999999999999997 99999999999999999999998 799999999999988766


Q ss_pred             CCC
Q 008442          470 KQR  472 (565)
Q Consensus       470 ~~~  472 (565)
                      +..
T Consensus       162 ~~~  164 (243)
T KOG0533|consen  162 PSQ  164 (243)
T ss_pred             ccc
Confidence            544

>PRK12370 invasion protein regulator; Provisional

Probab=98.82  E-value=2e-06  Score=92.66  Aligned_cols=213  Identities=9%  Similarity=-0.093  Sum_probs=128.4

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHH---------hcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcch
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQ---------SSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKV   73 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~---------~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~   73 (565)
                      ++...|+.++..+|.    +...|........         ..++...+...+++||...|.+...|..++..+. ..++
T Consensus       279 ~A~~~~~~Al~ldP~----~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~ldP~~~~a~~~lg~~~~-~~g~  353 (553)
T PRK12370        279 QALKLLTQCVNMSPN----SIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATELDHNNPQALGLLGLINT-IHSE  353 (553)
T ss_pred             HHHHHHHHHHhcCCc----cHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHH-HccC
Confidence            356677777777775    4555543332211         1233567888888888888888888887765443 3346


Q ss_pred             hhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchh
Q 008442           74 GNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEG  153 (565)
Q Consensus        74 ~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~  153 (565)
                      .+.+...|++|+...|.+...|..+...+ ...+..+++...|++|+...+.....+......++  .            
T Consensus       354 ~~~A~~~~~~Al~l~P~~~~a~~~lg~~l-~~~G~~~eAi~~~~~Al~l~P~~~~~~~~~~~~~~--~------------  418 (553)
T PRK12370        354 YIVGSLLFKQANLLSPISADIKYYYGWNL-FMAGQLEEALQTINECLKLDPTRAAAGITKLWITY--Y------------  418 (553)
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHH-HHCCCHHHHHHHHHHHHhcCCCChhhHHHHHHHHH--h------------
Confidence            77788888888888888888887666533 34677888888888888765543221111111010  0            


Q ss_pred             hhhHHHHHHHHHHHHHHHHhhhcCC-chhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCC
Q 008442          154 VLDYSLIRETFQRASDYLSEQMKNT-DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDH  232 (565)
Q Consensus       154 ~~~~~~~~~~~~~a~~~l~~~~~~~-~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~  232 (565)
                             ..-+++|+..+...+... +.....+...+.++...| ++++|+..+.+++...|.....+...+......| 
T Consensus       419 -------~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G-~~~eA~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-  489 (553)
T PRK12370        419 -------HTGIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKG-KHELARKLTKEISTQEITGLIAVNLLYAEYCQNS-  489 (553)
T ss_pred             -------ccCHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCC-CHHHHHHHHHHhhhccchhHHHHHHHHHHHhccH-
Confidence                   011233333333333221 222334455566666667 8888888888877777776666666666555555 


Q ss_pred             hHHHHHHHHHHHh
Q 008442          233 INEARSIYKRCYS  245 (565)
Q Consensus       233 ~~~aR~i~~~al~  245 (565)
                       +.+...++..+.
T Consensus       490 -~~a~~~l~~ll~  501 (553)
T PRK12370        490 -ERALPTIREFLE  501 (553)
T ss_pred             -HHHHHHHHHHHH
Confidence             366666666544

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=98.82  E-value=5.4e-06  Score=92.84  Aligned_cols=109  Identities=7%  Similarity=-0.013  Sum_probs=79.5

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...|+.+|...|.    +...|...+......++++.+..++++++...|.+.. |..++..+. ..+..+.+..+|+
T Consensus        67 ~A~~~~~~al~~~P~----~~~a~~~la~~l~~~g~~~eA~~~l~~~l~~~P~~~~-~~~la~~l~-~~g~~~~Al~~l~  140 (765)
T PRK10049         67 NSLTLWQKALSLEPQ----NDDYQRGLILTLADAGQYDEALVKAKQLVSGAPDKAN-LLALAYVYK-RAGRHWDELRAMT  140 (765)
T ss_pred             HHHHHHHHHHHhCCC----CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHH-HHHHHHHHH-HCCCHHHHHHHHH
Confidence            356677777777776    6777888877777888888888888999888888888 887766544 3446777888999


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 008442           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEK  118 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~r  118 (565)
                      +++...|....+|..+...+.. .+..+.+...+++
T Consensus       141 ~al~~~P~~~~~~~~la~~l~~-~~~~e~Al~~l~~  175 (765)
T PRK10049        141 QALPRAPQTQQYPTEYVQALRN-NRLSAPALGAIDD  175 (765)
T ss_pred             HHHHhCCCCHHHHHHHHHHHHH-CCChHHHHHHHHh
Confidence            9998888888888877764443 3444444444443

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=98.81  E-value=4.6e-06  Score=93.43  Aligned_cols=267  Identities=12%  Similarity=0.059  Sum_probs=168.8

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchh--------
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVG--------   74 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~--------   74 (565)
                      ++...++.++...|.    +.. |..+.......|+++.+...|++++...|.+..+|..|+..+.... ..        
T Consensus       101 eA~~~l~~~l~~~P~----~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~P~~~~~~~~la~~l~~~~-~~e~Al~~l~  174 (765)
T PRK10049        101 EALVKAKQLVSGAPD----KAN-LLALAYVYKRAGRHWDELRAMTQALPRAPQTQQYPTEYVQALRNNR-LSAPALGAID  174 (765)
T ss_pred             HHHHHHHHHHHhCCC----CHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCC-ChHHHHHHHH
Confidence            466778888888776    677 8888888888999999999999999999999999999887654211 11        


Q ss_pred             --------------------------------------hHHHHHHHHHHHcCCCCHHH-------HHHHHHHHHHhcCCH
Q 008442           75 --------------------------------------NVVRDVYSRATKNCPWVGEL-------WVRSLLSLERSRASE  109 (565)
Q Consensus        75 --------------------------------------~~~~~v~erAl~~~p~~~~l-------W~~yi~~le~~~~~~  109 (565)
                                                            +.+...|++++..+|..+..       +...+..+ ...+..
T Consensus       175 ~~~~~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~L-l~~g~~  253 (765)
T PRK10049        175 DANLTPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLGAL-LARDRY  253 (765)
T ss_pred             hCCCCHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHH-HHhhhH
Confidence                                                  23445566666544333222       12112222 234677


Q ss_pred             HHHHHHHHHHHhccc---ccHHHHH-HHHHH------HHHHHHHHhhcccc------chhhhhHH---HHHHHHHHHHHH
Q 008442          110 EEISTVFEKSLLCAF---STFEEYL-DLFLT------RIDGLRRRILFSGE------VEGVLDYS---LIRETFQRASDY  170 (565)
Q Consensus       110 ~~~~~if~ral~~~~---~~~~~~~-~~~~~------~~~~~~r~~~~~~~------~e~~~~~~---~~~~~~~~a~~~  170 (565)
                      +++...|++++....   .....++ .++..      -...+++ ++....      .+....+.   .-.+-+++|+.+
T Consensus       254 ~eA~~~~~~ll~~~~~~P~~a~~~la~~yl~~g~~e~A~~~l~~-~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~  332 (765)
T PRK10049        254 KDVISEYQRLKAEGQIIPPWAQRWVASAYLKLHQPEKAQSILTE-LFYHPETIADLSDEELADLFYSLLESENYPGALTV  332 (765)
T ss_pred             HHHHHHHHHhhccCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHH-HhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHH
Confidence            889999999887532   1111111 11111      1111111 111111      01111111   112445667776


Q ss_pred             HHhhhcCCc---------------hhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHH
Q 008442          171 LSEQMKNTD---------------GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINE  235 (565)
Q Consensus       171 l~~~~~~~~---------------~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~  235 (565)
                      +.......+               .....+...+.+....+ +.++|..++++++...|.+..+|+..+......|+++.
T Consensus       333 l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g-~~~eA~~~l~~al~~~P~n~~l~~~lA~l~~~~g~~~~  411 (765)
T PRK10049        333 TAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSN-DLPQAEMRARELAYNAPGNQGLRIDYASVLQARGWPRA  411 (765)
T ss_pred             HHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHH
Confidence            655443322               22345566777777777 99999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          236 ARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       236 aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      |.++|++++..  ..+.+ .++..........|+.+.+..++++++
T Consensus       412 A~~~l~~al~l--~Pd~~-~l~~~~a~~al~~~~~~~A~~~~~~ll  454 (765)
T PRK10049        412 AENELKKAEVL--EPRNI-NLEVEQAWTALDLQEWRQMDVLTDDVV  454 (765)
T ss_pred             HHHHHHHHHhh--CCCCh-HHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            99999999873  22223 355444445666778777777766654

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.80  E-value=4.1e-06  Score=94.61  Aligned_cols=246  Identities=9%  Similarity=0.014  Sum_probs=151.0

Q ss_pred             hhHHHHHHHhcCCCCChH--hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSE--KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVY   81 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~--~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~   81 (565)
                      +...++..+...+ .+|.  +...|..+...... +.+..+...|.+++...|.+.. .+..+ +.....+..+.+...|
T Consensus       457 ~~~~~~~~~~al~-~~p~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~~Pd~~~-~L~lA-~al~~~Gr~eeAi~~~  532 (987)
T PRK09782        457 IADNCPAIVRLLG-DMSPSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQRQPDAWQ-HRAVA-YQAYQVEDYATALAAW  532 (987)
T ss_pred             hhhhHHHHHHhcc-cCCCCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHhCCchHH-HHHHH-HHHHHCCCHHHHHHHH
Confidence            3444555554443 2333  56788888877765 6777788888899888886532 22222 2223445677788889


Q ss_pred             HHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHH
Q 008442           82 SRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIR  161 (565)
Q Consensus        82 erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~  161 (565)
                      ++++..-|. ...|......+ ...++.+.+...|.+++...+.....+..+.....       ..       .++..+.
T Consensus       533 rka~~~~p~-~~a~~~la~al-l~~Gd~~eA~~~l~qAL~l~P~~~~l~~~La~~l~-------~~-------Gr~~eAl  596 (987)
T PRK09782        533 QKISLHDMS-NEDLLAAANTA-QAAGNGAARDRWLQQAEQRGLGDNALYWWLHAQRY-------IP-------GQPELAL  596 (987)
T ss_pred             HHHhccCCC-cHHHHHHHHHH-HHCCCHHHHHHHHHHHHhcCCccHHHHHHHHHHHH-------hC-------CCHHHHH
Confidence            888776444 34566555433 33678888889999888765443332222211110       00       1233334


Q ss_pred             HHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHH
Q 008442          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYK  241 (565)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~  241 (565)
                      ..|.+++..       .+. ...+...+.+....+ +.+.|...|++++...|++..++..+..+....|+++.|..+|+
T Consensus       597 ~~~~~AL~l-------~P~-~~a~~~LA~~l~~lG-~~deA~~~l~~AL~l~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~  667 (987)
T PRK09782        597 NDLTRSLNI-------APS-ANAYVARATIYRQRH-NVPAAVSDLRAALELEPNNSNYQAALGYALWDSGDIAQSREMLE  667 (987)
T ss_pred             HHHHHHHHh-------CCC-HHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            444444332       222 455666677777777 78888888888888888878888888777777788888888888


Q ss_pred             HHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          242 RCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       242 ~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      +++..  . +....++......-...|+.+.+..++++++
T Consensus       668 ~AL~l--~-P~~~~a~~nLA~al~~lGd~~eA~~~l~~Al  704 (987)
T PRK09782        668 RAHKG--L-PDDPALIRQLAYVNQRLDDMAATQHYARLVI  704 (987)
T ss_pred             HHHHh--C-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            88762  1 2233455555555566777777777777765

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.79  E-value=1.7e-08  Score=97.23  Aligned_cols=85  Identities=26%  Similarity=0.484  Sum_probs=79.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecCC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~~  469 (565)
                      ...+|||++||.++++.++++.|.+||.|..+.++.|..+.+++||+||.|.+++++..++...-+.|+|+.+.|..|.|
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            35699999999999999999999999999999999999999999999999999999999999888999999999999998


Q ss_pred             CCCCC
Q 008442          470 KQRKD  474 (565)
Q Consensus       470 ~~~~~  474 (565)
                      +....
T Consensus       176 k~~~~  180 (311)
T KOG4205|consen  176 KEVMQ  180 (311)
T ss_pred             hhhcc
Confidence            86543

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=98.79  E-value=1.3e-08  Score=108.80  Aligned_cols=76  Identities=24%  Similarity=0.354  Sum_probs=63.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccC------------CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcC
Q 008442          386 KGFTDECTAFLSNINLKATYEDLRRFFSDV------------GGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKN  453 (565)
Q Consensus       386 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~------------G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~  453 (565)
                      ......++|||||||+.+++++|+.+|..+            +.|..+.+      +..+|||||+|.+.++|..||.|+
T Consensus       170 ~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~l~  243 (509)
T TIGR01642       170 QATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMALD  243 (509)
T ss_pred             cCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhcCC
Confidence            345677899999999999999999999875            23444433      445799999999999999999999


Q ss_pred             CcccCCeEEEEeec
Q 008442          454 KQMFLGKKLSIARS  467 (565)
Q Consensus       454 ~~~~~g~~l~v~~a  467 (565)
                      |..|.|++|.|...
T Consensus       244 g~~~~g~~l~v~r~  257 (509)
T TIGR01642       244 SIIYSNVFLKIRRP  257 (509)
T ss_pred             CeEeeCceeEecCc
Confidence            99999999999754

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=98.78  E-value=1.3e-08  Score=95.70  Aligned_cols=81  Identities=11%  Similarity=0.260  Sum_probs=75.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCCC
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNPK  470 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~~  470 (565)
                      .+|||..+.++.+++||+.+|+.||.|..|.+-+++..+.++||||++|.+..+...|+. ||-..++|.-|+|..+..+
T Consensus       211 nRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTP  290 (544)
T KOG0124|consen  211 NRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTP  290 (544)
T ss_pred             heEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccCC
Confidence            689999999999999999999999999999999998777899999999999999999998 8999999999999998655


Q ss_pred             CC
Q 008442          471 QR  472 (565)
Q Consensus       471 ~~  472 (565)
                      +.
T Consensus       291 P~  292 (544)
T KOG0124|consen  291 PD  292 (544)
T ss_pred             Cc
Confidence            44

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.74  E-value=1.6e-08  Score=91.41  Aligned_cols=83  Identities=23%  Similarity=0.450  Sum_probs=74.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCc-ccCC--eEEEE
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQ-MFLG--KKLSI  464 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~-~~~g--~~l~v  464 (565)
                      .+.++||||-|...-+|+|++.+|..||.|.++.+.+.. .|.++|||||.|.+..+|++||. ++|. .+-|  ..|.|
T Consensus        17 ~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVV   95 (371)
T KOG0146|consen   17 GDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVV   95 (371)
T ss_pred             ccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEE
Confidence            467899999999999999999999999999999999986 89999999999999999999998 8764 4554  47999


Q ss_pred             eecCCCCC
Q 008442          465 ARSNPKQR  472 (565)
Q Consensus       465 ~~a~~~~~  472 (565)
                      ++++..+.
T Consensus        96 K~ADTdkE  103 (371)
T KOG0146|consen   96 KFADTDKE  103 (371)
T ss_pred             EeccchHH
Confidence            99987765

>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=98.72  E-value=2.4e-06  Score=77.06  Aligned_cols=182  Identities=18%  Similarity=0.180  Sum_probs=141.9

Q ss_pred             HhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHH
Q 008442           34 QSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEIS  113 (565)
Q Consensus        34 ~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~  113 (565)
                      ...|+...+..-+|.||...|.++..|...+.+... .+..+.+.+-|++|+..-|.++.|-..|--||..+ +..+++.
T Consensus        46 L~~gd~~~A~~nlekAL~~DPs~~~a~~~~A~~Yq~-~Ge~~~A~e~YrkAlsl~p~~GdVLNNYG~FLC~q-g~~~eA~  123 (250)
T COG3063          46 LQQGDYAQAKKNLEKALEHDPSYYLAHLVRAHYYQK-LGENDLADESYRKALSLAPNNGDVLNNYGAFLCAQ-GRPEEAM  123 (250)
T ss_pred             HHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHH-cCChhhHHHHHHHHHhcCCCccchhhhhhHHHHhC-CChHHHH
Confidence            357899999999999999999999999999886654 44778899999999999999999999999888774 5889999


Q ss_pred             HHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHH
Q 008442          114 TVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQ  193 (565)
Q Consensus       114 ~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~  193 (565)
                      .-|++|+..|.-.                                ..-.+|+..            ..|         -.
T Consensus       124 q~F~~Al~~P~Y~--------------------------------~~s~t~eN~------------G~C---------al  150 (250)
T COG3063         124 QQFERALADPAYG--------------------------------EPSDTLENL------------GLC---------AL  150 (250)
T ss_pred             HHHHHHHhCCCCC--------------------------------Ccchhhhhh------------HHH---------Hh
Confidence            9999999755210                                000111100            001         12


Q ss_pred             HcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHH
Q 008442          194 SMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDF  273 (565)
Q Consensus       194 ~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~  273 (565)
                      +.| ..+.|+.+|+++|...|+....-+..++.+...|++-.||..+++.... .. ...+.||. -++++...||.+.+
T Consensus       151 ~~g-q~~~A~~~l~raL~~dp~~~~~~l~~a~~~~~~~~y~~Ar~~~~~~~~~-~~-~~A~sL~L-~iriak~~gd~~~a  226 (250)
T COG3063         151 KAG-QFDQAEEYLKRALELDPQFPPALLELARLHYKAGDYAPARLYLERYQQR-GG-AQAESLLL-GIRIAKRLGDRAAA  226 (250)
T ss_pred             hcC-CchhHHHHHHHHHHhCcCCChHHHHHHHHHHhcccchHHHHHHHHHHhc-cc-ccHHHHHH-HHHHHHHhccHHHH
Confidence            445 8889999999999999999999999999999999999999999998763 22 33445554 56899999987755


Q ss_pred             H
Q 008442          274 D  274 (565)
Q Consensus       274 ~  274 (565)
                      .
T Consensus       227 ~  227 (250)
T COG3063         227 Q  227 (250)
T ss_pred             H
Confidence            4

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.70  E-value=2e-05  Score=89.12  Aligned_cols=237  Identities=12%  Similarity=-0.045  Sum_probs=163.0

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (565)
                      +...|..++...|.    .. ..+..+......|+.+.+...|++++...|. ...|..++..+.. .++.+.+...|++
T Consensus       495 Ai~a~~~Al~~~Pd----~~-~~L~lA~al~~~Gr~eeAi~~~rka~~~~p~-~~a~~~la~all~-~Gd~~eA~~~l~q  567 (987)
T PRK09782        495 ALYAWLQAEQRQPD----AW-QHRAVAYQAYQVEDYATALAAWQKISLHDMS-NEDLLAAANTAQA-AGNGAARDRWLQQ  567 (987)
T ss_pred             HHHHHHHHHHhCCc----hH-HHHHHHHHHHHCCCHHHHHHHHHHHhccCCC-cHHHHHHHHHHHH-CCCHHHHHHHHHH
Confidence            45557777777764    22 2333333345688999999999998777555 4557777665544 4477789999999


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHH
Q 008442           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRET  163 (565)
Q Consensus        84 Al~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~  163 (565)
                      ++...|....++......+ ...++.+++...|++|+...+. ...+..+-..+.                     ...-
T Consensus       568 AL~l~P~~~~l~~~La~~l-~~~Gr~~eAl~~~~~AL~l~P~-~~a~~~LA~~l~---------------------~lG~  624 (987)
T PRK09782        568 AEQRGLGDNALYWWLHAQR-YIPGQPELALNDLTRSLNIAPS-ANAYVARATIYR---------------------QRHN  624 (987)
T ss_pred             HHhcCCccHHHHHHHHHHH-HhCCCHHHHHHHHHHHHHhCCC-HHHHHHHHHHHH---------------------HCCC
Confidence            9998887766655432212 2358899999999999986664 333333222211                     1122


Q ss_pred             HHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHH
Q 008442          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRC  243 (565)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~a  243 (565)
                      +.+|+..+...+...+....++..++.+....+ +.+.|..+|++++...|++..+|...+......|+++.|...|+++
T Consensus       625 ~deA~~~l~~AL~l~Pd~~~a~~nLG~aL~~~G-~~eeAi~~l~~AL~l~P~~~~a~~nLA~al~~lGd~~eA~~~l~~A  703 (987)
T PRK09782        625 VPAAVSDLRAALELEPNNSNYQAALGYALWDSG-DIAQSREMLERAHKGLPDDPALIRQLAYVNQRLDDMAATQHYARLV  703 (987)
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            344444444444445556677888888888888 9999999999999999999999999999999999999999999999


Q ss_pred             HhcccCCCCcHHHHHHHHHHHHHhCCHHHHH
Q 008442          244 YSKRFTGTGSEDICHAWLRFEREYGTLEDFD  274 (565)
Q Consensus       244 l~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~  274 (565)
                      +..   .+....|-..+-.++....+...+.
T Consensus       704 l~l---~P~~a~i~~~~g~~~~~~~~~~~a~  731 (987)
T PRK09782        704 IDD---IDNQALITPLTPEQNQQRFNFRRLH  731 (987)
T ss_pred             Hhc---CCCCchhhhhhhHHHHHHHHHHHHH
Confidence            873   2344466665555555544444333

>PRK12370 invasion protein regulator; Provisional

Probab=98.69  E-value=1.1e-05  Score=87.09  Aligned_cols=203  Identities=10%  Similarity=-0.061  Sum_probs=135.8

Q ss_pred             hHhHHHHHHHHHHHHh--c---CCchhHHHHHHHHHhcCCCCHHHHHHHHHHHH---H-----hcchhhHHHHHHHHHHH
Q 008442           20 SEKFQQYMIYLKYEQS--S---GDPGRVQLLYERAITDFPVSSDLWLDYTQYLD---K-----TLKVGNVVRDVYSRATK   86 (565)
Q Consensus        20 ~~~~~~W~~yi~~e~~--~---~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~---~-----~~~~~~~~~~v~erAl~   86 (565)
                      +++++.|..|+.-...  .   .+.+.+..+|++|+...|.+...|...+....   .     ..+..+.+...+++|+.
T Consensus       253 ~~~~da~~~~lrg~~~~~~~~~~~~~~A~~~~~~Al~ldP~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~  332 (553)
T PRK12370        253 LNSIDSTMVYLRGKHELNQYTPYSLQQALKLLTQCVNMSPNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATE  332 (553)
T ss_pred             CCChHHHHHHHHhHHHHHccCHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHh
Confidence            3467777777775322  1   23467899999999999999988865543211   1     11235679999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHH
Q 008442           87 NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQR  166 (565)
Q Consensus        87 ~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~  166 (565)
                      .-|.....|..... +....+..+++...|++|+...+.....+..+-..+.                     ...-+++
T Consensus       333 ldP~~~~a~~~lg~-~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~---------------------~~G~~~e  390 (553)
T PRK12370        333 LDHNNPQALGLLGL-INTIHSEYIVGSLLFKQANLLSPISADIKYYYGWNLF---------------------MAGQLEE  390 (553)
T ss_pred             cCCCCHHHHHHHHH-HHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH---------------------HCCCHHH
Confidence            99999999887765 3344678999999999999877664443332222211                     0122333


Q ss_pred             HHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHc-cchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          167 ASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS-GAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       167 a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~-~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      |+..+...+...+.....+...+......+ ++++|...+++++... |+....+.....+....|+++.|+..+.+.+.
T Consensus       391 Ai~~~~~Al~l~P~~~~~~~~~~~~~~~~g-~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~  469 (553)
T PRK12370        391 ALQTINECLKLDPTRAAAGITKLWITYYHT-GIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEIST  469 (553)
T ss_pred             HHHHHHHHHhcCCCChhhHHHHHHHHHhcc-CHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhh
Confidence            444444433322222222222222344456 8899999999999874 77788888888888899999999999998765

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.68  E-value=3.5e-07  Score=80.73  Aligned_cols=84  Identities=18%  Similarity=0.212  Sum_probs=66.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeec-CCCCCcceEEEEEecCHHHHHHHHH-cCCcccC---CeEEE
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHD-KFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFL---GKKLS  463 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~-~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~---g~~l~  463 (565)
                      ..-+||||.+||.++...+|..+|..|-.-....+... +.....+-+|||+|.+..+|++|+. +||..++   +..|.
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLh  111 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLH  111 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeE
Confidence            34689999999999999999999999866665555332 2122245799999999999999998 8999885   77899


Q ss_pred             EeecCCCCC
Q 008442          464 IARSNPKQR  472 (565)
Q Consensus       464 v~~a~~~~~  472 (565)
                      |+.++...+
T Consensus       112 iElAKSNtK  120 (284)
T KOG1457|consen  112 IELAKSNTK  120 (284)
T ss_pred             eeehhcCcc
Confidence            988876544

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.67  E-value=5.3e-08  Score=96.81  Aligned_cols=83  Identities=14%  Similarity=0.288  Sum_probs=75.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ..-++.|||++|+..+...+|+.+|++||.|.-..||++..+--.+||+||++.+.++|.+||. |+...|.|+.|.|..
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            3456899999999999999999999999999999999987677779999999999999999998 899999999999999


Q ss_pred             cCCC
Q 008442          467 SNPK  470 (565)
Q Consensus       467 a~~~  470 (565)
                      ++..
T Consensus       482 aKNE  485 (940)
T KOG4661|consen  482 AKNE  485 (940)
T ss_pred             cccC
Confidence            8644

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.67  E-value=4.4e-08  Score=100.58  Aligned_cols=76  Identities=34%  Similarity=0.498  Sum_probs=68.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCC----cceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGK----SRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~----~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ++|||.||+++++.++|...|...|.|.++.|...+ .+.    |.|||||+|.++++|++|+. |+|..|+|+.|.|.+
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkk-d~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~  594 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKK-DPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKI  594 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccc-cccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEe
Confidence            349999999999999999999999999999987765 332    45999999999999999998 899999999999999


Q ss_pred             cC
Q 008442          467 SN  468 (565)
Q Consensus       467 a~  468 (565)
                      +.
T Consensus       595 S~  596 (725)
T KOG0110|consen  595 SE  596 (725)
T ss_pred             cc
Confidence            87

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.65  E-value=6.2e-06  Score=81.42  Aligned_cols=201  Identities=14%  Similarity=0.109  Sum_probs=137.5

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      .++..|+.+|..+|.    +...|..........|+.+.+...|+++|...|.+...|......+. ..+..+.+...|+
T Consensus        82 ~A~~~~~~Al~l~P~----~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~-~~g~~~eA~~~~~  156 (296)
T PRK11189         82 LARNDFSQALALRPD----MADAYNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAYLNRGIALY-YGGRYELAQDDLL  156 (296)
T ss_pred             HHHHHHHHHHHcCCC----CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH-HCCCHHHHHHHHH
Confidence            467788899998887    78899999999999999999999999999999999999988776554 4457888999999


Q ss_pred             HHHHcCCCCH--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHH
Q 008442           83 RATKNCPWVG--ELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLI  160 (565)
Q Consensus        83 rAl~~~p~~~--~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~  160 (565)
                      +++...|..+  .+|.. +  .+ .....+++...|.+++....+..+.+ .+...+   +      .+       +.. 
T Consensus       157 ~al~~~P~~~~~~~~~~-l--~~-~~~~~~~A~~~l~~~~~~~~~~~~~~-~~~~~~---l------g~-------~~~-  214 (296)
T PRK11189        157 AFYQDDPNDPYRALWLY-L--AE-SKLDPKQAKENLKQRYEKLDKEQWGW-NIVEFY---L------GK-------ISE-  214 (296)
T ss_pred             HHHHhCCCCHHHHHHHH-H--HH-ccCCHHHHHHHHHHHHhhCCccccHH-HHHHHH---c------cC-------CCH-
Confidence            9999999876  35542 2  22 24678888899977764322211111 100000   0      11       101 


Q ss_pred             HHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHcc-chHHHHHHHHHHHHHcC
Q 008442          161 RETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG-AMLEAWQSYISMEIELD  231 (565)
Q Consensus       161 ~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~-~~~~lw~~yi~~e~~~~  231 (565)
                      ...+..+...+.......+.....|.+.+.+....| ++++|+..|++++..+| +.++.-...++++...+
T Consensus       215 ~~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g-~~~~A~~~~~~Al~~~~~~~~e~~~~~~e~~~~~~  285 (296)
T PRK11189        215 ETLMERLKAGATDNTELAERLCETYFYLAKYYLSLG-DLDEAAALFKLALANNVYNFVEHRYALLELALLGQ  285 (296)
T ss_pred             HHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHh
Confidence            123333333222222222334567888889998888 99999999999999875 65666666666665433

>COG5191 Uncharacterized conserved protein, contains HAT (Half-A-TPR) repeat [General function prediction only]

Probab=98.62  E-value=1.1e-07  Score=88.77  Aligned_cols=135  Identities=22%  Similarity=0.370  Sum_probs=106.3

Q ss_pred             chhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhc-------------C---------CchhHHHHHHHHHhcCCCCHHH
Q 008442            2 CNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS-------------G---------DPGRVQLLYERAITDFPVSSDL   59 (565)
Q Consensus         2 ~~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~-------------~---------~~~~~~~lyERal~~~p~~~~l   59 (565)
                      .+.|-.||..|.+-..    .+.-++.||++|...             +         -+.++..+|.|+...+|.++.+
T Consensus        34 vktRr~fE~rL~rr~~----klnDf~~YI~yE~nleklRaKR~Kr~~v~~K~s~sD~sipqk~~f~~~R~tnkff~D~k~  109 (435)
T COG5191          34 VKTRRKFELRLQRREK----KLNDFMRYIKYECNLEKLRAKRVKRKKVGKKASFSDMSIPQKKIFELYRSTNKFFNDPKI  109 (435)
T ss_pred             HHHHHHHHHHHhcccc----hHHHHHHHHHHHhhHHHHHHHHHHHHHhcccccchhccccceeeEeeehhhhcCCCCcHH
Confidence            4689999999988766    678899999998531             1         1235567889999999999999


Q ss_pred             HHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc---cHHHHHHHHHH
Q 008442           60 WLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS---TFEEYLDLFLT  136 (565)
Q Consensus        60 W~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~---~~~~~~~~~~~  136 (565)
                      |.+|+.|+.+.. ....+-.||..|++..|.+.+||+-.+.+--....+++..|.+|.++|..+..   .|.+|..+.+.
T Consensus       110 w~~y~~Y~~k~k-~y~~~~nI~~~~l~khP~nvdlWI~~c~~e~~~~ani~s~Ra~f~~glR~N~~~p~iw~eyfr~El~  188 (435)
T COG5191         110 WSQYAAYVIKKK-MYGEMKNIFAECLTKHPLNVDLWIYCCAFELFEIANIESSRAMFLKGLRMNSRSPRIWIEYFRMELM  188 (435)
T ss_pred             HHHHHHHHHHHH-HHHHHHHHHHHHHhcCCCCceeeeeeccchhhhhccHHHHHHHHHhhhccCCCCchHHHHHHHHHHH
Confidence            999999998655 55668899999999999999999875543333468899999999999987654   46667776666


Q ss_pred             HHHHH
Q 008442          137 RIDGL  141 (565)
Q Consensus       137 ~~~~~  141 (565)
                      |+.-+
T Consensus       189 yiTKL  193 (435)
T COG5191         189 YITKL  193 (435)
T ss_pred             HHHHH
Confidence            66433

>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.62  E-value=1.2e-05  Score=79.84  Aligned_cols=222  Identities=13%  Similarity=0.136  Sum_probs=157.8

Q ss_pred             HhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHH
Q 008442           34 QSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEIS  113 (565)
Q Consensus        34 ~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~  113 (565)
                      .-.|+...++..|..+|...|....+++..+..+. ...+.+.....|..|.+..|..+.++.+... +....+.++++.
T Consensus       337 fL~g~~~~a~~d~~~~I~l~~~~~~lyI~~a~~y~-d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQ-m~flL~q~e~A~  414 (606)
T KOG0547|consen  337 FLKGDSLGAQEDFDAAIKLDPAFNSLYIKRAAAYA-DENQSEKMWKDFNKAEDLDPENPDVYYHRGQ-MRFLLQQYEEAI  414 (606)
T ss_pred             hhcCCchhhhhhHHHHHhcCcccchHHHHHHHHHh-hhhccHHHHHHHHHHHhcCCCCCchhHhHHH-HHHHHHHHHHHH
Confidence            34578888999999999999999998665544322 2335677899999999999999999877654 323346688999


Q ss_pred             HHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHH
Q 008442          114 TVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQ  193 (565)
Q Consensus       114 ~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~  193 (565)
                      .-|++|+...+.....|+.+........              .+......|++++.-       .|.+.+.+.+++++..
T Consensus       415 aDF~Kai~L~pe~~~~~iQl~~a~Yr~~--------------k~~~~m~~Fee~kkk-------FP~~~Evy~~fAeiLt  473 (606)
T KOG0547|consen  415 ADFQKAISLDPENAYAYIQLCCALYRQH--------------KIAESMKTFEEAKKK-------FPNCPEVYNLFAEILT  473 (606)
T ss_pred             HHHHHHhhcChhhhHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHh-------CCCCchHHHHHHHHHh
Confidence            9999999877765555665544322110              223344556655543       4567788999999998


Q ss_pred             HcCCChHHHHHHHHHHHHHccc------hHH--HHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHH
Q 008442          194 SMGKDMVSARGVWERLLKISGA------MLE--AWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFER  265 (565)
Q Consensus       194 ~~~~~~~~ar~i~e~~l~~~~~------~~~--lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~  265 (565)
                      ..+ +++.|.+.|.+++..-|.      +..  +-...+.+ .=.+++..|..++.+|++.   .+..+.-+.-..+||.
T Consensus       474 Dqq-qFd~A~k~YD~ai~LE~~~~~~~v~~~plV~Ka~l~~-qwk~d~~~a~~Ll~KA~e~---Dpkce~A~~tlaq~~l  548 (606)
T KOG0547|consen  474 DQQ-QFDKAVKQYDKAIELEPREHLIIVNAAPLVHKALLVL-QWKEDINQAENLLRKAIEL---DPKCEQAYETLAQFEL  548 (606)
T ss_pred             hHH-hHHHHHHHHHHHHhhccccccccccchhhhhhhHhhh-chhhhHHHHHHHHHHHHcc---CchHHHHHHHHHHHHH
Confidence            888 999999999999988655      222  22222222 1238999999999999872   2334455677788999


Q ss_pred             HhCCHHHHHHHHHHHhhH
Q 008442          266 EYGTLEDFDHSVQKVTPR  283 (565)
Q Consensus       266 ~~G~~~~~~~~~~k~~~~  283 (565)
                      ..|+++.+-+.++++..-
T Consensus       549 Q~~~i~eAielFEksa~l  566 (606)
T KOG0547|consen  549 QRGKIDEAIELFEKSAQL  566 (606)
T ss_pred             HHhhHHHHHHHHHHHHHH
Confidence            999998888888877543

>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=98.61  E-value=9.2e-06  Score=73.43  Aligned_cols=117  Identities=14%  Similarity=0.148  Sum_probs=97.5

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      .++..+|.+|..+|.    .+..|...+-.-...|..+.+..-|++||...|.+.++-..|.-||-..+ .++.+..-|+
T Consensus        53 ~A~~nlekAL~~DPs----~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~~GdVLNNYG~FLC~qg-~~~eA~q~F~  127 (250)
T COG3063          53 QAKKNLEKALEHDPS----YYLAHLVRAHYYQKLGENDLADESYRKALSLAPNNGDVLNNYGAFLCAQG-RPEEAMQQFE  127 (250)
T ss_pred             HHHHHHHHHHHhCcc----cHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCCccchhhhhhHHHHhCC-ChHHHHHHHH
Confidence            578999999999998    88999999999999999999999999999999999999999999998777 7888999999


Q ss_pred             HHHHc--CCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc
Q 008442           83 RATKN--CPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (565)
Q Consensus        83 rAl~~--~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~  125 (565)
                      +|+..  .|.....|..--. .-...+..+.++..|+|+|...+.
T Consensus       128 ~Al~~P~Y~~~s~t~eN~G~-Cal~~gq~~~A~~~l~raL~~dp~  171 (250)
T COG3063         128 RALADPAYGEPSDTLENLGL-CALKAGQFDQAEEYLKRALELDPQ  171 (250)
T ss_pred             HHHhCCCCCCcchhhhhhHH-HHhhcCCchhHHHHHHHHHHhCcC
Confidence            99983  3444455555332 223457788999999999975544

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=98.60  E-value=7.2e-08  Score=93.08  Aligned_cols=74  Identities=27%  Similarity=0.466  Sum_probs=68.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      .+..|+|||.|||+++|++.|++-|..||.|..+.|+.   +|+++|  .|.|.++++|+.|+. |++..++||.|.|.+
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            36679999999999999999999999999999999853   688888  899999999999998 799999999999976

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=98.60  E-value=7.2e-08  Score=88.49  Aligned_cols=74  Identities=27%  Similarity=0.415  Sum_probs=68.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      ..+|+|+|+.+.++.++|+..|.+||.|.++.|+.+        |+||.|.-.++|..|+. |++.++.|+++.|..+..
T Consensus        78 stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~sts  149 (346)
T KOG0109|consen   78 STKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTS  149 (346)
T ss_pred             ccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeeeeecc
Confidence            468999999999999999999999999999999864        99999999999999997 999999999999999876


Q ss_pred             CCC
Q 008442          470 KQR  472 (565)
Q Consensus       470 ~~~  472 (565)
                      +-+
T Consensus       150 rlr  152 (346)
T KOG0109|consen  150 RLR  152 (346)
T ss_pred             ccc
Confidence            644

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.59  E-value=1.6e-07  Score=87.19  Aligned_cols=84  Identities=21%  Similarity=0.439  Sum_probs=77.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEee
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIAR  466 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~  466 (565)
                      ...+...+||+|+.+.++.+++...|+.||.|..+.++.++.+|.++||+||+|.+.+.++.|+.|++..|.|+.+.|..
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVTL  176 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceeee
Confidence            34566899999999999999999999999999999999999888999999999999999999999999999999999988


Q ss_pred             cCCC
Q 008442          467 SNPK  470 (565)
Q Consensus       467 a~~~  470 (565)
                      ..-.
T Consensus       177 ~r~~  180 (231)
T KOG4209|consen  177 KRTN  180 (231)
T ss_pred             eeee
Confidence            6543

>PF08424 NRDE-2: NRDE-2, necessary for RNA interference; InterPro: IPR013633 This is domain is found in eukaryotic proteins of unknown function

Probab=98.59  E-value=4.3e-06  Score=83.18  Aligned_cols=170  Identities=16%  Similarity=0.205  Sum_probs=119.3

Q ss_pred             HHHHHHHHhcCCCCHHHHHHHHHHHHHhcc-----------hhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHH
Q 008442           43 QLLYERAITDFPVSSDLWLDYTQYLDKTLK-----------VGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEE  111 (565)
Q Consensus        43 ~~lyERal~~~p~~~~lW~~Y~~~l~~~~~-----------~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~  111 (565)
                      ..-|++.|..+|.+.+.|+.|+.|-.....           ..+.-..||+|||++.|.+..||+.||...+. ..+.+.
T Consensus         5 ~~el~~~v~~~P~di~~Wl~li~~Qd~~~~~~~~~~~~~~a~~E~klsilerAL~~np~~~~L~l~~l~~~~~-~~~~~~   83 (321)
T PF08424_consen    5 TAELNRRVRENPHDIEAWLELIEFQDELFRLQSSSKAERRALAERKLSILERALKHNPDSERLLLGYLEEGEK-VWDSEK   83 (321)
T ss_pred             HHHHHHHHHhCcccHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-hCCHHH
Confidence            346899999999999999999998765432           12346689999999999999999999986655 457788


Q ss_pred             HHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHH
Q 008442          112 ISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHL  191 (565)
Q Consensus       112 ~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~  191 (565)
                      +...+++++...+.    ...+|..|+++.......       ..+..++.+|.+|+..+.......             
T Consensus        84 l~~~we~~l~~~~~----~~~LW~~yL~~~q~~~~~-------f~v~~~~~~y~~~l~~L~~~~~~~-------------  139 (321)
T PF08424_consen   84 LAKKWEELLFKNPG----SPELWREYLDFRQSNFAS-------FTVSDVRDVYEKCLRALSRRRSGR-------------  139 (321)
T ss_pred             HHHHHHHHHHHCCC----ChHHHHHHHHHHHHHhcc-------CcHHHHHHHHHHHHHHHHHhhccc-------------
Confidence            89999999875543    346777777766543221       145677788888877664322111             


Q ss_pred             HHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhccc
Q 008442          192 EQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRF  248 (565)
Q Consensus       192 e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~  248 (565)
                      ..... +...    .      ....+.+.+.++.|+...|..+.|..+++-.++..|
T Consensus       140 ~~~~~-~~~~----~------e~~~l~v~~r~~~fl~~aG~~E~Ava~~Qa~lE~n~  185 (321)
T PF08424_consen  140 MTSHP-DLPE----L------EEFMLYVFLRLCRFLRQAGYTERAVALWQALLEFNF  185 (321)
T ss_pred             ccccc-chhh----H------HHHHHHHHHHHHHHHHHCCchHHHHHHHHHHHHHHc
Confidence            00000 1111    1      111256788899999999999999999999987543

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.58  E-value=3.7e-08  Score=101.09  Aligned_cols=82  Identities=22%  Similarity=0.451  Sum_probs=74.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      ...|+|.|||+..+..+++.+|..||.+.+|+|+.....+.++|||||+|-++.+|.+|+. +....+.||+|.+.++..
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            4689999999999999999999999999999999875567789999999999999999997 788889999999999976


Q ss_pred             CCC
Q 008442          470 KQR  472 (565)
Q Consensus       470 ~~~  472 (565)
                      ...
T Consensus       693 d~~  695 (725)
T KOG0110|consen  693 DNT  695 (725)
T ss_pred             chH
Confidence            543

>PF05391 Lsm_interact: Lsm interaction motif; InterPro: IPR008669 This short motif is found at the C terminus of Prp24 proteins and probably interacts with the Lsm proteins to promote U4/U6 formation []

Probab=98.57  E-value=3.9e-08  Score=51.76  Aligned_cols=16  Identities=75%  Similarity=1.215  Sum_probs=14.6

Q ss_pred             CCCCCChHHHHhhhcc
Q 008442          548 DLKPKSNDEFRKMFIK  563 (565)
Q Consensus       548 ~~~~~sn~~f~~~~~~  563 (565)
                      .++||||||||||||+
T Consensus         6 ~~~p~SNddFrkmfl~   21 (21)
T PF05391_consen    6 TAKPKSNDDFRKMFLK   21 (21)
T ss_pred             ccCccchHHHHHHHcC
Confidence            5789999999999986

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.56  E-value=2.1e-07  Score=87.62  Aligned_cols=84  Identities=21%  Similarity=0.392  Sum_probs=74.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCee--------EEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccC
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVS--------SIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFL  458 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--------~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~  458 (565)
                      ...+..|||+|||.++|.+++.++|+.||.|.        .|.|.++. .|+.+|=|.+.|...+++.-|+. |++..+.
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCccccc
Confidence            34567899999999999999999999999874        47888886 79999999999999999999998 7999999


Q ss_pred             CeEEEEeecCCCCC
Q 008442          459 GKKLSIARSNPKQR  472 (565)
Q Consensus       459 g~~l~v~~a~~~~~  472 (565)
                      |+.|+|..|+=...
T Consensus       210 g~~~rVerAkfq~K  223 (382)
T KOG1548|consen  210 GKKLRVERAKFQMK  223 (382)
T ss_pred             CcEEEEehhhhhhc
Confidence            99999999864433

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.55  E-value=2.1e-07  Score=93.18  Aligned_cols=75  Identities=31%  Similarity=0.368  Sum_probs=69.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCCC
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNPK  470 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~~  470 (565)
                      ..||||   +++++..|.++|+++|.|.++++.+|. |  +-|||||.|.++.+|.+|+. +|...+.|++|+|.++...
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   899999999999999999999999996 5  99999999999999999998 8999999999999998655


Q ss_pred             CC
Q 008442          471 QR  472 (565)
Q Consensus       471 ~~  472 (565)
                      ..
T Consensus        76 ~~   77 (369)
T KOG0123|consen   76 PS   77 (369)
T ss_pred             Cc
Confidence            43

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.54  E-value=8.7e-05  Score=69.81  Aligned_cols=164  Identities=9%  Similarity=0.010  Sum_probs=108.8

Q ss_pred             HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHH
Q 008442           58 DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTR  137 (565)
Q Consensus        58 ~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~  137 (565)
                      .+|...+.... ..++.+.+...|++++...|.....|..... +....++.+.+...|++++...+.            
T Consensus        32 ~~~~~la~~~~-~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~-~~~~~~~~~~A~~~~~~al~~~~~------------   97 (234)
T TIGR02521        32 KIRVQLALGYL-EQGDLEVAKENLDKALEHDPDDYLAYLALAL-YYQQLGELEKAEDSFRRALTLNPN------------   97 (234)
T ss_pred             HHHHHHHHHHH-HCCCHHHHHHHHHHHHHhCcccHHHHHHHHH-HHHHcCCHHHHHHHHHHHHhhCCC------------
Confidence            44444443333 2335666777888888777777666665544 333356666666666666643211            


Q ss_pred             HHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH--ccc
Q 008442          138 IDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI--SGA  215 (565)
Q Consensus       138 ~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~--~~~  215 (565)
                                                                 ....+..++.+....+ ++++|...|++++..  .+.
T Consensus        98 -------------------------------------------~~~~~~~~~~~~~~~g-~~~~A~~~~~~~~~~~~~~~  133 (234)
T TIGR02521        98 -------------------------------------------NGDVLNNYGTFLCQQG-KYEQAMQQFEQAIEDPLYPQ  133 (234)
T ss_pred             -------------------------------------------CHHHHHHHHHHHHHcc-cHHHHHHHHHHHHhcccccc
Confidence                                                       1122334445555666 899999999999975  345


Q ss_pred             hHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhh
Q 008442          216 MLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTP  282 (565)
Q Consensus       216 ~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~  282 (565)
                      ...+|...+......|+++.|...|.+++..  . +.....+..+..+....|+.+.+...++++..
T Consensus       134 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  197 (234)
T TIGR02521       134 PARSLENAGLCALKAGDFDKAEKYLTRALQI--D-PQRPESLLELAELYYLRGQYKDARAYLERYQQ  197 (234)
T ss_pred             chHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--C-cCChHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            5678888888889999999999999999873  2 22335566666777778998888877777654

Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.

>TIGR00540 hemY_coli hemY protein

Probab=98.50  E-value=0.00023  Score=73.86  Aligned_cols=251  Identities=11%  Similarity=-0.000  Sum_probs=151.0

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCH-HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS-DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~-~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~  100 (565)
                      ..-.++--+......|+++.+...|++++...|.+. .+-..++..... .++.+.++..+++.++..|.+..++..+..
T Consensus       117 ~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~-~~~~~~Al~~l~~l~~~~P~~~~~l~ll~~  195 (409)
T TIGR00540       117 PVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLA-QNELHAARHGVDKLLEMAPRHKEVLKLAEE  195 (409)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHH-CCCHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            344455556666778999999999999999998885 677777775554 447788999999999999999988777766


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcccccHHHHH----HHHHHHHHH---------HHHHhh-cc----ccchh---hhhHHH
Q 008442          101 SLERSRASEEEISTVFEKSLLCAFSTFEEYL----DLFLTRIDG---------LRRRIL-FS----GEVEG---VLDYSL  159 (565)
Q Consensus       101 ~le~~~~~~~~~~~if~ral~~~~~~~~~~~----~~~~~~~~~---------~~r~~~-~~----~~~e~---~~~~~~  159 (565)
                       +....++.+.+..++.+.++........+.    ..+...++.         +..... ..    +....   +...-.
T Consensus       196 -~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~  274 (409)
T TIGR00540       196 -AYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLI  274 (409)
T ss_pred             -HHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHH
Confidence             444578889999999998865322222221    222111110         000000 00    00000   000011


Q ss_pred             HHHHHHHHHHHHHhhhcCCchhHH----HHHHHHHHHHHcCCChHHHHHHHHHHHHHccchH--HHHHHHHHHHHHcCCh
Q 008442          160 IRETFQRASDYLSEQMKNTDGLLR----LYAYWAHLEQSMGKDMVSARGVWERLLKISGAML--EAWQSYISMEIELDHI  233 (565)
Q Consensus       160 ~~~~~~~a~~~l~~~~~~~~~~~~----l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~--~lw~~yi~~e~~~~~~  233 (565)
                      ..+.+++|.+.+...+...+....    ++..+..+.  .+ +...+.+.++++++.+|+++  .+...+..+....|++
T Consensus       275 ~~g~~~~A~~~l~~~l~~~pd~~~~~~~~l~~~~~l~--~~-~~~~~~~~~e~~lk~~p~~~~~~ll~sLg~l~~~~~~~  351 (409)
T TIGR00540       275 DCDDHDSAQEIIFDGLKKLGDDRAISLPLCLPIPRLK--PE-DNEKLEKLIEKQAKNVDDKPKCCINRALGQLLMKHGEF  351 (409)
T ss_pred             HCCChHHHHHHHHHHHhhCCCcccchhHHHHHhhhcC--CC-ChHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHcccH
Confidence            112245566666555553222221    222222222  23 66777788888888877777  7777778777778888


Q ss_pred             HHHHHHHHH--HHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          234 NEARSIYKR--CYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       234 ~~aR~i~~~--al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      ++|++.|++  ++..   .+.++. +..+...-...|+.+.+.+..++++
T Consensus       352 ~~A~~~le~a~a~~~---~p~~~~-~~~La~ll~~~g~~~~A~~~~~~~l  397 (409)
T TIGR00540       352 IEAADAFKNVAACKE---QLDAND-LAMAADAFDQAGDKAEAAAMRQDSL  397 (409)
T ss_pred             HHHHHHHHHhHHhhc---CCCHHH-HHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            888888884  4431   223333 4466777777777777766655543

This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.

>KOG1155 consensus Anaphase-promoting complex (APC), Cdc23 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=98.47  E-value=6.4e-05  Score=74.49  Aligned_cols=81  Identities=19%  Similarity=0.199  Sum_probs=42.1

Q ss_pred             hhHHHHHHHHHhcCCCCHHHHHHHH-HHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 008442           40 GRVQLLYERAITDFPVSSDLWLDYT-QYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEK  118 (565)
Q Consensus        40 ~~~~~lyERal~~~p~~~~lW~~Y~-~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~r  118 (565)
                      +++...|.|||+.+|....+|..-. .|+  .+++...+.+.|.|||..||.+..-|..--+..+. .+...-+.--|++
T Consensus       347 EKAv~YFkRALkLNp~~~~aWTLmGHEyv--EmKNt~AAi~sYRrAvdi~p~DyRAWYGLGQaYei-m~Mh~YaLyYfqk  423 (559)
T KOG1155|consen  347 EKAVMYFKRALKLNPKYLSAWTLMGHEYV--EMKNTHAAIESYRRAVDINPRDYRAWYGLGQAYEI-MKMHFYALYYFQK  423 (559)
T ss_pred             HHHHHHHHHHHhcCcchhHHHHHhhHHHH--HhcccHHHHHHHHHHHhcCchhHHHHhhhhHHHHH-hcchHHHHHHHHH
Confidence            4556666666666666666666443 222  23344556666666666666666666554333322 1222233344445


Q ss_pred             HHhcc
Q 008442          119 SLLCA  123 (565)
Q Consensus       119 al~~~  123 (565)
                      |+.+.
T Consensus       424 A~~~k  428 (559)
T KOG1155|consen  424 ALELK  428 (559)
T ss_pred             HHhcC
Confidence            54443

>KOG1155 consensus Anaphase-promoting complex (APC), Cdc23 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=98.47  E-value=3.7e-05  Score=76.08  Aligned_cols=188  Identities=14%  Similarity=0.104  Sum_probs=114.3

Q ss_pred             hhhHHHHHHH---hcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHH
Q 008442            3 NARAHLEEQI---SRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRD   79 (565)
Q Consensus         3 ~~R~~~E~~l---~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~   79 (565)
                      ..|..+|.++   ++.-..+|....+|.--.-=-....+...+..-|.|||..||.+...|-...+..+ .++.+.-++-
T Consensus       341 Slr~eHEKAv~YFkRALkLNp~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~p~DyRAWYGLGQaYe-im~Mh~YaLy  419 (559)
T KOG1155|consen  341 SLRSEHEKAVMYFKRALKLNPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDINPRDYRAWYGLGQAYE-IMKMHFYALY  419 (559)
T ss_pred             HHHHhHHHHHHHHHHHHhcCcchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcCchhHHHHhhhhHHHH-HhcchHHHHH
Confidence            3455555554   22222233377888633322223456778999999999999999999998876433 4445666888


Q ss_pred             HHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHH
Q 008442           80 VYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSL  159 (565)
Q Consensus        80 v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~  159 (565)
                      -|++|+..-|++..+|...-...+. .+..+++...|.+|+.++-..-..++.+-..+-++              .+...
T Consensus       420 YfqkA~~~kPnDsRlw~aLG~CY~k-l~~~~eAiKCykrai~~~dte~~~l~~LakLye~l--------------~d~~e  484 (559)
T KOG1155|consen  420 YFQKALELKPNDSRLWVALGECYEK-LNRLEEAIKCYKRAILLGDTEGSALVRLAKLYEEL--------------KDLNE  484 (559)
T ss_pred             HHHHHHhcCCCchHHHHHHHHHHHH-hccHHHHHHHHHHHHhccccchHHHHHHHHHHHHH--------------HhHHH
Confidence            9999999999999999998776655 57789999999999986643222333333222111              13344


Q ss_pred             HHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHH
Q 008442          160 IRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWE  207 (565)
Q Consensus       160 ~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e  207 (565)
                      +...|+++++.....-...+.......+.+.++.+.+ +.++|-....
T Consensus       485 Aa~~yek~v~~~~~eg~~~~~t~ka~~fLA~~f~k~~-~~~~As~Ya~  531 (559)
T KOG1155|consen  485 AAQYYEKYVEVSELEGEIDDETIKARLFLAEYFKKMK-DFDEASYYAT  531 (559)
T ss_pred             HHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHhhc-chHHHHHHHH
Confidence            4555565555331111122323333344555555555 5555544333

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.46  E-value=3.5e-07  Score=94.78  Aligned_cols=77  Identities=22%  Similarity=0.337  Sum_probs=69.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      -.+|||||+|+.++++.+|..+|+.||.|.+|.++..      +|||||......+|.+|+. |....+.++.|+|.++.
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAV  493 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeec
Confidence            3589999999999999999999999999999988654      5999999999999999997 88889999999999986


Q ss_pred             CCCC
Q 008442          469 PKQR  472 (565)
Q Consensus       469 ~~~~  472 (565)
                      ....
T Consensus       494 g~G~  497 (894)
T KOG0132|consen  494 GKGP  497 (894)
T ss_pred             cCCc
Confidence            5544

>PF08311 Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro: IPR013212 Proteins containing this domain are checkpoint proteins involved in cell division

Probab=98.45  E-value=2e-06  Score=72.48  Aligned_cols=111  Identities=17%  Similarity=0.373  Sum_probs=85.8

Q ss_pred             CchhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhc----CCchhHHHHHHHHHhcCCCCH---------HHHHHHHHHH
Q 008442            1 MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS----GDPGRVQLLYERAITDFPVSS---------DLWLDYTQYL   67 (565)
Q Consensus         1 ~~~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~----~~~~~~~~lyERal~~~p~~~---------~lW~~Y~~~l   67 (565)
                      +...|..||..|.... ...+.++.|..||.|...+    +.......++|||+..+..+.         .+|+.|+++.
T Consensus         1 ~~~~r~~~e~~i~~~~-~~dDPL~~w~~yI~w~~~~~p~~~~~~~L~~lLer~~~~f~~~~~Y~nD~RylkiWi~ya~~~   79 (126)
T PF08311_consen    1 LEQQRQEFEEQIRSYE-EGDDPLDPWLRYIKWIEENYPSGGKQSGLLELLERCIRKFKDDERYKNDERYLKIWIKYADLS   79 (126)
T ss_dssp             -HHHHHHHHHHHHCCG-GSS-CHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHTTSGGGTT-HHHHHHHHHHHTTB
T ss_pred             CHHHHHHHHHHHHHcc-CCCCChHHHHHHHHHHHHHCCCCCchhHHHHHHHHHHHHHhhhHhhcCCHHHHHHHHHHHHHc
Confidence            3568999999998876 2233588999999998764    344667889999999876653         4999999864


Q ss_pred             HHhcchhhHHHHHHHHHHHc-C-CCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 008442           68 DKTLKVGNVVRDVYSRATKN-C-PWVGELWVRSLLSLERSRASEEEISTVFEKSL  120 (565)
Q Consensus        68 ~~~~~~~~~~~~v~erAl~~-~-p~~~~lW~~yi~~le~~~~~~~~~~~if~ral  120 (565)
                      .       ...+||.....+ + -....+|..|+..+|. .+++.++..||+.+|
T Consensus        80 ~-------~~~~if~~l~~~~IG~~~A~fY~~wA~~le~-~~~~~~A~~I~~~Gi  126 (126)
T PF08311_consen   80 S-------DPREIFKFLYSKGIGTKLALFYEEWAEFLEK-RGNFKKADEIYQLGI  126 (126)
T ss_dssp             S-------HHHHHHHHHHHHTTSTTBHHHHHHHHHHHHH-TT-HHHHHHHHHHHH
T ss_pred             c-------CHHHHHHHHHHcCccHHHHHHHHHHHHHHHH-cCCHHHHHHHHHhhC
Confidence            3       467888888873 3 4568999999997877 588999999999875

This region has been shown to be essential for the binding of BUB1 and MAD3 to CDC20p [].; PDB: 3ESL_B 4AEZ_I 4A1G_B 2LAH_A 2WVI_A 3SI5_B.

>PLN03218 maturation of RBCL 1; Provisional

Probab=98.44  E-value=0.00035  Score=79.91  Aligned_cols=270  Identities=7%  Similarity=-0.043  Sum_probs=166.8

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDF-PVSSDLWLDYTQYLDKTLKVGNVVRDVY   81 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~-p~~~~lW~~Y~~~l~~~~~~~~~~~~v~   81 (565)
                      .++..|+........   .+...|...|....+.|+.+.+..+|+++.... ..+...|...+..+-+. +..+.+.++|
T Consensus       490 ~A~~vf~eM~~~Gv~---PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~-G~~deA~~lf  565 (1060)
T PLN03218        490 AMFEVFHEMVNAGVE---ANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQS-GAVDRAFDVL  565 (1060)
T ss_pred             HHHHHHHHHHHcCCC---CCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHC-CCHHHHHHHH
Confidence            466778877765421   156789999999889999999999999987653 34567788777765544 4677889999


Q ss_pred             HHHHHc---CCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc----cHHHHHHHHHHHHHHHHHHhhcccc----
Q 008442           82 SRATKN---CPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS----TFEEYLDLFLTRIDGLRRRILFSGE----  150 (565)
Q Consensus        82 erAl~~---~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~----~~~~~~~~~~~~~~~~~r~~~~~~~----  150 (565)
                      +.....   +..+...|..-|..+-+ .+.++++..+|+.+......    .|...+..+....+......++..+    
T Consensus       566 ~eM~~~~~gi~PD~vTynaLI~ay~k-~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~G  644 (1060)
T PLN03218        566 AEMKAETHPIDPDHITVGALMKACAN-AGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKG  644 (1060)
T ss_pred             HHHHHhcCCCCCcHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Confidence            998752   22234566665654443 57888999999988875431    2222222221111000000000000    


Q ss_pred             -chhhhhHHHHH------HHHHHHHHHHHhhhcC-CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH-ccchHHHHH
Q 008442          151 -VEGVLDYSLIR------ETFQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI-SGAMLEAWQ  221 (565)
Q Consensus       151 -~e~~~~~~~~~------~~~~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~-~~~~~~lw~  221 (565)
                       .-+..-+..+.      ..+++|.+++...... ..+....|...+..+.+.+ +++.|..+|+.+... ...+...|.
T Consensus       645 v~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tynsLI~ay~k~G-~~eeA~~lf~eM~~~g~~PdvvtyN  723 (1060)
T PLN03218        645 VKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAK-NWKKALELYEDIKSIKLRPTVSTMN  723 (1060)
T ss_pred             CCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCC-CHHHHHHHHHHHHHcCCCCCHHHHH
Confidence             00000111111      1234455555443332 2334456677777788888 899999999988765 344577899


Q ss_pred             HHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHH
Q 008442          222 SYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (565)
Q Consensus       222 ~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~  280 (565)
                      ..|......|+++.|.++|+.+...  ........|...+.--...|+.+.+..++...
T Consensus       724 ~LI~gy~k~G~~eeAlelf~eM~~~--Gi~Pd~~Ty~sLL~a~~k~G~le~A~~l~~~M  780 (1060)
T PLN03218        724 ALITALCEGNQLPKALEVLSEMKRL--GLCPNTITYSILLVASERKDDADVGLDLLSQA  780 (1060)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            9999999999999999999988653  22223455666666666778877777666554

>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.43  E-value=5.1e-05  Score=75.62  Aligned_cols=220  Identities=11%  Similarity=0.075  Sum_probs=140.2

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (565)
                      +...|..+|.-.|.    ..+.|+...-......+...-...|..|...+|.+++++..-.....- ....+.+..-|++
T Consensus       345 a~~d~~~~I~l~~~----~~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~fl-L~q~e~A~aDF~K  419 (606)
T KOG0547|consen  345 AQEDFDAAIKLDPA----FNSLYIKRAAAYADENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFL-LQQYEEAIADFQK  419 (606)
T ss_pred             hhhhHHHHHhcCcc----cchHHHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHH-HHHHHHHHHHHHH
Confidence            34456666666554    333344444444455677788899999999999999998877653332 2356778999999


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHH
Q 008442           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRET  163 (565)
Q Consensus        84 Al~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~  163 (565)
                      |++.-|.+.--++.... ++-....+++....|+.|+...+...+.|--+.....|.              .++..+..-
T Consensus       420 ai~L~pe~~~~~iQl~~-a~Yr~~k~~~~m~~Fee~kkkFP~~~Evy~~fAeiLtDq--------------qqFd~A~k~  484 (606)
T KOG0547|consen  420 AISLDPENAYAYIQLCC-ALYRQHKIAESMKTFEEAKKKFPNCPEVYNLFAEILTDQ--------------QQFDKAVKQ  484 (606)
T ss_pred             HhhcChhhhHHHHHHHH-HHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHhhH--------------HhHHHHHHH
Confidence            99998876544444433 333355789999999999864333222222211211110              134444455


Q ss_pred             HHHHHHHHHhhhc-CCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHH
Q 008442          164 FQRASDYLSEQMK-NTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKR  242 (565)
Q Consensus       164 ~~~a~~~l~~~~~-~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~  242 (565)
                      |..|+.+-...-. ......-+....+.+-  ..+|+..|..+++++++..|.+-......+.|+.+.|++++|.++|++
T Consensus       485 YD~ai~LE~~~~~~~v~~~plV~Ka~l~~q--wk~d~~~a~~Ll~KA~e~Dpkce~A~~tlaq~~lQ~~~i~eAielFEk  562 (606)
T KOG0547|consen  485 YDKAIELEPREHLIIVNAAPLVHKALLVLQ--WKEDINQAENLLRKAIELDPKCEQAYETLAQFELQRGKIDEAIELFEK  562 (606)
T ss_pred             HHHHHhhccccccccccchhhhhhhHhhhc--hhhhHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            5555553221000 0001111112222222  224999999999999999999999999999999999999999999999


Q ss_pred             HHh
Q 008442          243 CYS  245 (565)
Q Consensus       243 al~  245 (565)
                      ++.
T Consensus       563 sa~  565 (606)
T KOG0547|consen  563 SAQ  565 (606)
T ss_pred             HHH
Confidence            975

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.39  E-value=0.00052  Score=70.82  Aligned_cols=246  Identities=11%  Similarity=0.029  Sum_probs=156.1

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHH-HHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Q 008442           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSD-LWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLE  103 (565)
Q Consensus        25 ~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~-lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le  103 (565)
                      .+..-.......|+++.+...|+++....|.+.- ..+.-+... ...++.+.+...+++++...|.+..+...... +.
T Consensus       120 ~~llaA~aA~~~g~~~~A~~~l~~A~~~~~~~~~~~~l~~a~l~-l~~g~~~~Al~~l~~~~~~~P~~~~al~ll~~-~~  197 (398)
T PRK10747        120 NYLLAAEAAQQRGDEARANQHLERAAELADNDQLPVEITRVRIQ-LARNENHAARHGVDKLLEVAPRHPEVLRLAEQ-AY  197 (398)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHH-HHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHH-HH
Confidence            3444455556789999999999999998888753 322223332 34457888999999999999998766555444 33


Q ss_pred             HhcCCHHHHHHHHHHHHhcccccHHHHHHHH-HHHHHHHHHHhhcc-----------------ccchhh---hhHHHHHH
Q 008442          104 RSRASEEEISTVFEKSLLCAFSTFEEYLDLF-LTRIDGLRRRILFS-----------------GEVEGV---LDYSLIRE  162 (565)
Q Consensus       104 ~~~~~~~~~~~if~ral~~~~~~~~~~~~~~-~~~~~~~~r~~~~~-----------------~~~e~~---~~~~~~~~  162 (565)
                      ...++.+.+..++.+..+.........-.+. ..+...+.......                 +.....   ........
T Consensus       198 ~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g  277 (398)
T PRK10747        198 IRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRKTRHQVALQVAMAEHLIECD  277 (398)
T ss_pred             HHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCC
Confidence            3357888899888887764432222211111 11111111000000                 000000   00000112


Q ss_pred             HHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHH
Q 008442          163 TFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKR  242 (565)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~  242 (565)
                      ..+.|...+...+.. ++...+...|+.+..  + +.+++.+..++.++.+|++..+.+.+..+....++++.|++.|++
T Consensus       278 ~~~~A~~~L~~~l~~-~~~~~l~~l~~~l~~--~-~~~~al~~~e~~lk~~P~~~~l~l~lgrl~~~~~~~~~A~~~le~  353 (398)
T PRK10747        278 DHDTAQQIILDGLKR-QYDERLVLLIPRLKT--N-NPEQLEKVLRQQIKQHGDTPLLWSTLGQLLMKHGEWQEASLAFRA  353 (398)
T ss_pred             CHHHHHHHHHHHHhc-CCCHHHHHHHhhccC--C-ChHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            234566666665552 334456666666532  4 888999999999999999999999999999999999999999999


Q ss_pred             HHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHH
Q 008442          243 CYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (565)
Q Consensus       243 al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~  280 (565)
                      ++...   + ....+..+.......|..+....+..+.
T Consensus       354 al~~~---P-~~~~~~~La~~~~~~g~~~~A~~~~~~~  387 (398)
T PRK10747        354 ALKQR---P-DAYDYAWLADALDRLHKPEEAAAMRRDG  387 (398)
T ss_pred             HHhcC---C-CHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            98731   2 2234567788888899888777666554

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.38  E-value=9e-07  Score=84.39  Aligned_cols=85  Identities=25%  Similarity=0.318  Sum_probs=77.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCee--------EEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccC
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVS--------SIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFL  458 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--------~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~  458 (565)
                      ...+.+|||.+||..+++.+|..+|.+||.|.        .|.|.+++.|+.++|-|.|.|.++..|++|+. .++..+.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            46678999999999999999999999999874        47788888999999999999999999999999 7999999


Q ss_pred             CeEEEEeecCCCCC
Q 008442          459 GKKLSIARSNPKQR  472 (565)
Q Consensus       459 g~~l~v~~a~~~~~  472 (565)
                      |..|.|..+..+..
T Consensus       143 gn~ikvs~a~~r~~  156 (351)
T KOG1995|consen  143 GNTIKVSLAERRTG  156 (351)
T ss_pred             CCCchhhhhhhccC
Confidence            99999999876654

>PLN03218 maturation of RBCL 1; Provisional

Probab=98.38  E-value=0.00079  Score=77.06  Aligned_cols=270  Identities=9%  Similarity=-0.016  Sum_probs=176.9

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCC-CCHHHHHHHHHHHHHhcchhhHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFP-VSSDLWLDYTQYLDKTLKVGNVVRDVY   81 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p-~~~~lW~~Y~~~l~~~~~~~~~~~~v~   81 (565)
                      .++..|+..+.....   .+...|...|....+.|+.+.+..+|+++....+ .+...|...+.-+.+. +..+.+..+|
T Consensus       455 ~A~~lf~~M~~~Gl~---pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~-G~~eeAl~lf  530 (1060)
T PLN03218        455 GALRVLRLVQEAGLK---ADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARA-GQVAKAFGAY  530 (1060)
T ss_pred             HHHHHHHHHHHcCCC---CCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHC-cCHHHHHHHH
Confidence            467788887765432   1567899999999999999999999999998643 4788999888866544 4778899999


Q ss_pred             HHHHHc-CCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHh--cc--cc--cHHHHHHHHHHHHHHHHHHhhccccch--
Q 008442           82 SRATKN-CPWVGELWVRSLLSLERSRASEEEISTVFEKSLL--CA--FS--TFEEYLDLFLTRIDGLRRRILFSGEVE--  152 (565)
Q Consensus        82 erAl~~-~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~--~~--~~--~~~~~~~~~~~~~~~~~r~~~~~~~~e--  152 (565)
                      +..... +..+...|...|..+-+ .+..+++..+|++...  .+  ++  .+...+..+....+......++....+  
T Consensus       531 ~~M~~~Gv~PD~vTYnsLI~a~~k-~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~g  609 (1060)
T PLN03218        531 GIMRSKNVKPDRVVFNALISACGQ-SGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYN  609 (1060)
T ss_pred             HHHHHcCCCCCHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC
Confidence            999864 33356788887775554 6889999999999875  22  22  222223222211111110000000000  


Q ss_pred             ---hhhhHHHHH------HHHHHHHHHHHhhhcC-CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH-ccchHHHHH
Q 008442          153 ---GVLDYSLIR------ETFQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI-SGAMLEAWQ  221 (565)
Q Consensus       153 ---~~~~~~~~~------~~~~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~-~~~~~~lw~  221 (565)
                         ...-+..+.      ..+++|..++...... ..+....|...++...+.+ +++.|..+|+.+++. ...+...|.
T Consensus       610 i~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G-~~eeA~~l~~eM~k~G~~pd~~tyn  688 (1060)
T PLN03218        610 IKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAG-DLDKAFEILQDARKQGIKLGTVSYS  688 (1060)
T ss_pred             CCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCC-CHHHHHHHHHHHHHcCCCCCHHHHH
Confidence               000111111      2234455555443322 2233445666677777778 999999999999987 455688999


Q ss_pred             HHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHH
Q 008442          222 SYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (565)
Q Consensus       222 ~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~  280 (565)
                      ..+..+...|+++.|.++|+.....  ........|...+.--...|..+.+.+++...
T Consensus       689 sLI~ay~k~G~~eeA~~lf~eM~~~--g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM  745 (1060)
T PLN03218        689 SLMGACSNAKNWKKALELYEDIKSI--KLRPTVSTMNALITALCEGNQLPKALEVLSEM  745 (1060)
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            9999999999999999999998653  22233456777777777788888777776653

>PRK14574 hmsH outer membrane protein; Provisional

Probab=98.37  E-value=0.00046  Score=76.73  Aligned_cols=67  Identities=16%  Similarity=0.074  Sum_probs=57.7

Q ss_pred             CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          178 TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       178 ~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ++.+.+.....+......+ +...|.++++.++...|.+..+++.+++.+...|.+..|..+++.++.
T Consensus       412 n~d~~~~~~l~a~~~~~~g-dl~~Ae~~le~l~~~aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~  478 (822)
T PRK14574        412 NDDWIEGQTLLVQSLVALN-DLPTAQKKLEDLSSTAPANQNLRIALASIYLARDLPRKAEQELKAVES  478 (822)
T ss_pred             CccHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Confidence            3444555555667677777 999999999999999999999999999999999999999999988865

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.37  E-value=3e-07  Score=82.95  Aligned_cols=82  Identities=23%  Similarity=0.381  Sum_probs=74.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .+..+||.|.|..+++++-|-..|.+|-.-....+++++.||+++||+||.|.++.++..|+. |+|..++.++|....+
T Consensus       188 ~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  188 EDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             cccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            456899999999999999999999999888888899999999999999999999999999997 9999999999887666


Q ss_pred             CCC
Q 008442          468 NPK  470 (565)
Q Consensus       468 ~~~  470 (565)
                      ..+
T Consensus       268 ~wk  270 (290)
T KOG0226|consen  268 EWK  270 (290)
T ss_pred             hHH
Confidence            443

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.35  E-value=5e-05  Score=77.34  Aligned_cols=112  Identities=13%  Similarity=0.077  Sum_probs=85.6

Q ss_pred             HHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHH
Q 008442          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYK  241 (565)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~  241 (565)
                      .-|.++++++..++...|....||..+......-. ...+|..-|.+|++.-|..+.+|....--.+..|.+..|.+.|=
T Consensus       444 ~efdraiDcf~~AL~v~Pnd~~lWNRLGAtLAN~~-~s~EAIsAY~rALqLqP~yVR~RyNlgIS~mNlG~ykEA~~hlL  522 (579)
T KOG1125|consen  444 GEFDRAVDCFEAALQVKPNDYLLWNRLGATLANGN-RSEEAISAYNRALQLQPGYVRVRYNLGISCMNLGAYKEAVKHLL  522 (579)
T ss_pred             hHHHHHHHHHHHHHhcCCchHHHHHHhhHHhcCCc-ccHHHHHHHHHHHhcCCCeeeeehhhhhhhhhhhhHHHHHHHHH
Confidence            56788888888888888888899998887776655 77889999999999999999999888888888999999999999


Q ss_pred             HHHhcccC----CCC---cHHHHHHHHHHHHHhCCHHHHH
Q 008442          242 RCYSKRFT----GTG---SEDICHAWLRFEREYGTLEDFD  274 (565)
Q Consensus       242 ~al~~~~~----~~~---~~~i~~~~~~fE~~~G~~~~~~  274 (565)
                      .||.-.-.    .+.   .+.||...-.+-...+..+.+.
T Consensus       523 ~AL~mq~ks~~~~~~~~~se~iw~tLR~als~~~~~D~l~  562 (579)
T KOG1125|consen  523 EALSMQRKSRNHNKAPMASENIWQTLRLALSAMNRSDLLQ  562 (579)
T ss_pred             HHHHhhhcccccccCCcchHHHHHHHHHHHHHcCCchHHH
Confidence            98753211    111   2568876665555555555343

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.33  E-value=6.3e-07  Score=80.97  Aligned_cols=71  Identities=21%  Similarity=0.454  Sum_probs=64.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCCC
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNPK  470 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~~  470 (565)
                      ..||||+||+.+.+.+|..+|..||.|.++.+..        ||+||+|.+..+|..|+. +++..|.|-.+.|.++.+.
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            3689999999999999999999999999988742        799999999999999997 8999999998888887654

>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]

Probab=98.32  E-value=0.0015  Score=70.09  Aligned_cols=255  Identities=15%  Similarity=0.154  Sum_probs=158.4

Q ss_pred             ChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHH-
Q 008442           19 DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVR-   97 (565)
Q Consensus        19 ~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~-   97 (565)
                      +|.+.+.|....+.-.+.|++.+++..|-|||..+|.+..+-..++....+.+ ....+..-|.+++..+|.+.-.|+. 
T Consensus       203 ~p~d~e~W~~ladls~~~~~i~qA~~cy~rAI~~~p~n~~~~~ers~L~~~~G-~~~~Am~~f~~l~~~~p~~d~er~~d  281 (895)
T KOG2076|consen  203 NPKDYELWKRLADLSEQLGNINQARYCYSRAIQANPSNWELIYERSSLYQKTG-DLKRAMETFLQLLQLDPPVDIERIED  281 (895)
T ss_pred             CCCChHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhC-hHHHHHHHHHHHHhhCCchhHHHHHH
Confidence            34467899999999889999999999999999999999887777777555444 6667889999999999854433322 


Q ss_pred             ----HHHHHHHhcCCHHHHHHHHHHHHhcc-----cccHHHHHHHHHHHHHHHH--------HHhhcccc----------
Q 008442           98 ----SLLSLERSRASEEEISTVFEKSLLCA-----FSTFEEYLDLFLTRIDGLR--------RRILFSGE----------  150 (565)
Q Consensus        98 ----yi~~le~~~~~~~~~~~if~ral~~~-----~~~~~~~~~~~~~~~~~~~--------r~~~~~~~----------  150 (565)
                          ++.+.-. ....+.+.++++.++...     .+....+..+++..-.+-+        ++...++.          
T Consensus       282 ~i~~~~~~~~~-~~~~e~a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~  360 (895)
T KOG2076|consen  282 LIRRVAHYFIT-HNERERAAKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERR  360 (895)
T ss_pred             HHHHHHHHHHH-hhHHHHHHHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhc
Confidence                2222222 233377888888888622     2245555666655332211        11000100          


Q ss_pred             ---------chh--hhhHHHHH---HHH----HHHHHHHHhhhc----CCchhHHHHHHHHHHHHHcCCChHHHHHHHHH
Q 008442          151 ---------VEG--VLDYSLIR---ETF----QRASDYLSEQMK----NTDGLLRLYAYWAHLEQSMGKDMVSARGVWER  208 (565)
Q Consensus       151 ---------~e~--~~~~~~~~---~~~----~~a~~~l~~~~~----~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~  208 (565)
                               +..  ..++..++   ..+    ....+.+...+.    .......|+.-.++.....+ .+..|..+|..
T Consensus       361 ~~~~~~~~~~~~~~s~~l~v~rl~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~-~~~~Al~~l~~  439 (895)
T KOG2076|consen  361 REEPNALCEVGKELSYDLRVIRLMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIG-KYKEALRLLSP  439 (895)
T ss_pred             cccccccccCCCCCCccchhHhHhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcc-cHHHHHHHHHH
Confidence                     000  00111111   111    011111111111    12223456666777788888 88999999999


Q ss_pred             HHHHccc-hHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHH
Q 008442          209 LLKISGA-MLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQK  279 (565)
Q Consensus       209 ~l~~~~~-~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k  279 (565)
                      ++...+. +.-+|...+.++...|..+.|...|+++|.-   .+...++-.....+-..-|+.+.+-+++..
T Consensus       440 i~~~~~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~---~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~  508 (895)
T KOG2076|consen  440 ITNREGYQNAFVWYKLARCYMELGEYEEAIEFYEKVLIL---APDNLDARITLASLYQQLGNHEKALETLEQ  508 (895)
T ss_pred             HhcCccccchhhhHHHHHHHHHHhhHHHHHHHHHHHHhc---CCCchhhhhhHHHHHHhcCCHHHHHHHHhc
Confidence            9887543 3679999999999999999999999999872   223334444555566667777766655554

>TIGR00540 hemY_coli hemY protein

Probab=98.31  E-value=0.00015  Score=75.14  Aligned_cols=217  Identities=12%  Similarity=-0.002  Sum_probs=132.5

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHH----
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRD----   79 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~----   79 (565)
                      +...|+.++...|..   .......+.......++.+.+...+++.+...|.++.++..++......+ +.+.+..    
T Consensus       137 A~~~l~~a~~~~p~~---~l~~~~~~a~l~l~~~~~~~Al~~l~~l~~~~P~~~~~l~ll~~~~~~~~-d~~~a~~~l~~  212 (409)
T TIGR00540       137 ANQHLEEAAELAGND---NILVEIARTRILLAQNELHAARHGVDKLLEMAPRHKEVLKLAEEAYIRSG-AWQALDDIIDN  212 (409)
T ss_pred             HHHHHHHHHHhCCcC---chHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHh-hHHHHHHHHHH
Confidence            455666666655541   13455556777777788888888888888888888876666555432222 3333333    


Q ss_pred             ----------------------------------HHHHHHHcCC----CCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 008442           80 ----------------------------------VYSRATKNCP----WVGELWVRSLLSLERSRASEEEISTVFEKSLL  121 (565)
Q Consensus        80 ----------------------------------v~erAl~~~p----~~~~lW~~yi~~le~~~~~~~~~~~if~ral~  121 (565)
                                                        .++.+....|    .+..+|..|.. +....+..+.+..++++++.
T Consensus       213 l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~-~l~~~g~~~~A~~~l~~~l~  291 (409)
T TIGR00540       213 MAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAE-HLIDCDDHDSAQEIIFDGLK  291 (409)
T ss_pred             HHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHH-HHHHCCChHHHHHHHHHHHh
Confidence                                              3333344444    35566666665 33335667777777887777


Q ss_pred             cccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhH--HHHHHHHHHHHHcCCCh
Q 008442          122 CAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLL--RLYAYWAHLEQSMGKDM  199 (565)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~--~l~~~~a~~e~~~~~~~  199 (565)
                      ..++.....+.+...+.      .+..+      +.       ..+...++.++...+...  .+...++.+..+.+ ++
T Consensus       292 ~~pd~~~~~~~~l~~~~------~l~~~------~~-------~~~~~~~e~~lk~~p~~~~~~ll~sLg~l~~~~~-~~  351 (409)
T TIGR00540       292 KLGDDRAISLPLCLPIP------RLKPE------DN-------EKLEKLIEKQAKNVDDKPKCCINRALGQLLMKHG-EF  351 (409)
T ss_pred             hCCCcccchhHHHHHhh------hcCCC------Ch-------HHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHcc-cH
Confidence            54442211111111110      00000      11       222333334444333334  67888999998888 99


Q ss_pred             HHHHHHHH--HHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhc
Q 008442          200 VSARGVWE--RLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       200 ~~ar~i~e--~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~  246 (565)
                      ++|++.|+  .++...|+... +..++......|+.+.|+++|++++.-
T Consensus       352 ~~A~~~le~a~a~~~~p~~~~-~~~La~ll~~~g~~~~A~~~~~~~l~~  399 (409)
T TIGR00540       352 IEAADAFKNVAACKEQLDAND-LAMAADAFDQAGDKAEAAAMRQDSLGL  399 (409)
T ss_pred             HHHHHHHHHhHHhhcCCCHHH-HHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            99999999  57777887655 559999999999999999999999763

This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.

>COG5191 Uncharacterized conserved protein, contains HAT (Half-A-TPR) repeat [General function prediction only]

Probab=98.31  E-value=6.3e-07  Score=83.76  Aligned_cols=81  Identities=14%  Similarity=0.304  Sum_probs=74.8

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~  101 (565)
                      ++..|..|+.+-.+.+....+..+|-.||+.+|++++||+.-++|......+.+.++.+|.++|+..|.++.||..|.+ 
T Consensus       106 D~k~w~~y~~Y~~k~k~y~~~~nI~~~~l~khP~nvdlWI~~c~~e~~~~ani~s~Ra~f~~glR~N~~~p~iw~eyfr-  184 (435)
T COG5191         106 DPKIWSQYAAYVIKKKMYGEMKNIFAECLTKHPLNVDLWIYCCAFELFEIANIESSRAMFLKGLRMNSRSPRIWIEYFR-  184 (435)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCceeeeeeccchhhhhccHHHHHHHHHhhhccCCCCchHHHHHHH-
Confidence            7889999999999988888999999999999999999999988887777778888999999999999999999999987 


Q ss_pred             HH
Q 008442          102 LE  103 (565)
Q Consensus       102 le  103 (565)
                      +|
T Consensus       185 ~E  186 (435)
T COG5191         185 ME  186 (435)
T ss_pred             HH
Confidence            44

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.29  E-value=3.5e-06  Score=83.40  Aligned_cols=81  Identities=21%  Similarity=0.408  Sum_probs=70.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecC
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSN  468 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~  468 (565)
                      .+..-|-+.+||+++|+++|.+||+.|+ |.++.+++  .+|+..|-|||+|.++++++.|++++...+..|-|.|-.+.
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~   84 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR--RNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAG   84 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec--cCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccC
Confidence            3445677889999999999999999996 88866655  47999999999999999999999999999999999998886


Q ss_pred             CCCC
Q 008442          469 PKQR  472 (565)
Q Consensus       469 ~~~~  472 (565)
                      +...
T Consensus        85 ~~e~   88 (510)
T KOG4211|consen   85 GAEA   88 (510)
T ss_pred             Cccc
Confidence            5543

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.28  E-value=2.8e-07  Score=81.18  Aligned_cols=76  Identities=18%  Similarity=0.203  Sum_probs=68.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ..+||||+|+...++++-|.++|-+-|.|..+.|+.++ .++.+ ||||.|.++.++.-|+. +||..+.++.+.|..-
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            35799999999999999999999999999999999887 67777 99999999999999999 6999999988877664

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.28  E-value=0.00017  Score=74.50  Aligned_cols=212  Identities=14%  Similarity=0.088  Sum_probs=136.3

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      .++..|+.+....|..   .......-.+.....|+++.+...+++.+...|.++......+...... ++.+.+..+++
T Consensus       136 ~A~~~l~~A~~~~~~~---~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~P~~~~al~ll~~~~~~~-gdw~~a~~~l~  211 (398)
T PRK10747        136 RANQHLERAAELADND---QLPVEITRVRIQLARNENHAARHGVDKLLEVAPRHPEVLRLAEQAYIRT-GAWSSLLDILP  211 (398)
T ss_pred             HHHHHHHHHHhcCCcc---hHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHH-HhHHHHHHHHH
Confidence            3567788887766641   1222233356667789999999999999999999987655555433222 34555555555


Q ss_pred             HHHHcCC------------------------------------------CCHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 008442           83 RATKNCP------------------------------------------WVGELWVRSLLSLERSRASEEEISTVFEKSL  120 (565)
Q Consensus        83 rAl~~~p------------------------------------------~~~~lW~~yi~~le~~~~~~~~~~~if~ral  120 (565)
                      +..+..+                                          ..+.++..|...+. ..+..+.+..++++++
T Consensus       212 ~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~-~~g~~~~A~~~L~~~l  290 (398)
T PRK10747        212 SMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRKTRHQVALQVAMAEHLI-ECDDHDTAQQIILDGL  290 (398)
T ss_pred             HHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHhCCHHHHHHHHHHHH-HCCCHHHHHHHHHHHH
Confidence            5544332                                          23444445544222 2445555555666655


Q ss_pred             hcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChH
Q 008442          121 LCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMV  200 (565)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~  200 (565)
                      ..+++.     .+...+.     .+              ....+.+++..++...+..+....+...++++....+ +.+
T Consensus       291 ~~~~~~-----~l~~l~~-----~l--------------~~~~~~~al~~~e~~lk~~P~~~~l~l~lgrl~~~~~-~~~  345 (398)
T PRK10747        291 KRQYDE-----RLVLLIP-----RL--------------KTNNPEQLEKVLRQQIKQHGDTPLLWSTLGQLLMKHG-EWQ  345 (398)
T ss_pred             hcCCCH-----HHHHHHh-----hc--------------cCCChHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCC-CHH
Confidence            533221     0011110     00              0022344555555556656666778889999999988 999


Q ss_pred             HHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          201 SARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       201 ~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      +|+..|++++...|+. ..+..++..+...|+.+.|..+|++++.
T Consensus       346 ~A~~~le~al~~~P~~-~~~~~La~~~~~~g~~~~A~~~~~~~l~  389 (398)
T PRK10747        346 EASLAFRAALKQRPDA-YDYAWLADALDRLHKPEEAAAMRRDGLM  389 (398)
T ss_pred             HHHHHHHHHHhcCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            9999999999998884 4567899999999999999999999986

>KOG1129 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.27  E-value=6.7e-05  Score=71.10  Aligned_cols=185  Identities=17%  Similarity=0.201  Sum_probs=106.3

Q ss_pred             cCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHH----HHHHHHHHHHHhcCCHHH
Q 008442           36 SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGE----LWVRSLLSLERSRASEEE  111 (565)
Q Consensus        36 ~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~----lW~~yi~~le~~~~~~~~  111 (565)
                      ...|.++..+|-..|..+|.++.+-..-+... ..++..+.+.++|.++++..|...+    |=..|.     +.+..|.
T Consensus       269 idQP~~AL~~~~~gld~fP~~VT~l~g~ARi~-eam~~~~~a~~lYk~vlk~~~~nvEaiAcia~~yf-----Y~~~PE~  342 (478)
T KOG1129|consen  269 IDQPERALLVIGEGLDSFPFDVTYLLGQARIH-EAMEQQEDALQLYKLVLKLHPINVEAIACIAVGYF-----YDNNPEM  342 (478)
T ss_pred             hccHHHHHHHHhhhhhcCCchhhhhhhhHHHH-HHHHhHHHHHHHHHHHHhcCCccceeeeeeeeccc-----cCCChHH
Confidence            34455555555555555555555544444422 2222334455555555554443211    111111     1334444


Q ss_pred             HHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHH
Q 008442          112 ISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHL  191 (565)
Q Consensus       112 ~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~  191 (565)
                      +...|.|.|+.+....+.+..+-++.+        +.      ..++.+...|++|.....+    .+....+|-....+
T Consensus       343 AlryYRRiLqmG~~speLf~NigLCC~--------ya------qQ~D~~L~sf~RAlstat~----~~~aaDvWYNlg~v  404 (478)
T KOG1129|consen  343 ALRYYRRILQMGAQSPELFCNIGLCCL--------YA------QQIDLVLPSFQRALSTATQ----PGQAADVWYNLGFV  404 (478)
T ss_pred             HHHHHHHHHHhcCCChHHHhhHHHHHH--------hh------cchhhhHHHHHHHHhhccC----cchhhhhhhcccee
Confidence            555555555444333333333333211        11      1344556667777665432    22334567666666


Q ss_pred             HHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          192 EQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       192 e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ....| |+.-|...|.-+|..++++.+.....+-++.+.|+++.||.+|..|-+
T Consensus       405 aV~iG-D~nlA~rcfrlaL~~d~~h~ealnNLavL~~r~G~i~~Arsll~~A~s  457 (478)
T KOG1129|consen  405 AVTIG-DFNLAKRCFRLALTSDAQHGEALNNLAVLAARSGDILGARSLLNAAKS  457 (478)
T ss_pred             EEecc-chHHHHHHHHHHhccCcchHHHHHhHHHHHhhcCchHHHHHHHHHhhh
Confidence            66677 999999999999999999899999999999999999999999999865

>PLN02789 farnesyltranstransferase

Probab=98.27  E-value=0.00098  Score=66.04  Aligned_cols=201  Identities=11%  Similarity=0.007  Sum_probs=129.2

Q ss_pred             HHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Q 008442           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLE  103 (565)
Q Consensus        24 ~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le  103 (565)
                      ++|.-+-......+..+++..+++.+|..+|.+..+|..-...+.......+.+...+++++...|.+..+|......++
T Consensus        38 ~a~~~~ra~l~~~e~serAL~lt~~aI~lnP~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npknyqaW~~R~~~l~  117 (320)
T PLN02789         38 EAMDYFRAVYASDERSPRALDLTADVIRLNPGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPKNYQIWHHRRWLAE  117 (320)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCcchHHhHHHHHHHH
Confidence            34443333344456778999999999999999999999777666554435677899999999999999999987654455


Q ss_pred             HhcCC-HHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhH
Q 008442          104 RSRAS-EEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLL  182 (565)
Q Consensus       104 ~~~~~-~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~  182 (565)
                      ..... .+.....+++++...+..+..+...-..    +.                 ....|+++++++...+...+...
T Consensus       118 ~l~~~~~~~el~~~~kal~~dpkNy~AW~~R~w~----l~-----------------~l~~~~eeL~~~~~~I~~d~~N~  176 (320)
T PLN02789        118 KLGPDAANKELEFTRKILSLDAKNYHAWSHRQWV----LR-----------------TLGGWEDELEYCHQLLEEDVRNN  176 (320)
T ss_pred             HcCchhhHHHHHHHHHHHHhCcccHHHHHHHHHH----HH-----------------HhhhHHHHHHHHHHHHHHCCCch
Confidence            43322 3566778888887665543322211111    10                 01225556666666555333334


Q ss_pred             HHHHHHHHHHHHc---C---CChHHHHHHHHHHHHHccchHHHHHHHHHHHHHc----CChHHHHHHHHHHHh
Q 008442          183 RLYAYWAHLEQSM---G---KDMVSARGVWERLLKISGAMLEAWQSYISMEIEL----DHINEARSIYKRCYS  245 (565)
Q Consensus       183 ~l~~~~a~~e~~~---~---~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~----~~~~~aR~i~~~al~  245 (565)
                      ..|.....+....   +   ...+.......++|...|++...|.....+....    +....|...+..++.
T Consensus       177 sAW~~R~~vl~~~~~l~~~~~~~e~el~y~~~aI~~~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~  249 (320)
T PLN02789        177 SAWNQRYFVITRSPLLGGLEAMRDSELKYTIDAILANPRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLS  249 (320)
T ss_pred             hHHHHHHHHHHhccccccccccHHHHHHHHHHHHHhCCCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhc
Confidence            4444333222222   1   1134566777899999999999998888877663    344557777877765

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=98.25  E-value=4.2e-07  Score=91.00  Aligned_cols=86  Identities=31%  Similarity=0.514  Sum_probs=79.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEee
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIAR  466 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~  466 (565)
                      ..++.+|||+-.|+..++..+|.++|+.+|.|.+|+++.|+.++.++|.|||+|.+.+++..||.+.|..+.|.+|.|..
T Consensus       175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~  254 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQL  254 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEecc
Confidence            45778999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +...++
T Consensus       255 sEaekn  260 (549)
T KOG0147|consen  255 SEAEKN  260 (549)
T ss_pred             cHHHHH
Confidence            754443

>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]

Probab=98.25  E-value=0.0002  Score=76.52  Aligned_cols=237  Identities=14%  Similarity=0.083  Sum_probs=143.6

Q ss_pred             chhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHH-----HHHHHHHhcchhhH
Q 008442            2 CNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLD-----YTQYLDKTLKVGNV   76 (565)
Q Consensus         2 ~~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~-----Y~~~l~~~~~~~~~   76 (565)
                      ..+|.+|-.+|+.+|.    +.+...+++....+.|+..++..-|.+++..+|.+.-.|+.     ++.|.....+. +.
T Consensus       224 ~qA~~cy~rAI~~~p~----n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~-e~  298 (895)
T KOG2076|consen  224 NQARYCYSRAIQANPS----NWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNER-ER  298 (895)
T ss_pred             HHHHHHHHHHHhcCCc----chHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHH-HH
Confidence            3589999999999998    78888889999999999999999999999999944433332     44444444433 77


Q ss_pred             HHHHHHHHHHcCCC-----CHHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-------------------cc-cc----cH
Q 008442           77 VRDVYSRATKNCPW-----VGELWVRSLLSLERSRASEEEISTVFEKSLL-------------------CA-FS----TF  127 (565)
Q Consensus        77 ~~~v~erAl~~~p~-----~~~lW~~yi~~le~~~~~~~~~~~if~ral~-------------------~~-~~----~~  127 (565)
                      +.++++-++..+..     ...|...-+............+...-.+-++                   +. ..    ..
T Consensus       299 a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l  378 (895)
T KOG2076|consen  299 AAKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDL  378 (895)
T ss_pred             HHHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccc
Confidence            88999999984421     1123222111121111111112111111000                   00 00    01


Q ss_pred             HH-HHHHHHHHHH------HHHHHhhccc-----cchhhhhHHHH---HHHHHHHHHHHHhhhcC-CchhHHHHHHHHHH
Q 008442          128 EE-YLDLFLTRID------GLRRRILFSG-----EVEGVLDYSLI---RETFQRASDYLSEQMKN-TDGLLRLYAYWAHL  191 (565)
Q Consensus       128 ~~-~~~~~~~~~~------~~~r~~~~~~-----~~e~~~~~~~~---~~~~~~a~~~l~~~~~~-~~~~~~l~~~~a~~  191 (565)
                      .. .+.+.+...+      ++-......+     .++-+.|+..+   ..-|..|+.++...... .....-+|...+..
T Consensus       379 ~v~rl~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c  458 (895)
T KOG2076|consen  379 RVIRLMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARC  458 (895)
T ss_pred             hhHhHhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHH
Confidence            11 1222211110      1110000000     01111222111   13356788887654432 22224488888999


Q ss_pred             HHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHH
Q 008442          192 EQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCY  244 (565)
Q Consensus       192 e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al  244 (565)
                      +..++ .++.|...|+++|...|++.++-+..+.+....|+.++|-++++..+
T Consensus       459 ~~~l~-e~e~A~e~y~kvl~~~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~  510 (895)
T KOG2076|consen  459 YMELG-EYEEAIEFYEKVLILAPDNLDARITLASLYQQLGNHEKALETLEQII  510 (895)
T ss_pred             HHHHh-hHHHHHHHHHHHHhcCCCchhhhhhHHHHHHhcCCHHHHHHHHhccc
Confidence            99988 99999999999999999999999999999999999999999998865

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.12  E-value=1.9e-05  Score=62.28  Aligned_cols=78  Identities=21%  Similarity=0.154  Sum_probs=65.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhcc--CCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccC----CeEEEE
Q 008442          392 CTAFLSNINLKATYEDLRRFFSD--VGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFL----GKKLSI  464 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~--~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~----g~~l~v  464 (565)
                      +||.|+|+|...+.++|.+++..  .|....+-++.|-.++-+.|||||.|.+++.|..-.. .+|..+.    .+.+.|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            68999999999999999998854  3677888899998888999999999999999988887 6887764    446677


Q ss_pred             eecCC
Q 008442          465 ARSNP  469 (565)
Q Consensus       465 ~~a~~  469 (565)
                      .+|+-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            77754

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional

Probab=98.09  E-value=0.00075  Score=75.23  Aligned_cols=263  Identities=9%  Similarity=0.012  Sum_probs=153.6

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (565)
                      .+..+...+.....   .+...|...++...+.|..+.+..+|++...   .+...|...+...... +..+.+..+|+.
T Consensus       243 ~~~l~~~~~~~g~~---~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~---~~~vt~n~li~~y~~~-g~~~eA~~lf~~  315 (697)
T PLN03081        243 GQQLHCCVLKTGVV---GDTFVSCALIDMYSKCGDIEDARCVFDGMPE---KTTVAWNSMLAGYALH-GYSEEALCLYYE  315 (697)
T ss_pred             HHHHHHHHHHhCCC---ccceeHHHHHHHHHHCCCHHHHHHHHHhCCC---CChhHHHHHHHHHHhC-CCHHHHHHHHHH
Confidence            34445544444321   1455777788888888888888888887643   4666777777655443 366778888888


Q ss_pred             HHHc-CCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc----cHHHHHHHHHHHHHHHHHHhhccccch-hhhhH
Q 008442           84 ATKN-CPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS----TFEEYLDLFLTRIDGLRRRILFSGEVE-GVLDY  157 (565)
Q Consensus        84 Al~~-~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~----~~~~~~~~~~~~~~~~~r~~~~~~~~e-~~~~~  157 (565)
                      .... +..+...+..-|..+-. .+.++.+..++..+++..+.    .+...+..+....+......++....+ +..-|
T Consensus       316 M~~~g~~pd~~t~~~ll~a~~~-~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~d~~t~  394 (697)
T PLN03081        316 MRDSGVSIDQFTFSIMIRIFSR-LALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISW  394 (697)
T ss_pred             HHHcCCCCCHHHHHHHHHHHHh-ccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCCCCeeeH
Confidence            8763 22233445444443333 56677888888887765422    233333333221111111111111100 00112


Q ss_pred             HHHHHH------HHHHHHHHHhhhcC-CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHc--cchHHHHHHHHHHHH
Q 008442          158 SLIRET------FQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS--GAMLEAWQSYISMEI  228 (565)
Q Consensus       158 ~~~~~~------~~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~--~~~~~lw~~yi~~e~  228 (565)
                      ..+...      +++|++++...... ..+....+...+.-....| .+++|..+|+.+.+.+  ......|...++...
T Consensus       395 n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g-~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l~  473 (697)
T PLN03081        395 NALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSG-LSEQGWEIFQSMSENHRIKPRAMHYACMIELLG  473 (697)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCC-cHHHHHHHHHHHHHhcCCCCCccchHhHHHHHH
Confidence            222221      24455555443321 2222333444445555666 8999999999998753  334667888899999


Q ss_pred             HcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHH
Q 008442          229 ELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (565)
Q Consensus       229 ~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~  280 (565)
                      +.|.++.|.++++++-     ......+|...+.--..+|+.+..+.+.++.
T Consensus       474 r~G~~~eA~~~~~~~~-----~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l  520 (697)
T PLN03081        474 REGLLDEAYAMIRRAP-----FKPTVNMWAALLTACRIHKNLELGRLAAEKL  520 (697)
T ss_pred             hcCCHHHHHHHHHHCC-----CCCCHHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence            9999999999988752     2234568999998888999988877776654

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.08  E-value=4.2e-06  Score=80.69  Aligned_cols=84  Identities=26%  Similarity=0.518  Sum_probs=74.7

Q ss_pred             CCCCeEE-EcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          389 TDECTAF-LSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~-V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      ....++| |++|+++++.++|+..|..+|.|..++++.++.+|.++|||||.|.+......++..+...+.|+++.|...
T Consensus       182 ~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  261 (285)
T KOG4210|consen  182 GPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALNDQTRSIGGRPLRLEED  261 (285)
T ss_pred             CccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhcccCcccCcccccccC
Confidence            4455666 999999999999999999999999999999999999999999999999988888876667789999999998


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .|.+.
T Consensus       262 ~~~~~  266 (285)
T KOG4210|consen  262 EPRPK  266 (285)
T ss_pred             CCCcc
Confidence            87654

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.08  E-value=0.00013  Score=67.15  Aligned_cols=115  Identities=13%  Similarity=0.040  Sum_probs=91.7

Q ss_pred             HHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcch--hhHHHHHHHH
Q 008442            6 AHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKV--GNVVRDVYSR   83 (565)
Q Consensus         6 ~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~--~~~~~~v~er   83 (565)
                      ..|+.+|..+|.    +.+.|..........|+++.+...|++|+...|.+.++|..|+..+....+.  .+.+..++++
T Consensus        60 ~~l~~~L~~~P~----~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~  135 (198)
T PRK10370         60 QALQDKIRANPQ----NSEQWALLGEYYLWRNDYDNALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQTREMIDK  135 (198)
T ss_pred             HHHHHHHHHCCC----CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHH
Confidence            456666777776    8889999999888999999999999999999999999999998754333323  4779999999


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc
Q 008442           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (565)
Q Consensus        84 Al~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~  125 (565)
                      |++..|.....|..... .....++++++...|++++...++
T Consensus       136 al~~dP~~~~al~~LA~-~~~~~g~~~~Ai~~~~~aL~l~~~  176 (198)
T PRK10370        136 ALALDANEVTALMLLAS-DAFMQADYAQAIELWQKVLDLNSP  176 (198)
T ss_pred             HHHhCCCChhHHHHHHH-HHHHcCCHHHHHHHHHHHHhhCCC
Confidence            99999988887766654 334478899999999999875544

>smart00777 Mad3_BUB1_I Mad3/BUB1 hoMad3/BUB1 homology region 1

Probab=98.07  E-value=4.8e-05  Score=63.30  Aligned_cols=108  Identities=17%  Similarity=0.310  Sum_probs=79.1

Q ss_pred             chhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhc---C-CchhHHHHHHHHHhcCCCC---------HHHHHHHHHHHH
Q 008442            2 CNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS---G-DPGRVQLLYERAITDFPVS---------SDLWLDYTQYLD   68 (565)
Q Consensus         2 ~~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~---~-~~~~~~~lyERal~~~p~~---------~~lW~~Y~~~l~   68 (565)
                      ...|..||..|.... ....-++.|..||+|...+   | .......++|||+..+-.+         ..+|+.|+++..
T Consensus         2 ~~~r~~~e~~i~~~~-~~dDPL~~w~~yI~W~~~~~p~g~~~s~L~~lLerc~~~f~~~~~YknD~RyLkiWi~ya~~~~   80 (125)
T smart00777        2 EQQRQAFEQELQDLY-EGDDPLDLWLRYIKWTEENYPQGGKESGLLTLLERCIRYFEDDERYKNDPRYLKIWLKYADNCD   80 (125)
T ss_pred             hHHHHHHHHHHHhcc-cCCCChHHHHHHHHHHHHhCCCCCchhhHHHHHHHHHHHhhhhhhhcCCHHHHHHHHHHHHhcC
Confidence            357999999996432 2233578999999997753   2 3446789999999986433         359999998641


Q ss_pred             HhcchhhHHHHHHHHHHHcC-C-CCHHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 008442           69 KTLKVGNVVRDVYSRATKNC-P-WVGELWVRSLLSLERSRASEEEISTVFEK  118 (565)
Q Consensus        69 ~~~~~~~~~~~v~erAl~~~-p-~~~~lW~~yi~~le~~~~~~~~~~~if~r  118 (565)
                          +   ..++|.-..++- + ....+|..|+.++|. .+...++.+||+.
T Consensus        81 ----d---p~~if~~L~~~~IG~~~AlfYe~~A~~lE~-~g~~~~A~~iy~~  124 (125)
T smart00777       81 ----E---PRELFQFLYSKGIGTKLALFYEEWAQLLEA-AGRYKKADEVYQL  124 (125)
T ss_pred             ----C---HHHHHHHHHHCCcchhhHHHHHHHHHHHHH-cCCHHHHHHHHHc
Confidence                2   467888777643 3 356799999998887 6788999999875

Proteins containing this domain are checkpoint proteins involved in cell division. This region has been shown to be essential for the binding of the binding of BUB1 and MAD3 to CDC20p.

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.07  E-value=3.1e-06  Score=85.14  Aligned_cols=71  Identities=25%  Similarity=0.420  Sum_probs=64.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEE
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLS  463 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~  463 (565)
                      +....+|+|-|||..++.++|..+|+.||+|+.|+.     +-..+|.+||+|-|.-+|++|++ +++..|.|+.|.
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            456789999999999999999999999999999765     44567999999999999999998 899999998877

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=98.04  E-value=0.0097  Score=62.14  Aligned_cols=246  Identities=17%  Similarity=0.166  Sum_probs=149.3

Q ss_pred             ChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhc--------CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHc---
Q 008442           19 DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITD--------FPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKN---   87 (565)
Q Consensus        19 ~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~--------~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~---   87 (565)
                      +|....+-..........|.++.+..+|++||..        +|.-...-..|+.++. ..+...++..+|++||..   
T Consensus       195 ~P~~~~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~-~~~k~~eAv~ly~~AL~i~e~  273 (508)
T KOG1840|consen  195 DPERLRTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYR-SLGKYDEAVNLYEEALTIREE  273 (508)
T ss_pred             CchHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHH-HhccHHHHHHHHHHHHHHHHH
Confidence            3334455555555556678999999999999998        4444444444665544 444667799999999972   


Q ss_pred             -C----CCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcc-------cccHHHHH-HHHHHHHHHHHHHhhccccchhh
Q 008442           88 -C----PWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA-------FSTFEEYL-DLFLTRIDGLRRRILFSGEVEGV  154 (565)
Q Consensus        88 -~----p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~-------~~~~~~~~-~~~~~~~~~~~r~~~~~~~~e~~  154 (565)
                       +    |....+...-.. +--..+.+.+++..+++|+..-       .+.+...+ .+...+.  .      .      
T Consensus       274 ~~G~~h~~va~~l~nLa~-ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~--~------~------  338 (508)
T KOG1840|consen  274 VFGEDHPAVAATLNNLAV-LYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQ--S------M------  338 (508)
T ss_pred             hcCCCCHHHHHHHHHHHH-HHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHH--H------h------
Confidence             2    222233333111 2233578888888888888521       11111111 1111111  0      0      


Q ss_pred             hhHHHHHHHHHHHHHHHHhhhcCCc-hhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHc----cc-----hHHHHHHHH
Q 008442          155 LDYSLIRETFQRASDYLSEQMKNTD-GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS----GA-----MLEAWQSYI  224 (565)
Q Consensus       155 ~~~~~~~~~~~~a~~~l~~~~~~~~-~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~----~~-----~~~lw~~yi  224 (565)
                      .+++.+...++++...+...+...+ ....+...++.++...| .+++|+++|+++|+..    ..     ...+|.--.
T Consensus       339 ~~~Eea~~l~q~al~i~~~~~g~~~~~~a~~~~nl~~l~~~~g-k~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~  417 (508)
T KOG1840|consen  339 NEYEEAKKLLQKALKIYLDAPGEDNVNLAKIYANLAELYLKMG-KYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAE  417 (508)
T ss_pred             cchhHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHhc-chhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHH
Confidence            1344555666777777665555433 55667778888888888 9999999999999873    21     235777666


Q ss_pred             HHHHHcCChHHHHHHHHHHHhc--ccCCCCcHHHHHHHHHHH---HHhCCHHHHHHHHHHHhhH
Q 008442          225 SMEIELDHINEARSIYKRCYSK--RFTGTGSEDICHAWLRFE---REYGTLEDFDHSVQKVTPR  283 (565)
Q Consensus       225 ~~e~~~~~~~~aR~i~~~al~~--~~~~~~~~~i~~~~~~fE---~~~G~~~~~~~~~~k~~~~  283 (565)
                      .+ .+.+.+..|-.+|.+++..  .+..+.| ++...|..+-   +.-|+.+.+.+..+++...
T Consensus       418 ~~-~~~k~~~~a~~l~~~~~~i~~~~g~~~~-~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~~~  479 (508)
T KOG1840|consen  418 AY-EELKKYEEAEQLFEEAKDIMKLCGPDHP-DVTYTYLNLAALYRAQGNYEAAEELEEKVLNA  479 (508)
T ss_pred             HH-HHhcccchHHHHHHHHHHHHHHhCCCCC-chHHHHHHHHHHHHHcccHHHHHHHHHHHHHH
Confidence            66 5677788888888887543  2333333 3444454443   4458888777776666533

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.01  E-value=2.4e-05  Score=73.81  Aligned_cols=77  Identities=14%  Similarity=0.304  Sum_probs=65.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCC--CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVG--GVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G--~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ..-+|||||-+.+|++||-+.....|  .+.++.+..++.+|.++|||.|...+..++.+.+. +-.+.|.|+.-.|...
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeecc
Confidence            35689999999999999999887776  46778888888899999999999999998888888 6778899986555443

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.01  E-value=0.00043  Score=70.68  Aligned_cols=225  Identities=15%  Similarity=0.121  Sum_probs=137.1

Q ss_pred             HhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHH
Q 008442           34 QSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEIS  113 (565)
Q Consensus        34 ~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~  113 (565)
                      ++.|++..+..+||-||...|.+.+.|..... ....+.....+...+.||+..-|...++-....-..- ..+.-..+.
T Consensus       296 m~nG~L~~A~LafEAAVkqdP~haeAW~~LG~-~qaENE~E~~ai~AL~rcl~LdP~NleaLmaLAVSyt-Neg~q~~Al  373 (579)
T KOG1125|consen  296 MKNGDLSEAALAFEAAVKQDPQHAEAWQKLGI-TQAENENEQNAISALRRCLELDPTNLEALMALAVSYT-NEGLQNQAL  373 (579)
T ss_pred             HhcCCchHHHHHHHHHHhhChHHHHHHHHhhh-HhhhccchHHHHHHHHHHHhcCCccHHHHHHHHHHHh-hhhhHHHHH
Confidence            34677888999999999999999999997764 2223334456889999999999988665433221111 112223455


Q ss_pred             HHHHHHHhcccccHHHHHHHHHHHHHHHHHH---hhcc--ccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHH
Q 008442          114 TVFEKSLLCAFSTFEEYLDLFLTRIDGLRRR---ILFS--GEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYW  188 (565)
Q Consensus       114 ~if~ral~~~~~~~~~~~~~~~~~~~~~~r~---~~~~--~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~  188 (565)
                      ..++.-|...+...+            ++..   ...+  +...+...+..+...|-.+.....   ..  ....+...+
T Consensus       374 ~~L~~Wi~~~p~y~~------------l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~~~~---~~--~DpdvQ~~L  436 (579)
T KOG1125|consen  374 KMLDKWIRNKPKYVH------------LVSAGENEDFENTKSFLDSSHLAHIQELFLEAARQLP---TK--IDPDVQSGL  436 (579)
T ss_pred             HHHHHHHHhCccchh------------ccccCccccccCCcCCCCHHHHHHHHHHHHHHHHhCC---CC--CChhHHhhh
Confidence            555555543333111            0000   0000  011111122333344443333221   11  123445555


Q ss_pred             HHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhC
Q 008442          189 AHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYG  268 (565)
Q Consensus       189 a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G  268 (565)
                      .-|+.-.+ ++++|..+|+.||...|+++.+|..+.--...-...+.|..-|.+|++..      +.....++.+=..|=
T Consensus       437 GVLy~ls~-efdraiDcf~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqLq------P~yVR~RyNlgIS~m  509 (579)
T KOG1125|consen  437 GVLYNLSG-EFDRAVDCFEAALQVKPNDYLLWNRLGATLANGNRSEEAISAYNRALQLQ------PGYVRVRYNLGISCM  509 (579)
T ss_pred             HHHHhcch-HHHHHHHHHHHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhcC------CCeeeeehhhhhhhh
Confidence            54554445 99999999999999999999999999999888889999999999999731      233445555655565


Q ss_pred             CHHHHHHHHHHHhhHH
Q 008442          269 TLEDFDHSVQKVTPRL  284 (565)
Q Consensus       269 ~~~~~~~~~~k~~~~~  284 (565)
                      ++..+++|+.-.+..+
T Consensus       510 NlG~ykEA~~hlL~AL  525 (579)
T KOG1125|consen  510 NLGAYKEAVKHLLEAL  525 (579)
T ss_pred             hhhhHHHHHHHHHHHH
Confidence            6666666665554443

>PLN03077 Protein ECB2; Provisional

Probab=98.00  E-value=0.0034  Score=71.82  Aligned_cols=85  Identities=12%  Similarity=0.034  Sum_probs=62.6

Q ss_pred             HHHHHcCCChHHHHHHHHHHHHHc--cchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHh
Q 008442          190 HLEQSMGKDMVSARGVWERLLKIS--GAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREY  267 (565)
Q Consensus       190 ~~e~~~~~~~~~ar~i~e~~l~~~--~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~  267 (565)
                      ....+.| .+++|..+|+.+...+  ..+...+...++...+.|++++|.++++..-     ......+|...+.--+.+
T Consensus       597 ~a~~~~g-~v~ea~~~f~~M~~~~gi~P~~~~y~~lv~~l~r~G~~~eA~~~~~~m~-----~~pd~~~~~aLl~ac~~~  670 (857)
T PLN03077        597 CACSRSG-MVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMP-----ITPDPAVWGALLNACRIH  670 (857)
T ss_pred             HHHhhcC-hHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHhCCCHHHHHHHHHHCC-----CCCCHHHHHHHHHHHHHc
Confidence            3344556 8889999999888542  3346788888888889999999999988762     223457888888877888


Q ss_pred             CCHHHHHHHHHHH
Q 008442          268 GTLEDFDHSVQKV  280 (565)
Q Consensus       268 G~~~~~~~~~~k~  280 (565)
                      |+.+-.+.+.++.
T Consensus       671 ~~~e~~e~~a~~l  683 (857)
T PLN03077        671 RHVELGELAAQHI  683 (857)
T ss_pred             CChHHHHHHHHHH
Confidence            9888776655444

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.96  E-value=0.0027  Score=58.59  Aligned_cols=188  Identities=16%  Similarity=0.139  Sum_probs=131.3

Q ss_pred             cCCchhHHHHHHHHHhcCCCC---HHHHHHHHHHHHHhc--chhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHH
Q 008442           36 SGDPGRVQLLYERAITDFPVS---SDLWLDYTQYLDKTL--KVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEE  110 (565)
Q Consensus        36 ~~~~~~~~~lyERal~~~p~~---~~lW~~Y~~~l~~~~--~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~  110 (565)
                      .-+++.+..+++..+...+..   .++|.-|=.-...-.  ...+.+..++.+-...+|.|..+=..+...+|. .+..+
T Consensus        25 ~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~fp~S~RV~~lkam~lEa-~~~~~  103 (289)
T KOG3060|consen   25 VRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRFPGSKRVGKLKAMLLEA-TGNYK  103 (289)
T ss_pred             ccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhCCCChhHHHHHHHHHHH-hhchh
Confidence            347788888998888876544   789988744322211  234557788888777889999887777776776 57778


Q ss_pred             HHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHH
Q 008442          111 EISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAH  190 (565)
Q Consensus       111 ~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~  190 (565)
                      ++.++|++.++-.+.....+.    ..+-.++.   .++      ..    .+.+...+|++.++    ...+.|...++
T Consensus       104 ~A~e~y~~lL~ddpt~~v~~K----RKlAilka---~GK------~l----~aIk~ln~YL~~F~----~D~EAW~eLae  162 (289)
T KOG3060|consen  104 EAIEYYESLLEDDPTDTVIRK----RKLAILKA---QGK------NL----EAIKELNEYLDKFM----NDQEAWHELAE  162 (289)
T ss_pred             hHHHHHHHHhccCcchhHHHH----HHHHHHHH---cCC------cH----HHHHHHHHHHHHhc----CcHHHHHHHHH
Confidence            899999999875443222111    11101100   011      11    33344445555544    44678889999


Q ss_pred             HHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcC---ChHHHHHHHHHHHhc
Q 008442          191 LEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELD---HINEARSIYKRCYSK  246 (565)
Q Consensus       191 ~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~---~~~~aR~i~~~al~~  246 (565)
                      ++...+ ++.+|-=+||.++-..|.++.+...|++..-..|   |++.+|+.|.+++..
T Consensus       163 iY~~~~-~f~kA~fClEE~ll~~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl  220 (289)
T KOG3060|consen  163 IYLSEG-DFEKAAFCLEELLLIQPFNPLYFQRLAEVLYTQGGAENLELARKYYERALKL  220 (289)
T ss_pred             HHHhHh-HHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHh
Confidence            998888 9999999999999999999999999999875554   788899999999973

>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]

Probab=97.95  E-value=0.00091  Score=69.49  Aligned_cols=186  Identities=9%  Similarity=0.025  Sum_probs=127.5

Q ss_pred             cCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHH
Q 008442           36 SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTV  115 (565)
Q Consensus        36 ~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~i  115 (565)
                      .++++.+..+|+.+=...|.-.+=---|-.-|++-. +.-..--+.+--+..-|.+++-|+..-..+- .+++.+.+...
T Consensus       366 l~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq-~~v~Ls~Laq~Li~~~~~sPesWca~GNcfS-LQkdh~~Aik~  443 (638)
T KOG1126|consen  366 LIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQ-DEVALSYLAQDLIDTDPNSPESWCALGNCFS-LQKDHDTAIKC  443 (638)
T ss_pred             HHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHH-hhHHHHHHHHHHHhhCCCCcHHHHHhcchhh-hhhHHHHHHHH
Confidence            356778889999988887765543333333333222 1111223445555677899999998765333 35778889999


Q ss_pred             HHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHc
Q 008442          116 FEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSM  195 (565)
Q Consensus       116 f~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~  195 (565)
                      |+||++..+.-...|..     +...                ..+.+.|+.|..++..++...+..+..|--..-++.+.
T Consensus       444 f~RAiQldp~faYayTL-----lGhE----------------~~~~ee~d~a~~~fr~Al~~~~rhYnAwYGlG~vy~Kq  502 (638)
T KOG1126|consen  444 FKRAIQLDPRFAYAYTL-----LGHE----------------SIATEEFDKAMKSFRKALGVDPRHYNAWYGLGTVYLKQ  502 (638)
T ss_pred             HHHhhccCCccchhhhh-----cCCh----------------hhhhHHHHhHHHHHHhhhcCCchhhHHHHhhhhheecc
Confidence            99999865532222211     1000                12346677777777777776666677776666666676


Q ss_pred             CCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          196 GKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       196 ~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      + ..+.|.--|++|+..+|.+..+-..+..++...|..++|-.+|++|+.
T Consensus       503 e-k~e~Ae~~fqkA~~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~  551 (638)
T KOG1126|consen  503 E-KLEFAEFHFQKAVEINPSNSVILCHIGRIQHQLKRKDKALQLYEKAIH  551 (638)
T ss_pred             c-hhhHHHHHHHhhhcCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHh
Confidence            7 788899999999999999888888888899999999999999999986

>PLN02789 farnesyltranstransferase

Probab=97.95  E-value=0.0027  Score=62.92  Aligned_cols=200  Identities=11%  Similarity=0.012  Sum_probs=125.5

Q ss_pred             HHHHHHHhcCCCCChHhHHHHHHHHHHHHhcC-CchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcch-hhHHHHHHHH
Q 008442            6 AHLEEQISRQDLSDSEKFQQYMIYLKYEQSSG-DPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKV-GNVVRDVYSR   83 (565)
Q Consensus         6 ~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~-~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~-~~~~~~v~er   83 (565)
                      ..++.+|.-+|.    ++.+|..-.......+ +...+...+++++..+|.++.+|..-.-.+...... .+...+.+++
T Consensus        58 ~lt~~aI~lnP~----~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npknyqaW~~R~~~l~~l~~~~~~~el~~~~k  133 (320)
T PLN02789         58 DLTADVIRLNPG----NYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPKNYQIWHHRRWLAEKLGPDAANKELEFTRK  133 (320)
T ss_pred             HHHHHHHHHCch----hHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCcchHHhHHHHHHHHHcCchhhHHHHHHHHH
Confidence            345556666665    8899987777666666 568899999999999999999998665444333321 2457889999


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccccc--HHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHH
Q 008442           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFST--FEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIR  161 (565)
Q Consensus        84 Al~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~--~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~  161 (565)
                      ++..-|.+...|....-.++. .+..++....++++|...+..  .|.+..+......      ...       ..   .
T Consensus       134 al~~dpkNy~AW~~R~w~l~~-l~~~~eeL~~~~~~I~~d~~N~sAW~~R~~vl~~~~------~l~-------~~---~  196 (320)
T PLN02789        134 ILSLDAKNYHAWSHRQWVLRT-LGGWEDELEYCHQLLEEDVRNNSAWNQRYFVITRSP------LLG-------GL---E  196 (320)
T ss_pred             HHHhCcccHHHHHHHHHHHHH-hhhHHHHHHHHHHHHHHCCCchhHHHHHHHHHHhcc------ccc-------cc---c
Confidence            999999999999887654444 566788889999999865543  3322222111100      000       00   1


Q ss_pred             HHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCC---ChHHHHHHHHHHHHHccchHHHHHHHHHH
Q 008442          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGK---DMVSARGVWERLLKISGAMLEAWQSYISM  226 (565)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~---~~~~ar~i~e~~l~~~~~~~~lw~~yi~~  226 (565)
                      ..++..++++...+...+.....|.+..-+....+.   ....|..++..++...+.+...--..++.
T Consensus       197 ~~~e~el~y~~~aI~~~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~~~s~~al~~l~d~  264 (320)
T PLN02789        197 AMRDSELKYTIDAILANPRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKDSNHVFALSDLLDL  264 (320)
T ss_pred             ccHHHHHHHHHHHHHhCCCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhcccCCcHHHHHHHHHH
Confidence            123344555555555445556677777666655221   23457788888887666655433333443

>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]

Probab=97.93  E-value=0.0021  Score=69.54  Aligned_cols=239  Identities=12%  Similarity=0.104  Sum_probs=148.6

Q ss_pred             hhhHHHHHHHhcCC-CCChHh---HHHHHH--HHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhH
Q 008442            3 NARAHLEEQISRQD-LSDSEK---FQQYMI--YLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNV   76 (565)
Q Consensus         3 ~~R~~~E~~l~~~~-~~~~~~---~~~W~~--yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~   76 (565)
                      .++..|..++.... .++.+.   ..+=+.  .....+..++...+...|...|..+|...+-.+..+.+....+ +...
T Consensus       470 ~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YNlarl~E~l~~~~~A~e~Yk~Ilkehp~YId~ylRl~~ma~~k~-~~~e  548 (1018)
T KOG2002|consen  470 KALEHFKSALGKLLEVANKDEGKSTNLTLKYNLARLLEELHDTEVAEEMYKSILKEHPGYIDAYLRLGCMARDKN-NLYE  548 (1018)
T ss_pred             HHHHHHHHHhhhhhhhcCccccccchhHHHHHHHHHHHhhhhhhHHHHHHHHHHHHCchhHHHHHHhhHHHHhcc-CcHH
Confidence            46777888876621 122212   222222  2334456678889999999999999999998888876554444 4556


Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhh
Q 008442           77 VRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLD  156 (565)
Q Consensus        77 ~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~  156 (565)
                      +...+..++.....++.+|.-+-. +.......--+..-|++.++.+......|..+-+.- -++.+......      +
T Consensus       549 a~~~lk~~l~~d~~np~arsl~G~-~~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN-~~~~~l~~~~r------n  620 (1018)
T KOG2002|consen  549 ASLLLKDALNIDSSNPNARSLLGN-LHLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGN-VYIQALHNPSR------N  620 (1018)
T ss_pred             HHHHHHHHHhcccCCcHHHHHHHH-HHHhhhhhcccccHHHHHHhhhccCCchhHHHHhhH-HHHHHhccccc------C
Confidence            888999999987778889887653 333233333344445554443222112222222221 11111111111      1


Q ss_pred             HHHHHHHHHHHHHHHHhhhcCCchhHHHHH--HHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChH
Q 008442          157 YSLIRETFQRASDYLSEQMKNTDGLLRLYA--YWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHIN  234 (565)
Q Consensus       157 ~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~--~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~  234 (565)
                      -...+..+++|++.+.+.+...+..  +|.  -.+-+....+ .+..|+.||.+....-.+...+|+..+..+..+|++-
T Consensus       621 ~ek~kk~~~KAlq~y~kvL~~dpkN--~yAANGIgiVLA~kg-~~~~A~dIFsqVrEa~~~~~dv~lNlah~~~e~~qy~  697 (1018)
T KOG2002|consen  621 PEKEKKHQEKALQLYGKVLRNDPKN--MYAANGIGIVLAEKG-RFSEARDIFSQVREATSDFEDVWLNLAHCYVEQGQYR  697 (1018)
T ss_pred             hHHHHHHHHHHHHHHHHHHhcCcch--hhhccchhhhhhhcc-CchHHHHHHHHHHHHHhhCCceeeeHHHHHHHHHHHH
Confidence            1234466777777776666544332  221  1233445556 8999999999999987777899999999999999999


Q ss_pred             HHHHHHHHHHhcccCCCCc
Q 008442          235 EARSIYKRCYSKRFTGTGS  253 (565)
Q Consensus       235 ~aR~i~~~al~~~~~~~~~  253 (565)
                      .|.++|+.++.+.+..+.+
T Consensus       698 ~AIqmYe~~lkkf~~~~~~  716 (1018)
T KOG2002|consen  698 LAIQMYENCLKKFYKKNRS  716 (1018)
T ss_pred             HHHHHHHHHHHHhcccCCH
Confidence            9999999999865544444

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=97.93  E-value=1.7e-05  Score=81.72  Aligned_cols=82  Identities=15%  Similarity=0.291  Sum_probs=72.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCC---CCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEE
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKF---TGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLS  463 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~---~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~  463 (565)
                      +.....|||+||++.++++.|-..|..||+|.+++|+..+.   ....+-||||.|-+..+|++|+. |+|..+.+..++
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            45568899999999999999999999999999999987651   23456799999999999999998 899999999999


Q ss_pred             EeecCC
Q 008442          464 IARSNP  469 (565)
Q Consensus       464 v~~a~~  469 (565)
                      +.++++
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            988854

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.92  E-value=0.00069  Score=58.96  Aligned_cols=111  Identities=13%  Similarity=0.027  Sum_probs=89.0

Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHH
Q 008442            7 HLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATK   86 (565)
Q Consensus         7 ~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~   86 (565)
                      .|+.+|..+|.    +   |..........|+++.+...|++++...|.+...|...+.-+.. .+..+.+...|++|+.
T Consensus        15 ~~~~al~~~p~----~---~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~-~g~~~~A~~~y~~Al~   86 (144)
T PRK15359         15 ILKQLLSVDPE----T---VYASGYASWQEGDYSRAVIDFSWLVMAQPWSWRAHIALAGTWMM-LKEYTTAINFYGHALM   86 (144)
T ss_pred             HHHHHHHcCHH----H---HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHH-HhhHHHHHHHHHHHHh
Confidence            45666666653    3   44455556678999999999999999999999999999875554 4477889999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccccc
Q 008442           87 NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFST  126 (565)
Q Consensus        87 ~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~  126 (565)
                      ..|.....|......+.. .+..+++...|.+|+...+..
T Consensus        87 l~p~~~~a~~~lg~~l~~-~g~~~eAi~~~~~Al~~~p~~  125 (144)
T PRK15359         87 LDASHPEPVYQTGVCLKM-MGEPGLAREAFQTAIKMSYAD  125 (144)
T ss_pred             cCCCCcHHHHHHHHHHHH-cCCHHHHHHHHHHHHHhCCCC
Confidence            999999998887764544 688999999999999866553

>KOG1173 consensus Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=97.91  E-value=0.0042  Score=63.53  Aligned_cols=233  Identities=14%  Similarity=0.146  Sum_probs=127.4

Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHH
Q 008442            7 HLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATK   86 (565)
Q Consensus         7 ~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~   86 (565)
                      +++..+..+|.    +.....-+|-...+.|+..+...+=-+.+...|.++--|..-.-|..... ..+++|..|-+|..
T Consensus       266 it~~lle~dpf----h~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~yP~~a~sW~aVg~YYl~i~-k~seARry~SKat~  340 (611)
T KOG1173|consen  266 ITEELLEKDPF----HLPCLPLHIACLYELGKSNKLFLLSHKLVDLYPSKALSWFAVGCYYLMIG-KYSEARRYFSKATT  340 (611)
T ss_pred             HhHHHHhhCCC----CcchHHHHHHHHHHhcccchHHHHHHHHHHhCCCCCcchhhHHHHHHHhc-CcHHHHHHHHHHhh
Confidence            34444555555    44555555555455555444444445555566666666666555544333 33446666666666


Q ss_pred             cCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc--cHHHHHHHHHHHHHHHH--------HHhhcccc------
Q 008442           87 NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLR--------RRILFSGE------  150 (565)
Q Consensus        87 ~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~--~~~~~~~~~~~~~~~~~--------r~~~~~~~------  150 (565)
                      .-|..+.-|+.|...+-. .+.-+++...|.+|-+.-.+  ....|+.+.......+.        ...+....      
T Consensus       341 lD~~fgpaWl~fghsfa~-e~EhdQAmaaY~tAarl~~G~hlP~LYlgmey~~t~n~kLAe~Ff~~A~ai~P~Dplv~~E  419 (611)
T KOG1173|consen  341 LDPTFGPAWLAFGHSFAG-EGEHDQAMAAYFTAARLMPGCHLPSLYLGMEYMRTNNLKLAEKFFKQALAIAPSDPLVLHE  419 (611)
T ss_pred             cCccccHHHHHHhHHhhh-cchHHHHHHHHHHHHHhccCCcchHHHHHHHHHHhccHHHHHHHHHHHHhcCCCcchhhhh
Confidence            556666666666554432 23345555555555542211  12222222211111000        00000000      


Q ss_pred             ---ch-hhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHH
Q 008442          151 ---VE-GVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISM  226 (565)
Q Consensus       151 ---~e-~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~  226 (565)
                         +. ...++..+...|+.+....+........+..++........+++ ..+.|...|+++|...|.++...-...=.
T Consensus       420 lgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~-~~~eAI~~~q~aL~l~~k~~~~~asig~i  498 (611)
T KOG1173|consen  420 LGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLN-KYEEAIDYYQKALLLSPKDASTHASIGYI  498 (611)
T ss_pred             hhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHh-hHHHHHHHHHHHHHcCCCchhHHHHHHHH
Confidence               00 01233344444555544333333222235566777777888888 88899999999999999888877666666


Q ss_pred             HHHcCChHHHHHHHHHHHhc
Q 008442          227 EIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       227 e~~~~~~~~aR~i~~~al~~  246 (565)
                      .-..|+++.|...|.++|-.
T Consensus       499 y~llgnld~Aid~fhKaL~l  518 (611)
T KOG1173|consen  499 YHLLGNLDKAIDHFHKALAL  518 (611)
T ss_pred             HHHhcChHHHHHHHHHHHhc
Confidence            67799999999999999863

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=97.91  E-value=1.5e-05  Score=81.19  Aligned_cols=86  Identities=22%  Similarity=0.356  Sum_probs=79.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      .....+.+||++||...++..+.++...||.+....++.+..+|.++||||.+|-++.....|+. +||..+++.+|.|.
T Consensus       285 ~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq  364 (500)
T KOG0120|consen  285 VPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQ  364 (500)
T ss_pred             cccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEee
Confidence            34567899999999999999999999999999999999999889999999999999999999998 99999999999999


Q ss_pred             ecCCCCC
Q 008442          466 RSNPKQR  472 (565)
Q Consensus       466 ~a~~~~~  472 (565)
                      .+.+...
T Consensus       365 ~A~~g~~  371 (500)
T KOG0120|consen  365 RAIVGAS  371 (500)
T ss_pred             hhhccch
Confidence            9876543

>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=97.87  E-value=3.2e-05  Score=57.83  Aligned_cols=68  Identities=25%  Similarity=0.371  Sum_probs=46.5

Q ss_pred             CeEEEcCCCCCCCHH----HHHHHhccCCC-eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          392 CTAFLSNINLKATYE----DLRRFFSDVGG-VSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~----~l~~~f~~~G~-i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      ..|||.|||.+.+..    -|++++..||. |.+|       +   .|.|+|-|.+++.|..|.+ |+|..+.|++|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v-------~---~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV-------S---GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE-------e---CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            468999999998865    46677778974 4443       2   2689999999999999998 89999999999999


Q ss_pred             ecCC
Q 008442          466 RSNP  469 (565)
Q Consensus       466 ~a~~  469 (565)
                      +...
T Consensus        73 ~~~~   76 (90)
T PF11608_consen   73 FSPK   76 (90)
T ss_dssp             SS--
T ss_pred             EcCC
Confidence            8743

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=97.86  E-value=0.00065  Score=62.59  Aligned_cols=81  Identities=15%  Similarity=0.072  Sum_probs=40.3

Q ss_pred             hhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCC--HHHHHHHHH
Q 008442           40 GRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRAS--EEEISTVFE  117 (565)
Q Consensus        40 ~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~--~~~~~~if~  117 (565)
                      +.....|+++|..+|.+.+.|........ ..++.+.+...|++|++..|....+|..|...+-...+.  .+++..+|+
T Consensus        56 ~~~i~~l~~~L~~~P~~~~~w~~Lg~~~~-~~g~~~~A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~  134 (198)
T PRK10370         56 EAQLQALQDKIRANPQNSEQWALLGEYYL-WRNDYDNALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQTREMID  134 (198)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHH-HCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHH
Confidence            34445555666666666666655554333 223445555566666665555555555555432222222  244444454


Q ss_pred             HHHh
Q 008442          118 KSLL  121 (565)
Q Consensus       118 ral~  121 (565)
                      +++.
T Consensus       135 ~al~  138 (198)
T PRK10370        135 KALA  138 (198)
T ss_pred             HHHH
Confidence            4444

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=97.86  E-value=0.0048  Score=58.60  Aligned_cols=186  Identities=15%  Similarity=0.040  Sum_probs=123.0

Q ss_pred             hHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCH---HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHH--
Q 008442           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS---DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGEL--   94 (565)
Q Consensus        20 ~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~---~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~l--   94 (565)
                      +...+.+...+......|+.+.+...|++++..+|.++   ..|...+..+. ..++.+.+...|+++++..|.+..+  
T Consensus        30 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~-~~~~~~~A~~~~~~~l~~~p~~~~~~~  108 (235)
T TIGR03302        30 EWPAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYY-KSGDYAEAIAAADRFIRLHPNHPDADY  108 (235)
T ss_pred             cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHH-hcCCHHHHHHHHHHHHHHCcCCCchHH
Confidence            34567788888777888999999999999999999886   45555555433 3457888999999999999976543  


Q ss_pred             -HHHH-HHHHHH------hcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHH
Q 008442           95 -WVRS-LLSLER------SRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQR  166 (565)
Q Consensus        95 -W~~y-i~~le~------~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~  166 (565)
                       |..- +..+..      ..+..+.+...|++++...+........++.  ..                   .....   
T Consensus       109 a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~--~~-------------------~~~~~---  164 (235)
T TIGR03302       109 AYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPNSEYAPDAKKR--MD-------------------YLRNR---  164 (235)
T ss_pred             HHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCCCChhHHHHHHH--HH-------------------HHHHH---
Confidence             2111 111111      1134566777787777654432111111000  00                   00000   


Q ss_pred             HHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccc---hHHHHHHHHHHHHHcCChHHHHHHHHHH
Q 008442          167 ASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA---MLEAWQSYISMEIELDHINEARSIYKRC  243 (565)
Q Consensus       167 a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~---~~~lw~~yi~~e~~~~~~~~aR~i~~~a  243 (565)
                          +          .......+.++...+ ++..|...|+.++..+|+   ..+.|...+......|+.+.|..+++..
T Consensus       165 ----~----------~~~~~~~a~~~~~~g-~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l  229 (235)
T TIGR03302       165 ----L----------AGKELYVARFYLKRG-AYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVL  229 (235)
T ss_pred             ----H----------HHHHHHHHHHHHHcC-ChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence                0          001123455666777 999999999999999765   3679999999999999999999988887


Q ss_pred             Hh
Q 008442          244 YS  245 (565)
Q Consensus       244 l~  245 (565)
                      ..
T Consensus       230 ~~  231 (235)
T TIGR03302       230 GA  231 (235)
T ss_pred             Hh
Confidence            64

Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=97.86  E-value=4.8e-05  Score=75.54  Aligned_cols=78  Identities=23%  Similarity=0.390  Sum_probs=66.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeE-EEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSS-IRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~-~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      .....|-+.+||+.|++++|.+||+..-.|.. |.++.+. .+++.|-|||.|++.+.|+.|+..+...|+-|-|.|-.|
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRS  179 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHHHHHhhccceEEeehh
Confidence            35578889999999999999999998755544 5667775 788999999999999999999998888888888888665

>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala

Probab=97.84  E-value=0.043  Score=57.98  Aligned_cols=66  Identities=12%  Similarity=0.163  Sum_probs=53.8

Q ss_pred             chhHHHHHHH--HHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          179 DGLLRLYAYW--AHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       179 ~~~~~l~~~~--a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ++..-+|..|  ++.+...+ ++++|.++.+++|...|..+++.+.-+.+....|++..|-..++.|-.
T Consensus       189 ~p~~~lw~~~~lAqhyd~~g-~~~~Al~~Id~aI~htPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~  256 (517)
T PF12569_consen  189 PPSTLLWTLYFLAQHYDYLG-DYEKALEYIDKAIEHTPTLVELYMTKARILKHAGDLKEAAEAMDEARE  256 (517)
T ss_pred             CchHHHHHHHHHHHHHHHhC-CHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            3455567554  77777778 899999999999999999899999889999889998888888888753

N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].

>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]

Probab=97.83  E-value=0.023  Score=54.39  Aligned_cols=224  Identities=12%  Similarity=0.142  Sum_probs=136.6

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCC-C--HHH------H
Q 008442           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPW-V--GEL------W   95 (565)
Q Consensus        25 ~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~-~--~~l------W   95 (565)
                      .|..=++|... ..++++..+|-..+...|..+++=+.... +...-+..+++..|.+--+.. |. .  ..+      =
T Consensus        38 ~Yv~GlNfLLs-~Q~dKAvdlF~e~l~~d~~t~e~~ltLGn-LfRsRGEvDRAIRiHQ~L~~s-pdlT~~qr~lAl~qL~  114 (389)
T COG2956          38 DYVKGLNFLLS-NQPDKAVDLFLEMLQEDPETFEAHLTLGN-LFRSRGEVDRAIRIHQTLLES-PDLTFEQRLLALQQLG  114 (389)
T ss_pred             HHHhHHHHHhh-cCcchHHHHHHHHHhcCchhhHHHHHHHH-HHHhcchHHHHHHHHHHHhcC-CCCchHHHHHHHHHHH
Confidence            45555666554 36789999999999999999998888777 444555777777777666552 32 1  112      1


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcc-c--ccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHH
Q 008442           96 VRSLLSLERSRASEEEISTVFEKSLLCA-F--STFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLS  172 (565)
Q Consensus        96 ~~yi~~le~~~~~~~~~~~if~ral~~~-~--~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~  172 (565)
                      ..|+.     .+-++.++.+|......+ +  ......+.++.                        ...-|++|++...
T Consensus       115 ~Dym~-----aGl~DRAE~~f~~L~de~efa~~AlqqLl~IYQ------------------------~treW~KAId~A~  165 (389)
T COG2956         115 RDYMA-----AGLLDRAEDIFNQLVDEGEFAEGALQQLLNIYQ------------------------ATREWEKAIDVAE  165 (389)
T ss_pred             HHHHH-----hhhhhHHHHHHHHHhcchhhhHHHHHHHHHHHH------------------------HhhHHHHHHHHHH
Confidence            22221     355678888888766532 1  11222223332                        2233444444433


Q ss_pred             hhhcC--CchhHHHHHHHHHHH--HHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhccc
Q 008442          173 EQMKN--TDGLLRLYAYWAHLE--QSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRF  248 (565)
Q Consensus       173 ~~~~~--~~~~~~l~~~~a~~e--~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~  248 (565)
                      .....  .+....+-.+|..+-  ....++.++|+..+.++++.+|+++..-+...+.+...|+++.|.+.|++.++.  
T Consensus       166 ~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kAlqa~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQ--  243 (389)
T COG2956         166 RLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKALQADKKCVRASIILGRVELAKGDYQKAVEALERVLEQ--  243 (389)
T ss_pred             HHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhhCccceehhhhhhHHHHhccchHHHHHHHHHHHHh--
Confidence            22221  222234444444332  233448889999999999999999998899999999999999999999999874  


Q ss_pred             CCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhh
Q 008442          249 TGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTP  282 (565)
Q Consensus       249 ~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~  282 (565)
                      +.+.-..+......-=...|.++.....+.+++.
T Consensus       244 n~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~  277 (389)
T COG2956         244 NPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAME  277 (389)
T ss_pred             ChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            2222223333333333345777777666666553

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=97.81  E-value=0.0013  Score=56.45  Aligned_cols=114  Identities=13%  Similarity=0.064  Sum_probs=91.8

Q ss_pred             HHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHH
Q 008442            6 AHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRAT   85 (565)
Q Consensus         6 ~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl   85 (565)
                      ..|+.+|...|.    +...-..++......++...+...|++++...|.+..+|...+..+... ++.+.+..+|++++
T Consensus         4 ~~~~~~l~~~p~----~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~-~~~~~A~~~~~~~~   78 (135)
T TIGR02552         4 ATLKDLLGLDSE----QLEQIYALAYNLYQQGRYDEALKLFQLLAAYDPYNSRYWLGLAACCQML-KEYEEAIDAYALAA   78 (135)
T ss_pred             hhHHHHHcCChh----hHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHH-HHHHHHHHHHHHHH
Confidence            357777777775    5666666777777889999999999999999999999999988766544 46778999999999


Q ss_pred             HcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc
Q 008442           86 KNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (565)
Q Consensus        86 ~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~  125 (565)
                      ...|.+..+|..... +....++.+.+...|++++...+.
T Consensus        79 ~~~p~~~~~~~~la~-~~~~~g~~~~A~~~~~~al~~~p~  117 (135)
T TIGR02552        79 ALDPDDPRPYFHAAE-CLLALGEPESALKALDLAIEICGE  117 (135)
T ss_pred             hcCCCChHHHHHHHH-HHHHcCCHHHHHHHHHHHHHhccc
Confidence            999998888877655 334468899999999999986544

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>smart00386 HAT HAT (Half-A-TPR) repeats

Probab=97.79  E-value=3.2e-05  Score=48.13  Aligned_cols=30  Identities=43%  Similarity=0.909  Sum_probs=20.0

Q ss_pred             CchhHHHHHHHHHhcCCCCHHHHHHHHHHH
Q 008442           38 DPGRVQLLYERAITDFPVSSDLWLDYTQYL   67 (565)
Q Consensus        38 ~~~~~~~lyERal~~~p~~~~lW~~Y~~~l   67 (565)
                      +.+.++.+|+++|..+|.+.++|+.|++|+
T Consensus         2 ~~~~~r~i~e~~l~~~~~~~~~W~~y~~~e   31 (33)
T smart00386        2 DIERARKIYERALEKFPKSVELWLKYAEFE   31 (33)
T ss_pred             cHHHHHHHHHHHHHHCCCChHHHHHHHHHH
Confidence            445666677777777777777777776664

Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=97.78  E-value=0.011  Score=65.50  Aligned_cols=236  Identities=10%  Similarity=0.014  Sum_probs=137.2

Q ss_pred             ChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCH------
Q 008442           19 DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVG------   92 (565)
Q Consensus        19 ~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~------   92 (565)
                      ++.+..+|...+......++++.+..+.+.++..+|....+|....- +..+.+..+.+..|  +++...+...      
T Consensus        27 ~p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~P~~i~~yy~~G~-l~~q~~~~~~~~lv--~~l~~~~~~~~~~~ve  103 (906)
T PRK14720         27 SLSKFKELDDLIDAYKSENLTDEAKDICEEHLKEHKKSISALYISGI-LSLSRRPLNDSNLL--NLIDSFSQNLKWAIVE  103 (906)
T ss_pred             CcchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCcceehHHHHHH-HHHhhcchhhhhhh--hhhhhcccccchhHHH
Confidence            45688999999999989999999999999999999999998887665 33233233333333  5665554322      


Q ss_pred             -------------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHH
Q 008442           93 -------------ELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSL  159 (565)
Q Consensus        93 -------------~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~  159 (565)
                                   .........++ ..+..+++..+|+++|...+......-.+...+.             +.  +++.
T Consensus       104 ~~~~~i~~~~~~k~Al~~LA~~Yd-k~g~~~ka~~~yer~L~~D~~n~~aLNn~AY~~a-------------e~--dL~K  167 (906)
T PRK14720        104 HICDKILLYGENKLALRTLAEAYA-KLNENKKLKGVWERLVKADRDNPEIVKKLATSYE-------------EE--DKEK  167 (906)
T ss_pred             HHHHHHHhhhhhhHHHHHHHHHHH-HcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHH-------------Hh--hHHH
Confidence                         11111112122 2466788999999999866543222111111110             00  2233


Q ss_pred             HHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH--ccchHHHHHHHHHHHHHcCChHHHH
Q 008442          160 IRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI--SGAMLEAWQSYISMEIELDHINEAR  237 (565)
Q Consensus       160 ~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~--~~~~~~lw~~yi~~e~~~~~~~~aR  237 (565)
                      +...+.+|+..+-.    ...+..+...|..+......+++---.|.++++..  +...+.+|....+.+...++++.+-
T Consensus       168 A~~m~~KAV~~~i~----~kq~~~~~e~W~k~~~~~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~y~~~~~~~~~i  243 (906)
T PRK14720        168 AITYLKKAIYRFIK----KKQYVGIEEIWSKLVHYNSDDFDFFLRIERKVLGHREFTRLVGLLEDLYEPYKALEDWDEVI  243 (906)
T ss_pred             HHHHHHHHHHHHHh----hhcchHHHHHHHHHHhcCcccchHHHHHHHHHHhhhccchhHHHHHHHHHHHhhhhhhhHHH
Confidence            34444444443211    11122233334444333333555555666666665  4556778888888888889999999


Q ss_pred             HHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHH
Q 008442          238 SIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQK  279 (565)
Q Consensus       238 ~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k  279 (565)
                      .+++.+|..  ..++...+...-..|-..|++-..+++++..
T Consensus       244 ~iLK~iL~~--~~~n~~a~~~l~~~y~~kY~~~~~~ee~l~~  283 (906)
T PRK14720        244 YILKKILEH--DNKNNKAREELIRFYKEKYKDHSLLEDYLKM  283 (906)
T ss_pred             HHHHHHHhc--CCcchhhHHHHHHHHHHHccCcchHHHHHHH
Confidence            999999973  2223323333333344666665555555543

>PF08311 Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro: IPR013212 Proteins containing this domain are checkpoint proteins involved in cell division

Probab=97.78  E-value=0.00041  Score=58.53  Aligned_cols=79  Identities=15%  Similarity=0.277  Sum_probs=60.7

Q ss_pred             HHHHHHHHHHHHHHh--hhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH--ccchHHHHHHHHHHHHHcCChH
Q 008442          159 LIRETFQRASDYLSE--QMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI--SGAMLEAWQSYISMEIELDHIN  234 (565)
Q Consensus       159 ~~~~~~~~a~~~l~~--~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~--~~~~~~lw~~yi~~e~~~~~~~  234 (565)
                      .+..++++|+..+..  .+.+...++++|+.|+++-       +.++.+|..+...  ......+|..|+.++...|+++
T Consensus        44 ~L~~lLer~~~~f~~~~~Y~nD~RylkiWi~ya~~~-------~~~~~if~~l~~~~IG~~~A~fY~~wA~~le~~~~~~  116 (126)
T PF08311_consen   44 GLLELLERCIRKFKDDERYKNDERYLKIWIKYADLS-------SDPREIFKFLYSKGIGTKLALFYEEWAEFLEKRGNFK  116 (126)
T ss_dssp             HHHHHHHHHHHHHTTSGGGTT-HHHHHHHHHHHTTB-------SHHHHHHHHHHHHTTSTTBHHHHHHHHHHHHHTT-HH
T ss_pred             HHHHHHHHHHHHHhhhHhhcCCHHHHHHHHHHHHHc-------cCHHHHHHHHHHcCccHHHHHHHHHHHHHHHHcCCHH
Confidence            455677777777643  3445666788888887543       2788999999886  4556889999999999999999


Q ss_pred             HHHHHHHHHH
Q 008442          235 EARSIYKRCY  244 (565)
Q Consensus       235 ~aR~i~~~al  244 (565)
                      .|.+||..+|
T Consensus       117 ~A~~I~~~Gi  126 (126)
T PF08311_consen  117 KADEIYQLGI  126 (126)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHhhC
Confidence            9999999986

This region has been shown to be essential for the binding of BUB1 and MAD3 to CDC20p [].; PDB: 3ESL_B 4AEZ_I 4A1G_B 2LAH_A 2WVI_A 3SI5_B.

>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]

Probab=97.77  E-value=0.0048  Score=64.29  Aligned_cols=177  Identities=12%  Similarity=0.069  Sum_probs=99.5

Q ss_pred             HHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccc
Q 008442           45 LYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAF  124 (565)
Q Consensus        45 lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~  124 (565)
                      +-+..+...|++++-|....... ...++.+.+...|+||+..-|...--+...-. .-.....+|.+...|..||...+
T Consensus       409 Laq~Li~~~~~sPesWca~GNcf-SLQkdh~~Aik~f~RAiQldp~faYayTLlGh-E~~~~ee~d~a~~~fr~Al~~~~  486 (638)
T KOG1126|consen  409 LAQDLIDTDPNSPESWCALGNCF-SLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGH-ESIATEEFDKAMKSFRKALGVDP  486 (638)
T ss_pred             HHHHHHhhCCCCcHHHHHhcchh-hhhhHHHHHHHHHHHhhccCCccchhhhhcCC-hhhhhHHHHhHHHHHHhhhcCCc
Confidence            44555566677777777766643 33446666777777777766643211111000 00112345666666666666555


Q ss_pred             ccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHH
Q 008442          125 STFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARG  204 (565)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~  204 (565)
                      ..+..|..+-+.|.                     -.+-|+.|.-++..++..++....+...+..++.+.+ ..++|..
T Consensus       487 rhYnAwYGlG~vy~---------------------Kqek~e~Ae~~fqkA~~INP~nsvi~~~~g~~~~~~k-~~d~AL~  544 (638)
T KOG1126|consen  487 RHYNAWYGLGTVYL---------------------KQEKLEFAEFHFQKAVEINPSNSVILCHIGRIQHQLK-RKDKALQ  544 (638)
T ss_pred             hhhHHHHhhhhhee---------------------ccchhhHHHHHHHhhhcCCccchhHHhhhhHHHHHhh-hhhHHHH
Confidence            44444443333221                     1144566666666666666655556666666666666 6777777


Q ss_pred             HHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          205 VWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       205 i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      +|++|+...|.++.--..-+......++.+.|-..++..-.
T Consensus       545 ~~~~A~~ld~kn~l~~~~~~~il~~~~~~~eal~~LEeLk~  585 (638)
T KOG1126|consen  545 LYEKAIHLDPKNPLCKYHRASILFSLGRYVEALQELEELKE  585 (638)
T ss_pred             HHHHHHhcCCCCchhHHHHHHHHHhhcchHHHHHHHHHHHH
Confidence            77777777666655555555555566666777666666543

>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]

Probab=97.75  E-value=0.028  Score=61.29  Aligned_cols=270  Identities=10%  Similarity=0.025  Sum_probs=126.5

Q ss_pred             hHHHHHHHhcCCCCCh-HhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc--chhhHHHHHH
Q 008442            5 RAHLEEQISRQDLSDS-EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL--KVGNVVRDVY   81 (565)
Q Consensus         5 R~~~E~~l~~~~~~~~-~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~--~~~~~~~~v~   81 (565)
                      =..|..+|..+|..-+ .....|..+.+    .+..+.+...|+||++.+|.+++.-+....+.....  ........++
T Consensus       184 l~yyk~al~inp~~~aD~rIgig~Cf~k----l~~~~~a~~a~~ralqLdp~~v~alv~L~~~~l~~~d~~s~~~~~~ll  259 (1018)
T KOG2002|consen  184 LKYYKKALRINPACKADVRIGIGHCFWK----LGMSEKALLAFERALQLDPTCVSALVALGEVDLNFNDSDSYKKGVQLL  259 (1018)
T ss_pred             HHHHHHHHhcCcccCCCccchhhhHHHh----ccchhhHHHHHHHHHhcChhhHHHHHHHHHHHHHccchHHHHHHHHHH
Confidence            3456666666553211 12334544433    355666777777777777777776555544333222  1223466677


Q ss_pred             HHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccccc-HH--HHH---HHHHHHHHHHHHHhhcc-------
Q 008442           82 SRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFST-FE--EYL---DLFLTRIDGLRRRILFS-------  148 (565)
Q Consensus        82 erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~-~~--~~~---~~~~~~~~~~~r~~~~~-------  148 (565)
                      .+|....|.++.+-......+ -..++.+.+-.+.+-|+...... ..  .+.   .-+....++......+.       
T Consensus       260 ~~ay~~n~~nP~~l~~LAn~f-yfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~~~  338 (1018)
T KOG2002|consen  260 QRAYKENNENPVALNHLANHF-YFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKADN  338 (1018)
T ss_pred             HHHHhhcCCCcHHHHHHHHHH-hhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccCC
Confidence            777765555544322222111 11355556666666655433211 00  011   11111111111111110       


Q ss_pred             cc-c---hhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHc---CCChHHHHHHHHHHHHHccchHHHHH
Q 008442          149 GE-V---EGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSM---GKDMVSARGVWERLLKISGAMLEAWQ  221 (565)
Q Consensus       149 ~~-~---e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~---~~~~~~ar~i~e~~l~~~~~~~~lw~  221 (565)
                      +. +   -.+.....-+.-++.+..++...+...+..+........++...   ....++|..+..+++...|...+.|+
T Consensus       339 d~~~l~~~GlgQm~i~~~dle~s~~~fEkv~k~~p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~K~~~~~~~d~~a~l  418 (1018)
T KOG2002|consen  339 DNFVLPLVGLGQMYIKRGDLEESKFCFEKVLKQLPNNYETMKILGCLYAHSAKKQEKRDKASNVLGKVLEQTPVDSEAWL  418 (1018)
T ss_pred             CCccccccchhHHHHHhchHHHHHHHHHHHHHhCcchHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHHHhcccccHHHHH
Confidence            00 0   00112222333445555555555544444444444444443332   11356888888888888888888998


Q ss_pred             HHHHHHHHcCChHHHHHHHHHHHhccc--CCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHH
Q 008442          222 SYISMEIELDHINEARSIYKRCYSKRF--TGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (565)
Q Consensus       222 ~yi~~e~~~~~~~~aR~i~~~al~~~~--~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~  280 (565)
                      ..+.+... +++-.+-..|.+|+....  ....|..+...-..+--..|+++.+..-+..+
T Consensus       419 ~laql~e~-~d~~~sL~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A  478 (1018)
T KOG2002|consen  419 ELAQLLEQ-TDPWASLDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSA  478 (1018)
T ss_pred             HHHHHHHh-cChHHHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHH
Confidence            88887644 344444666666652210  11234444443333333345554444444333

>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional

Probab=97.72  E-value=0.007  Score=67.53  Aligned_cols=264  Identities=11%  Similarity=0.015  Sum_probs=153.6

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDF-PVSSDLWLDYTQYLDKTLKVGNVVRDVY   81 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~-p~~~~lW~~Y~~~l~~~~~~~~~~~~v~   81 (565)
                      ++...|++.+......   +...|...+......+....+..++..++... ..+..+|...+....+.+ ..+.+..+|
T Consensus       207 ~A~~lf~~M~~~g~~p---~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g-~~~~A~~vf  282 (697)
T PLN03081        207 EAFALFREMWEDGSDA---EPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCG-DIEDARCVF  282 (697)
T ss_pred             HHHHHHHHHHHhCCCC---ChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCC-CHHHHHHHH
Confidence            4567777777654321   34567777777777888888889988887763 345567777777555444 677899999


Q ss_pred             HHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc-cHHHHHHHHHHHHH------------HHHHHhhcc
Q 008442           82 SRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS-TFEEYLDLFLTRID------------GLRRRILFS  148 (565)
Q Consensus        82 erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~-~~~~~~~~~~~~~~------------~~~r~~~~~  148 (565)
                      +....   .+...|..-|..+.+ .+..+++..+|++....... ....|..+...+..            .+.+.....
T Consensus       283 ~~m~~---~~~vt~n~li~~y~~-~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~  358 (697)
T PLN03081        283 DGMPE---KTTVAWNSMLAGYAL-HGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPL  358 (697)
T ss_pred             HhCCC---CChhHHHHHHHHHHh-CCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCC
Confidence            87643   355678887765544 68889999999998764321 22223322222211            111111000


Q ss_pred             ccc--hhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH-ccchHHHHHHHHH
Q 008442          149 GEV--EGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI-SGAMLEAWQSYIS  225 (565)
Q Consensus       149 ~~~--e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~-~~~~~~lw~~yi~  225 (565)
                      +..  ...++.-.-...++.|...+.....   +....|...+.-+.+.| +.++|.++|++++.. ...+...+...+.
T Consensus       359 d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~---~d~~t~n~lI~~y~~~G-~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~  434 (697)
T PLN03081        359 DIVANTALVDLYSKWGRMEDARNVFDRMPR---KNLISWNALIAGYGNHG-RGTKAVEMFERMIAEGVAPNHVTFLAVLS  434 (697)
T ss_pred             CeeehHHHHHHHHHCCCHHHHHHHHHhCCC---CCeeeHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence            000  0000100001123444444443322   12234566666666777 788888888887765 3333555666777


Q ss_pred             HHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHH
Q 008442          226 MEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQK  279 (565)
Q Consensus       226 ~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k  279 (565)
                      -....|..+.|..+|+..... .........|...++.--+.|.++.+.+.+++
T Consensus       435 a~~~~g~~~~a~~~f~~m~~~-~g~~p~~~~y~~li~~l~r~G~~~eA~~~~~~  487 (697)
T PLN03081        435 ACRYSGLSEQGWEIFQSMSEN-HRIKPRAMHYACMIELLGREGLLDEAYAMIRR  487 (697)
T ss_pred             HHhcCCcHHHHHHHHHHHHHh-cCCCCCccchHhHHHHHHhcCCHHHHHHHHHH
Confidence            677778888888888887652 12222223455566666667777777766654

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.72  E-value=0.0056  Score=66.97  Aligned_cols=138  Identities=14%  Similarity=0.115  Sum_probs=98.0

Q ss_pred             hcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHH
Q 008442           51 TDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEY  130 (565)
Q Consensus        51 ~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~  130 (565)
                      ..+|.+.+.-...+.... ..+..+.+..++++++..+|.....+..|+..|-+ .+.++++...+++++...+..    
T Consensus        80 ~~~~~~~~~~~~La~i~~-~~g~~~ea~~~l~~~~~~~Pd~~~a~~~~a~~L~~-~~~~eeA~~~~~~~l~~~p~~----  153 (694)
T PRK15179         80 RRYPHTELFQVLVARALE-AAHRSDEGLAVWRGIHQRFPDSSEAFILMLRGVKR-QQGIEAGRAEIELYFSGGSSS----  153 (694)
T ss_pred             HhccccHHHHHHHHHHHH-HcCCcHHHHHHHHHHHhhCCCcHHHHHHHHHHHHH-hccHHHHHHHHHHHhhcCCCC----
Confidence            345666666666555333 33455667777777777777777777777764443 456677766666666544332    


Q ss_pred             HHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHH
Q 008442          131 LDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLL  210 (565)
Q Consensus       131 ~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l  210 (565)
                                                                         .......+.....+| .+++|..+|++++
T Consensus       154 ---------------------------------------------------~~~~~~~a~~l~~~g-~~~~A~~~y~~~~  181 (694)
T PRK15179        154 ---------------------------------------------------AREILLEAKSWDEIG-QSEQADACFERLS  181 (694)
T ss_pred             ---------------------------------------------------HHHHHHHHHHHHHhc-chHHHHHHHHHHH
Confidence                                                               222223444445667 8999999999999


Q ss_pred             HHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhc
Q 008442          211 KISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       211 ~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~  246 (565)
                      ..+|+....|+.|....+..|+.+.|...|++++..
T Consensus       182 ~~~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~  217 (694)
T PRK15179        182 RQHPEFENGYVGWAQSLTRRGALWRARDVLQAGLDA  217 (694)
T ss_pred             hcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            988888999999999999999999999999999873

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=97.71  E-value=0.031  Score=55.25  Aligned_cols=228  Identities=13%  Similarity=0.028  Sum_probs=113.6

Q ss_pred             HHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcC
Q 008442            9 EEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNC   88 (565)
Q Consensus         9 E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~   88 (565)
                      -+.++..+.    +....+...+.+...|+...+...||.+...+|....---.|+-.+...+ ..+....+-.+-+...
T Consensus       222 le~~~~lr~----NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~dpy~i~~MD~Ya~LL~~eg-~~e~~~~L~~~Lf~~~  296 (564)
T KOG1174|consen  222 LHDNTTLRC----NEHLMMALGKCLYYNGDYFQAEDIFSSTLCANPDNVEAMDLYAVLLGQEG-GCEQDSALMDYLFAKV  296 (564)
T ss_pred             HHhhccCCc----cHHHHHHHhhhhhhhcCchHHHHHHHHHhhCChhhhhhHHHHHHHHHhcc-CHhhHHHHHHHHHhhh
Confidence            334455554    88889999999999999999999999999999988887777776554433 4444555555554433


Q ss_pred             CCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHH----------HHHHHH-----HH--HHhhccccc
Q 008442           89 PWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLF----------LTRIDG-----LR--RRILFSGEV  151 (565)
Q Consensus        89 p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~----------~~~~~~-----~~--r~~~~~~~~  151 (565)
                      .+...-|.--+. +-...++++.+...-+++|.........+|.--          .+.+.+     ++  |--.+.+.+
T Consensus       297 ~~ta~~wfV~~~-~l~~~K~~~rAL~~~eK~I~~~~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~Lap~rL~~Y~GL~  375 (564)
T KOG1174|consen  297 KYTASHWFVHAQ-LLYDEKKFERALNFVEKCIDSEPRNHEALILKGRLLIALERHTQAVIAFRTAQMLAPYRLEIYRGLF  375 (564)
T ss_pred             hcchhhhhhhhh-hhhhhhhHHHHHHHHHHHhccCcccchHHHhccHHHHhccchHHHHHHHHHHHhcchhhHHHHHHHH
Confidence            222233322221 111123344444444555543322222221000          000000     00  000011111


Q ss_pred             hhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcC
Q 008442          152 EGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELD  231 (565)
Q Consensus       152 e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~  231 (565)
                      +.++.+...+++.--|...+.. +...-..+.|.-.-.-++.-.  .-++|.++++++|+..|.........+++....|
T Consensus       376 hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~--~rEKAKkf~ek~L~~~P~Y~~AV~~~AEL~~~Eg  452 (564)
T KOG1174|consen  376 HSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPR--MREKAKKFAEKSLKINPIYTPAVNLIAELCQVEG  452 (564)
T ss_pred             HHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCch--hHHHHHHHHHhhhccCCccHHHHHHHHHHHHhhC
Confidence            1111222222222222221111 111111111111011111111  2357888888888888888777777777777777


Q ss_pred             ChHHHHHHHHHHHh
Q 008442          232 HINEARSIYKRCYS  245 (565)
Q Consensus       232 ~~~~aR~i~~~al~  245 (565)
                      ....+.+++++++.
T Consensus       453 ~~~D~i~LLe~~L~  466 (564)
T KOG1174|consen  453 PTKDIIKLLEKHLI  466 (564)
T ss_pred             ccchHHHHHHHHHh
Confidence            77788888888876

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.70  E-value=0.014  Score=54.00  Aligned_cols=159  Identities=19%  Similarity=0.136  Sum_probs=109.7

Q ss_pred             CCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHH
Q 008442           37 GDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVF  116 (565)
Q Consensus        37 ~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if  116 (565)
                      +....++..+.+.-..+|.|..+=..++-+++... ....+.++|++-|..-|.+..+..+-+-.+-....+.+.|+.+-
T Consensus        66 ~~~~lAq~C~~~L~~~fp~S~RV~~lkam~lEa~~-~~~~A~e~y~~lL~ddpt~~v~~KRKlAilka~GK~l~aIk~ln  144 (289)
T KOG3060|consen   66 GRDDLAQKCINQLRDRFPGSKRVGKLKAMLLEATG-NYKEAIEYYESLLEDDPTDTVIRKRKLAILKAQGKNLEAIKELN  144 (289)
T ss_pred             cchHHHHHHHHHHHHhCCCChhHHHHHHHHHHHhh-chhhHHHHHHHHhccCcchhHHHHHHHHHHHHcCCcHHHHHHHH
Confidence            34455677788877888999999999998887655 56669999999999999998899888876666666666555543


Q ss_pred             HHHHhcccc--cHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHH
Q 008442          117 EKSLLCAFS--TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQS  194 (565)
Q Consensus       117 ~ral~~~~~--~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~  194 (565)
                      +=.-.+..+  .|++..+++.                        ....|++|.-+++..+-..|..+.++..|+++...
T Consensus       145 ~YL~~F~~D~EAW~eLaeiY~------------------------~~~~f~kA~fClEE~ll~~P~n~l~f~rlae~~Yt  200 (289)
T KOG3060|consen  145 EYLDKFMNDQEAWHELAEIYL------------------------SEGDFEKAAFCLEELLLIQPFNPLYFQRLAEVLYT  200 (289)
T ss_pred             HHHHHhcCcHHHHHHHHHHHH------------------------hHhHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHH
Confidence            322222222  2332222222                        23556666666666555555556677888888776


Q ss_pred             cCC--ChHHHHHHHHHHHHHccchHHHH
Q 008442          195 MGK--DMVSARGVWERLLKISGAMLEAW  220 (565)
Q Consensus       195 ~~~--~~~~ar~i~e~~l~~~~~~~~lw  220 (565)
                      .|+  ++.-+|+.|+++++.++.+..-|
T Consensus       201 ~gg~eN~~~arkyy~~alkl~~~~~ral  228 (289)
T KOG3060|consen  201 QGGAENLELARKYYERALKLNPKNLRAL  228 (289)
T ss_pred             HhhHHHHHHHHHHHHHHHHhChHhHHHH
Confidence            653  56789999999999988654433

>KOG1173 consensus Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=97.68  E-value=0.021  Score=58.61  Aligned_cols=253  Identities=9%  Similarity=-0.023  Sum_probs=144.9

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~  101 (565)
                      +.++-..-++-....+.+.....+++..+...|.+.....-+|.-+.... +......+=-+-++..|.++--|..-..+
T Consensus       243 ~~dll~~~ad~~y~~c~f~~c~kit~~lle~dpfh~~~~~~~ia~l~el~-~~n~Lf~lsh~LV~~yP~~a~sW~aVg~Y  321 (611)
T KOG1173|consen  243 NLDLLAEKADRLYYGCRFKECLKITEELLEKDPFHLPCLPLHIACLYELG-KSNKLFLLSHKLVDLYPSKALSWFAVGCY  321 (611)
T ss_pred             cHHHHHHHHHHHHHcChHHHHHHHhHHHHhhCCCCcchHHHHHHHHHHhc-ccchHHHHHHHHHHhCCCCCcchhhHHHH
Confidence            56677777777777788889999999999999999998888887555443 33333344444555669888889775543


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcc--cccHHHHHHHHHH--------HHHHHHHHhhcccc-ch-hhhhHHHH-HHHHHHHH
Q 008442          102 LERSRASEEEISTVFEKSLLCA--FSTFEEYLDLFLT--------RIDGLRRRILFSGE-VE-GVLDYSLI-RETFQRAS  168 (565)
Q Consensus       102 le~~~~~~~~~~~if~ral~~~--~~~~~~~~~~~~~--------~~~~~~r~~~~~~~-~e-~~~~~~~~-~~~~~~a~  168 (565)
                      .-. .+...++|..|.+|....  ++..|....--.+        .--|-....+..+. .- -++..+-. ...+..|-
T Consensus       322 Yl~-i~k~seARry~SKat~lD~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~~G~hlP~LYlgmey~~t~n~kLAe  400 (611)
T KOG1173|consen  322 YLM-IGKYSEARRYFSKATTLDPTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHLPSLYLGMEYMRTNNLKLAE  400 (611)
T ss_pred             HHH-hcCcHHHHHHHHHHhhcCccccHHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCcchHHHHHHHHHHhccHHHHH
Confidence            433 377899999999998644  3333322211111        00011111111111 00 01111112 13344555


Q ss_pred             HHHHhhhcCCchhHHHHHHHHH-HHHHcCCChHHHHHHHHHHHHHc----cc---hHHHHHHHHHHHHHcCChHHHHHHH
Q 008442          169 DYLSEQMKNTDGLLRLYAYWAH-LEQSMGKDMVSARGVWERLLKIS----GA---MLEAWQSYISMEIELDHINEARSIY  240 (565)
Q Consensus       169 ~~l~~~~~~~~~~~~l~~~~a~-~e~~~~~~~~~ar~i~e~~l~~~----~~---~~~lw~~yi~~e~~~~~~~~aR~i~  240 (565)
                      .|+.+++..+|..+ +.....- +..... .+.+|..+|..++..-    +.   -..+|.......+.++.++.|...|
T Consensus       401 ~Ff~~A~ai~P~Dp-lv~~Elgvvay~~~-~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~  478 (611)
T KOG1173|consen  401 KFFKQALAIAPSDP-LVLHELGVVAYTYE-EYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYY  478 (611)
T ss_pred             HHHHHHHhcCCCcc-hhhhhhhheeehHh-hhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHH
Confidence            55555544322221 2222211 222223 6778888888888431    11   2346777778888999999999999


Q ss_pred             HHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          241 KRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       241 ~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      +++|. ..+.++  ..+..-.-.-..-|+++.+-..++|++
T Consensus       479 q~aL~-l~~k~~--~~~asig~iy~llgnld~Aid~fhKaL  516 (611)
T KOG1173|consen  479 QKALL-LSPKDA--STHASIGYIYHLLGNLDKAIDHFHKAL  516 (611)
T ss_pred             HHHHH-cCCCch--hHHHHHHHHHHHhcChHHHHHHHHHHH
Confidence            99987 223222  222222222234588888877777765

>PF02184 HAT: HAT (Half-A-TPR) repeat; InterPro: IPR003107 The HAT (Half A TPR) repeat has a repetitive pattern characterised by three aromatic residues with a conserved spacing

Probab=97.62  E-value=6.8e-05  Score=45.13  Aligned_cols=30  Identities=23%  Similarity=0.577  Sum_probs=25.7

Q ss_pred             ChHHHHHHHHHHHHHccchHHHHHHHHHHHH
Q 008442          198 DMVSARGVWERLLKISGAMLEAWQSYISMEI  228 (565)
Q Consensus       198 ~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~  228 (565)
                      .+++||.||++.+..+|+ +..|+.|+.||.
T Consensus         2 E~dRAR~IyeR~v~~hp~-~k~WikyAkFEe   31 (32)
T PF02184_consen    2 EFDRARSIYERFVLVHPE-VKNWIKYAKFEE   31 (32)
T ss_pred             hHHHHHHHHHHHHHhCCC-chHHHHHHHhhc
Confidence            578899999999988865 889999999984

They are structurally and sequentially similar to TPRs (tetratricopeptide repeats), though they lack the highly conserved alanine and glycine residues found in TPRs. The number of HAT repeats found in different proteins varies between 9 and 12. HAT-repeat-containing proteins appear to be components of macromolecular complexes that are required for RNA processing []. The repeats may be involved in protein-protein interactions. The HAT motif has striking structural similarities to HEAT repeats (IPR000357 from INTERPRO), being of a similar length and consisting of two short helices connected by a loop domain, as in HEAT repeats.; GO: 0006396 RNA processing, 0005622 intracellular

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=97.61  E-value=0.032  Score=58.19  Aligned_cols=203  Identities=15%  Similarity=0.125  Sum_probs=119.4

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~  101 (565)
                      +.-.|.-|.-.-....+++.+...|..||...|++..||.+.+ ++..++.+.+.....-.+-+...|....-|+.|+..
T Consensus        74 S~vCwHv~gl~~R~dK~Y~eaiKcy~nAl~~~~dN~qilrDls-lLQ~QmRd~~~~~~tr~~LLql~~~~ra~w~~~Avs  152 (700)
T KOG1156|consen   74 SHVCWHVLGLLQRSDKKYDEAIKCYRNALKIEKDNLQILRDLS-LLQIQMRDYEGYLETRNQLLQLRPSQRASWIGFAVA  152 (700)
T ss_pred             cchhHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcHHHHHHHH-HHHHHHHhhhhHHHHHHHHHHhhhhhHHHHHHHHHH
Confidence            4457888877766677778888888888888888888888865 366666666666677777777778777888888753


Q ss_pred             HHHhcCCHHHHHHHH---HHHHhcccccHHHHH--HHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhc
Q 008442          102 LERSRASEEEISTVF---EKSLLCAFSTFEEYL--DLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMK  176 (565)
Q Consensus       102 le~~~~~~~~~~~if---~ral~~~~~~~~~~~--~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~  176 (565)
                      ... .+....+..+.   ++....+++ ...+-  ...+-....+     .        +.    ..++.+.+.+...-.
T Consensus       153 ~~L-~g~y~~A~~il~ef~~t~~~~~s-~~~~e~se~~Ly~n~i~-----~--------E~----g~~q~ale~L~~~e~  213 (700)
T KOG1156|consen  153 QHL-LGEYKMALEILEEFEKTQNTSPS-KEDYEHSELLLYQNQIL-----I--------EA----GSLQKALEHLLDNEK  213 (700)
T ss_pred             HHH-HHHHHHHHHHHHHHHHhhccCCC-HHHHHHHHHHHHHHHHH-----H--------Hc----ccHHHHHHHHHhhhh
Confidence            322 23334443433   333322222 11111  1111111000     0        00    123333333322111


Q ss_pred             CCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHH-HHcCChHHHHHHHHHHHh
Q 008442          177 NTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISME-IELDHINEARSIYKRCYS  245 (565)
Q Consensus       177 ~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e-~~~~~~~~aR~i~~~al~  245 (565)
                      ..-....+...-+.++..++ .+++|-.+|..++..+|+++.....+.... .-.+..+....+|...-+
T Consensus       214 ~i~Dkla~~e~ka~l~~kl~-~lEeA~~~y~~Ll~rnPdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~  282 (700)
T KOG1156|consen  214 QIVDKLAFEETKADLLMKLG-QLEEAVKVYRRLLERNPDNLDYYEGLEKALGKIKDMLEALKALYAILSE  282 (700)
T ss_pred             HHHHHHHHhhhHHHHHHHHh-hHHhHHHHHHHHHhhCchhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhh
Confidence            00011223334577888888 999999999999999999888776666655 244555555577777644

>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals

Probab=97.54  E-value=0.013  Score=59.36  Aligned_cols=202  Identities=8%  Similarity=-0.085  Sum_probs=118.9

Q ss_pred             hHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHH---HHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHH
Q 008442           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSD---LWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWV   96 (565)
Q Consensus        20 ~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~---lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~   96 (565)
                      |+....|.....+....+++..+...|.++....+.+.+   .+...+. +....++.+.+..++++++...|.+...|.
T Consensus         3 p~~~~a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~-~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~   81 (355)
T cd05804           3 PDFALGHAAAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEAL-SAWIAGDLPKALALLEQLLDDYPRDLLALK   81 (355)
T ss_pred             CccHHHHHHHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHH-HHHHcCCHHHHHHHHHHHHHHCCCcHHHHH
Confidence            445555555566666667777778888888887775533   4332222 222344677899999999999998887766


Q ss_pred             ---HHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHh
Q 008442           97 ---RSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSE  173 (565)
Q Consensus        97 ---~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~  173 (565)
                         .+.. +-...+....+..++.......+..+.....+-..+.                     ...-+.+|...+..
T Consensus        82 ~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~a~~~~---------------------~~G~~~~A~~~~~~  139 (355)
T cd05804          82 LHLGAFG-LGDFSGMRDHVARVLPLWAPENPDYWYLLGMLAFGLE---------------------EAGQYDRAEEAARR  139 (355)
T ss_pred             HhHHHHH-hcccccCchhHHHHHhccCcCCCCcHHHHHHHHHHHH---------------------HcCCHHHHHHHHHH
Confidence               2222 1111233344444444322222221111111001000                     01113333333333


Q ss_pred             hhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccch----HHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          174 QMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM----LEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       174 ~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~----~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      .+...+.....+..++.+....+ ++++|...+++++...+..    ...|..++.+....|+++.|..+|++++.
T Consensus       140 al~~~p~~~~~~~~la~i~~~~g-~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~  214 (355)
T cd05804         140 ALELNPDDAWAVHAVAHVLEMQG-RFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIA  214 (355)
T ss_pred             HHhhCCCCcHHHHHHHHHHHHcC-CHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhc
Confidence            33333333455667788888888 9999999999999875422    34677888899999999999999999864

A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.

>PRK14574 hmsH outer membrane protein; Provisional

Probab=97.53  E-value=0.018  Score=64.29  Aligned_cols=183  Identities=13%  Similarity=0.075  Sum_probs=119.6

Q ss_pred             HHhcCCchhHHHHHHHHHhcCCCCH-HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHH
Q 008442           33 EQSSGDPGRVQLLYERAITDFPVSS-DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEE  111 (565)
Q Consensus        33 e~~~~~~~~~~~lyERal~~~p~~~-~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~  111 (565)
                      ....|+...+...|++++...|.+. .+. +++.++... +..+.++.++++|+...|.....-..-.. +-...+..+.
T Consensus        44 ~~r~Gd~~~Al~~L~qaL~~~P~~~~av~-dll~l~~~~-G~~~~A~~~~eka~~p~n~~~~~llalA~-ly~~~gdyd~  120 (822)
T PRK14574         44 RARAGDTAPVLDYLQEESKAGPLQSGQVD-DWLQIAGWA-GRDQEVIDVYERYQSSMNISSRGLASAAR-AYRNEKRWDQ  120 (822)
T ss_pred             HHhCCCHHHHHHHHHHHHhhCccchhhHH-HHHHHHHHc-CCcHHHHHHHHHhccCCCCCHHHHHHHHH-HHHHcCCHHH
Confidence            4567999999999999999999995 444 776654433 46678999999999433333322221122 3334688999


Q ss_pred             HHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHH
Q 008442          112 ISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHL  191 (565)
Q Consensus       112 ~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~  191 (565)
                      +..+|++++...+.....+..+...+.+.                     .-.++|+..+.......+. ...+...+.+
T Consensus       121 Aiely~kaL~~dP~n~~~l~gLa~~y~~~---------------------~q~~eAl~~l~~l~~~dp~-~~~~l~layL  178 (822)
T PRK14574        121 ALALWQSSLKKDPTNPDLISGMIMTQADA---------------------GRGGVVLKQATELAERDPT-VQNYMTLSYL  178 (822)
T ss_pred             HHHHHHHHHhhCCCCHHHHHHHHHHHhhc---------------------CCHHHHHHHHHHhcccCcc-hHHHHHHHHH
Confidence            99999999988776655554443333211                     2223333444333332222 2223444555


Q ss_pred             HHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHH
Q 008442          192 EQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYK  241 (565)
Q Consensus       192 e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~  241 (565)
                      ....+ +...|..+|++++...|++.++...|+......|-...|-++.+
T Consensus       179 ~~~~~-~~~~AL~~~ekll~~~P~n~e~~~~~~~~l~~~~~~~~a~~l~~  227 (822)
T PRK14574        179 NRATD-RNYDALQASSEAVRLAPTSEEVLKNHLEILQRNRIVEPALRLAK  227 (822)
T ss_pred             HHhcc-hHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCcHHHHHHHH
Confidence            54445 55569999999999999999999999999988887666655544

>PLN03077 Protein ECB2; Provisional

Probab=97.51  E-value=0.024  Score=64.97  Aligned_cols=257  Identities=8%  Similarity=-0.008  Sum_probs=135.6

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (565)
                      ++..|+..+.....   .+...|...|+...+.|+.+.+..+|++...   .+...|...+.-+.... ..+.+..+|++
T Consensus       408 a~~l~~~~~~~g~~---~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~---~d~vs~~~mi~~~~~~g-~~~eA~~lf~~  480 (857)
T PLN03077        408 GVKLHELAERKGLI---SYVVVANALIEMYSKCKCIDKALEVFHNIPE---KDVISWTSIIAGLRLNN-RCFEALIFFRQ  480 (857)
T ss_pred             HHHHHHHHHHhCCC---cchHHHHHHHHHHHHcCCHHHHHHHHHhCCC---CCeeeHHHHHHHHHHCC-CHHHHHHHHHH
Confidence            45666666655422   1455677777777777777778777777543   23445666655443322 44556666666


Q ss_pred             HHHcCCCCHHHH-----------------------------------HHHHHHHHHhcCCHHHHHHHHHHHHhcccccHH
Q 008442           84 ATKNCPWVGELW-----------------------------------VRSLLSLERSRASEEEISTVFEKSLLCAFSTFE  128 (565)
Q Consensus        84 Al~~~p~~~~lW-----------------------------------~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~  128 (565)
                      .+..++.+...+                                   ...|..+. ..+.++++..+|+.. ......|.
T Consensus       481 m~~~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~-k~G~~~~A~~~f~~~-~~d~~s~n  558 (857)
T PLN03077        481 MLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYV-RCGRMNYAWNQFNSH-EKDVVSWN  558 (857)
T ss_pred             HHhCCCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceechHHHHHHH-HcCCHHHHHHHHHhc-CCChhhHH
Confidence            654432111111                                   11122122 246667777777665 21111233


Q ss_pred             HHHHHHHHHHHHHHH-----HhhccccchhhhhHHHHH------HHHHHHHHHHHhhhc--CCchhHHHHHHHHHHHHHc
Q 008442          129 EYLDLFLTRIDGLRR-----RILFSGEVEGVLDYSLIR------ETFQRASDYLSEQMK--NTDGLLRLYAYWAHLEQSM  195 (565)
Q Consensus       129 ~~~~~~~~~~~~~~r-----~~~~~~~~e~~~~~~~~~------~~~~~a~~~l~~~~~--~~~~~~~l~~~~a~~e~~~  195 (565)
                      ..+..+.........     .+...+..-+...+..+.      ..++++..++.....  ...+....+...+++..+.
T Consensus       559 ~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~~~~y~~lv~~l~r~  638 (857)
T PLN03077        559 ILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRA  638 (857)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHhC
Confidence            333222111000000     000000000000111111      234555565554331  2334456677888999999


Q ss_pred             CCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHH
Q 008442          196 GKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDH  275 (565)
Q Consensus       196 ~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~  275 (565)
                      | .+++|.++++++-  ...+..+|...+.-...+++.+.+....++++. ..+. .+ ..+......--..|..+++.+
T Consensus       639 G-~~~eA~~~~~~m~--~~pd~~~~~aLl~ac~~~~~~e~~e~~a~~l~~-l~p~-~~-~~y~ll~n~ya~~g~~~~a~~  712 (857)
T PLN03077        639 G-KLTEAYNFINKMP--ITPDPAVWGALLNACRIHRHVELGELAAQHIFE-LDPN-SV-GYYILLCNLYADAGKWDEVAR  712 (857)
T ss_pred             C-CHHHHHHHHHHCC--CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHh-hCCC-Cc-chHHHHHHHHHHCCChHHHHH
Confidence            9 9999999998762  233478999999988899999999998888876 2222 22 222222233345576665553

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=97.50  E-value=0.071  Score=55.73  Aligned_cols=199  Identities=17%  Similarity=0.130  Sum_probs=119.2

Q ss_pred             CCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHH
Q 008442           37 GDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVF  116 (565)
Q Consensus        37 ~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if  116 (565)
                      |+.+.+...-.+++...+.+.-.|.-|.- +.+..+..+.+...|..|++.-|.+.+||-.... |..+.++.+-....-
T Consensus        55 g~~~ea~~~vr~glr~d~~S~vCwHv~gl-~~R~dK~Y~eaiKcy~nAl~~~~dN~qilrDlsl-LQ~QmRd~~~~~~tr  132 (700)
T KOG1156|consen   55 GKKEEAYELVRLGLRNDLKSHVCWHVLGL-LQRSDKKYDEAIKCYRNALKIEKDNLQILRDLSL-LQIQMRDYEGYLETR  132 (700)
T ss_pred             cchHHHHHHHHHHhccCcccchhHHHHHH-HHhhhhhHHHHHHHHHHHHhcCCCcHHHHHHHHH-HHHHHHhhhhHHHHH
Confidence            55667777778888888888888888876 4455667778888889998888888888877543 555555555444444


Q ss_pred             HHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcC----Cch----hHHHHHHH
Q 008442          117 EKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKN----TDG----LLRLYAYW  188 (565)
Q Consensus       117 ~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~----~~~----~~~l~~~~  188 (565)
                      .+.++-.+..-..|+.+....       .              +...+..|...+..+...    .++    ...+.++-
T Consensus       133 ~~LLql~~~~ra~w~~~Avs~-------~--------------L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~  191 (700)
T KOG1156|consen  133 NQLLQLRPSQRASWIGFAVAQ-------H--------------LLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQ  191 (700)
T ss_pred             HHHHHhhhhhHHHHHHHHHHH-------H--------------HHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHH
Confidence            444443322111122221111       1              112222222222221111    111    11222333


Q ss_pred             HHHHHHcCCChHHHHHHHHHHHHH---ccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHH
Q 008442          189 AHLEQSMGKDMVSARGVWERLLKI---SGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFER  265 (565)
Q Consensus       189 a~~e~~~~~~~~~ar~i~e~~l~~---~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~  265 (565)
                      .++..+.+ ..+.   .++.....   .-+...+-..-++++...++++.|..+|...+.+      .++-+..|..++.
T Consensus       192 n~i~~E~g-~~q~---ale~L~~~e~~i~Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~r------nPdn~~Yy~~l~~  261 (700)
T KOG1156|consen  192 NQILIEAG-SLQK---ALEHLLDNEKQIVDKLAFEETKADLLMKLGQLEEAVKVYRRLLER------NPDNLDYYEGLEK  261 (700)
T ss_pred             HHHHHHcc-cHHH---HHHHHHhhhhHHHHHHHHhhhHHHHHHHHhhHHhHHHHHHHHHhh------CchhHHHHHHHHH
Confidence            44455555 4333   44444433   3344667778888999999999999999999974      2367788888888


Q ss_pred             HhC
Q 008442          266 EYG  268 (565)
Q Consensus       266 ~~G  268 (565)
                      ..|
T Consensus       262 ~lg  264 (700)
T KOG1156|consen  262 ALG  264 (700)
T ss_pred             HHH
Confidence            888

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.49  E-value=0.0019  Score=56.25  Aligned_cols=91  Identities=9%  Similarity=-0.065  Sum_probs=78.7

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (565)
                      +...|..++...|.    +...|..........|+.+.+...|++++...|.++..|......+.. .+..+.+...|++
T Consensus        43 A~~~~~~al~~~P~----~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~~~~a~~~lg~~l~~-~g~~~eAi~~~~~  117 (144)
T PRK15359         43 AVIDFSWLVMAQPW----SWRAHIALAGTWMMLKEYTTAINFYGHALMLDASHPEPVYQTGVCLKM-MGEPGLAREAFQT  117 (144)
T ss_pred             HHHHHHHHHHcCCC----cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHH-cCCHHHHHHHHHH
Confidence            55667778877777    889999999999999999999999999999999999999998875554 4578889999999


Q ss_pred             HHHcCCCCHHHHHHHH
Q 008442           84 ATKNCPWVGELWVRSL   99 (565)
Q Consensus        84 Al~~~p~~~~lW~~yi   99 (565)
                      |+..+|.....|...-
T Consensus       118 Al~~~p~~~~~~~~~~  133 (144)
T PRK15359        118 AIKMSYADASWSEIRQ  133 (144)
T ss_pred             HHHhCCCChHHHHHHH
Confidence            9999999988885543

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=97.48  E-value=9.8e-05  Score=65.62  Aligned_cols=65  Identities=22%  Similarity=0.374  Sum_probs=52.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCccc
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMF  457 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~  457 (565)
                      +-..||||.||..++++++|+.+|+.|.....++|...  .|.  +.|||+|++.+.|..|+. ++|..|
T Consensus       208 ~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~g~--~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  208 RACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--GGM--PVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--CCc--ceEeecHHHHHHHHHHHHHhhccee
Confidence            44579999999999999999999999976655555331  343  699999999999999997 777654

>smart00386 HAT HAT (Half-A-TPR) repeats

Probab=97.46  E-value=0.00021  Score=44.28  Aligned_cols=31  Identities=32%  Similarity=0.527  Sum_probs=27.8

Q ss_pred             ChHHHHHHHHHHHHHccchHHHHHHHHHHHH
Q 008442          198 DMVSARGVWERLLKISGAMLEAWQSYISMEI  228 (565)
Q Consensus       198 ~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~  228 (565)
                      +++.||.+|++++..+|.+..+|+.|++|+.
T Consensus         2 ~~~~~r~i~e~~l~~~~~~~~~W~~y~~~e~   32 (33)
T smart00386        2 DIERARKIYERALEKFPKSVELWLKYAEFEE   32 (33)
T ss_pred             cHHHHHHHHHHHHHHCCCChHHHHHHHHHHh
Confidence            6788999999999999988999999999985

Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.44  E-value=0.0054  Score=67.08  Aligned_cols=114  Identities=13%  Similarity=0.024  Sum_probs=92.5

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (565)
                      +...++.++.-.|.    +..++..|+.-..+.+.++++...++++|...|.+...-..++..+... +..+.+..+|++
T Consensus       105 a~~~l~~~~~~~Pd----~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~p~~~~~~~~~a~~l~~~-g~~~~A~~~y~~  179 (694)
T PRK15179        105 GLAVWRGIHQRFPD----SSEAFILMLRGVKRQQGIEAGRAEIELYFSGGSSSAREILLEAKSWDEI-GQSEQADACFER  179 (694)
T ss_pred             HHHHHHHHHhhCCC----cHHHHHHHHHHHHHhccHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHh-cchHHHHHHHHH
Confidence            55667777777776    8888999999888888889999999999999999998888888766543 467789999999


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcc
Q 008442           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA  123 (565)
Q Consensus        84 Al~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~  123 (565)
                      ++...|.....|..|...|. ..+..+++...|++|+...
T Consensus       180 ~~~~~p~~~~~~~~~a~~l~-~~G~~~~A~~~~~~a~~~~  218 (694)
T PRK15179        180 LSRQHPEFENGYVGWAQSLT-RRGALWRARDVLQAGLDAI  218 (694)
T ss_pred             HHhcCCCcHHHHHHHHHHHH-HcCCHHHHHHHHHHHHHhh
Confidence            99877888889999887444 4688889999999998643

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=97.42  E-value=0.00047  Score=66.90  Aligned_cols=75  Identities=25%  Similarity=0.338  Sum_probs=67.6

Q ss_pred             CCeEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          391 ECTAFLSNINLK-ATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       391 ~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      ++.|.|.||... +|.+.|..+|..||.|..|.|..++.     --|.|.+.+...|+-|+. ++|..+.|++|+|.+++
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            689999999766 89999999999999999999988652     479999999999999998 89999999999999986


Q ss_pred             CC
Q 008442          469 PK  470 (565)
Q Consensus       469 ~~  470 (565)
                      -.
T Consensus       372 H~  373 (492)
T KOG1190|consen  372 HT  373 (492)
T ss_pred             Cc
Confidence            43

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=97.31  E-value=0.00076  Score=60.74  Aligned_cols=76  Identities=24%  Similarity=0.390  Sum_probs=64.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccC-CeEEEEe
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFL-GKKLSIA  465 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~-g~~l~v~  465 (565)
                      ...+..+|+.|||..++.+.+..+|.+|+.-..|+++..+     ++.|||+|.+...+..|.. +++..+- ...|.|.
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            3567899999999999999999999999999999997654     4899999999988888887 7777765 7778887


Q ss_pred             ecC
Q 008442          466 RSN  468 (565)
Q Consensus       466 ~a~  468 (565)
                      ++.
T Consensus       218 ~a~  220 (221)
T KOG4206|consen  218 FAK  220 (221)
T ss_pred             ccC
Confidence            654

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=97.30  E-value=0.014  Score=64.83  Aligned_cols=177  Identities=15%  Similarity=0.101  Sum_probs=108.0

Q ss_pred             HHHHHHhc--CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 008442           45 LYERAITD--FPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLC  122 (565)
Q Consensus        45 lyERal~~--~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~  122 (565)
                      .|-|+...  .|.+.+.|...+... ...+..+.+..+++.++...|....+|..... +..+.+.....-.+  +++..
T Consensus        17 ~~~r~~~~~~~p~n~~a~~~Li~~~-~~~~~~deai~i~~~~l~~~P~~i~~yy~~G~-l~~q~~~~~~~~lv--~~l~~   92 (906)
T PRK14720         17 KWTRADANNYSLSKFKELDDLIDAY-KSENLTDEAKDICEEHLKEHKKSISALYISGI-LSLSRRPLNDSNLL--NLIDS   92 (906)
T ss_pred             hhhhcccccCCcchHHHHHHHHHHH-HhcCCHHHHHHHHHHHHHhCCcceehHHHHHH-HHHhhcchhhhhhh--hhhhh
Confidence            45565444  477888999988744 34457888999999999999988777655433 33333333333333  33332


Q ss_pred             ccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHH
Q 008442          123 AFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSA  202 (565)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~a  202 (565)
                      ....                            .++..+...+..-..+.        ..-.....++..+.+.+ +.++|
T Consensus        93 ~~~~----------------------------~~~~~ve~~~~~i~~~~--------~~k~Al~~LA~~Ydk~g-~~~ka  135 (906)
T PRK14720         93 FSQN----------------------------LKWAIVEHICDKILLYG--------ENKLALRTLAEAYAKLN-ENKKL  135 (906)
T ss_pred             cccc----------------------------cchhHHHHHHHHHHhhh--------hhhHHHHHHHHHHHHcC-ChHHH
Confidence            1110                            01111111111001111        11113334566667777 89999


Q ss_pred             HHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHH
Q 008442          203 RGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRF  263 (565)
Q Consensus       203 r~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~f  263 (565)
                      ..+|+++|+..|+++.+-..|+-+.... ++++|..++.+|+...........+...|..+
T Consensus       136 ~~~yer~L~~D~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV~~~i~~kq~~~~~e~W~k~  195 (906)
T PRK14720        136 KGVWERLVKADRDNPEIVKKLATSYEEE-DKEKAITYLKKAIYRFIKKKQYVGIEEIWSKL  195 (906)
T ss_pred             HHHHHHHHhcCcccHHHHHHHHHHHHHh-hHHHHHHHHHHHHHHHHhhhcchHHHHHHHHH
Confidence            9999999999999999999999988777 99999999999987544333344444444443

>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=97.29  E-value=0.00081  Score=54.54  Aligned_cols=70  Identities=23%  Similarity=0.346  Sum_probs=42.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-c--C---CcccCCeEEEE
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-K--N---KQMFLGKKLSI  464 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~--~---~~~~~g~~l~v  464 (565)
                      ++.|.|.+++..++.++|+..|+.||.|..|.+...    .  .-|||-|.+++.|+.|+. +  .   +..|.+..+.+
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G----~--~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~   74 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG----D--TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTL   74 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEE
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC----C--CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEE
Confidence            367889999999999999999999999999988543    2  389999999999999986 3  3   34566666555


Q ss_pred             ee
Q 008442          465 AR  466 (565)
Q Consensus       465 ~~  466 (565)
                      ..
T Consensus        75 ~v   76 (105)
T PF08777_consen   75 EV   76 (105)
T ss_dssp             E-
T ss_pred             EE
Confidence            44

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=97.27  E-value=0.00061  Score=61.89  Aligned_cols=72  Identities=21%  Similarity=0.473  Sum_probs=62.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      .....+.++|.+++..+.+.+|...|.++|.+....+        .++++||+|...+++..|+. +++..+.|+.|.+.
T Consensus        95 p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~  166 (216)
T KOG0106|consen   95 PSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVE  166 (216)
T ss_pred             cccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeeec
Confidence            3466799999999999999999999999999844333        35799999999999999998 79999999999993


Q ss_pred             e
Q 008442          466 R  466 (565)
Q Consensus       466 ~  466 (565)
                      .
T Consensus       167 ~  167 (216)
T KOG0106|consen  167 K  167 (216)
T ss_pred             c
Confidence            3

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=97.22  E-value=0.0063  Score=52.10  Aligned_cols=67  Identities=9%  Similarity=-0.054  Sum_probs=55.4

Q ss_pred             CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          178 TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       178 ~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      .+....+|...+.+....+ +++.|..+|++++...|+...+|.....+....|+.+.|...|++++.
T Consensus        47 ~p~~~~~~~~la~~~~~~~-~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  113 (135)
T TIGR02552        47 DPYNSRYWLGLAACCQMLK-EYEEAIDAYALAAALDPDDPRPYFHAAECLLALGEPESALKALDLAIE  113 (135)
T ss_pred             CCCcHHHHHHHHHHHHHHH-HHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3445567777777777777 888999999999888888888888888888888999999999998886

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C

Probab=97.19  E-value=0.0085  Score=46.56  Aligned_cols=96  Identities=18%  Similarity=0.109  Sum_probs=73.9

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Q 008442           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER  104 (565)
Q Consensus        25 ~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~  104 (565)
                      .|...+......++.+.+..+|++++...|.+..+|..++..+... ++.+.+...|++++...|....+|......+..
T Consensus         2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (100)
T cd00189           2 ALLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKL-GKYEEALEDYEKALELDPDNAKAYYNLGLAYYK   80 (100)
T ss_pred             HHHHHHHHHHHHhcHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhCCCcchhHHHHHHHHHHH
Confidence            3555566666678899999999999999999988888887755543 467789999999999998887777776653333


Q ss_pred             hcCCHHHHHHHHHHHHhc
Q 008442          105 SRASEEEISTVFEKSLLC  122 (565)
Q Consensus       105 ~~~~~~~~~~if~ral~~  122 (565)
                       .++.+.+...|.+++..
T Consensus        81 -~~~~~~a~~~~~~~~~~   97 (100)
T cd00189          81 -LGKYEEALEAYEKALEL   97 (100)
T ss_pred             -HHhHHHHHHHHHHHHcc
Confidence             46677888888887753

>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals

Probab=97.18  E-value=0.12  Score=52.28  Aligned_cols=204  Identities=12%  Similarity=-0.088  Sum_probs=123.4

Q ss_pred             CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCC---HHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHH
Q 008442           54 PVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV---GELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEY  130 (565)
Q Consensus        54 p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~---~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~  130 (565)
                      |....-|...+.+... .+..+.....|.++.+..|.+   .+.+..... +....++.+.+..++++++...+.....+
T Consensus         3 p~~~~a~~~~a~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~-~~~~~g~~~~A~~~~~~~l~~~P~~~~a~   80 (355)
T cd05804           3 PDFALGHAAAALLLLL-GGERPAAAAKAAAAAQALAARATERERAHVEAL-SAWIAGDLPKALALLEQLLDDYPRDLLAL   80 (355)
T ss_pred             CccHHHHHHHHHHHHh-cCCcchHHHHHHHHHHHhccCCCHHHHHHHHHH-HHHHcCCHHHHHHHHHHHHHHCCCcHHHH
Confidence            4444444444443332 234555578888888877643   233332222 33446889999999999997655433211


Q ss_pred             HHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHH
Q 008442          131 LDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLL  210 (565)
Q Consensus       131 ~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l  210 (565)
                      .. -..+....    ....      ..    ....   ..+.......+.....+...+.+....| +++.|...+++++
T Consensus        81 ~~-~~~~~~~~----~~~~------~~----~~~~---~~l~~~~~~~~~~~~~~~~~a~~~~~~G-~~~~A~~~~~~al  141 (355)
T cd05804          81 KL-HLGAFGLG----DFSG------MR----DHVA---RVLPLWAPENPDYWYLLGMLAFGLEEAG-QYDRAEEAARRAL  141 (355)
T ss_pred             HH-hHHHHHhc----cccc------Cc----hhHH---HHHhccCcCCCCcHHHHHHHHHHHHHcC-CHHHHHHHHHHHH
Confidence            10 00110000    0000      11    1111   2221122223333334445566777778 9999999999999


Q ss_pred             HHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcH---HHHHHHHHHHHHhCCHHHHHHHHHHH
Q 008442          211 KISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSE---DICHAWLRFEREYGTLEDFDHSVQKV  280 (565)
Q Consensus       211 ~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~---~i~~~~~~fE~~~G~~~~~~~~~~k~  280 (565)
                      ...|++..++..++......|+++.|..++.+++.. .+. .+.   ..|..+..+....|+.+.+...++++
T Consensus       142 ~~~p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~-~~~-~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~  212 (355)
T cd05804         142 ELNPDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDT-WDC-SSMLRGHNWWHLALFYLERGDYEAALAIYDTH  212 (355)
T ss_pred             hhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhc-cCC-CcchhHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            999999889999999999999999999999999863 221 122   23445566777889999888887775

A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=97.17  E-value=0.0021  Score=47.80  Aligned_cols=68  Identities=16%  Similarity=0.082  Sum_probs=51.9

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCC
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCP   89 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p   89 (565)
                      +...|..........++++.+...|++||..+|.++.+|..........++....+...|++|+...|
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l~P   69 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKLDP   69 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHcCc
Confidence            45678888888888888888888888888888888888888776544433256778888888887655

...

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=97.15  E-value=0.014  Score=61.64  Aligned_cols=192  Identities=14%  Similarity=0.134  Sum_probs=109.9

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCC-CCHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCP-WVGELWVRSLL  100 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p-~~~~lW~~yi~  100 (565)
                      ....|..-|.+....|...++..+.-+-+. .|.++.+|....+++..        -..||+|....- .+..- .+|+.
T Consensus       423 rlemw~~vi~CY~~lg~~~kaeei~~q~le-k~~d~~lyc~LGDv~~d--------~s~yEkawElsn~~sarA-~r~~~  492 (777)
T KOG1128|consen  423 RLEMWDPVILCYLLLGQHGKAEEINRQELE-KDPDPRLYCLLGDVLHD--------PSLYEKAWELSNYISARA-QRSLA  492 (777)
T ss_pred             hHHHHHHHHHHHHHhcccchHHHHHHHHhc-CCCcchhHHHhhhhccC--------hHHHHHHHHHhhhhhHHH-HHhhc
Confidence            445566666655555555555444444444 55666666655554321        124444443211 01110 01110


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCch
Q 008442          101 SLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG  180 (565)
Q Consensus       101 ~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~  180 (565)
                      .+-..+.+++++...|++++...+.....|...=.+.+..              .++......|..|..       -.+.
T Consensus       493 ~~~~~~~~fs~~~~hle~sl~~nplq~~~wf~~G~~ALql--------------ek~q~av~aF~rcvt-------L~Pd  551 (777)
T KOG1128|consen  493 LLILSNKDFSEADKHLERSLEINPLQLGTWFGLGCAALQL--------------EKEQAAVKAFHRCVT-------LEPD  551 (777)
T ss_pred             cccccchhHHHHHHHHHHHhhcCccchhHHHhccHHHHHH--------------hhhHHHHHHHHHHhh-------cCCC
Confidence            0111245677777777777765443222221111111100              123333344444433       2344


Q ss_pred             hHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       181 ~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ...-|..++..+.+++ ...+|+..+..+++.+-.+..+|..|.-.....|+++.|.+.|.+.+.
T Consensus       552 ~~eaWnNls~ayi~~~-~k~ra~~~l~EAlKcn~~~w~iWENymlvsvdvge~eda~~A~~rll~  615 (777)
T KOG1128|consen  552 NAEAWNNLSTAYIRLK-KKKRAFRKLKEALKCNYQHWQIWENYMLVSVDVGEFEDAIKAYHRLLD  615 (777)
T ss_pred             chhhhhhhhHHHHHHh-hhHHHHHHHHHHhhcCCCCCeeeechhhhhhhcccHHHHHHHHHHHHH
Confidence            5567888888888888 888999999999998877899999999999999999999999999875

>PF02184 HAT: HAT (Half-A-TPR) repeat; InterPro: IPR003107 The HAT (Half A TPR) repeat has a repetitive pattern characterised by three aromatic residues with a conserved spacing

Probab=97.14  E-value=0.0005  Score=41.43  Aligned_cols=29  Identities=21%  Similarity=0.497  Sum_probs=20.0

Q ss_pred             chhHHHHHHHHHhcCCCCHHHHHHHHHHHH
Q 008442           39 PGRVQLLYERAITDFPVSSDLWLDYTQYLD   68 (565)
Q Consensus        39 ~~~~~~lyERal~~~p~~~~lW~~Y~~~l~   68 (565)
                      .++++.+|||.|... .++..|+.|++|.+
T Consensus         3 ~dRAR~IyeR~v~~h-p~~k~WikyAkFEe   31 (32)
T PF02184_consen    3 FDRARSIYERFVLVH-PEVKNWIKYAKFEE   31 (32)
T ss_pred             HHHHHHHHHHHHHhC-CCchHHHHHHHhhc
Confidence            467777777777766 34777777777653

They are structurally and sequentially similar to TPRs (tetratricopeptide repeats), though they lack the highly conserved alanine and glycine residues found in TPRs. The number of HAT repeats found in different proteins varies between 9 and 12. HAT-repeat-containing proteins appear to be components of macromolecular complexes that are required for RNA processing []. The repeats may be involved in protein-protein interactions. The HAT motif has striking structural similarities to HEAT repeats (IPR000357 from INTERPRO), being of a similar length and consisting of two short helices connected by a loop domain, as in HEAT repeats.; GO: 0006396 RNA processing, 0005622 intracellular

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=97.10  E-value=0.0015  Score=43.77  Aligned_cols=42  Identities=19%  Similarity=0.360  Sum_probs=36.7

Q ss_pred             HHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHH
Q 008442           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQ   65 (565)
Q Consensus        24 ~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~   65 (565)
                      ..|..+.......|+++++..+|+++|..+|.+.++|..++.
T Consensus         2 ~~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~~~a~~~La~   43 (44)
T PF13428_consen    2 AAWLALARAYRRLGQPDEAERLLRRALALDPDDPEAWRALAQ   43 (44)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCHHHHHHhhh
Confidence            468888888889999999999999999999999999988764

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.06  E-value=0.0027  Score=46.55  Aligned_cols=61  Identities=18%  Similarity=0.159  Sum_probs=49.1

Q ss_pred             HHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCC
Q 008442           30 LKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV   91 (565)
Q Consensus        30 i~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~   91 (565)
                      .......|+++.+..+|+++|...|.+.+.|..+...+.. .+..+.+..+|++++...|.+
T Consensus         4 a~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~-~g~~~~A~~~~~~a~~~~P~~   64 (65)
T PF13432_consen    4 ARALYQQGDYDEAIAAFEQALKQDPDNPEAWYLLGRILYQ-QGRYDEALAYYERALELDPDN   64 (65)
T ss_dssp             HHHHHHCTHHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHSTT-
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHHCcCC
Confidence            4445667888999999999999999999999999886664 447777889999999988865

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.06  E-value=0.0023  Score=46.93  Aligned_cols=56  Identities=25%  Similarity=0.264  Sum_probs=50.8

Q ss_pred             HHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          189 AHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       189 a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      +......+ +++.|..+|+.++..+|++..+|..+..+....|+++.|...|++++.
T Consensus         4 a~~~~~~g-~~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~   59 (65)
T PF13432_consen    4 ARALYQQG-DYDEAIAAFEQALKQDPDNPEAWYLLGRILYQQGRYDEALAYYERALE   59 (65)
T ss_dssp             HHHHHHCT-HHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHcC-CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            45566777 999999999999999999999999999999999999999999999987

>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]

Probab=97.04  E-value=0.34  Score=46.74  Aligned_cols=228  Identities=15%  Similarity=0.127  Sum_probs=131.1

Q ss_pred             hHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHH--HHHHH---HHHHHHhcchhhHHHHHHHHHHHcCCCC-HH
Q 008442           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSD--LWLDY---TQYLDKTLKVGNVVRDVYSRATKNCPWV-GE   93 (565)
Q Consensus        20 ~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~--lW~~Y---~~~l~~~~~~~~~~~~v~erAl~~~p~~-~~   93 (565)
                      ++.++.-....++-..-|..+++..+.+-.+..--...+  +-..+   =+|+.  .+-.+++..+|..-+.. |.. ..
T Consensus        66 ~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~--aGl~DRAE~~f~~L~de-~efa~~  142 (389)
T COG2956          66 PETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMA--AGLLDRAEDIFNQLVDE-GEFAEG  142 (389)
T ss_pred             chhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHH--hhhhhHHHHHHHHHhcc-hhhhHH
Confidence            346777777777777778888988887766544222221  11111   11211  11234455555444331 111 11


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHh
Q 008442           94 LWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSE  173 (565)
Q Consensus        94 lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~  173 (565)
                      --...+. +-....+.+++.++-++..+.....+...|.  ..||+..              .-....+.+++|+..+.+
T Consensus       143 AlqqLl~-IYQ~treW~KAId~A~~L~k~~~q~~~~eIA--qfyCELA--------------q~~~~~~~~d~A~~~l~k  205 (389)
T COG2956         143 ALQQLLN-IYQATREWEKAIDVAERLVKLGGQTYRVEIA--QFYCELA--------------QQALASSDVDRARELLKK  205 (389)
T ss_pred             HHHHHHH-HHHHhhHHHHHHHHHHHHHHcCCccchhHHH--HHHHHHH--------------HHHhhhhhHHHHHHHHHH
Confidence            1111111 2122334444555544444444333333333  3333322              112333556667777777


Q ss_pred             hhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchH-HHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCC
Q 008442          174 QMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAML-EAWQSYISMEIELDHINEARSIYKRCYSKRFTGTG  252 (565)
Q Consensus       174 ~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~-~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~  252 (565)
                      ++..++.+.+.-+...+++...| ++..|-+.|+++++.+|... ++-......+...|.++.....+.+++.. +  ..
T Consensus       206 Alqa~~~cvRAsi~lG~v~~~~g-~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~-~--~g  281 (389)
T COG2956         206 ALQADKKCVRASIILGRVELAKG-DYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMET-N--TG  281 (389)
T ss_pred             HHhhCccceehhhhhhHHHHhcc-chHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHc-c--CC
Confidence            77767777788888899999999 99999999999999999875 45566666778899999999999999873 2  23


Q ss_pred             cHHHHHHHHHHHHHhCCHH
Q 008442          253 SEDICHAWLRFEREYGTLE  271 (565)
Q Consensus       253 ~~~i~~~~~~fE~~~G~~~  271 (565)
                      ++.+...+--.|...|..+
T Consensus       282 ~~~~l~l~~lie~~~G~~~  300 (389)
T COG2956         282 ADAELMLADLIELQEGIDA  300 (389)
T ss_pred             ccHHHHHHHHHHHhhChHH
Confidence            4344444444555666444

>KOG2003 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.01  E-value=0.25  Score=49.48  Aligned_cols=228  Identities=14%  Similarity=0.085  Sum_probs=120.9

Q ss_pred             hcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHH
Q 008442           35 SSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEIST  114 (565)
Q Consensus        35 ~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~  114 (565)
                      -+|+.+++...|..||.....+.+....-. ...+..++.+.+++.|-+.-..+-.+.++...-....|. ..+..++.+
T Consensus       502 ~ngd~dka~~~ykeal~ndasc~ealfnig-lt~e~~~~ldeald~f~klh~il~nn~evl~qianiye~-led~aqaie  579 (840)
T KOG2003|consen  502 ANGDLDKAAEFYKEALNNDASCTEALFNIG-LTAEALGNLDEALDCFLKLHAILLNNAEVLVQIANIYEL-LEDPAQAIE  579 (840)
T ss_pred             ecCcHHHHHHHHHHHHcCchHHHHHHHHhc-ccHHHhcCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH-hhCHHHHHH
Confidence            457788888888888876544444222111 112233456667776666554444455555554443444 334455667


Q ss_pred             HHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHH
Q 008442          115 VFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQS  194 (565)
Q Consensus       115 if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~  194 (565)
                      ++-++.+..+.....+..+-..|-.        +.      |-.   .+|+-..+    .+...+...+...+++.++..
T Consensus       580 ~~~q~~slip~dp~ilskl~dlydq--------eg------dks---qafq~~yd----syryfp~nie~iewl~ayyid  638 (840)
T KOG2003|consen  580 LLMQANSLIPNDPAILSKLADLYDQ--------EG------DKS---QAFQCHYD----SYRYFPCNIETIEWLAAYYID  638 (840)
T ss_pred             HHHHhcccCCCCHHHHHHHHHHhhc--------cc------chh---hhhhhhhh----cccccCcchHHHHHHHHHHHh
Confidence            7777766444433333333322210        00      111   22221111    112223333444444444433


Q ss_pred             cCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhC--CHHH
Q 008442          195 MGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYG--TLED  272 (565)
Q Consensus       195 ~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G--~~~~  272 (565)
                      .. =.+++..+|+++.-.-|+....-+--+...++.|++++|-.+|+..-. .|+.+  .+.+...+.+.-..|  +...
T Consensus       639 tq-f~ekai~y~ekaaliqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hr-kfped--ldclkflvri~~dlgl~d~ke  714 (840)
T KOG2003|consen  639 TQ-FSEKAINYFEKAALIQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHR-KFPED--LDCLKFLVRIAGDLGLKDAKE  714 (840)
T ss_pred             hH-HHHHHHHHHHHHHhcCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHH-hCccc--hHHHHHHHHHhccccchhHHH
Confidence            32 356888999999888777554445555677889999999999998855 45543  244555666665555  3334


Q ss_pred             HHHHHHHHhhHHHHHHHH
Q 008442          273 FDHSVQKVTPRLEELRLF  290 (565)
Q Consensus       273 ~~~~~~k~~~~~~~~~~~  290 (565)
                      +..-++++ .++.+++++
T Consensus       715 y~~klek~-eki~eir~q  731 (840)
T KOG2003|consen  715 YADKLEKA-EKIKEIREQ  731 (840)
T ss_pred             HHHHHHHH-HHHHHHHHH
Confidence            44455554 445555543

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=97.00  E-value=0.034  Score=53.69  Aligned_cols=78  Identities=24%  Similarity=0.222  Sum_probs=62.1

Q ss_pred             CCCCeEEEc--CCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCC--eEEE
Q 008442          389 TDECTAFLS--NINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLG--KKLS  463 (565)
Q Consensus       389 ~~~~~l~V~--nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g--~~l~  463 (565)
                      ..+.-|.++  |--+.+|.+-|..+...+|.|..|.|...  +|.   -|.|+|++.+.|++|.. |||..|..  -.|+
T Consensus       118 ~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ngV---QAmVEFdsv~~AqrAk~alNGADIYsGCCTLK  192 (494)
T KOG1456|consen  118 TPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NGV---QAMVEFDSVEVAQRAKAALNGADIYSGCCTLK  192 (494)
T ss_pred             CCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cce---eeEEeechhHHHHHHHhhcccccccccceeEE
Confidence            344555554  44456889999999999999999988774  554   69999999999999998 89998753  3789


Q ss_pred             EeecCCCC
Q 008442          464 IARSNPKQ  471 (565)
Q Consensus       464 v~~a~~~~  471 (565)
                      |++|+|.+
T Consensus       193 IeyAkP~r  200 (494)
T KOG1456|consen  193 IEYAKPTR  200 (494)
T ss_pred             EEecCcce
Confidence            99998864

>KOG2003 consensus TPR repeat-containing protein [General function prediction only]

Probab=96.97  E-value=0.43  Score=47.86  Aligned_cols=191  Identities=14%  Similarity=0.038  Sum_probs=117.4

Q ss_pred             HHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHH-HHHHHHHHHHHhcCC
Q 008442           30 LKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGE-LWVRSLLSLERSRAS  108 (565)
Q Consensus        30 i~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~-lW~~yi~~le~~~~~  108 (565)
                      +.|..-..++..+...-..||...-.+...-..-..... -+++.+.+.+.|..||.+-..+.+ |+.-=+ ..+. .++
T Consensus       463 l~flqggk~~~~aqqyad~aln~dryn~~a~~nkgn~~f-~ngd~dka~~~ykeal~ndasc~ealfnigl-t~e~-~~~  539 (840)
T KOG2003|consen  463 LRFLQGGKDFADAQQYADIALNIDRYNAAALTNKGNIAF-ANGDLDKAAEFYKEALNNDASCTEALFNIGL-TAEA-LGN  539 (840)
T ss_pred             HHHHhcccchhHHHHHHHHHhcccccCHHHhhcCCceee-ecCcHHHHHHHHHHHHcCchHHHHHHHHhcc-cHHH-hcC
Confidence            333333345666777777787766556554443322222 234778899999999997654443 332222 2333 577


Q ss_pred             HHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHH
Q 008442          109 EEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYW  188 (565)
Q Consensus       109 ~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~  188 (565)
                      ++++.+.|-+.--........++.+...|-                     +.+.-.+|++++.+.....+....+...+
T Consensus       540 ldeald~f~klh~il~nn~evl~qianiye---------------------~led~aqaie~~~q~~slip~dp~ilskl  598 (840)
T KOG2003|consen  540 LDEALDCFLKLHAILLNNAEVLVQIANIYE---------------------LLEDPAQAIELLMQANSLIPNDPAILSKL  598 (840)
T ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHH---------------------HhhCHHHHHHHHHHhcccCCCCHHHHHHH
Confidence            888888887743322233333333333221                     11223345666665555445556788899


Q ss_pred             HHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          189 AHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       189 a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ++++.+-| +...|-.++-.....+|.+.+...=.+.|+....-.+++...|++|..
T Consensus       599 ~dlydqeg-dksqafq~~ydsyryfp~nie~iewl~ayyidtqf~ekai~y~ekaal  654 (840)
T KOG2003|consen  599 ADLYDQEG-DKSQAFQCHYDSYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAAL  654 (840)
T ss_pred             HHHhhccc-chhhhhhhhhhcccccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHh
Confidence            99999988 999999999888888999877533334445555557888899999843

>smart00777 Mad3_BUB1_I Mad3/BUB1 hoMad3/BUB1 homology region 1

Probab=96.96  E-value=0.012  Score=49.11  Aligned_cols=76  Identities=14%  Similarity=0.260  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHHH--hhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH-c-cchHHHHHHHHHHHHHcCChHHH
Q 008442          161 RETFQRASDYLS--EQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI-S-GAMLEAWQSYISMEIELDHINEA  236 (565)
Q Consensus       161 ~~~~~~a~~~l~--~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~-~-~~~~~lw~~yi~~e~~~~~~~~a  236 (565)
                      ..++++|+..+.  ....+.+.++++|+.|+++-   . +   .+++|..+... . .....+|..|+.+....|++..|
T Consensus        46 ~~lLerc~~~f~~~~~YknD~RyLkiWi~ya~~~---~-d---p~~if~~L~~~~IG~~~AlfYe~~A~~lE~~g~~~~A  118 (125)
T smart00777       46 LTLLERCIRYFEDDERYKNDPRYLKIWLKYADNC---D-E---PRELFQFLYSKGIGTKLALFYEEWAQLLEAAGRYKKA  118 (125)
T ss_pred             HHHHHHHHHHhhhhhhhcCCHHHHHHHHHHHHhc---C-C---HHHHHHHHHHCCcchhhHHHHHHHHHHHHHcCCHHHH
Confidence            345555555542  23445666788999988652   2 3   67899888876 3 34577999999999999999999


Q ss_pred             HHHHHHH
Q 008442          237 RSIYKRC  243 (565)
Q Consensus       237 R~i~~~a  243 (565)
                      .+||+.+
T Consensus       119 ~~iy~~G  125 (125)
T smart00777      119 DEVYQLG  125 (125)
T ss_pred             HHHHHcc
Confidence            9999863

Proteins containing this domain are checkpoint proteins involved in cell division. This region has been shown to be essential for the binding of the binding of BUB1 and MAD3 to CDC20p.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.93  E-value=0.0025  Score=62.50  Aligned_cols=64  Identities=28%  Similarity=0.378  Sum_probs=53.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeec---CCC--CCc--------ceEEEEEecCHHHHHHHHHc
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHD---KFT--GKS--------RGLAYVDFIDDEHLAAAVAK  452 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~---~~~--g~~--------~g~afv~f~~~~~a~~a~~~  452 (565)
                      ...+||.+-|||.+-.-+.|.++|+.||.|..|+|...   +.+  |.+        +-+|+|+|...+.|.+|.++
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~  305 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAREL  305 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHh
Confidence            34689999999999888999999999999999999765   222  222        45899999999999999984

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=96.92  E-value=0.25  Score=49.06  Aligned_cols=251  Identities=10%  Similarity=-0.029  Sum_probs=128.0

Q ss_pred             hHHHHHHHHHHHHhc-CCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSS-GDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~-~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~  100 (565)
                      ....|..-..+.-.. ........++-.-....|.++.|-...++.+...+ +...+...|+.+....|..-.---.|..
T Consensus       196 wls~wika~Aq~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~G-dn~~a~~~Fe~~~~~dpy~i~~MD~Ya~  274 (564)
T KOG1174|consen  196 WLSKWIKALAQMFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNG-DYFQAEDIFSSTLCANPDNVEAMDLYAV  274 (564)
T ss_pred             HHHHHHHHHHHHHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhc-CchHHHHHHHHHhhCChhhhhhHHHHHH
Confidence            445666544443322 22334456677777889999999999988666555 5556889999999888865544445554


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcccc---cHHHHH-HHH-----HHHHHHHHHHhh-ccccchhhhhHHH-HH--HHHHHH
Q 008442          101 SLERSRASEEEISTVFEKSLLCAFS---TFEEYL-DLF-----LTRIDGLRRRIL-FSGEVEGVLDYSL-IR--ETFQRA  167 (565)
Q Consensus       101 ~le~~~~~~~~~~~if~ral~~~~~---~~~~~~-~~~-----~~~~~~~~r~~~-~~~~~e~~~~~~~-~~--~~~~~a  167 (565)
                      .| ...+..+.+..+..+.+....-   .|-... -+|     ..-+.+....+. ..+.++.++--.. ++  .-.++|
T Consensus       275 LL-~~eg~~e~~~~L~~~Lf~~~~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~~r~~~alilKG~lL~~~~R~~~A  353 (564)
T KOG1174|consen  275 LL-GQEGGCEQDSALMDYLFAKVKYTASHWFVHAQLLYDEKKFERALNFVEKCIDSEPRNHEALILKGRLLIALERHTQA  353 (564)
T ss_pred             HH-HhccCHhhHHHHHHHHHhhhhcchhhhhhhhhhhhhhhhHHHHHHHHHHHhccCcccchHHHhccHHHHhccchHHH
Confidence            33 3357778877777776653211   111000 111     111112211111 1222222111000 11  112333


Q ss_pred             HHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHH---HHHHHHcCChHHHHHHHHHHH
Q 008442          168 SDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSY---ISMEIELDHINEARSIYKRCY  244 (565)
Q Consensus       168 ~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~y---i~~e~~~~~~~~aR~i~~~al  244 (565)
                      +-.+..+...-+.-++.|.-...-+.-.+ .+.+|-..-+.+++.+|.+.....-+   +-|+...+ -++|.++|++++
T Consensus       354 ~IaFR~Aq~Lap~rL~~Y~GL~hsYLA~~-~~kEA~~~An~~~~~~~~sA~~LtL~g~~V~~~dp~~-rEKAKkf~ek~L  431 (564)
T KOG1174|consen  354 VIAFRTAQMLAPYRLEIYRGLFHSYLAQK-RFKEANALANWTIRLFQNSARSLTLFGTLVLFPDPRM-REKAKKFAEKSL  431 (564)
T ss_pred             HHHHHHHHhcchhhHHHHHHHHHHHHhhc-hHHHHHHHHHHHHHHhhcchhhhhhhcceeeccCchh-HHHHHHHHHhhh
Confidence            33333222222222333433333333445 77888888888888877776543333   33433333 578999999998


Q ss_pred             hcccCCCCcHH--HHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          245 SKRFTGTGSED--ICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       245 ~~~~~~~~~~~--i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      ..  ..+....  ........|..+||   +-..+++++
T Consensus       432 ~~--~P~Y~~AV~~~AEL~~~Eg~~~D---~i~LLe~~L  465 (564)
T KOG1174|consen  432 KI--NPIYTPAVNLIAELCQVEGPTKD---IIKLLEKHL  465 (564)
T ss_pred             cc--CCccHHHHHHHHHHHHhhCccch---HHHHHHHHH
Confidence            74  2222222  22333444444444   444555554

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=96.91  E-value=0.0046  Score=45.75  Aligned_cols=49  Identities=18%  Similarity=0.151  Sum_probs=45.9

Q ss_pred             ChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhc
Q 008442          198 DMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       198 ~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~  246 (565)
                      +++.|..+|++++..+|++..+|+.++.+....|+++.|+.++++++..
T Consensus         6 ~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~   54 (68)
T PF14559_consen    6 DYDEAIELLEKALQRNPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQ   54 (68)
T ss_dssp             HHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG
T ss_pred             CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            8899999999999999999999999999999999999999999999873

...

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=96.88  E-value=0.5  Score=49.68  Aligned_cols=164  Identities=15%  Similarity=0.163  Sum_probs=104.1

Q ss_pred             HHHhcchhhHHHHHHHHHHHc--------CCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcc---cc-----cHHHH
Q 008442           67 LDKTLKVGNVVRDVYSRATKN--------CPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA---FS-----TFEEY  130 (565)
Q Consensus        67 l~~~~~~~~~~~~v~erAl~~--------~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~---~~-----~~~~~  130 (565)
                      .....+..+.+..+|++|++.        +|.....-..+.. +-+..+.+.++..+|++|+...   +.     ....+
T Consensus       208 ~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~-~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h~~va~~l  286 (508)
T KOG1840|consen  208 MYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILAL-VYRSLGKYDEAVNLYEEALTIREEVFGEDHPAVAATL  286 (508)
T ss_pred             HHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHH-HHHHhccHHHHHHHHHHHHHHHHHhcCCCCHHHHHHH
Confidence            334456778899999999986        3322222122222 3345678899999999999632   11     11122


Q ss_pred             HHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCch-hHHHHHHHHHHHHHcCCChHHHHHHHHHH
Q 008442          131 LDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG-LLRLYAYWAHLEQSMGKDMVSARGVWERL  209 (565)
Q Consensus       131 ~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~-~~~l~~~~a~~e~~~~~~~~~ar~i~e~~  209 (565)
                      ..+-..|+.       .       .++..++..++.|..+....+...++ ....+...+.+....+ .++.|..++.++
T Consensus       287 ~nLa~ly~~-------~-------GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~-~~Eea~~l~q~a  351 (508)
T KOG1840|consen  287 NNLAVLYYK-------Q-------GKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMN-EYEEAKKLLQKA  351 (508)
T ss_pred             HHHHHHHhc-------c-------CChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhc-chhHHHHHHHHH
Confidence            222222210       0       14556677778888877664433333 2334444555555555 899999999988


Q ss_pred             HHHc--------cchHHHHHHHHHHHHHcCChHHHHHHHHHHHhc
Q 008442          210 LKIS--------GAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       210 l~~~--------~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~  246 (565)
                      ++..        +.-..+...+..+....|.++.|+++|+.||++
T Consensus       352 l~i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~  396 (508)
T KOG1840|consen  352 LKIYLDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQI  396 (508)
T ss_pred             HHHHHhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHH
Confidence            8762        122457778888888999999999999999986

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=96.87  E-value=0.0032  Score=46.59  Aligned_cols=63  Identities=21%  Similarity=0.090  Sum_probs=51.6

Q ss_pred             hcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHH
Q 008442           35 SSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRS   98 (565)
Q Consensus        35 ~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~y   98 (565)
                      ..|+++.+..+|++++..+|.+.++|..++..+...+ ..+.+..++++++...|..+.+|...
T Consensus         3 ~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~g-~~~~A~~~l~~~~~~~~~~~~~~~l~   65 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQRNPDNPEARLLLAQCYLKQG-QYDEAEELLERLLKQDPDNPEYQQLL   65 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHTT--HHHHHHHHHCCHGGGTTHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHHCcCHHHHHHHH
Confidence            4678888999999999999999999999988766554 77889999999999988876666543

...

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.86  E-value=0.0029  Score=63.70  Aligned_cols=65  Identities=22%  Similarity=0.265  Sum_probs=59.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhc-cCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHc
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFS-DVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK  452 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~-~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~  452 (565)
                      ....+|||||+||.-++.++|..+|. -||.|..+.|=+|+.-+.++|-|=|+|.+..+-.+||..
T Consensus       367 lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  367 IDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            35578999999999999999999998 699999999999976788999999999999999999963

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=96.85  E-value=0.029  Score=56.86  Aligned_cols=94  Identities=19%  Similarity=0.045  Sum_probs=77.7

Q ss_pred             HHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCH
Q 008442           30 LKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASE  109 (565)
Q Consensus        30 i~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~  109 (565)
                      +.-....+++..+..+|++||...|.+..+|..++..+.. .+..+.+...|++|+...|.....|..... +....+.+
T Consensus         9 a~~a~~~~~~~~Ai~~~~~Al~~~P~~~~a~~~~a~~~~~-~g~~~eAl~~~~~Al~l~P~~~~a~~~lg~-~~~~lg~~   86 (356)
T PLN03088          9 AKEAFVDDDFALAVDLYTQAIDLDPNNAELYADRAQANIK-LGNFTEAVADANKAIELDPSLAKAYLRKGT-ACMKLEEY   86 (356)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHhCcCCHHHHHHHHH-HHHHhCCH
Confidence            3334557899999999999999999999999988876554 457788999999999999999888887765 33447889


Q ss_pred             HHHHHHHHHHHhcccc
Q 008442          110 EEISTVFEKSLLCAFS  125 (565)
Q Consensus       110 ~~~~~if~ral~~~~~  125 (565)
                      +.+...|++|+...+.
T Consensus        87 ~eA~~~~~~al~l~P~  102 (356)
T PLN03088         87 QTAKAALEKGASLAPG  102 (356)
T ss_pred             HHHHHHHHHHHHhCCC
Confidence            9999999999986654

>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala

Probab=96.85  E-value=0.85  Score=48.37  Aligned_cols=220  Identities=15%  Similarity=0.136  Sum_probs=134.9

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh----cchhhHHHHHHHHHHHcCCCCHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKT----LKVGNVVRDVYSRATKNCPWVGELWVR   97 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~----~~~~~~~~~v~erAl~~~p~~~~lW~~   97 (565)
                      .......-+++..+.|..+.+..+|...|..+|.+......|...+.-.    ....+...++|+.--...|.+..  ..
T Consensus        37 k~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNPdn~~Yy~~L~~~~g~~~~~~~~~~~~~~~~y~~l~~~yp~s~~--~~  114 (517)
T PF12569_consen   37 KLAVLEKRAELLLKLGRKEEAEKIYRELIDRNPDNYDYYRGLEEALGLQLQLSDEDVEKLLELYDELAEKYPRSDA--PR  114 (517)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHhCccccc--hh
Confidence            3444555566677889999999999999999999999888887765222    12345677888877777776532  22


Q ss_pred             HHHHHHHhc-CCHH-HHHHHHHHHHhcc-cccHHHH-------------HHHHHHHHHHHHHHhhcccc----ch--h--
Q 008442           98 SLLSLERSR-ASEE-EISTVFEKSLLCA-FSTFEEY-------------LDLFLTRIDGLRRRILFSGE----VE--G--  153 (565)
Q Consensus        98 yi~~le~~~-~~~~-~~~~if~ral~~~-~~~~~~~-------------~~~~~~~~~~~~r~~~~~~~----~e--~--  153 (565)
                      +|- |.... ..+. .+...+...+..+ ++.+...             ..+...+...+.........    .+  .  
T Consensus       115 rl~-L~~~~g~~F~~~~~~yl~~~l~KgvPslF~~lk~Ly~d~~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~  193 (517)
T PF12569_consen  115 RLP-LDFLEGDEFKERLDEYLRPQLRKGVPSLFSNLKPLYKDPEKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTL  193 (517)
T ss_pred             Hhh-cccCCHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHcChhHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHH
Confidence            221 11101 1111 1222222223221 1111111             12222222222111010000    00  0  


Q ss_pred             -h-----hhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHH
Q 008442          154 -V-----LDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISME  227 (565)
Q Consensus       154 -~-----~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e  227 (565)
                       +     ...-.....+++|+++++.++...|..+.++..-+++....| ++..|-..++.+-.....+--+=...+.+.
T Consensus       194 lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~~ely~~KarilKh~G-~~~~Aa~~~~~Ar~LD~~DRyiNsK~aKy~  272 (517)
T PF12569_consen  194 LWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPTLVELYMTKARILKHAG-DLKEAAEAMDEARELDLADRYINSKCAKYL  272 (517)
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHCC-CHHHHHHHHHHHHhCChhhHHHHHHHHHHH
Confidence             0     000111234578999999999888888999999999999999 999999999999987665555667788888


Q ss_pred             HHcCChHHHHHHHHHHHh
Q 008442          228 IELDHINEARSIYKRCYS  245 (565)
Q Consensus       228 ~~~~~~~~aR~i~~~al~  245 (565)
                      .+.|.++.|.+++.....
T Consensus       273 LRa~~~e~A~~~~~~Ftr  290 (517)
T PF12569_consen  273 LRAGRIEEAEKTASLFTR  290 (517)
T ss_pred             HHCCCHHHHHHHHHhhcC
Confidence            899999999999988854

N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=96.85  E-value=0.013  Score=50.93  Aligned_cols=71  Identities=23%  Similarity=0.410  Sum_probs=58.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCccc--CCeEEE
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMF--LGKKLS  463 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~--~g~~l~  463 (565)
                      .-+...+|.|++||++.++++|+.....-|.|+...+.+|       |.+.|+|...++..-|+. ++...+  .|-...
T Consensus       111 srrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~seGe~~y  183 (241)
T KOG0105|consen  111 SRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFRSEGETAY  183 (241)
T ss_pred             ccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhccccccCcCcEee
Confidence            3456789999999999999999999999999999998876       589999999999999997 655443  354433


Q ss_pred             E
Q 008442          464 I  464 (565)
Q Consensus       464 v  464 (565)
                      +
T Consensus       184 i  184 (241)
T KOG0105|consen  184 I  184 (241)
T ss_pred             E
Confidence            3

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=96.82  E-value=0.0082  Score=44.52  Aligned_cols=62  Identities=15%  Similarity=0.179  Sum_probs=56.2

Q ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcC-ChHHHHHHHHHHHh
Q 008442          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELD-HINEARSIYKRCYS  245 (565)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~-~~~~aR~i~~~al~  245 (565)
                      ..|...+......+ ++++|...|+++|..+|++..+|..........| +++.|.+.|++++.
T Consensus         4 ~~~~~~g~~~~~~~-~~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen    4 EAWYNLGQIYFQQG-DYEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcC-CHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence            45667777777878 9999999999999999999999999999999999 79999999999986

...

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.81  E-value=0.0027  Score=44.25  Aligned_cols=52  Identities=13%  Similarity=0.245  Sum_probs=41.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHH
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV  450 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~  450 (565)
                      +.|-|.|.|++.. +.+...|..||+|..+.+...      .-+.||.|.++.+|+.||
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            5788999997766 455558889999999888522      248999999999999885

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=96.80  E-value=0.0049  Score=49.12  Aligned_cols=77  Identities=14%  Similarity=0.167  Sum_probs=51.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEE-EeecC------CCCCcceEEEEEecCHHHHHHHHHcCCcccCCeE-E
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIR-ILHDK------FTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKK-L  462 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~-~~~~~------~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~-l  462 (565)
                      .+.|.|=+.|+. ....|-..|++||.|.+.. +..+.      ........-.|.|.++.+|.+||..||..+.|.- +
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~mv   84 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSLMV   84 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCEEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcEEE
Confidence            467888899988 5577888999999998764 10000      0011224889999999999999999999999874 4


Q ss_pred             EEeecC
Q 008442          463 SIARSN  468 (565)
Q Consensus       463 ~v~~a~  468 (565)
                      -|.+++
T Consensus        85 GV~~~~   90 (100)
T PF05172_consen   85 GVKPCD   90 (100)
T ss_dssp             EEEE-H
T ss_pred             EEEEcH
Confidence            466653

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.

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=96.73  E-value=0.3  Score=46.24  Aligned_cols=174  Identities=13%  Similarity=-0.030  Sum_probs=103.7

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHH---HHHHHHHHHHh-------cch
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDL---WLDYTQYLDKT-------LKV   73 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~l---W~~Y~~~l~~~-------~~~   73 (565)
                      +...|+..+...|. ++.....|..........++++.+...|++++...|.++.+   |..........       .+.
T Consensus        52 A~~~~~~~~~~~p~-~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~g~~~~~~~~~~~~~~~~  130 (235)
T TIGR03302        52 AIKYFEALESRYPF-SPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYLRGLSNYNQIDRVDRDQTA  130 (235)
T ss_pred             HHHHHHHHHHhCCC-chhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHHHHHHHHHHhcccccCCHHH
Confidence            56677787777764 22234577778888888899999999999999999988863   32222211111       134


Q ss_pred             hhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchh
Q 008442           74 GNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEG  153 (565)
Q Consensus        74 ~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~  153 (565)
                      .+.+...|++++...|.+...|..+.. +...       ........       ...-.++...                
T Consensus       131 ~~~A~~~~~~~~~~~p~~~~~~~a~~~-~~~~-------~~~~~~~~-------~~~a~~~~~~----------------  179 (235)
T TIGR03302       131 AREAFEAFQELIRRYPNSEYAPDAKKR-MDYL-------RNRLAGKE-------LYVARFYLKR----------------  179 (235)
T ss_pred             HHHHHHHHHHHHHHCCCChhHHHHHHH-HHHH-------HHHHHHHH-------HHHHHHHHHc----------------
Confidence            567899999999999988776655433 1110       00000000       0000011100                


Q ss_pred             hhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccc
Q 008442          154 VLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA  215 (565)
Q Consensus       154 ~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~  215 (565)
                       .++......|..++..+    .+.+.....+...+..+...+ +.++|..+++.+...+|+
T Consensus       180 -g~~~~A~~~~~~al~~~----p~~~~~~~a~~~l~~~~~~lg-~~~~A~~~~~~l~~~~~~  235 (235)
T TIGR03302       180 -GAYVAAINRFETVVENY----PDTPATEEALARLVEAYLKLG-LKDLAQDAAAVLGANYPD  235 (235)
T ss_pred             -CChHHHHHHHHHHHHHC----CCCcchHHHHHHHHHHHHHcC-CHHHHHHHHHHHHhhCCC
Confidence             02223333444333322    112334567777888888888 999999999988877663

Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=96.69  E-value=1.2  Score=47.90  Aligned_cols=88  Identities=10%  Similarity=0.084  Sum_probs=57.2

Q ss_pred             HHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHH--HHHHHHhcccCCCCcHHHHHHHHHHHHH
Q 008442          189 AHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARS--IYKRCYSKRFTGTGSEDICHAWLRFERE  266 (565)
Q Consensus       189 a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~--i~~~al~~~~~~~~~~~i~~~~~~fE~~  266 (565)
                      ..+....+ ...+|...|.-++..+|+++..-...+.+....|+...|-+  ++..++..  +.. ....|...-..-+.
T Consensus       691 G~~~~~~~-~~~EA~~af~~Al~ldP~hv~s~~Ala~~lle~G~~~la~~~~~L~dalr~--dp~-n~eaW~~LG~v~k~  766 (799)
T KOG4162|consen  691 GLLLEVKG-QLEEAKEAFLVALALDPDHVPSMTALAELLLELGSPRLAEKRSLLSDALRL--DPL-NHEAWYYLGEVFKK  766 (799)
T ss_pred             hHHHHHHH-hhHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCcchHHHHHHHHHHHhh--CCC-CHHHHHHHHHHHHH
Confidence            33444444 66677777777777778777777777777777776554444  77777752  222 33566666666667


Q ss_pred             hCCHHHHHHHHHHH
Q 008442          267 YGTLEDFDHSVQKV  280 (565)
Q Consensus       267 ~G~~~~~~~~~~k~  280 (565)
                      .|+.+.+.++++.+
T Consensus       767 ~Gd~~~Aaecf~aa  780 (799)
T KOG4162|consen  767 LGDSKQAAECFQAA  780 (799)
T ss_pred             ccchHHHHHHHHHH
Confidence            78777777676654

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=96.63  E-value=0.0057  Score=40.85  Aligned_cols=42  Identities=19%  Similarity=0.260  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHH
Q 008442          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYIS  225 (565)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~  225 (565)
                      ..|..++..+...| ++++|+.+|+++++.+|++..+|..+++
T Consensus         2 ~~~~~la~~~~~~G-~~~~A~~~~~~~l~~~P~~~~a~~~La~   43 (44)
T PF13428_consen    2 AAWLALARAYRRLG-QPDEAERLLRRALALDPDDPEAWRALAQ   43 (44)
T ss_pred             HHHHHHHHHHHHcC-CHHHHHHHHHHHHHHCcCCHHHHHHhhh
Confidence            35667888888888 8999999999999999998999888764

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.61  E-value=0.0047  Score=58.50  Aligned_cols=79  Identities=16%  Similarity=0.294  Sum_probs=60.4

Q ss_pred             CCCeEEEcCCCCCCCHHH------HHHHhccCCCeeEEEEeecCCCCC-cceEE--EEEecCHHHHHHHHH-cCCcccCC
Q 008442          390 DECTAFLSNINLKATYED------LRRFFSDVGGVSSIRILHDKFTGK-SRGLA--YVDFIDDEHLAAAVA-KNKQMFLG  459 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~------l~~~f~~~G~i~~~~~~~~~~~g~-~~g~a--fv~f~~~~~a~~a~~-~~~~~~~g  459 (565)
                      +..-+||-+||+.+..++      -.++|.+||.|..|.|-....+.. ..+.+  ||+|.+.++|..||. .+|..++|
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG  192 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG  192 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC
Confidence            446789999999887666      246899999999987754321111 12323  999999999999998 79999999


Q ss_pred             eEEEEeecC
Q 008442          460 KKLSIARSN  468 (565)
Q Consensus       460 ~~l~v~~a~  468 (565)
                      |.|+..+..
T Consensus       193 r~lkatYGT  201 (480)
T COG5175         193 RVLKATYGT  201 (480)
T ss_pred             ceEeeecCc
Confidence            999887754

>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C

Probab=96.59  E-value=0.041  Score=42.51  Aligned_cols=88  Identities=16%  Similarity=0.139  Sum_probs=55.3

Q ss_pred             HHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHh
Q 008442          188 WAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREY  267 (565)
Q Consensus       188 ~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~  267 (565)
                      .+..+...+ +++.|..++++++...|....+|..++......++++.|..+|++++.. .+.  ...++..+.......
T Consensus         6 ~a~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~-~~~--~~~~~~~~~~~~~~~   81 (100)
T cd00189           6 LGNLYYKLG-DYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKALEL-DPD--NAKAYYNLGLAYYKL   81 (100)
T ss_pred             HHHHHHHHh-cHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC-CCc--chhHHHHHHHHHHHH
Confidence            344444455 7778888888888877776777777777777778888888888888762 111  223444444444455


Q ss_pred             CCHHHHHHHHHH
Q 008442          268 GTLEDFDHSVQK  279 (565)
Q Consensus       268 G~~~~~~~~~~k  279 (565)
                      |+.+.+...+.+
T Consensus        82 ~~~~~a~~~~~~   93 (100)
T cd00189          82 GKYEEALEAYEK   93 (100)
T ss_pred             HhHHHHHHHHHH
Confidence            555544444433

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.56  E-value=0.0089  Score=50.63  Aligned_cols=72  Identities=24%  Similarity=0.321  Sum_probs=52.4

Q ss_pred             CCeEEEcCCCC------CCCH---HHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeE
Q 008442          391 ECTAFLSNINL------KATY---EDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKK  461 (565)
Q Consensus       391 ~~~l~V~nl~~------~~~~---~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~  461 (565)
                      ..||.|.=+.+      ..++   .+|-+.|..||.+.-+|++.+        .-+|+|.+-.+|.+|+.++|..++|+.
T Consensus        27 DaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals~dg~~v~g~~   98 (146)
T PF08952_consen   27 DATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALSLDGIQVNGRT   98 (146)
T ss_dssp             T-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHHGCCSEETTEE
T ss_pred             CceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHccCCcEECCEE
Confidence            35777765541      1222   367778899999998888753        579999999999999999999999999


Q ss_pred             EEEeecCCC
Q 008442          462 LSIARSNPK  470 (565)
Q Consensus       462 l~v~~a~~~  470 (565)
                      |.|....|.
T Consensus        99 l~i~LKtpd  107 (146)
T PF08952_consen   99 LKIRLKTPD  107 (146)
T ss_dssp             EEEEE----
T ss_pred             EEEEeCCcc
Confidence            999997665

; PDB: 1UFW_A 2DNR_A.

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=96.54  E-value=0.011  Score=56.46  Aligned_cols=81  Identities=20%  Similarity=0.291  Sum_probs=63.5

Q ss_pred             CCCCCCeEEEcCCCC----CCC-------HHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCC
Q 008442          387 GFTDECTAFLSNINL----KAT-------YEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNK  454 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~----~~~-------~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~  454 (565)
                      ..+..+||.+.|+=.    ..+       .++|.+-..+||.|.+|.|.-    ..+.|.+-|.|.+.+.|..||. |+|
T Consensus       261 k~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d----~hPdGvvtV~f~n~eeA~~ciq~m~G  336 (382)
T KOG1548|consen  261 KARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYD----RHPDGVVTVSFRNNEEADQCIQTMDG  336 (382)
T ss_pred             cccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEec----cCCCceeEEEeCChHHHHHHHHHhcC
Confidence            346678999999822    223       245556678999999988752    3467999999999999999998 899


Q ss_pred             cccCCeEEEEeecCCCC
Q 008442          455 QMFLGKKLSIARSNPKQ  471 (565)
Q Consensus       455 ~~~~g~~l~v~~a~~~~  471 (565)
                      ..++||.|..+......
T Consensus       337 R~fdgRql~A~i~DG~t  353 (382)
T KOG1548|consen  337 RWFDGRQLTASIWDGKT  353 (382)
T ss_pred             eeecceEEEEEEeCCcc
Confidence            99999999988876543

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=96.53  E-value=0.25  Score=52.48  Aligned_cols=179  Identities=12%  Similarity=0.036  Sum_probs=103.6

Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHhc----CCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHH
Q 008442           83 RATKNCPWVGELWVRSLLSLERSR----ASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYS  158 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~~~----~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~  158 (565)
                      ++.+.-|.+..-|..|++......    .....+..+|++|+...+.....+..+..++.  .+ ..... ..+  .++.
T Consensus       328 ~~~~~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ldP~~a~a~A~la~~~~--~~-~~~~~-~~~--~~l~  401 (517)
T PRK10153        328 RLQQGLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSEPDFTYAQAEKALADI--VR-HSQQP-LDE--KQLA  401 (517)
T ss_pred             HHhccCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH--HH-HhcCC-ccH--HHHH
Confidence            333445677788888887544321    23567889999999877664333333333221  11 11111 000  0122


Q ss_pred             HHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHH
Q 008442          159 LIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARS  238 (565)
Q Consensus       159 ~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~  238 (565)
                      .+.....++...     ...+.....+..++-.....+ +++.|...+++++...++ ...|..+..+....|+.+.|-.
T Consensus       402 ~a~~~~~~a~al-----~~~~~~~~~~~ala~~~~~~g-~~~~A~~~l~rAl~L~ps-~~a~~~lG~~~~~~G~~~eA~~  474 (517)
T PRK10153        402 ALSTELDNIVAL-----PELNVLPRIYEILAVQALVKG-KTDEAYQAINKAIDLEMS-WLNYVLLGKVYELKGDNRLAAD  474 (517)
T ss_pred             HHHHHHHHhhhc-----ccCcCChHHHHHHHHHHHhcC-CHHHHHHHHHHHHHcCCC-HHHHHHHHHHHHHcCCHHHHHH
Confidence            222223322221     111112345555555555556 999999999999999985 7788899999999999999999


Q ss_pred             HHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHH
Q 008442          239 IYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQK  279 (565)
Q Consensus       239 i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k  279 (565)
                      .|++|+.  +....|...|..=+-|   |-|++++.-++-+
T Consensus       475 ~~~~A~~--L~P~~pt~~~~~~~~f---~~~~~~~~~~~~~  510 (517)
T PRK10153        475 AYSTAFN--LRPGENTLYWIENLVF---QTSVETVVPYLYR  510 (517)
T ss_pred             HHHHHHh--cCCCCchHHHHHhccc---cccHHHHHHHHHh
Confidence            9999986  2444454333222223   3456666544433

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.51  E-value=0.0091  Score=62.11  Aligned_cols=77  Identities=25%  Similarity=0.261  Sum_probs=64.8

Q ss_pred             CCCC-eEEEcCCCCCCCHHHHHHHhccCCCee-EEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          389 TDEC-TAFLSNINLKATYEDLRRFFSDVGGVS-SIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       389 ~~~~-~l~V~nl~~~~~~~~l~~~f~~~G~i~-~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      +.++ -|-|.|+|++++-+||-+||..|-.+. +|++... ..|...|-|-|.|++.+.|.+|.. +++..|..+.|.+.
T Consensus       864 ~pGp~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~  942 (944)
T KOG4307|consen  864 SPGPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLR  942 (944)
T ss_pred             CCCCeEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEE
Confidence            4455 566889999999999999999997553 4555554 489999999999999999999998 89999999998875


Q ss_pred             e
Q 008442          466 R  466 (565)
Q Consensus       466 ~  466 (565)
                      +
T Consensus       943 i  943 (944)
T KOG4307|consen  943 I  943 (944)
T ss_pred             e
Confidence            4

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=96.47  E-value=0.034  Score=56.32  Aligned_cols=81  Identities=16%  Similarity=0.227  Sum_probs=65.3

Q ss_pred             HHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHH
Q 008442          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRC  243 (565)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~a  243 (565)
                      |..|+.++...+...+....+|...+......+ +++.|...+++++...|++...|..........|+++.|...|+++
T Consensus        18 ~~~Ai~~~~~Al~~~P~~~~a~~~~a~~~~~~g-~~~eAl~~~~~Al~l~P~~~~a~~~lg~~~~~lg~~~eA~~~~~~a   96 (356)
T PLN03088         18 FALAVDLYTQAIDLDPNNAELYADRAQANIKLG-NFTEAVADANKAIELDPSLAKAYLRKGTACMKLEEYQTAKAALEKG   96 (356)
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            444555555555444555667777788888888 9999999999999999999999999988888999999999999999


Q ss_pred             Hh
Q 008442          244 YS  245 (565)
Q Consensus       244 l~  245 (565)
                      +.
T Consensus        97 l~   98 (356)
T PLN03088         97 AS   98 (356)
T ss_pred             HH
Confidence            87

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.43  E-value=0.0025  Score=58.28  Aligned_cols=71  Identities=24%  Similarity=0.281  Sum_probs=58.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCC--------CCcce----EEEEEecCHHHHHHHHH-cCCccc
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFT--------GKSRG----LAYVDFIDDEHLAAAVA-KNKQMF  457 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~--------g~~~g----~afv~f~~~~~a~~a~~-~~~~~~  457 (565)
                      ..-||++++|+.+....|+++|+.||.|-.|.+-....+        |.+.+    -|.|+|.+...|..+.. ||+..|
T Consensus        74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~I  153 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPI  153 (278)
T ss_pred             ceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCcc
Confidence            468999999999999999999999999999887654333        33322    46799999999988777 799999


Q ss_pred             CCeE
Q 008442          458 LGKK  461 (565)
Q Consensus       458 ~g~~  461 (565)
                      +|++
T Consensus       154 ggkk  157 (278)
T KOG3152|consen  154 GGKK  157 (278)
T ss_pred             CCCC
Confidence            9874

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.43  E-value=0.017  Score=43.37  Aligned_cols=60  Identities=20%  Similarity=0.127  Sum_probs=50.3

Q ss_pred             HhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHH
Q 008442           34 QSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGEL   94 (565)
Q Consensus        34 ~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~l   94 (565)
                      ...++++.+..++++++...|.++.+|..++..+...+ ..+.+...|++++..+|.....
T Consensus         6 ~~~~~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g-~~~~A~~~l~~~l~~~p~~~~~   65 (73)
T PF13371_consen    6 LQQEDYEEALEVLERALELDPDDPELWLQRARCLFQLG-RYEEALEDLERALELSPDDPDA   65 (73)
T ss_pred             HhCCCHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhc-cHHHHHHHHHHHHHHCCCcHHH
Confidence            45678889999999999999999999999998666544 7788999999999999976543

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.36  E-value=0.02  Score=42.90  Aligned_cols=55  Identities=22%  Similarity=0.191  Sum_probs=50.4

Q ss_pred             HHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhc
Q 008442          191 LEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       191 ~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~  246 (565)
                      +....+ +++.|.+++++++..+|+++.+|..++.+....|+++.|...|++++..
T Consensus         4 ~~~~~~-~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~   58 (73)
T PF13371_consen    4 IYLQQE-DYEEALEVLERALELDPDDPELWLQRARCLFQLGRYEEALEDLERALEL   58 (73)
T ss_pred             HHHhCC-CHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            344556 9999999999999999999999999999999999999999999999973

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=96.34  E-value=0.0023  Score=61.64  Aligned_cols=74  Identities=24%  Similarity=0.367  Sum_probs=59.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhcc-C---CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          393 TAFLSNINLKATYEDLRRFFSD-V---GGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       393 ~l~V~nl~~~~~~~~l~~~f~~-~---G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      .|-.++||+++++.++..||.+ |   |....|-+++.+ .|+..|-|||.|..+++|+.|+..+...|+-|-|.+-.+
T Consensus       163 ivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElFRS  240 (508)
T KOG1365|consen  163 IVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELFRS  240 (508)
T ss_pred             EEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            4556799999999999999963 2   355667677655 899999999999999999999988877777776655444

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=96.31  E-value=2.2  Score=46.42  Aligned_cols=100  Identities=9%  Similarity=0.096  Sum_probs=64.7

Q ss_pred             HHHHHHcCCChHHHHHHHHHH------HHH------------------ccchHHHHHHHHHHHHHcCChHHHHHHH----
Q 008442          189 AHLEQSMGKDMVSARGVWERL------LKI------------------SGAMLEAWQSYISMEIELDHINEARSIY----  240 (565)
Q Consensus       189 a~~e~~~~~~~~~ar~i~e~~------l~~------------------~~~~~~lw~~yi~~e~~~~~~~~aR~i~----  240 (565)
                      +.+++..+....+|-.+|.++      |..                  ..+.+.+....++|...+.++++|..++    
T Consensus      1028 ArYyEe~g~~~~~AVmLYHkAGm~~kALelAF~tqQf~aL~lIa~DLd~~sDp~ll~RcadFF~~~~qyekAV~lL~~ar 1107 (1416)
T KOG3617|consen 1028 ARYYEELGGYAHKAVMLYHKAGMIGKALELAFRTQQFSALDLIAKDLDAGSDPKLLRRCADFFENNQQYEKAVNLLCLAR 1107 (1416)
T ss_pred             HHHHHHcchhhhHHHHHHHhhcchHHHHHHHHhhcccHHHHHHHHhcCCCCCHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            555556665777777666532      211                  1345789999999999998999888774    


Q ss_pred             --HHHHhcccCCCC-----------------c-----HHHHHHHHHHHHHhCCHHHHHHHHHHHhhHHHHHH
Q 008442          241 --KRCYSKRFTGTG-----------------S-----EDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELR  288 (565)
Q Consensus       241 --~~al~~~~~~~~-----------------~-----~~i~~~~~~fE~~~G~~~~~~~~~~k~~~~~~~~~  288 (565)
                        ..|++.+...+.                 +     ..|+....+|..+.|+...+.+-+-.+-+++..++
T Consensus      1108 ~~~~AlqlC~~~nv~vtee~aE~mTp~Kd~~~~e~~R~~vLeqvae~c~qQG~Yh~AtKKfTQAGdKl~AMr 1179 (1416)
T KOG3617|consen 1108 EFSGALQLCKNRNVRVTEEFAELMTPTKDDMPNEQERKQVLEQVAELCLQQGAYHAATKKFTQAGDKLSAMR 1179 (1416)
T ss_pred             HHHHHHHHHhcCCCchhHHHHHhcCcCcCCCccHHHHHHHHHHHHHHHHhccchHHHHHHHhhhhhHHHHHH
Confidence              444442111111                 1     14778888888888988877777766666665553

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=96.25  E-value=0.13  Score=49.28  Aligned_cols=112  Identities=13%  Similarity=0.075  Sum_probs=78.9

Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcc--hhhHHHHHHHHH
Q 008442            7 HLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLK--VGNVVRDVYSRA   84 (565)
Q Consensus         7 ~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~--~~~~~~~v~erA   84 (565)
                      .+|..|.++|.    +.+-|......-...++...+...|.+|+...|.++++|..|+.-+..+.+  ....+..+|..|
T Consensus       144 ~Le~~L~~nP~----d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~a  219 (287)
T COG4235         144 RLETHLQQNPG----DAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALLRQA  219 (287)
T ss_pred             HHHHHHHhCCC----CchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHH
Confidence            45666777776    778888888888888888888888888888888888888888876654442  345678888888


Q ss_pred             HHcCCCCH-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhccc
Q 008442           85 TKNCPWVG-ELWVRSLLSLERSRASEEEISTVFEKSLLCAF  124 (565)
Q Consensus        85 l~~~p~~~-~lW~~yi~~le~~~~~~~~~~~if~ral~~~~  124 (565)
                      ++.-|... .+|.--+..+  ..+++.++...|+..+...+
T Consensus       220 l~~D~~~iral~lLA~~af--e~g~~~~A~~~Wq~lL~~lp  258 (287)
T COG4235         220 LALDPANIRALSLLAFAAF--EQGDYAEAAAAWQMLLDLLP  258 (287)
T ss_pred             HhcCCccHHHHHHHHHHHH--HcccHHHHHHHHHHHHhcCC
Confidence            88777543 3443333323  34677777777777776443

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=96.23  E-value=0.43  Score=44.65  Aligned_cols=47  Identities=15%  Similarity=-0.026  Sum_probs=32.2

Q ss_pred             ChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHH
Q 008442          198 DMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCY  244 (565)
Q Consensus       198 ~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al  244 (565)
                      +.+.|+.++..+....+....+-...+-.....|++..|+.|-..-+
T Consensus       183 d~~~A~~lll~a~l~~~ad~~v~~NLAl~~~~~g~~~~A~~i~~~e~  229 (257)
T COG5010         183 DLEDAETLLLPAYLSPAADSRVRQNLALVVGLQGDFREAEDIAVQEL  229 (257)
T ss_pred             CHHHHHHHHHHHHhCCCCchHHHHHHHHHHhhcCChHHHHhhccccc
Confidence            77777777777777766556666666666666777777777665544

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=96.22  E-value=0.15  Score=44.20  Aligned_cols=100  Identities=9%  Similarity=-0.075  Sum_probs=81.7

Q ss_pred             hHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHH
Q 008442           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSL   99 (565)
Q Consensus        20 ~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi   99 (565)
                      ++.++.--.|.-.....|+.+.+..+|+-.+...|.+.+.|..... +....++.+.+...|.+|+..-|.++.....-.
T Consensus        32 ~~~l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~Dp~~~~y~~gLG~-~~Q~~g~~~~AI~aY~~A~~L~~ddp~~~~~ag  110 (157)
T PRK15363         32 TQPLNTLYRYAMQLMEVKEFAGAARLFQLLTIYDAWSFDYWFRLGE-CCQAQKHWGEAIYAYGRAAQIKIDAPQAPWAAA  110 (157)
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHH-HHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHH
Confidence            4567766677777788999999999999999999999999999987 444556888899999999998888776654433


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHh
Q 008442          100 LSLERSRASEEEISTVFEKSLL  121 (565)
Q Consensus       100 ~~le~~~~~~~~~~~if~ral~  121 (565)
                      . .-...++.+.++..|+.|+.
T Consensus       111 ~-c~L~lG~~~~A~~aF~~Ai~  131 (157)
T PRK15363        111 E-CYLACDNVCYAIKALKAVVR  131 (157)
T ss_pred             H-HHHHcCCHHHHHHHHHHHHH
Confidence            3 22336889999999999996

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=96.22  E-value=0.23  Score=52.87  Aligned_cols=116  Identities=15%  Similarity=0.157  Sum_probs=92.9

Q ss_pred             HHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHH
Q 008442          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYK  241 (565)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~  241 (565)
                      .-|+++...+...+.-++.....|..+.-....+. +...|-+.|.+++.-.|++.+.|..+....+..+.-.+|+..++
T Consensus       499 ~~fs~~~~hle~sl~~nplq~~~wf~~G~~ALqle-k~q~av~aF~rcvtL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~  577 (777)
T KOG1128|consen  499 KDFSEADKHLERSLEINPLQLGTWFGLGCAALQLE-KEQAAVKAFHRCVTLEPDNAEAWNNLSTAYIRLKKKKRAFRKLK  577 (777)
T ss_pred             hhHHHHHHHHHHHhhcCccchhHHHhccHHHHHHh-hhHHHHHHHHHHhhcCCCchhhhhhhhHHHHHHhhhHHHHHHHH
Confidence            45666666666666656666667766555555666 88899999999999999999999999999999999999999999


Q ss_pred             HHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          242 RCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       242 ~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      .|+..  + ..+..+|+-|...-...|..+++-+|.++..
T Consensus       578 EAlKc--n-~~~w~iWENymlvsvdvge~eda~~A~~rll  614 (777)
T KOG1128|consen  578 EALKC--N-YQHWQIWENYMLVSVDVGEFEDAIKAYHRLL  614 (777)
T ss_pred             HHhhc--C-CCCCeeeechhhhhhhcccHHHHHHHHHHHH
Confidence            99963  3 4566789888888888898888887776654

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=96.19  E-value=0.021  Score=58.17  Aligned_cols=77  Identities=14%  Similarity=0.230  Sum_probs=61.1

Q ss_pred             CCCCeEEEcCCCCCCCH------HHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccC-Ce
Q 008442          389 TDECTAFLSNINLKATY------EDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFL-GK  460 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~------~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~-g~  460 (565)
                      ....-|+|.|.|---..      .-|..+|+++|.|....++.+. .|.++||.|++|.+..+|+.|++ +||+.|+ .+
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e-~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknH  134 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDE-EGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNH  134 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCc-cCCeeeEEEEEecChhhHHHHHHhcccceecccc
Confidence            44567899999864222      2356789999999999999886 55699999999999999999998 8998875 56


Q ss_pred             EEEEee
Q 008442          461 KLSIAR  466 (565)
Q Consensus       461 ~l~v~~  466 (565)
                      ...|..
T Consensus       135 tf~v~~  140 (698)
T KOG2314|consen  135 TFFVRL  140 (698)
T ss_pred             eEEeeh
Confidence            666643

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=96.13  E-value=0.032  Score=53.86  Aligned_cols=79  Identities=23%  Similarity=0.360  Sum_probs=68.7

Q ss_pred             CCCCCCeEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEE
Q 008442          387 GFTDECTAFLSNINLK-ATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSI  464 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v  464 (565)
                      ...+++-+.|-+|... +.-+.|..+|-.||.|..|.+++.+     .|-|.|++.+...+++|+. ||+..+-|.+|.|
T Consensus       283 g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v  357 (494)
T KOG1456|consen  283 GGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNV  357 (494)
T ss_pred             CCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEE
Confidence            3467889999999887 5668899999999999999998865     3789999999999999998 8999999999999


Q ss_pred             eecCCC
Q 008442          465 ARSNPK  470 (565)
Q Consensus       465 ~~a~~~  470 (565)
                      ..++..
T Consensus       358 ~~SkQ~  363 (494)
T KOG1456|consen  358 CVSKQN  363 (494)
T ss_pred             eecccc
Confidence            887543

>KOG1129 consensus TPR repeat-containing protein [General function prediction only]

Probab=96.12  E-value=1.2  Score=43.21  Aligned_cols=219  Identities=9%  Similarity=0.129  Sum_probs=129.8

Q ss_pred             HhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHH
Q 008442           34 QSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEIS  113 (565)
Q Consensus        34 ~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~  113 (565)
                      ...|-+.++...++.+|...|+-..+-+ ..+ +....+.+..++.+|...|..+|....+-+.-.+ +....+..+++.
T Consensus       234 lrLgm~r~AekqlqssL~q~~~~dTfll-Lsk-vY~ridQP~~AL~~~~~gld~fP~~VT~l~g~AR-i~eam~~~~~a~  310 (478)
T KOG1129|consen  234 LRLGMPRRAEKQLQSSLTQFPHPDTFLL-LSK-VYQRIDQPERALLVIGEGLDSFPFDVTYLLGQAR-IHEAMEQQEDAL  310 (478)
T ss_pred             HHhcChhhhHHHHHHHhhcCCchhHHHH-HHH-HHHHhccHHHHHHHHhhhhhcCCchhhhhhhhHH-HHHHHHhHHHHH
Confidence            3457788899999999999876554322 222 2333456778999999999999987665555444 222345667888


Q ss_pred             HHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHH
Q 008442          114 TVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQ  193 (565)
Q Consensus       114 ~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~  193 (565)
                      ++|+++++..+..++....+-..|+        +.+      +-+.+..-|.+.+++       +-...+|+....---.
T Consensus       311 ~lYk~vlk~~~~nvEaiAcia~~yf--------Y~~------~PE~AlryYRRiLqm-------G~~speLf~NigLCC~  369 (478)
T KOG1129|consen  311 QLYKLVLKLHPINVEAIACIAVGYF--------YDN------NPEMALRYYRRILQM-------GAQSPELFCNIGLCCL  369 (478)
T ss_pred             HHHHHHHhcCCccceeeeeeeeccc--------cCC------ChHHHHHHHHHHHHh-------cCCChHHHhhHHHHHH
Confidence            9999988744332221110000000        010      111111112211111       0111222222111111


Q ss_pred             HcCCChHHHHHHHHHHHHH--ccc-hHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCH
Q 008442          194 SMGKDMVSARGVWERLLKI--SGA-MLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTL  270 (565)
Q Consensus       194 ~~~~~~~~ar~i~e~~l~~--~~~-~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~  270 (565)
                      . +..++-+...|++++..  .+. -.++|..........|++.-|...|.-||..   ......-+.-..-++.+-|++
T Consensus       370 y-aqQ~D~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~---d~~h~ealnNLavL~~r~G~i  445 (478)
T KOG1129|consen  370 Y-AQQIDLVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTS---DAQHGEALNNLAVLAARSGDI  445 (478)
T ss_pred             h-hcchhhhHHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhcc---CcchHHHHHhHHHHHhhcCch
Confidence            1 22677888899999986  344 3679999888888899999999999999873   233344455566678889999


Q ss_pred             HHHHHHHHHH
Q 008442          271 EDFDHSVQKV  280 (565)
Q Consensus       271 ~~~~~~~~k~  280 (565)
                      +.++..+..+
T Consensus       446 ~~Arsll~~A  455 (478)
T KOG1129|consen  446 LGARSLLNAA  455 (478)
T ss_pred             HHHHHHHHHh
Confidence            9888666544

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=96.03  E-value=0.0093  Score=57.62  Aligned_cols=77  Identities=18%  Similarity=0.340  Sum_probs=63.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCC-eeE--EEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGG-VSS--IRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~-i~~--~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ..-|-+++||+..+-++|-.||..|.. |..  |+++.+. .|++.|-|||+|.+.+.|.+|.. .+.+...+|-|.|-.
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp  358 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFP  358 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEee
Confidence            346788999999999999999998863 444  7888774 89999999999999999999887 466666788888866


Q ss_pred             cC
Q 008442          467 SN  468 (565)
Q Consensus       467 a~  468 (565)
                      +.
T Consensus       359 ~S  360 (508)
T KOG1365|consen  359 CS  360 (508)
T ss_pred             cc
Confidence            54

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=95.98  E-value=0.74  Score=50.89  Aligned_cols=93  Identities=12%  Similarity=-0.021  Sum_probs=76.4

Q ss_pred             HHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhc--CC
Q 008442           31 KYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSR--AS  108 (565)
Q Consensus        31 ~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~--~~  108 (565)
                      +-+..+.+++.+.+.-+.+|...|+++..|.....++.....+.+++.+.|-.|.+..|...--|......+++..  .+
T Consensus        10 k~al~nk~YeealEqskkvLk~dpdNYnA~vFLGvAl~sl~q~le~A~ehYv~AaKldpdnlLAWkGL~nLye~~~dIl~   89 (1238)
T KOG1127|consen   10 KDALRNKEYEEALEQSKKVLKEDPDNYNAQVFLGVALWSLGQDLEKAAEHYVLAAKLDPDNLLAWKGLGNLYERYNDILD   89 (1238)
T ss_pred             HHHHhhccHHHHHHHHHHHHhcCCCcchhhhHHHHHHHhccCCHHHHHHHHHHHHhcChhhhHHHHHHHHHHHccchhhh
Confidence            3445567888899999999999999999999999999888877999999999999999988888887776666632  34


Q ss_pred             HHHHHHHHHHHHhcc
Q 008442          109 EEEISTVFEKSLLCA  123 (565)
Q Consensus       109 ~~~~~~if~ral~~~  123 (565)
                      .+++-.+|.+++...
T Consensus        90 ld~~~~~yq~~~l~l  104 (1238)
T KOG1127|consen   90 LDRAAKCYQRAVLIL  104 (1238)
T ss_pred             hhHhHHHHHHHHHhh
Confidence            567888888887543

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=95.97  E-value=0.29  Score=40.30  Aligned_cols=100  Identities=10%  Similarity=0.069  Sum_probs=73.6

Q ss_pred             HHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCC---HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCC---HHHHHH
Q 008442           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVS---SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV---GELWVR   97 (565)
Q Consensus        24 ~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~---~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~---~~lW~~   97 (565)
                      +++..-+......|+.+.+...|++++..+|.+   ...+..++..... .++.+.+...|++++...|..   ..+|..
T Consensus         3 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~   81 (119)
T TIGR02795         3 EAYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYA-QGKYADAAKAFLAVVKKYPKSPKAPDALLK   81 (119)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHh-hccHHHHHHHHHHHHHHCCCCCcccHHHHH
Confidence            345566666677899999999999999988766   4566666664443 346778999999999988764   456666


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcccc
Q 008442           98 SLLSLERSRASEEEISTVFEKSLLCAFS  125 (565)
Q Consensus        98 yi~~le~~~~~~~~~~~if~ral~~~~~  125 (565)
                      ....+. ..+..+.+...|.+++...+.
T Consensus        82 ~~~~~~-~~~~~~~A~~~~~~~~~~~p~  108 (119)
T TIGR02795        82 LGMSLQ-ELGDKEKAKATLQQVIKRYPG  108 (119)
T ss_pred             HHHHHH-HhCChHHHHHHHHHHHHHCcC
Confidence            555443 367788899999999876544

Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=95.86  E-value=0.31  Score=42.36  Aligned_cols=93  Identities=12%  Similarity=0.002  Sum_probs=73.8

Q ss_pred             HHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHh
Q 008442          188 WAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREY  267 (565)
Q Consensus       188 ~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~  267 (565)
                      |+-.....| +++.|..+|+-++...|.+...|+.+.-.....|+++.|...|.+|+..  ..++|...+..=. --...
T Consensus        41 ~A~~ly~~G-~l~~A~~~f~~L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L--~~ddp~~~~~ag~-c~L~l  116 (157)
T PRK15363         41 YAMQLMEVK-EFAGAARLFQLLTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQI--KIDAPQAPWAAAE-CYLAC  116 (157)
T ss_pred             HHHHHHHCC-CHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc--CCCCchHHHHHHH-HHHHc
Confidence            444455667 9999999999999999999999999999999999999999999999873  4556654443222 22356


Q ss_pred             CCHHHHHHHHHHHhhHH
Q 008442          268 GTLEDFDHSVQKVTPRL  284 (565)
Q Consensus       268 G~~~~~~~~~~k~~~~~  284 (565)
                      |+.+..+++++.++..-
T Consensus       117 G~~~~A~~aF~~Ai~~~  133 (157)
T PRK15363        117 DNVCYAIKALKAVVRIC  133 (157)
T ss_pred             CCHHHHHHHHHHHHHHh
Confidence            89999998888877555

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=95.79  E-value=0.011  Score=57.29  Aligned_cols=76  Identities=18%  Similarity=0.349  Sum_probs=62.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCC---CCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKF---TGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~---~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      .-|-|.||.+.++.++++.+|...|.|..++|+....   .......|||.|.|...+..|..|...++-|+.|.|-..
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEec
Confidence            3788999999999999999999999999999875321   123457999999999999999998777777777777654

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=95.74  E-value=0.36  Score=39.67  Aligned_cols=88  Identities=16%  Similarity=0.078  Sum_probs=48.1

Q ss_pred             HHHHHcCCChHHHHHHHHHHHHHccch---HHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCC-CcHHHHHHHHHHHH
Q 008442          190 HLEQSMGKDMVSARGVWERLLKISGAM---LEAWQSYISMEIELDHINEARSIYKRCYSKRFTGT-GSEDICHAWLRFER  265 (565)
Q Consensus       190 ~~e~~~~~~~~~ar~i~e~~l~~~~~~---~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~-~~~~i~~~~~~fE~  265 (565)
                      ......+ +++.|...|+.++..+|++   ...+..++......|+++.|..+|+.++.. .+.. ....++........
T Consensus        10 ~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~p~~~~~~~~~~~~~~~~~   87 (119)
T TIGR02795        10 LLVLKAG-DYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKK-YPKSPKAPDALLKLGMSLQ   87 (119)
T ss_pred             HHHHHcC-CHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHH-CCCCCcccHHHHHHHHHHH
Confidence            3334445 6777777777777765543   345666666666677777777777777652 1211 11233333333334


Q ss_pred             HhCCHHHHHHHHHH
Q 008442          266 EYGTLEDFDHSVQK  279 (565)
Q Consensus       266 ~~G~~~~~~~~~~k  279 (565)
                      ..|+.+.+...+.+
T Consensus        88 ~~~~~~~A~~~~~~  101 (119)
T TIGR02795        88 ELGDKEKAKATLQQ  101 (119)
T ss_pred             HhCChHHHHHHHHH
Confidence            45555554444433

Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=95.74  E-value=1.4  Score=45.12  Aligned_cols=85  Identities=13%  Similarity=0.015  Sum_probs=52.4

Q ss_pred             HhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHH
Q 008442           34 QSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEIS  113 (565)
Q Consensus        34 ~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~  113 (565)
                      ...+.++.++..+...+...|.|+-+|..-.+.....+ ....+.+-|++|+...|...-||+.|...+-. .+...++.
T Consensus       317 ~~~~~~d~A~~~l~~L~~~~P~N~~~~~~~~~i~~~~n-k~~~A~e~~~kal~l~P~~~~l~~~~a~all~-~g~~~eai  394 (484)
T COG4783         317 YLAGQYDEALKLLQPLIAAQPDNPYYLELAGDILLEAN-KAKEAIERLKKALALDPNSPLLQLNLAQALLK-GGKPQEAI  394 (484)
T ss_pred             HHhcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcC-ChHHHHHHHHHHHhcCCCccHHHHHHHHHHHh-cCChHHHH
Confidence            34456666777777777777777777766666555444 33446777777777777777777777764443 33334444


Q ss_pred             HHHHHHH
Q 008442          114 TVFEKSL  120 (565)
Q Consensus       114 ~if~ral  120 (565)
                      .++++.+
T Consensus       395 ~~L~~~~  401 (484)
T COG4783         395 RILNRYL  401 (484)
T ss_pred             HHHHHHh
Confidence            4444444

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.74  E-value=0.93  Score=44.27  Aligned_cols=177  Identities=15%  Similarity=0.065  Sum_probs=92.3

Q ss_pred             CCchhHHHHHHHHHhcCC---CCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHH
Q 008442           37 GDPGRVQLLYERAITDFP---VSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEIS  113 (565)
Q Consensus        37 ~~~~~~~~lyERal~~~p---~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~  113 (565)
                      .|+..++.++|-.+...-   .+.++|+.|..|   +.++.+++..+|+-+...---..+||....- .--..+...++.
T Consensus        36 rDytGAislLefk~~~~~EEE~~~~lWia~C~f---hLgdY~~Al~~Y~~~~~~~~~~~el~vnLAc-c~FyLg~Y~eA~  111 (557)
T KOG3785|consen   36 RDYTGAISLLEFKLNLDREEEDSLQLWIAHCYF---HLGDYEEALNVYTFLMNKDDAPAELGVNLAC-CKFYLGQYIEAK  111 (557)
T ss_pred             ccchhHHHHHHHhhccchhhhHHHHHHHHHHHH---hhccHHHHHHHHHHHhccCCCCcccchhHHH-HHHHHHHHHHHH
Confidence            355555556555543321   245688888876   4557777888888777643233456644321 000112233444


Q ss_pred             HHHHHHHhcccc------------cHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchh
Q 008442          114 TVFEKSLLCAFS------------TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGL  181 (565)
Q Consensus       114 ~if~ral~~~~~------------~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~  181 (565)
                      .+-++|-..+..            .-+.+..+.....|.+..+..       ...+.-+|.-|++|++.+...+..++.+
T Consensus       112 ~~~~ka~k~pL~~RLlfhlahklndEk~~~~fh~~LqD~~EdqLS-------LAsvhYmR~HYQeAIdvYkrvL~dn~ey  184 (557)
T KOG3785|consen  112 SIAEKAPKTPLCIRLLFHLAHKLNDEKRILTFHSSLQDTLEDQLS-------LASVHYMRMHYQEAIDVYKRVLQDNPEY  184 (557)
T ss_pred             HHHhhCCCChHHHHHHHHHHHHhCcHHHHHHHHHHHhhhHHHHHh-------HHHHHHHHHHHHHHHHHHHHHHhcChhh
Confidence            444443332211            111112222222222111111       1123446788899999888887777666


Q ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchH-HHHHHHHH
Q 008442          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAML-EAWQSYIS  225 (565)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~-~lw~~yi~  225 (565)
                      ..+-.+.+--+.++. -++-+.+++.-.|..+|++. .+=+....
T Consensus       185 ~alNVy~ALCyyKlD-Yydvsqevl~vYL~q~pdStiA~NLkacn  228 (557)
T KOG3785|consen  185 IALNVYMALCYYKLD-YYDVSQEVLKVYLRQFPDSTIAKNLKACN  228 (557)
T ss_pred             hhhHHHHHHHHHhcc-hhhhHHHHHHHHHHhCCCcHHHHHHHHHH
Confidence            555444444455555 67778888888888888763 33333333

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=95.73  E-value=0.24  Score=50.33  Aligned_cols=100  Identities=16%  Similarity=-0.039  Sum_probs=82.3

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      .++..+...|...|.    +.-.|..-.+.....+...++.+.|++++...|.+.-+|+.|+.-+...+ .+..+..++.
T Consensus       324 ~A~~~l~~L~~~~P~----N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l~P~~~~l~~~~a~all~~g-~~~eai~~L~  398 (484)
T COG4783         324 EALKLLQPLIAAQPD----NPYYLELAGDILLEANKAKEAIERLKKALALDPNSPLLQLNLAQALLKGG-KPQEAIRILN  398 (484)
T ss_pred             hHHHHHHHHHHhCCC----CHHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCCccHHHHHHHHHHHhcC-ChHHHHHHHH
Confidence            356666666677776    77777777777888899999999999999999999999999999877555 5567899999


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHhcC
Q 008442           83 RATKNCPWVGELWVRSLLSLERSRA  107 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~~~~  107 (565)
                      +.+...|..+..|....+..+....
T Consensus       399 ~~~~~~p~dp~~w~~LAqay~~~g~  423 (484)
T COG4783         399 RYLFNDPEDPNGWDLLAQAYAELGN  423 (484)
T ss_pred             HHhhcCCCCchHHHHHHHHHHHhCc
Confidence            9999999999999888776665433

>PRK11906 transcriptional regulator; Provisional

Probab=95.73  E-value=0.63  Score=47.56  Aligned_cols=164  Identities=12%  Similarity=-0.015  Sum_probs=95.8

Q ss_pred             HHHcCCCCH---HHH--HHHHHHHHHh----cCCHHHHHHHHHHHH---hcccccHHHHHHHHHHHHHHHHHHhhccccc
Q 008442           84 ATKNCPWVG---ELW--VRSLLSLERS----RASEEEISTVFEKSL---LCAFSTFEEYLDLFLTRIDGLRRRILFSGEV  151 (565)
Q Consensus        84 Al~~~p~~~---~lW--~~yi~~le~~----~~~~~~~~~if~ral---~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~  151 (565)
                      +.+.-|.+.   .-|  ..|++.+...    ....+.+..+|.+|+   ...+.....|..+..++  +.+...-...  
T Consensus       240 ~~r~~~~~l~~~~a~~~d~ylrg~~~~~~~t~~~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h--~~~~~~g~~~--  315 (458)
T PRK11906        240 SVRLAKQDQGYKNHYLSDEMLAGKKELYDFTPESIYRAMTIFDRLQNKSDIQTLKTECYCLLAECH--MSLALHGKSE--  315 (458)
T ss_pred             hhcCCCCCcccccchhhHHHHHHHHHhhccCHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHH--HHHHHhcCCC--
Confidence            444445555   678  6677644331    123566788999999   43333333333322222  2211111111  


Q ss_pred             hhhhhHHHHHHHHHHHHHHHHhhh--cCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHH
Q 008442          152 EGVLDYSLIRETFQRASDYLSEQM--KNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE  229 (565)
Q Consensus       152 e~~~~~~~~~~~~~~a~~~l~~~~--~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~  229 (565)
                              .......|......+.  ...|+......-++  ....+ +.+.|...|++++..+|+....|..+.....-
T Consensus       316 --------~~~~~~~a~~~A~rAveld~~Da~a~~~~g~~--~~~~~-~~~~a~~~f~rA~~L~Pn~A~~~~~~~~~~~~  384 (458)
T PRK11906        316 --------LELAAQKALELLDYVSDITTVDGKILAIMGLI--TGLSG-QAKVSHILFEQAKIHSTDIASLYYYRALVHFH  384 (458)
T ss_pred             --------chHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH--HHhhc-chhhHHHHHHHHhhcCCccHHHHHHHHHHHHH
Confidence                    1112222223332222  23444433333333  33345 68899999999999999999999999999999


Q ss_pred             cCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHH
Q 008442          230 LDHINEARSIYKRCYSKRFTGTGSEDICHAWLRF  263 (565)
Q Consensus       230 ~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~f  263 (565)
                      .|+.+.|+..+++|+. .-+..-...+...|++.
T Consensus       385 ~G~~~~a~~~i~~alr-LsP~~~~~~~~~~~~~~  417 (458)
T PRK11906        385 NEKIEEARICIDKSLQ-LEPRRRKAVVIKECVDM  417 (458)
T ss_pred             cCCHHHHHHHHHHHhc-cCchhhHHHHHHHHHHH
Confidence            9999999999999986 32333334577777743

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=95.71  E-value=0.13  Score=49.03  Aligned_cols=91  Identities=15%  Similarity=0.004  Sum_probs=72.1

Q ss_pred             HHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHH
Q 008442           33 EQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEI  112 (565)
Q Consensus        33 e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~  112 (565)
                      ..+.+++..+...|.+||...|.+.-++..-+.-+. ..+..+.+..-++.||..-|+....|.+--. .-...+.++++
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~l~P~nAVyycNRAAAy~-~Lg~~~~AVkDce~Al~iDp~yskay~RLG~-A~~~~gk~~~A  168 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIELDPTNAVYYCNRAAAYS-KLGEYEDAVKDCESALSIDPHYSKAYGRLGL-AYLALGKYEEA  168 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHhcCCCcchHHHHHHHHHH-HhcchHHHHHHHHHHHhcChHHHHHHHHHHH-HHHccCcHHHH
Confidence            345678889999999999999999999888776433 4446677999999999998988888877544 33346778888


Q ss_pred             HHHHHHHHhcccc
Q 008442          113 STVFEKSLLCAFS  125 (565)
Q Consensus       113 ~~if~ral~~~~~  125 (565)
                      ..-|++||...+.
T Consensus       169 ~~aykKaLeldP~  181 (304)
T KOG0553|consen  169 IEAYKKALELDPD  181 (304)
T ss_pred             HHHHHhhhccCCC
Confidence            8889999987665

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=95.68  E-value=0.033  Score=56.38  Aligned_cols=63  Identities=13%  Similarity=0.241  Sum_probs=48.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCC---CCCcce---EEEEEecCHHHHHHHHH
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKF---TGKSRG---LAYVDFIDDEHLAAAVA  451 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~---~g~~~g---~afv~f~~~~~a~~a~~  451 (565)
                      ..-.++||||+||++++|+.|...|..||.+. |.++....   --.++|   |+|+.|+++.+++.-|.
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~  324 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLS  324 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHH
Confidence            34568999999999999999999999999753 55553110   112456   99999999988877664

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=95.63  E-value=0.43  Score=42.75  Aligned_cols=80  Identities=11%  Similarity=-0.027  Sum_probs=59.5

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCH---HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS---DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRS   98 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~---~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~y   98 (565)
                      ....+..........|+.+.+...|++++...|...   .+|..++... ...+..+.+...|++|+...|.....|..+
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~-~~~g~~~~A~~~~~~al~~~p~~~~~~~~l  112 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIY-ASNGEHDKALEYYHQALELNPKQPSALNNI  112 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHhCcccHHHHHHH
Confidence            445566677777778999999999999998766543   4666665533 344577889999999999999887777665


Q ss_pred             HHHH
Q 008442           99 LLSL  102 (565)
Q Consensus        99 i~~l  102 (565)
                      ...+
T Consensus       113 g~~~  116 (172)
T PRK02603        113 AVIY  116 (172)
T ss_pred             HHHH
Confidence            5433

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=95.56  E-value=2.5  Score=41.31  Aligned_cols=221  Identities=16%  Similarity=0.113  Sum_probs=103.3

Q ss_pred             HhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHH-HHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHH
Q 008442           21 EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDL-WLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSL   99 (565)
Q Consensus        21 ~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~l-W~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi   99 (565)
                      ...+.-+...+-....+....+..-|--||..+|+++.. +..-..||-  ++..--+..-++|.|..-|.....-+...
T Consensus        36 advekhlElGk~lla~~Q~sDALt~yHaAve~dp~~Y~aifrRaT~yLA--mGksk~al~Dl~rVlelKpDF~~ARiQRg  113 (504)
T KOG0624|consen   36 ADVEKHLELGKELLARGQLSDALTHYHAAVEGDPNNYQAIFRRATVYLA--MGKSKAALQDLSRVLELKPDFMAARIQRG  113 (504)
T ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhHHHHHHHHHHHhh--hcCCccchhhHHHHHhcCccHHHHHHHhc
Confidence            345555555554455566666777777777777766653 322223332  11112245566677776664333333332


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcccc---cHHHHHHHHHH-----HHHHHHHHhhcccc---ch---hhh-------hHH
Q 008442          100 LSLERSRASEEEISTVFEKSLLCAFS---TFEEYLDLFLT-----RIDGLRRRILFSGE---VE---GVL-------DYS  158 (565)
Q Consensus       100 ~~le~~~~~~~~~~~if~ral~~~~~---~~~~~~~~~~~-----~~~~~~r~~~~~~~---~e---~~~-------~~~  158 (565)
                      . +...++.++++..-|...|+..++   .-+.+-.+.+.     ....+....-.++.   ++   .++       .+-
T Consensus       114 ~-vllK~Gele~A~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~~Wda~l~  192 (504)
T KOG0624|consen  114 V-VLLKQGELEQAEADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQPWDASLR  192 (504)
T ss_pred             h-hhhhcccHHHHHHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcCcchhHHH
Confidence            2 222356677777777777765432   11111111100     00011100000010   00   000       000


Q ss_pred             HHH-HHH------HHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHH-----
Q 008442          159 LIR-ETF------QRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISM-----  226 (565)
Q Consensus       159 ~~~-~~~------~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~-----  226 (565)
                      .+| ..|      ..||.-+....+........+-..+++++..+ +.+.+......+|+.+|++-..+-.|-.+     
T Consensus       193 ~~Rakc~i~~~e~k~AI~Dlk~askLs~DnTe~~ykis~L~Y~vg-d~~~sL~~iRECLKldpdHK~Cf~~YKklkKv~K  271 (504)
T KOG0624|consen  193 QARAKCYIAEGEPKKAIHDLKQASKLSQDNTEGHYKISQLLYTVG-DAENSLKEIRECLKLDPDHKLCFPFYKKLKKVVK  271 (504)
T ss_pred             HHHHHHHHhcCcHHHHHHHHHHHHhccccchHHHHHHHHHHHhhh-hHHHHHHHHHHHHccCcchhhHHHHHHHHHHHHH
Confidence            111 111      23443333332221222334445678888888 88888888889998888754433333332     


Q ss_pred             -----H--HHcCChHHHHHHHHHHHh
Q 008442          227 -----E--IELDHINEARSIYKRCYS  245 (565)
Q Consensus       227 -----e--~~~~~~~~aR~i~~~al~  245 (565)
                           +  ++.+++..|.+-++..+.
T Consensus       272 ~les~e~~ie~~~~t~cle~ge~vlk  297 (504)
T KOG0624|consen  272 SLESAEQAIEEKHWTECLEAGEKVLK  297 (504)
T ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHh
Confidence                 1  233455666666666664

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=95.55  E-value=4.4  Score=43.83  Aligned_cols=241  Identities=15%  Similarity=0.144  Sum_probs=137.1

Q ss_pred             HHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcC--CCCH-HHHHHHH
Q 008442           23 FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNC--PWVG-ELWVRSL   99 (565)
Q Consensus        23 ~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~--p~~~-~lW~~yi   99 (565)
                      ..+|..+.-+....|.+..+.+.||+++..+-...+.|..+.--+..... ...+..+.+.++..-  |... .+-..+-
T Consensus       323 ~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~~~~~e~w~~~als~saag~-~s~Av~ll~~~~~~~~~ps~~s~~Lmask  401 (799)
T KOG4162|consen  323 AAIFDHLTFALSRCGQFEVLAEQFEQALPFSFGEHERWYQLALSYSAAGS-DSKAVNLLRESLKKSEQPSDISVLLMASK  401 (799)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhHHHHHHHHHHHHHhcc-chHHHHHHHhhcccccCCCcchHHHHHHH
Confidence            34566555556666777788888888888877788888888654443332 344667777777655  3222 2222222


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHh-cc----cccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHH-HHHHHHHHHh
Q 008442          100 LSLERSRASEEEISTVFEKSLL-CA----FSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRET-FQRASDYLSE  173 (565)
Q Consensus       100 ~~le~~~~~~~~~~~if~ral~-~~----~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~-~~~a~~~l~~  173 (565)
                      ...|+ .+..+++.+.-.+|+. +.    .-....|.-+-.+|....+  .  .       +....|.. ..++++.++.
T Consensus       402 lc~e~-l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~--~--a-------~~~seR~~~h~kslqale~  469 (799)
T KOG4162|consen  402 LCIER-LKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQAR--Q--A-------NLKSERDALHKKSLQALEE  469 (799)
T ss_pred             HHHhc-hhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhh--c--C-------CChHHHHHHHHHHHHHHHH
Confidence            22222 3344444444455553 10    0011112222222221110  0  0       11112222 2334444444


Q ss_pred             hhc--CCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH-ccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCC
Q 008442          174 QMK--NTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI-SGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTG  250 (565)
Q Consensus       174 ~~~--~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~-~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~  250 (565)
                      +..  .+|+   ..++|..++.....+++.|..+..+++.- ..++...|.-.+-.....+++..|-.+.+.++.. ++.
T Consensus       470 av~~d~~dp---~~if~lalq~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~E-~~~  545 (799)
T KOG4162|consen  470 AVQFDPTDP---LVIFYLALQYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALEE-FGD  545 (799)
T ss_pred             HHhcCCCCc---hHHHHHHHHHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHH-hhh
Confidence            332  2333   44455555544444999999999999998 6778999999999999999999999999999973 222


Q ss_pred             CCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhhHHH
Q 008442          251 TGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLE  285 (565)
Q Consensus       251 ~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~~~~  285 (565)
                        .-.+..-=+.+|..+|+.+.   ++..|...+.
T Consensus       546 --N~~l~~~~~~i~~~~~~~e~---~l~t~~~~L~  575 (799)
T KOG4162|consen  546 --NHVLMDGKIHIELTFNDREE---ALDTCIHKLA  575 (799)
T ss_pred             --hhhhchhhhhhhhhcccHHH---HHHHHHHHHH
Confidence              22345555677888777664   4445544444

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=95.52  E-value=0.5  Score=45.32  Aligned_cols=84  Identities=10%  Similarity=-0.026  Sum_probs=66.7

Q ss_pred             chhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcC--CHHHHHHHH
Q 008442           39 PGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRA--SEEEISTVF  116 (565)
Q Consensus        39 ~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~--~~~~~~~if  116 (565)
                      .+....-.|..|..+|.+.+=|..........+ +.+.+...|.+|++.-|.+.++|..|...+-...+  ...+++.+|
T Consensus       138 ~~~l~a~Le~~L~~nP~d~egW~~Lg~~ym~~~-~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll  216 (287)
T COG4235         138 MEALIARLETHLQQNPGDAEGWDLLGRAYMALG-RASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALL  216 (287)
T ss_pred             HHHHHHHHHHHHHhCCCCchhHHHHHHHHHHhc-chhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccHHHHHHH
Confidence            456677889999999999999999988655444 67779999999999999999999999887765443  345677777


Q ss_pred             HHHHhcc
Q 008442          117 EKSLLCA  123 (565)
Q Consensus       117 ~ral~~~  123 (565)
                      .+++...
T Consensus       217 ~~al~~D  223 (287)
T COG4235         217 RQALALD  223 (287)
T ss_pred             HHHHhcC
Confidence            7777543

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=95.43  E-value=2.1  Score=41.81  Aligned_cols=124  Identities=15%  Similarity=0.156  Sum_probs=78.1

Q ss_pred             hHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHc-CCChHHHHHHHHHHHHHc---cc---hHHHHHHHHHHHH
Q 008442          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSM-GKDMVSARGVWERLLKIS---GA---MLEAWQSYISMEI  228 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~-~~~~~~ar~i~e~~l~~~---~~---~~~lw~~yi~~e~  228 (565)
                      ++..+...|++|+.++.. .+.......+....+.++... + +++.|.+.|++++..+   ..   ...+.+..+.+..
T Consensus        89 ~~~~Ai~~~~~A~~~y~~-~G~~~~aA~~~~~lA~~ye~~~~-d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~  166 (282)
T PF14938_consen   89 DPDEAIECYEKAIEIYRE-AGRFSQAAKCLKELAEIYEEQLG-DYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYA  166 (282)
T ss_dssp             THHHHHHHHHHHHHHHHH-CT-HHHHHHHHHHHHHHHCCTT---HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHh-cCcHHHHHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence            344555677777776632 222233455667778888777 6 9999999999999873   21   2458889999999


Q ss_pred             HcCChHHHHHHHHHHHhcccCCCC-cHHHHHHHHH---HHHHhCCHHHHHHHHHHHh
Q 008442          229 ELDHINEARSIYKRCYSKRFTGTG-SEDICHAWLR---FEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       229 ~~~~~~~aR~i~~~al~~~~~~~~-~~~i~~~~~~---fE~~~G~~~~~~~~~~k~~  281 (565)
                      ..|+++.|.++|++........+. ...+-..++.   .-...||...++.++++..
T Consensus       167 ~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~  223 (282)
T PF14938_consen  167 RLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYC  223 (282)
T ss_dssp             HTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHG
T ss_pred             HhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            999999999999999764322221 1112222222   2334588888887777754

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=95.40  E-value=0.089  Score=40.73  Aligned_cols=58  Identities=14%  Similarity=0.094  Sum_probs=40.6

Q ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHH
Q 008442          184 LYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRC  243 (565)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~a  243 (565)
                      +|...+......+ ++++|..++++ +...+.+..+...++......|+++.|+++|+++
T Consensus        27 ~~~~la~~~~~~~-~y~~A~~~~~~-~~~~~~~~~~~~l~a~~~~~l~~y~eAi~~l~~~   84 (84)
T PF12895_consen   27 YLYNLAQCYFQQG-KYEEAIELLQK-LKLDPSNPDIHYLLARCLLKLGKYEEAIKALEKA   84 (84)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHC-HTHHHCHHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCC-CHHHHHHHHHH-hCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHhcC
Confidence            4444677777777 78888888877 5555666666666677777788888888887764

>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi

Probab=95.39  E-value=0.33  Score=49.46  Aligned_cols=57  Identities=18%  Similarity=0.057  Sum_probs=34.2

Q ss_pred             HHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          188 WAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       188 ~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      .+++....+ +-.+|-.+++++++.+|.+..+....++|....++++.|..+.++|+.
T Consensus       206 LA~v~l~~~-~E~~AI~ll~~aL~~~p~d~~LL~~Qa~fLl~k~~~~lAL~iAk~av~  262 (395)
T PF09295_consen  206 LARVYLLMN-EEVEAIRLLNEALKENPQDSELLNLQAEFLLSKKKYELALEIAKKAVE  262 (395)
T ss_pred             HHHHHHhcC-cHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            344444333 445566666666666666666666666666666666666666666655

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=95.34  E-value=2.5  Score=39.70  Aligned_cols=92  Identities=8%  Similarity=0.074  Sum_probs=69.2

Q ss_pred             hHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHH
Q 008442          181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAW  260 (565)
Q Consensus       181 ~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~  260 (565)
                      ..++|...+-.+.+.| +.+.||.-|.++++..+....+--...-...-.|+.+.|+.++..+...   ......|-+..
T Consensus       133 d~~~~~~lgaaldq~G-r~~~Ar~ay~qAl~L~~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~---~~ad~~v~~NL  208 (257)
T COG5010         133 DWEAWNLLGAALDQLG-RFDEARRAYRQALELAPNEPSIANNLGMSLLLRGDLEDAETLLLPAYLS---PAADSRVRQNL  208 (257)
T ss_pred             ChhhhhHHHHHHHHcc-ChhHHHHHHHHHHHhccCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhC---CCCchHHHHHH
Confidence            3445555556667888 9999999999999999998888888888888899999999999999752   23334555555


Q ss_pred             HHHHHHhCCHHHHHHH
Q 008442          261 LRFEREYGTLEDFDHS  276 (565)
Q Consensus       261 ~~fE~~~G~~~~~~~~  276 (565)
                      .-.-...|++...+.+
T Consensus       209 Al~~~~~g~~~~A~~i  224 (257)
T COG5010         209 ALVVGLQGDFREAEDI  224 (257)
T ss_pred             HHHHhhcCChHHHHhh
Confidence            5555566776666544

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=95.29  E-value=0.052  Score=53.20  Aligned_cols=77  Identities=23%  Similarity=0.266  Sum_probs=62.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCe-EEEEee
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGK-KLSIAR  466 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~-~l~v~~  466 (565)
                      ....++-..|+|.++++++++..|..-|...+....    -++.+-+|++.+.+.+.|-.|+. ++.+.+++. .++|++
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkf----f~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSF  487 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKF----FQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSF  487 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeee----cCCCcceeecccCChhHhhhhccccccccCCCCceEEEEe
Confidence            456789999999999999999999998876554432    34445699999999999999987 788887654 899999


Q ss_pred             cCC
Q 008442          467 SNP  469 (565)
Q Consensus       467 a~~  469 (565)
                      ++.
T Consensus       488 Sks  490 (492)
T KOG1190|consen  488 SKS  490 (492)
T ss_pred             ecc
Confidence            764

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=95.24  E-value=0.015  Score=56.94  Aligned_cols=75  Identities=25%  Similarity=0.371  Sum_probs=57.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCc-ccCCeEEEEeecCC
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQ-MFLGKKLSIARSNP  469 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~-~~~g~~l~v~~a~~  469 (565)
                      ..+|++||.+.++..+|..+|...---.+-.++.      -.||+||.+.+..-+.+|++ ++|+ .+.|.++.|..+-|
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            4689999999999999999997541111111221      13899999999999999998 7765 58999999999877


Q ss_pred             CCC
Q 008442          470 KQR  472 (565)
Q Consensus       470 ~~~  472 (565)
                      ++.
T Consensus        76 kkq   78 (584)
T KOG2193|consen   76 KKQ   78 (584)
T ss_pred             HHH
Confidence            654

>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi

Probab=95.18  E-value=0.38  Score=48.99  Aligned_cols=85  Identities=14%  Similarity=-0.062  Sum_probs=40.5

Q ss_pred             CCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHH
Q 008442           37 GDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVF  116 (565)
Q Consensus        37 ~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if  116 (565)
                      +..+.+..+|++.....|.   ++...+..+.... ....+..+..++|...|.+..|+.....++-. .+..+.+..+.
T Consensus       183 ~~~~~ai~lle~L~~~~pe---v~~~LA~v~l~~~-~E~~AI~ll~~aL~~~p~d~~LL~~Qa~fLl~-k~~~~lAL~iA  257 (395)
T PF09295_consen  183 QRYDEAIELLEKLRERDPE---VAVLLARVYLLMN-EEVEAIRLLNEALKENPQDSELLNLQAEFLLS-KKKYELALEIA  257 (395)
T ss_pred             ccHHHHHHHHHHHHhcCCc---HHHHHHHHHHhcC-cHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHh-cCCHHHHHHHH
Confidence            4445555555555555442   2222333222222 22335555555555555555555555554433 33445555555


Q ss_pred             HHHHhccccc
Q 008442          117 EKSLLCAFST  126 (565)
Q Consensus       117 ~ral~~~~~~  126 (565)
                      ++|+.+.++.
T Consensus       258 k~av~lsP~~  267 (395)
T PF09295_consen  258 KKAVELSPSE  267 (395)
T ss_pred             HHHHHhCchh
Confidence            5555554443

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=95.18  E-value=0.31  Score=46.53  Aligned_cols=83  Identities=20%  Similarity=0.194  Sum_probs=68.4

Q ss_pred             HHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHH
Q 008442          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYK  241 (565)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~  241 (565)
                      ..|+.|+..+..++...|...-++..-+..+.+++ .++.|.+-.+.+|...|++...|...-......|+++.|..-|+
T Consensus        95 ~~Y~eAv~kY~~AI~l~P~nAVyycNRAAAy~~Lg-~~~~AVkDce~Al~iDp~yskay~RLG~A~~~~gk~~~A~~ayk  173 (304)
T KOG0553|consen   95 KDYQEAVDKYTEAIELDPTNAVYYCNRAAAYSKLG-EYEDAVKDCESALSIDPHYSKAYGRLGLAYLALGKYEEAIEAYK  173 (304)
T ss_pred             hhHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHhc-chHHHHHHHHHHHhcChHHHHHHHHHHHHHHccCcHHHHHHHHH
Confidence            44556666555555555555566777788888999 99999999999999999988999888888889999999999999


Q ss_pred             HHHh
Q 008442          242 RCYS  245 (565)
Q Consensus       242 ~al~  245 (565)
                      +||.
T Consensus       174 KaLe  177 (304)
T KOG0553|consen  174 KALE  177 (304)
T ss_pred             hhhc
Confidence            9997

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=95.17  E-value=0.055  Score=55.76  Aligned_cols=65  Identities=22%  Similarity=0.296  Sum_probs=52.1

Q ss_pred             HHHHHHhccCCCeeEEEEeecCCC---CCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCCC
Q 008442          406 EDLRRFFSDVGGVSSIRILHDKFT---GKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNPK  470 (565)
Q Consensus       406 ~~l~~~f~~~G~i~~~~~~~~~~~---g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~~  470 (565)
                      ++++.-+.+||.|.+|.++++-..   .-..|--||+|.+.++++.|++ |.|..+.||.|...+..+.
T Consensus       424 Edvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeD  492 (500)
T KOG0120|consen  424 EDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDED  492 (500)
T ss_pred             HHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHH
Confidence            345555678999999999887212   2335778999999999999998 9999999999998887654

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=95.05  E-value=0.34  Score=46.61  Aligned_cols=56  Identities=13%  Similarity=0.120  Sum_probs=27.4

Q ss_pred             HHHHHHcCCChHHHHHHHHHHHHHccch---HHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          189 AHLEQSMGKDMVSARGVWERLLKISGAM---LEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       189 a~~e~~~~~~~~~ar~i~e~~l~~~~~~---~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      +.++...+ +++.|...|.++++.+|++   .+.|...+......|+.+.|+.+|++++.
T Consensus       187 G~~y~~~g-~~~~A~~~f~~vv~~yP~s~~~~dAl~klg~~~~~~g~~~~A~~~~~~vi~  245 (263)
T PRK10803        187 GQLNYNKG-KKDDAAYYFASVVKNYPKSPKAADAMFKVGVIMQDKGDTAKAKAVYQQVIK  245 (263)
T ss_pred             HHHHHHcC-CHHHHHHHHHHHHHHCCCCcchhHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            34444444 5555555555555554432   33444444444445555555555555544

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=94.89  E-value=0.17  Score=38.23  Aligned_cols=51  Identities=16%  Similarity=0.291  Sum_probs=39.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA  451 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~  451 (565)
                      +-.+|+ +|......||.++|++||.|. |.++.|.       -|||...+.+.|..++.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~~~~~v~~   60 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRDQAKVVMN   60 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCHHHHHHHH
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHHHHHHHHH
Confidence            455665 999999999999999999764 6676653       79999999999998886

; 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.

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=94.82  E-value=4.4  Score=39.68  Aligned_cols=47  Identities=19%  Similarity=0.018  Sum_probs=29.4

Q ss_pred             ChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHH
Q 008442          198 DMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCY  244 (565)
Q Consensus       198 ~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al  244 (565)
                      |...|......+|+..|-.+.+...-++.+...|++..|..-++.+-
T Consensus       170 D~~~ai~~i~~llEi~~Wda~l~~~Rakc~i~~~e~k~AI~Dlk~as  216 (504)
T KOG0624|consen  170 DCQNAIEMITHLLEIQPWDASLRQARAKCYIAEGEPKKAIHDLKQAS  216 (504)
T ss_pred             chhhHHHHHHHHHhcCcchhHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            55566666666666666666666666666666666666666665553

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=94.75  E-value=1.7  Score=48.23  Aligned_cols=192  Identities=10%  Similarity=0.047  Sum_probs=103.5

Q ss_pred             CCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHH
Q 008442           55 VSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLF  134 (565)
Q Consensus        55 ~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~  134 (565)
                      .....|..|....    ++...+...|=||++.-+.....|..--.+.... .+...++..|.+|+......+...-..-
T Consensus       459 e~~~~w~a~~~~r----K~~~~al~ali~alrld~~~apaf~~LG~iYrd~-~Dm~RA~kCf~KAFeLDatdaeaaaa~a  533 (1238)
T KOG1127|consen  459 ENSEFWVALGCMR----KNSALALHALIRALRLDVSLAPAFAFLGQIYRDS-DDMKRAKKCFDKAFELDATDAEAAAASA  533 (1238)
T ss_pred             HHHHHHHHHHHhh----hhHHHHHHHHHHHHhcccchhHHHHHHHHHHHHH-HHHHHHHHHHHHHhcCCchhhhhHHHHH
Confidence            3445666665422    2345577788888887777777775544433222 2555677788888765433222222222


Q ss_pred             HHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhH--HHHHHHHHHHHHcCCChHHHHHHHHHHHHH
Q 008442          135 LTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLL--RLYAYWAHLEQSMGKDMVSARGVWERLLKI  212 (565)
Q Consensus       135 ~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~--~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~  212 (565)
                      .++.+         .     .+|+.+..+.-.+       -...+...  .-|....-++.+.+ +...+..-|+.++..
T Consensus       534 dtyae---------~-----~~we~a~~I~l~~-------~qka~a~~~k~nW~~rG~yyLea~-n~h~aV~~fQsALR~  591 (1238)
T KOG1127|consen  534 DTYAE---------E-----STWEEAFEICLRA-------AQKAPAFACKENWVQRGPYYLEAH-NLHGAVCEFQSALRT  591 (1238)
T ss_pred             HHhhc---------c-----ccHHHHHHHHHHH-------hhhchHHHHHhhhhhccccccCcc-chhhHHHHHHHHhcC
Confidence            22210         0     0222222221100       00000000  01111111223334 677788888899988


Q ss_pred             ccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHH--HHHHhCCHHHHHHHHH
Q 008442          213 SGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLR--FEREYGTLEDFDHSVQ  278 (565)
Q Consensus       213 ~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~--fE~~~G~~~~~~~~~~  278 (565)
                      .|.++..|....+.+-+.|.+..|-++|.+|..-     .|...+-.|-.  .|...|.....-.++.
T Consensus       592 dPkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~L-----rP~s~y~~fk~A~~ecd~GkYkeald~l~  654 (1238)
T KOG1127|consen  592 DPKDYNLWLGLGEAYPESGRYSHALKVFTKASLL-----RPLSKYGRFKEAVMECDNGKYKEALDALG  654 (1238)
T ss_pred             CchhHHHHHHHHHHHHhcCceehHHHhhhhhHhc-----CcHhHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence            9999999999999998999999999999998652     24454444432  4555565444333333

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=94.60  E-value=1.2  Score=39.66  Aligned_cols=77  Identities=12%  Similarity=-0.012  Sum_probs=59.3

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCH---HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS---DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRS   98 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~---~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~y   98 (565)
                      ....|...+......++++.+...|++|+...|.+.   .+|...... ....+..+.+...|++|+...|.....|...
T Consensus        34 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~-~~~~g~~~eA~~~~~~Al~~~~~~~~~~~~l  112 (168)
T CHL00033         34 EAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLI-HTSNGEHTKALEYYFQALERNPFLPQALNNM  112 (168)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHH-HHHcCCHHHHHHHHHHHHHhCcCcHHHHHHH
Confidence            456788888888888999999999999998876543   367666554 3445577889999999999888877766554


Q ss_pred             H
Q 008442           99 L   99 (565)
Q Consensus        99 i   99 (565)
                      .
T Consensus       113 a  113 (168)
T CHL00033        113 A  113 (168)
T ss_pred             H
Confidence            3

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=94.58  E-value=0.046  Score=34.09  Aligned_cols=34  Identities=12%  Similarity=0.282  Sum_probs=31.1

Q ss_pred             HHHHHHHHccchHHHHHHHHHHHHHcCChHHHHH
Q 008442          205 VWERLLKISGAMLEAWQSYISMEIELDHINEARS  238 (565)
Q Consensus       205 i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~  238 (565)
                      +|+++|+.+|+++..|..++.+....|+++.|++
T Consensus         1 ~y~kAie~~P~n~~a~~nla~~~~~~g~~~~A~~   34 (34)
T PF13431_consen    1 CYKKAIELNPNNAEAYNNLANLYLNQGDYEEAIA   34 (34)
T ss_pred             ChHHHHHHCCCCHHHHHHHHHHHHHCcCHHhhcC
Confidence            3789999999999999999999999999998863

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=94.54  E-value=4.5  Score=38.52  Aligned_cols=173  Identities=16%  Similarity=0.061  Sum_probs=99.5

Q ss_pred             HHHHHHhcCCchhHHHHHHHHHhcCCCCHH-----HHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHH-HHHHHHHH
Q 008442           29 YLKYEQSSGDPGRVQLLYERAITDFPVSSD-----LWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGEL-WVRSLLSL  102 (565)
Q Consensus        29 yi~~e~~~~~~~~~~~lyERal~~~p~~~~-----lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~l-W~~yi~~l  102 (565)
                      -+.-....|+.+.+...|+..+...|.++-     +|+.|+-|-   .++.+.+...|++.++..|.++.+ |..|+..+
T Consensus        38 ~A~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a~~a~l~la~ayy~---~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~g~  114 (243)
T PRK10866         38 TAQQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYK---NADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGL  114 (243)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHh---cCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHH
Confidence            333345578999999999999999998753     677777653   456788999999999999977643 44444322


Q ss_pred             HHh----------------cCCHH---HHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHH
Q 008442          103 ERS----------------RASEE---EISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRET  163 (565)
Q Consensus       103 e~~----------------~~~~~---~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~  163 (565)
                      -..                ..+..   .+...|++.+..-+.+  .|......++..+                      
T Consensus       115 ~~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~yP~S--~ya~~A~~rl~~l----------------------  170 (243)
T PRK10866        115 TNMALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRGYPNS--QYTTDATKRLVFL----------------------  170 (243)
T ss_pred             hhhhcchhhhhhccCCCccccCHHHHHHHHHHHHHHHHHCcCC--hhHHHHHHHHHHH----------------------
Confidence            100                01111   2234444444322211  0111111111111                      


Q ss_pred             HHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchH---HHHHHHHHHHHHcCChHHHHHHH
Q 008442          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAML---EAWQSYISMEIELDHINEARSIY  240 (565)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~---~lw~~yi~~e~~~~~~~~aR~i~  240 (565)
                          ...+.          +-...-++++.+.+ .+..|..=++.+++.+|+..   +.-...++-....|..+.|..+.
T Consensus       171 ----~~~la----------~~e~~ia~~Y~~~~-~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~  235 (243)
T PRK10866        171 ----KDRLA----------KYELSVAEYYTKRG-AYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVA  235 (243)
T ss_pred             ----HHHHH----------HHHHHHHHHHHHcC-chHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHH
Confidence                11110          01113356666666 78888888999998877653   33333344455678888887766


Q ss_pred             HHH
Q 008442          241 KRC  243 (565)
Q Consensus       241 ~~a  243 (565)
                      ...
T Consensus       236 ~~l  238 (243)
T PRK10866        236 KII  238 (243)
T ss_pred             HHH
Confidence            554

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=94.47  E-value=0.091  Score=48.44  Aligned_cols=78  Identities=15%  Similarity=0.179  Sum_probs=63.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cC-C---cccCCeEEEE
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KN-K---QMFLGKKLSI  464 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~-~---~~~~g~~l~v  464 (565)
                      ....|||.||+.-++-+.+..-|+.||.|....++.|- .+++.|-++|.|...-.+..|+. +. +   ....+++..|
T Consensus        30 ~~a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~V  108 (275)
T KOG0115|consen   30 MHAELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGV  108 (275)
T ss_pred             ccceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCC
Confidence            34789999999999999999999999999988777774 78888999999999998988886 42 2   2345666666


Q ss_pred             eecC
Q 008442          465 ARSN  468 (565)
Q Consensus       465 ~~a~  468 (565)
                      ....
T Consensus       109 eP~e  112 (275)
T KOG0115|consen  109 EPME  112 (275)
T ss_pred             Chhh
Confidence            5543

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=94.44  E-value=1.9  Score=35.85  Aligned_cols=91  Identities=18%  Similarity=0.077  Sum_probs=66.8

Q ss_pred             HHHHHHHhcCCchhHHHHHHHHHhcCCCC---HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCC---CHHHHHHHHHH
Q 008442           28 IYLKYEQSSGDPGRVQLLYERAITDFPVS---SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPW---VGELWVRSLLS  101 (565)
Q Consensus        28 ~yi~~e~~~~~~~~~~~lyERal~~~p~~---~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~---~~~lW~~yi~~  101 (565)
                      ......-..|.++++..+|++++..-...   ...|+.+..-+. +.+..+.+..+++.++...|.   +..++..|...
T Consensus         6 ~~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr-~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~   84 (120)
T PF12688_consen    6 ELAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLR-NLGRYDEALALLEEALEEFPDDELNAALRVFLALA   84 (120)
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHH-HcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHH
Confidence            33444556799999999999999975444   458888887555 556888899999999999887   77888777765


Q ss_pred             HHHhcCCHHHHHHHHHHHH
Q 008442          102 LERSRASEEEISTVFEKSL  120 (565)
Q Consensus       102 le~~~~~~~~~~~if~ral  120 (565)
                      +.. .+..+++...+-.++
T Consensus        85 L~~-~gr~~eAl~~~l~~l  102 (120)
T PF12688_consen   85 LYN-LGRPKEALEWLLEAL  102 (120)
T ss_pred             HHH-CCCHHHHHHHHHHHH
Confidence            555 455566656555555

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=94.35  E-value=0.22  Score=35.71  Aligned_cols=52  Identities=23%  Similarity=0.407  Sum_probs=44.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccC---CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDV---GGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA  451 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~---G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~  451 (565)
                      .+|.|.|+. +++.++|+.+|..|   .....|.++-|.       -|=|.|.+++.|.+||.
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 68999999999988   236789998885       58899999999999986

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=94.35  E-value=0.29  Score=37.10  Aligned_cols=63  Identities=19%  Similarity=0.255  Sum_probs=48.8

Q ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHH---ccc----hHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKI---SGA----MLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~---~~~----~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ..++...+.+....+ ++++|...|++++..   .++    ....+..........|+++.|.+.|++++.
T Consensus         5 a~~~~~la~~~~~~~-~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~   74 (78)
T PF13424_consen    5 ANAYNNLARVYRELG-RYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALD   74 (78)
T ss_dssp             HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcC-CHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            345566777888888 999999999999975   332    244667777778899999999999999985

...

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=94.26  E-value=0.06  Score=58.11  Aligned_cols=77  Identities=18%  Similarity=0.226  Sum_probs=66.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCC--eEEEE
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLG--KKLSI  464 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g--~~l~v  464 (565)
                      ......+||++|+.++....|...|..||.|..|.+-    .|.  -||||.|.+...+++|+. |.|..|+|  +++.|
T Consensus       452 st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~----hgq--~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rv  525 (975)
T KOG0112|consen  452 STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR----HGQ--PYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRV  525 (975)
T ss_pred             cccceeeccCCCCCCChHHHHHHHhhccCcceeeecc----cCC--cceeeecccCccchhhHHHHhcCcCCCCCccccc
Confidence            3567889999999999999999999999999998873    233  499999999999999998 89999875  57899


Q ss_pred             eecCCC
Q 008442          465 ARSNPK  470 (565)
Q Consensus       465 ~~a~~~  470 (565)
                      .++.+.
T Consensus       526 dla~~~  531 (975)
T KOG0112|consen  526 DLASPP  531 (975)
T ss_pred             ccccCC
Confidence            888654

>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=94.07  E-value=1.5  Score=42.97  Aligned_cols=97  Identities=16%  Similarity=0.214  Sum_probs=67.6

Q ss_pred             chhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHH
Q 008442          179 DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICH  258 (565)
Q Consensus       179 ~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~  258 (565)
                      .....|...|+.+..-. +.+..|.-+|+.+...++..+.+..-.+-.....|+++.|.+++..++..  ...++ +.+.
T Consensus       164 ~~l~qLa~awv~l~~g~-e~~~~A~y~f~El~~~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~--~~~~~-d~La  239 (290)
T PF04733_consen  164 SILTQLAEAWVNLATGG-EKYQDAFYIFEELSDKFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEK--DPNDP-DTLA  239 (290)
T ss_dssp             HHHHHHHHHHHHHHHTT-TCCCHHHHHHHHHHCCS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC---CCHH-HHHH
T ss_pred             HHHHHHHHHHHHHHhCc-hhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh--ccCCH-HHHH
Confidence            34466777787777543 37889999999988888888888888888889999999999999999873  33334 4444


Q ss_pred             HHHHHHHHhCCH-HHHHHHHHH
Q 008442          259 AWLRFEREYGTL-EDFDHSVQK  279 (565)
Q Consensus       259 ~~~~fE~~~G~~-~~~~~~~~k  279 (565)
                      -.+......|.. +.+.+.+..
T Consensus       240 Nliv~~~~~gk~~~~~~~~l~q  261 (290)
T PF04733_consen  240 NLIVCSLHLGKPTEAAERYLSQ  261 (290)
T ss_dssp             HHHHHHHHTT-TCHHHHHHHHH
T ss_pred             HHHHHHHHhCCChhHHHHHHHH
Confidence            567777777865 445545543

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.

>PRK11906 transcriptional regulator; Provisional

Probab=94.01  E-value=2.3  Score=43.59  Aligned_cols=172  Identities=10%  Similarity=0.049  Sum_probs=92.9

Q ss_pred             HHhcCCCCH---HHH--HHHHHHHHH----hcchhhHHHHHHHHHH---HcCCCCHH-----HHHHHHHHHHH---hcCC
Q 008442           49 AITDFPVSS---DLW--LDYTQYLDK----TLKVGNVVRDVYSRAT---KNCPWVGE-----LWVRSLLSLER---SRAS  108 (565)
Q Consensus        49 al~~~p~~~---~lW--~~Y~~~l~~----~~~~~~~~~~v~erAl---~~~p~~~~-----lW~~yi~~le~---~~~~  108 (565)
                      +...-|.+.   +-|  -.|+.-...    .......+..+|.||+   ..-|....     -|+.....+..   ....
T Consensus       240 ~~r~~~~~l~~~~a~~~d~ylrg~~~~~~~t~~~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h~~~~~~g~~~~~~~  319 (458)
T PRK11906        240 SVRLAKQDQGYKNHYLSDEMLAGKKELYDFTPESIYRAMTIFDRLQNKSDIQTLKTECYCLLAECHMSLALHGKSELELA  319 (458)
T ss_pred             hhcCCCCCcccccchhhHHHHHHHHHhhccCHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhcCCCchHH
Confidence            334446666   777  556554333    1223455778899999   54454332     23332221211   1223


Q ss_pred             HHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHH
Q 008442          109 EEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYW  188 (565)
Q Consensus       109 ~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~  188 (565)
                      ..++...-++|+...........  ...+.-.+                   ..-+..+...++++...++.....|.++
T Consensus       320 ~~~a~~~A~rAveld~~Da~a~~--~~g~~~~~-------------------~~~~~~a~~~f~rA~~L~Pn~A~~~~~~  378 (458)
T PRK11906        320 AQKALELLDYVSDITTVDGKILA--IMGLITGL-------------------SGQAKVSHILFEQAKIHSTDIASLYYYR  378 (458)
T ss_pred             HHHHHHHHHHHHhcCCCCHHHHH--HHHHHHHh-------------------hcchhhHHHHHHHHhhcCCccHHHHHHH
Confidence            44566777888876554322111  11111000                   0113344444444444456666677777


Q ss_pred             HHHHHHcCCChHHHHHHHHHHHHHccchH--HHHHHHHHHHHHcCChHHHHHHHHHH
Q 008442          189 AHLEQSMGKDMVSARGVWERLLKISGAML--EAWQSYISMEIELDHINEARSIYKRC  243 (565)
Q Consensus       189 a~~e~~~~~~~~~ar~i~e~~l~~~~~~~--~lw~~yi~~e~~~~~~~~aR~i~~~a  243 (565)
                      +-+..-.| +.+.|+..+++++...|...  .+-..+++.+. ...+++|.++|-+-
T Consensus       379 ~~~~~~~G-~~~~a~~~i~~alrLsP~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~  433 (458)
T PRK11906        379 ALVHFHNE-KIEEARICIDKSLQLEPRRRKAVVIKECVDMYV-PNPLKNNIKLYYKE  433 (458)
T ss_pred             HHHHHHcC-CHHHHHHHHHHHhccCchhhHHHHHHHHHHHHc-CCchhhhHHHHhhc
Confidence            77776677 99999999999999877653  34455554443 33467777776554

>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production

Probab=93.83  E-value=1.1  Score=38.79  Aligned_cols=46  Identities=17%  Similarity=0.145  Sum_probs=20.0

Q ss_pred             hhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 008442           73 VGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKS  119 (565)
Q Consensus        73 ~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ra  119 (565)
                      +.+.+..++++++...|.+..+|...|..+.. .++...+..+|+++
T Consensus        77 ~~~~a~~~~~~~l~~dP~~E~~~~~lm~~~~~-~g~~~~A~~~Y~~~  122 (146)
T PF03704_consen   77 DYEEALRLLQRALALDPYDEEAYRLLMRALAA-QGRRAEALRVYERY  122 (146)
T ss_dssp             -HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHH-TT-HHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHH-CcCHHHHHHHHHHH
Confidence            34445555555555555555555554442222 34444444444443

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=93.81  E-value=7.1  Score=38.10  Aligned_cols=121  Identities=20%  Similarity=0.234  Sum_probs=75.9

Q ss_pred             hHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHcc----chH---HHHHHHHHHHH
Q 008442          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG----AML---EAWQSYISMEI  228 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~----~~~---~lw~~yi~~e~  228 (565)
                      +++.+...|++|.+++...- .......+....+.+....+ ++++|.++|+++....-    ..+   .+++..+-...
T Consensus       130 d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l~~~l~-~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L  207 (282)
T PF14938_consen  130 DYEKAIEYYQKAAELYEQEG-SPHSAAECLLKAADLYARLG-RYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHL  207 (282)
T ss_dssp             -HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHHHHHhC-CHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHH
Confidence            66778888999998875433 12223456778899999999 99999999999998631    112   46666666777


Q ss_pred             HcCChHHHHHHHHHHHhcc--cCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHH
Q 008442          229 ELDHINEARSIYKRCYSKR--FTGTGSEDICHAWLRFEREYGTLEDFDHSVQK  279 (565)
Q Consensus       229 ~~~~~~~aR~i~~~al~~~--~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k  279 (565)
                      ..||+..|+..|++.....  |..+.-..+....++=- +.||.+.+..++..
T Consensus       208 ~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~-~~~D~e~f~~av~~  259 (282)
T PF14938_consen  208 AMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAY-EEGDVEAFTEAVAE  259 (282)
T ss_dssp             HTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHH-HTT-CCCHHHHCHH
T ss_pred             HcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHH-HhCCHHHHHHHHHH
Confidence            7899999999999997631  22211122333333211 34666666655543

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=93.75  E-value=0.018  Score=61.97  Aligned_cols=80  Identities=20%  Similarity=0.305  Sum_probs=63.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      ....+.|||+|||+..+++.+|+..|..+|.|.+|.|-+.+ -+.---|+||.|.+.+.+-.|.. +.+..|....+.+.
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 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIG  446 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCccccc
Confidence            44678999999999999999999999999999999986653 34444699999999888877775 77766654445554


Q ss_pred             ec
Q 008442          466 RS  467 (565)
Q Consensus       466 ~a  467 (565)
                      +.
T Consensus       447 lG  448 (975)
T KOG0112|consen  447 LG  448 (975)
T ss_pred             cc
Confidence            44

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=93.68  E-value=0.37  Score=37.22  Aligned_cols=81  Identities=16%  Similarity=0.078  Sum_probs=52.4

Q ss_pred             cCCchhHHHHHHHHHhcCCC--CHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHH
Q 008442           36 SGDPGRVQLLYERAITDFPV--SSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEIS  113 (565)
Q Consensus        36 ~~~~~~~~~lyERal~~~p~--~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~  113 (565)
                      +++++.+..+|++++...|.  +..+|..++.-+. ..+..+.+..++++ +...|....++..+...+. ..+..+++.
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~-~~~~y~~A~~~~~~-~~~~~~~~~~~~l~a~~~~-~l~~y~eAi   78 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYF-QQGKYEEAIELLQK-LKLDPSNPDIHYLLARCLL-KLGKYEEAI   78 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHH-HTTHHHHHHHHHHC-HTHHHCHHHHHHHHHHHHH-HTT-HHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHH-HCCCHHHHHHHHHH-hCCCCCCHHHHHHHHHHHH-HhCCHHHHH
Confidence            46778899999999999885  3556776555333 44477778888888 5444444344434344333 357788888


Q ss_pred             HHHHHH
Q 008442          114 TVFEKS  119 (565)
Q Consensus       114 ~if~ra  119 (565)
                      .+|++|
T Consensus        79 ~~l~~~   84 (84)
T PF12895_consen   79 KALEKA   84 (84)
T ss_dssp             HHHHHH
T ss_pred             HHHhcC
Confidence            888875

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=93.58  E-value=1.1  Score=40.07  Aligned_cols=49  Identities=10%  Similarity=0.034  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCC
Q 008442          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDH  232 (565)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~  232 (565)
                      .++..++.+....+ +++.|..+|++++...|.....|..+.......|+
T Consensus        73 ~~~~~la~~~~~~g-~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~  121 (172)
T PRK02603         73 YILYNMGIIYASNG-EHDKALEYYHQALELNPKQPSALNNIAVIYHKRGE  121 (172)
T ss_pred             HHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCC
Confidence            45666777777777 89999999999999888888877777776665554

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=93.41  E-value=2.6  Score=36.39  Aligned_cols=53  Identities=21%  Similarity=0.274  Sum_probs=25.2

Q ss_pred             cCCchhHHHHHHHHHhcCCCCH---HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCC
Q 008442           36 SGDPGRVQLLYERAITDFPVSS---DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCP   89 (565)
Q Consensus        36 ~~~~~~~~~lyERal~~~p~~~---~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p   89 (565)
                      .++...+...++..+..+|.+.   ..++..+.... ..++.+.+..+|+.++...|
T Consensus        24 ~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~-~~g~~~~A~~~l~~~~~~~~   79 (145)
T PF09976_consen   24 AGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAY-EQGDYDEAKAALEKALANAP   79 (145)
T ss_pred             CCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHH-HCCCHHHHHHHHHHHHhhCC
Confidence            4455555555666666555552   22222233222 22345555566666665543

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=93.36  E-value=2.3  Score=40.92  Aligned_cols=86  Identities=9%  Similarity=0.009  Sum_probs=58.8

Q ss_pred             HcCCChHHHHHHHHHHHHHccch---HHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCC-CCcHHHHHHHHHHHHHhCC
Q 008442          194 SMGKDMVSARGVWERLLKISGAM---LEAWQSYISMEIELDHINEARSIYKRCYSKRFTG-TGSEDICHAWLRFEREYGT  269 (565)
Q Consensus       194 ~~~~~~~~ar~i~e~~l~~~~~~---~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~-~~~~~i~~~~~~fE~~~G~  269 (565)
                      ..+ +++.|...|+.+++.+|++   ...+..........|+++.|...|++++.. ++. ....+.+......-...|+
T Consensus       155 ~~~-~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~-yP~s~~~~dAl~klg~~~~~~g~  232 (263)
T PRK10803        155 DKS-RQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKN-YPKSPKAADAMFKVGVIMQDKGD  232 (263)
T ss_pred             hcC-CHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-CCCCcchhHHHHHHHHHHHHcCC
Confidence            345 8999999999999998876   345555556666799999999999999974 332 2222333222222335688


Q ss_pred             HHHHHHHHHHHh
Q 008442          270 LEDFDHSVQKVT  281 (565)
Q Consensus       270 ~~~~~~~~~k~~  281 (565)
                      .+.+...+++++
T Consensus       233 ~~~A~~~~~~vi  244 (263)
T PRK10803        233 TAKAKAVYQQVI  244 (263)
T ss_pred             HHHHHHHHHHHH
Confidence            888877776654

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=93.30  E-value=2.1  Score=45.59  Aligned_cols=173  Identities=13%  Similarity=0.057  Sum_probs=95.0

Q ss_pred             HHHHHhcCCCCHHHHHHHHHHHHHhc----chhhHHHHHHHHHHHcCCCCHHHHHHHHH--HHHHhcCC-----HHHHHH
Q 008442           46 YERAITDFPVSSDLWLDYTQYLDKTL----KVGNVVRDVYSRATKNCPWVGELWVRSLL--SLERSRAS-----EEEIST  114 (565)
Q Consensus        46 yERal~~~p~~~~lW~~Y~~~l~~~~----~~~~~~~~v~erAl~~~p~~~~lW~~yi~--~le~~~~~-----~~~~~~  114 (565)
                      -+++....|.+.+.|-.|+.-...-.    .....++.+|++|+..-|.....|.....  ........     ...+..
T Consensus       326 ~~~~~~~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ldP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~  405 (517)
T PRK10153        326 QERLQQGLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSEPDFTYAQAEKALADIVRHSQQPLDEKQLAALST  405 (517)
T ss_pred             HHHHhccCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHH
Confidence            34555667788888888876543211    23456889999999999988766654221  11111111     233444


Q ss_pred             HHHHHHhcccc--cHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHH
Q 008442          115 VFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLE  192 (565)
Q Consensus       115 if~ral~~~~~--~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e  192 (565)
                      ...+++..+..  ....+..+-....        ..      .+++.....+++|+..       .+ ....|..++++.
T Consensus       406 ~~~~a~al~~~~~~~~~~~ala~~~~--------~~------g~~~~A~~~l~rAl~L-------~p-s~~a~~~lG~~~  463 (517)
T PRK10153        406 ELDNIVALPELNVLPRIYEILAVQAL--------VK------GKTDEAYQAINKAIDL-------EM-SWLNYVLLGKVY  463 (517)
T ss_pred             HHHHhhhcccCcCChHHHHHHHHHHH--------hc------CCHHHHHHHHHHHHHc-------CC-CHHHHHHHHHHH
Confidence            45555443211  1111111111000        00      1334444555554443       33 344677788888


Q ss_pred             HHcCCChHHHHHHHHHHHHHccchH-HHHHHHHHHHHHcCChHHHHHHHHHHH
Q 008442          193 QSMGKDMVSARGVWERLLKISGAML-EAWQSYISMEIELDHINEARSIYKRCY  244 (565)
Q Consensus       193 ~~~~~~~~~ar~i~e~~l~~~~~~~-~lw~~yi~~e~~~~~~~~aR~i~~~al  244 (565)
                      ...| +.++|...|++++...|... -+|..=.-|.   -+++...-.+-+++
T Consensus       464 ~~~G-~~~eA~~~~~~A~~L~P~~pt~~~~~~~~f~---~~~~~~~~~~~~~~  512 (517)
T PRK10153        464 ELKG-DNRLAADAYSTAFNLRPGENTLYWIENLVFQ---TSVETVVPYLYRFL  512 (517)
T ss_pred             HHcC-CHHHHHHHHHHHHhcCCCCchHHHHHhcccc---ccHHHHHHHHHhcc
Confidence            8888 99999999999999877654 3555444443   34444444444443

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=92.97  E-value=5.5  Score=34.33  Aligned_cols=91  Identities=13%  Similarity=0.018  Sum_probs=65.3

Q ss_pred             HHHHHHHHHHcCCChHHHHHHHHHHHHHccch---HHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHH
Q 008442          185 YAYWAHLEQSMGKDMVSARGVWERLLKISGAM---LEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWL  261 (565)
Q Consensus       185 ~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~---~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~  261 (565)
                      ....++.....+ ++++|..+|+.++...++.   ...++..+.+....|+++.|..+++...    ........+..--
T Consensus        51 ~l~lA~~~~~~g-~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~~~----~~~~~~~~~~~~G  125 (145)
T PF09976_consen   51 ALQLAKAAYEQG-DYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQYDEALATLQQIP----DEAFKALAAELLG  125 (145)
T ss_pred             HHHHHHHHHHCC-CHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhcc----CcchHHHHHHHHH
Confidence            344566777777 9999999999999986543   3466777777888999999999996642    2233334555555


Q ss_pred             HHHHHhCCHHHHHHHHHHH
Q 008442          262 RFEREYGTLEDFDHSVQKV  280 (565)
Q Consensus       262 ~fE~~~G~~~~~~~~~~k~  280 (565)
                      +.-...|+.+.+..+.+++
T Consensus       126 di~~~~g~~~~A~~~y~~A  144 (145)
T PF09976_consen  126 DIYLAQGDYDEARAAYQKA  144 (145)
T ss_pred             HHHHHCCCHHHHHHHHHHh
Confidence            6666778888888777665

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=92.90  E-value=4.3  Score=35.99  Aligned_cols=64  Identities=11%  Similarity=-0.021  Sum_probs=51.5

Q ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccch---HHHHHHHHHHHHHcCChHHHHHHHHHHHhc
Q 008442          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM---LEAWQSYISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~---~~lw~~yi~~e~~~~~~~~aR~i~~~al~~  246 (565)
                      ...|...+......+ +++.|...|++++...++.   ..+|..........|+++.|..+|++++..
T Consensus        35 a~~~~~~g~~~~~~g-~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~  101 (168)
T CHL00033         35 AFTYYRDGMSAQSEG-EYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALER  101 (168)
T ss_pred             HHHHHHHHHHHHHcC-CHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            344555666666667 9999999999999875543   358888888899999999999999999873

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=92.86  E-value=0.3  Score=45.82  Aligned_cols=63  Identities=21%  Similarity=0.214  Sum_probs=48.8

Q ss_pred             HHHHHHhccCCCeeEEEEeecCCCCCcc-eEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          406 EDLRRFFSDVGGVSSIRILHDKFTGKSR-GLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       406 ~~l~~~f~~~G~i~~~~~~~~~~~g~~~-g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      ++++.-..+||.|..|-|...+..-... ---||+|+..++|.+|+. |||..|+||.+...+.+
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            5677778899999998887765222222 246999999999999997 89999999988766643

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=92.78  E-value=0.48  Score=49.92  Aligned_cols=80  Identities=14%  Similarity=0.245  Sum_probs=64.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      ..+.+.+=+.+.+++.+..+++++|... .|..+.|..+...+...|-++|.|....+++.|+..|...+-.|.+.|..+
T Consensus       308 v~d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R~~q~~P~  386 (944)
T KOG4307|consen  308 VSDKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNRPFQTGPP  386 (944)
T ss_pred             cchhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhcCchhhhhcceeecCC
Confidence            3567777888999999999999999654 356666666655555579999999999999999998888888888887665


Q ss_pred             C
Q 008442          468 N  468 (565)
Q Consensus       468 ~  468 (565)
                      .
T Consensus       387 g  387 (944)
T KOG4307|consen  387 G  387 (944)
T ss_pred             C
Confidence            3

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=92.75  E-value=8  Score=35.62  Aligned_cols=64  Identities=23%  Similarity=0.223  Sum_probs=45.3

Q ss_pred             HHHHHHHHhcCCchhHHHHHHHHHhcCCCCH-----HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHH
Q 008442           27 MIYLKYEQSSGDPGRVQLLYERAITDFPVSS-----DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGE   93 (565)
Q Consensus        27 ~~yi~~e~~~~~~~~~~~lyERal~~~p~~~-----~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~   93 (565)
                      -.-+.-....|+...+...|+..+..+|.+.     .+|+.++.|.   .++.+.+...|++-++..|.+..
T Consensus         9 Y~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~---~~~y~~A~~~~~~fi~~yP~~~~   77 (203)
T PF13525_consen    9 YQKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYK---QGDYEEAIAAYERFIKLYPNSPK   77 (203)
T ss_dssp             HHHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHH---TT-HHHHHHHHHHHHHH-TT-TT
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHH---cCCHHHHHHHHHHHHHHCCCCcc
Confidence            3344445678999999999999999999875     3777776653   34677899999999999997653

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=92.73  E-value=0.052  Score=50.08  Aligned_cols=60  Identities=18%  Similarity=0.298  Sum_probs=47.4

Q ss_pred             HHHHhc-cCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          408 LRRFFS-DVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       408 l~~~f~-~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      |...|+ +||+|.++.|-.+. .-.-+|-+||.|..+++|++|+. +|+.-+.|++|...++.
T Consensus        85 ~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   85 VFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            333334 89999998665442 44567999999999999999998 89999999999877753

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=92.69  E-value=0.43  Score=49.31  Aligned_cols=78  Identities=18%  Similarity=0.173  Sum_probs=61.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhc-cCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCccc---CCeE
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFS-DVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMF---LGKK  461 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~-~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~---~g~~  461 (565)
                      +....+.|+|.||-.-+|.-.|+.++. .+|.|.+.  ..|+    -+..|||.|.+.+.|.+... |+|...   +++.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~--WmDk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF--WMDK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHH--HHHH----hhcceeEecccHHHHHHHHHHHhccccCCCCCce
Confidence            445568999999999999999999998 56777665  3332    35689999999999998887 888764   5778


Q ss_pred             EEEeecCCC
Q 008442          462 LSIARSNPK  470 (565)
Q Consensus       462 l~v~~a~~~  470 (565)
                      |.|.+....
T Consensus       514 L~adf~~~d  522 (718)
T KOG2416|consen  514 LIADFVRAD  522 (718)
T ss_pred             eEeeecchh
Confidence            888887543

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=92.26  E-value=1.7  Score=47.64  Aligned_cols=68  Identities=6%  Similarity=0.108  Sum_probs=47.2

Q ss_pred             eEEEc-CCCCCCCHHHHHHHhccCCCe-----eEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          393 TAFLS-NINLKATYEDLRRFFSDVGGV-----SSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       393 ~l~V~-nl~~~~~~~~l~~~f~~~G~i-----~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      ++||. +=-..++..+|-.++..-+.|     -.|+|..        .|.||+... ..+...+. +++..+.|++|.|.
T Consensus       488 ~~~~~~g~~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~~--------~~s~v~~~~-~~~~~~~~~~~~~~~~~~~~~~~  558 (629)
T PRK11634        488 LYRIEVGRDDGVEVRHIVGAIANEGDISSRYIGNIKLFA--------SHSTIELPK-GMPGEVLQHFTRTRILNKPMNMQ  558 (629)
T ss_pred             EEEEecccccCCCHHHHHHHHHhhcCCChhhCCcEEEeC--------CceEEEcCh-hhHHHHHHHhccccccCCceEEE
Confidence            45553 223458888888888765544     3455543        389999875 44666676 78888999999999


Q ss_pred             ecCC
Q 008442          466 RSNP  469 (565)
Q Consensus       466 ~a~~  469 (565)
                      .+..
T Consensus       559 ~~~~  562 (629)
T PRK11634        559 LLGD  562 (629)
T ss_pred             ECCC
Confidence            8753

>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=92.25  E-value=0.34  Score=43.46  Aligned_cols=81  Identities=12%  Similarity=0.091  Sum_probs=48.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhcc-CCCe---eEEEEeecCC-CC-CcceEEEEEecCHHHHHHHHH-cCCcccCC--
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSD-VGGV---SSIRILHDKF-TG-KSRGLAYVDFIDDEHLAAAVA-KNKQMFLG--  459 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~-~G~i---~~~~~~~~~~-~g-~~~g~afv~f~~~~~a~~a~~-~~~~~~~g--  459 (565)
                      .+..+|.|++||++++++++...++. ++.-   ..+.-..... .. ..-.-|||.|.+.+++..-.. ++|+.+.+  
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            34679999999999999999997776 5554   3333212211 11 123578999999999887776 78877632  


Q ss_pred             -e--EEEEeecCC
Q 008442          460 -K--KLSIARSNP  469 (565)
Q Consensus       460 -~--~l~v~~a~~  469 (565)
                       .  +..|.+|.-
T Consensus        85 g~~~~~~VE~Apy   97 (176)
T PF03467_consen   85 GNEYPAVVEFAPY   97 (176)
T ss_dssp             S-EEEEEEEE-SS
T ss_pred             CCCcceeEEEcch
Confidence             2  456677644

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.

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=92.01  E-value=0.17  Score=31.46  Aligned_cols=26  Identities=15%  Similarity=0.254  Sum_probs=19.6

Q ss_pred             HHHHHHhcCCCCHHHHHHHHHHHHHh
Q 008442           45 LYERAITDFPVSSDLWLDYTQYLDKT   70 (565)
Q Consensus        45 lyERal~~~p~~~~lW~~Y~~~l~~~   70 (565)
                      +|++||..+|.++..|..|+.++...
T Consensus         1 ~y~kAie~~P~n~~a~~nla~~~~~~   26 (34)
T PF13431_consen    1 CYKKAIELNPNNAEAYNNLANLYLNQ   26 (34)
T ss_pred             ChHHHHHHCCCCHHHHHHHHHHHHHC
Confidence            37788888888888888888765543

>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=91.37  E-value=3.9  Score=40.05  Aligned_cols=61  Identities=15%  Similarity=0.119  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCCh-HHHHHHHHHH
Q 008442          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHI-NEARSIYKRC  243 (565)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~-~~aR~i~~~a  243 (565)
                      ..+....+-.....+ ++++|.++++.++...|.+.+.....|-+....|+. +.+...+...
T Consensus       201 ~~~lng~A~~~l~~~-~~~eAe~~L~~al~~~~~~~d~LaNliv~~~~~gk~~~~~~~~l~qL  262 (290)
T PF04733_consen  201 PKLLNGLAVCHLQLG-HYEEAEELLEEALEKDPNDPDTLANLIVCSLHLGKPTEAAERYLSQL  262 (290)
T ss_dssp             HHHHHHHHHHHHHCT--HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHTT-TCHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHhC-CHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCChhHHHHHHHHH
Confidence            334444444555555 666666666666666666666666666666666655 4455555444

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=90.94  E-value=1.3  Score=45.25  Aligned_cols=67  Identities=12%  Similarity=-0.023  Sum_probs=58.6

Q ss_pred             CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHH---HHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          178 TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLE---AWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       178 ~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~---lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      .+.....|..++..+...+ ++++|...|+++|...|++.+   .|...+-.+..+|+++.|...|++|+.
T Consensus        71 dP~~a~a~~NLG~AL~~lG-ryeEAIa~f~rALeL~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALe  140 (453)
T PLN03098         71 DVKTAEDAVNLGLSLFSKG-RVKDALAQFETALELNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALR  140 (453)
T ss_pred             CCCCHHHHHHHHHHHHHcC-CHHHHHHHHHHHHhhCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3445667777887788888 999999999999999999875   499999999999999999999999997

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=90.45  E-value=1.2  Score=45.43  Aligned_cols=69  Identities=13%  Similarity=0.075  Sum_probs=57.4

Q ss_pred             CChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHH---HHHHHHHHHHhcchhhHHHHHHHHHHHc
Q 008442           18 SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDL---WLDYTQYLDKTLKVGNVVRDVYSRATKN   87 (565)
Q Consensus        18 ~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~l---W~~Y~~~l~~~~~~~~~~~~v~erAl~~   87 (565)
                      .+|.....|..+.......|+++.+...|++||..+|.+.+.   |...+..+. ..+..+.+.+.|++|+..
T Consensus        70 ~dP~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~aeA~~A~yNLAcaya-~LGr~dEAla~LrrALel  141 (453)
T PLN03098         70 ADVKTAEDAVNLGLSLFSKGRVKDALAQFETALELNPNPDEAQAAYYNKACCHA-YREEGKKAADCLRTALRD  141 (453)
T ss_pred             CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHHHH-HcCCHHHHHHHHHHHHHh
Confidence            356688899999999999999999999999999999999864   766665444 445788899999999995

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=90.32  E-value=5.4  Score=34.15  Aligned_cols=69  Identities=16%  Similarity=0.123  Sum_probs=53.8

Q ss_pred             HHHHHHhcCCchhHHHHHHHHHhcCCCCH-----HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHH-HHHHHH
Q 008442           29 YLKYEQSSGDPGRVQLLYERAITDFPVSS-----DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGEL-WVRSLL  100 (565)
Q Consensus        29 yi~~e~~~~~~~~~~~lyERal~~~p~~~-----~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~l-W~~yi~  100 (565)
                      =..-..+.|+...+...||.....+|...     .||+.|+-|..   ++.+.+...++|-|+..|.++.+ |..|+.
T Consensus        16 ~a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~---~~y~~A~a~~~rFirLhP~hp~vdYa~Y~~   90 (142)
T PF13512_consen   16 EAQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQ---GDYEEAIAAYDRFIRLHPTHPNVDYAYYMR   90 (142)
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHc---cCHHHHHHHHHHHHHhCCCCCCccHHHHHH
Confidence            33445667899999999999999999764     69999998753   36678999999999999987654 444444

>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production

Probab=89.91  E-value=2.6  Score=36.34  Aligned_cols=61  Identities=20%  Similarity=0.150  Sum_probs=50.8

Q ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          184 LYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      .....+......+ +++.|..++.+++...|.+..+|...+......|+...|..+|.++..
T Consensus        64 ~~~~l~~~~~~~~-~~~~a~~~~~~~l~~dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~  124 (146)
T PF03704_consen   64 ALERLAEALLEAG-DYEEALRLLQRALALDPYDEEAYRLLMRALAAQGRRAEALRVYERYRR  124 (146)
T ss_dssp             HHHHHHHHHHHTT--HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcc-CHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3445566666777 999999999999999999999999999999999999999999999854

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=89.43  E-value=0.2  Score=48.38  Aligned_cols=82  Identities=13%  Similarity=0.258  Sum_probs=60.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHH-H--HHhccCCCeeEEEEeecCC--CCC-cceEEEEEecCHHHHHHHHH-cCCcccCCeE
Q 008442          389 TDECTAFLSNINLKATYEDL-R--RFFSDVGGVSSIRILHDKF--TGK-SRGLAYVDFIDDEHLAAAVA-KNKQMFLGKK  461 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l-~--~~f~~~G~i~~~~~~~~~~--~g~-~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~  461 (565)
                      ....-+||-+|+.....+.+ +  ..|.+||.|..|.+-.+..  .+. .-.-+||+|...++|..||. .+|..++|+.
T Consensus        75 Vqknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~  154 (327)
T KOG2068|consen   75 VQKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRA  154 (327)
T ss_pred             hhhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhh
Confidence            34567899999988655443 3  4688999999998877651  111 12347999999999999998 7999999998


Q ss_pred             EEEeecCCC
Q 008442          462 LSIARSNPK  470 (565)
Q Consensus       462 l~v~~a~~~  470 (565)
                      ++..+..++
T Consensus       155 lka~~gttk  163 (327)
T KOG2068|consen  155 LKASLGTTK  163 (327)
T ss_pred             hHHhhCCCc
Confidence            766665443

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=89.23  E-value=4.4  Score=34.67  Aligned_cols=54  Identities=26%  Similarity=0.327  Sum_probs=43.4

Q ss_pred             hhhHHHHHHHhcCCCCCh-HhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHH
Q 008442            3 NARAHLEEQISRQDLSDS-EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSD   58 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~-~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~   58 (565)
                      ++.+.||....+.|.... +..++|+.|+-|  +.++.+.+...|+|-|..+|.++.
T Consensus        28 ~A~~~le~L~~ryP~g~ya~qAqL~l~yayy--~~~~y~~A~a~~~rFirLhP~hp~   82 (142)
T PF13512_consen   28 EAIKQLEALDTRYPFGEYAEQAQLDLAYAYY--KQGDYEEAIAAYDRFIRLHPTHPN   82 (142)
T ss_pred             HHHHHHHHHHhcCCCCcccHHHHHHHHHHHH--HccCHHHHHHHHHHHHHhCCCCCC
Confidence            467888888888876532 456678888775  467889999999999999999987

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=89.13  E-value=33  Score=36.32  Aligned_cols=117  Identities=12%  Similarity=0.119  Sum_probs=73.2

Q ss_pred             HHHHHHHHHhhhcCCchh-HHHHHHHHHHHHHcCCChHHHHHHHHHHHHH-------ccchHHHHHHHHHHHHHcCChHH
Q 008442          164 FQRASDYLSEQMKNTDGL-LRLYAYWAHLEQSMGKDMVSARGVWERLLKI-------SGAMLEAWQSYISMEIELDHINE  235 (565)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~-~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~-------~~~~~~lw~~yi~~e~~~~~~~~  235 (565)
                      ..+++.++......++.. ..+....+++....| ++..|.+|+...+..       ..+.+.+.-.-+.+....++.+.
T Consensus       357 ~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is~g-n~~~A~~il~~~~~~~~ss~~~~~~~P~~V~aiv~l~~~~~~~~~  435 (652)
T KOG2376|consen  357 HKKAIELLLQFADGHPEKSKVVLLLRAQLKISQG-NPEVALEILSLFLESWKSSILEAKHLPGTVGAIVALYYKIKDNDS  435 (652)
T ss_pred             HhhhHHHHHHHhccCCchhHHHHHHHHHHHHhcC-CHHHHHHHHHHHhhhhhhhhhhhccChhHHHHHHHHHHhccCCcc
Confidence            455666665555444333 334455678888888 999999999844422       22334444444445566778888


Q ss_pred             HHHHHHHHHhccc---CCC-CcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          236 ARSIYKRCYSKRF---TGT-GSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       236 aR~i~~~al~~~~---~~~-~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      |-.++..|+.-.-   +.. .-..+|.....|+.++|+.++....++...
T Consensus       436 a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~lr~G~~~ea~s~leel~  485 (652)
T KOG2376|consen  436 ASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKLRHGNEEEASSLLEELV  485 (652)
T ss_pred             HHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHHhcCchHHHHHHHHHHH
Confidence            8889988875210   111 112466777889999999887776665544

>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]

Probab=89.02  E-value=27  Score=35.09  Aligned_cols=49  Identities=10%  Similarity=-0.054  Sum_probs=35.5

Q ss_pred             ChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhc
Q 008442          198 DMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       198 ~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~  246 (565)
                      +...-.+..++.++.+|+++.+|.....+...++.+.+|...|+.|+..
T Consensus       309 d~~~l~k~~e~~l~~h~~~p~L~~tLG~L~~k~~~w~kA~~~leaAl~~  357 (400)
T COG3071         309 DPEPLIKAAEKWLKQHPEDPLLLSTLGRLALKNKLWGKASEALEAALKL  357 (400)
T ss_pred             CchHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhHHHHHHHHHHHHHhc
Confidence            5666666777777777777777777777777777777777777777753

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=89.00  E-value=12  Score=37.65  Aligned_cols=84  Identities=12%  Similarity=0.216  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcC-ChHHHHHHH
Q 008442          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELD-HINEARSIY  240 (565)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~-~~~~aR~i~  240 (565)
                      ..|..|+..+...+...++.+.-.-.-.+.....+ +++.||..|+++++..|.+-.+-..++.+-.... ..++.+++|
T Consensus       271 ~~~~~Ai~~c~kvLe~~~~N~KALyRrG~A~l~~~-e~~~A~~df~ka~k~~P~Nka~~~el~~l~~k~~~~~~kekk~y  349 (397)
T KOG0543|consen  271 KEYKEAIESCNKVLELDPNNVKALYRRGQALLALG-EYDLARDDFQKALKLEPSNKAARAELIKLKQKIREYEEKEKKMY  349 (397)
T ss_pred             hhHHHHHHHHHHHHhcCCCchhHHHHHHHHHHhhc-cHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555666666666543333333333344455566 8888888888888888888888888887765443 445668888


Q ss_pred             HHHHhc
Q 008442          241 KRCYSK  246 (565)
Q Consensus       241 ~~al~~  246 (565)
                      .+++.+
T Consensus       350 ~~mF~k  355 (397)
T KOG0543|consen  350 ANMFAK  355 (397)
T ss_pred             HHHhhc
Confidence            888764

>KOG3824 consensus Huntingtin interacting protein HYPE [General function prediction only]

Probab=88.82  E-value=1.7  Score=41.63  Aligned_cols=59  Identities=17%  Similarity=0.243  Sum_probs=50.2

Q ss_pred             HhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHH
Q 008442           34 QSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGE   93 (565)
Q Consensus        34 ~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~   93 (565)
                      .+.|+.+++..+||.||...|.++++.+.|..|.+.+. ++-.+-..|-+||...|...+
T Consensus       127 ~~~Gk~ekA~~lfeHAlalaP~~p~~L~e~G~f~E~~~-~iv~ADq~Y~~ALtisP~nse  185 (472)
T KOG3824|consen  127 RKDGKLEKAMTLFEHALALAPTNPQILIEMGQFREMHN-EIVEADQCYVKALTISPGNSE  185 (472)
T ss_pred             HhccchHHHHHHHHHHHhcCCCCHHHHHHHhHHHHhhh-hhHhhhhhhheeeeeCCCchH
Confidence            35688899999999999999999999999999998774 555577899999998886554

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=88.33  E-value=9  Score=31.89  Aligned_cols=60  Identities=13%  Similarity=-0.042  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHHHHHccc---hHHHHHHHHHHHHHcCChHHHHHHHHHHH
Q 008442          184 LYAYWAHLEQSMGKDMVSARGVWERLLKISGA---MLEAWQSYISMEIELDHINEARSIYKRCY  244 (565)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~---~~~lw~~yi~~e~~~~~~~~aR~i~~~al  244 (565)
                      .++.++.....+| .+++|..+++.++..+|+   ...++..++.-....|..+.|...+-.++
T Consensus        40 a~i~lastlr~LG-~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L~~~gr~~eAl~~~l~~l  102 (120)
T PF12688_consen   40 ALIQLASTLRNLG-RYDEALALLEEALEEFPDDELNAALRVFLALALYNLGRPKEALEWLLEAL  102 (120)
T ss_pred             HHHHHHHHHHHcC-CHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3444444444455 555555555555555444   33444444444444555555544444443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=88.03  E-value=2.8  Score=35.27  Aligned_cols=69  Identities=22%  Similarity=0.214  Sum_probs=49.4

Q ss_pred             CCeEEEcCCCCCCCH-HHHH---HHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEee
Q 008442          391 ECTAFLSNINLKATY-EDLR---RFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIAR  466 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~-~~l~---~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~  466 (565)
                      =.||.|.=|..++.. +|++   ..++.||+|.+|.+     .|+  --|.|.|.|..+|-.|+..-+....|..+..++
T Consensus        86 MsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~-----cGr--qsavVvF~d~~SAC~Av~Af~s~~pgtm~qCsW  158 (166)
T PF15023_consen   86 MSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTL-----CGR--QSAVVVFKDITSACKAVSAFQSRAPGTMFQCSW  158 (166)
T ss_pred             ceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeee-----cCC--ceEEEEehhhHHHHHHHHhhcCCCCCceEEeec
Confidence            468999877766543 4444   45688999999876     444  379999999999999997433355566666655

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=88.01  E-value=0.33  Score=47.17  Aligned_cols=79  Identities=18%  Similarity=0.140  Sum_probs=64.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCC-cccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK-QMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a  467 (565)
                      ...+++|++++...+.+.+...++..+|.+....+........++|++++.|...+.+..|+.+.+ ..+.+..+.....
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            456899999999999999999999999988777766655688899999999999999999999765 4566665554443

>PF06552 TOM20_plant: Plant specific mitochondrial import receptor subunit TOM20; InterPro: IPR010547 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins

Probab=87.98  E-value=9.6  Score=33.96  Aligned_cols=58  Identities=21%  Similarity=0.241  Sum_probs=33.1

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCC-------chhHHHHHHHHHhcCCCCHH-HHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGD-------PGRVQLLYERAITDFPVSSD-LWL   61 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~-------~~~~~~lyERal~~~p~~~~-lW~   61 (565)
                      .+|+.+|..+..+|. |.+++-.|-..+...-....       ++.+..-||.||..+|...+ +|.
T Consensus         9 ~ark~aea~y~~nP~-DadnL~~WG~ALLELAqfk~g~es~~miedAisK~eeAL~I~P~~hdAlw~   74 (186)
T PF06552_consen    9 HARKKAEAAYAKNPL-DADNLTNWGGALLELAQFKQGPESKKMIEDAISKFEEALKINPNKHDALWC   74 (186)
T ss_dssp             HHHHHHHHHHHH-TT--HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHH
T ss_pred             HHHHHHHHHHHhCcH-hHHHHHHHHHHHHHHHhccCcchHHHHHHHHHHHHHHHHhcCCchHHHHHH
Confidence            378888888888885 55555566555554433222       23456677788888887654 444

Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [].; GO: 0045040 protein import into mitochondrial outer membrane, 0005742 mitochondrial outer membrane translocase complex; PDB: 1ZU2_A.

>PRK15331 chaperone protein SicA; Provisional

Probab=87.18  E-value=20  Score=31.51  Aligned_cols=88  Identities=9%  Similarity=0.015  Sum_probs=67.3

Q ss_pred             HcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHH
Q 008442          194 SMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDF  273 (565)
Q Consensus       194 ~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~  273 (565)
                      ..| +++.|..+|.-+....+.+..+|+-++-.....++++.|..+|..|...  ..++|...+..- +.-..-|+.+.+
T Consensus        49 ~~G-k~~eA~~~F~~L~~~d~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l--~~~dp~p~f~ag-qC~l~l~~~~~A  124 (165)
T PRK15331         49 NQG-RLDEAETFFRFLCIYDFYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTL--LKNDYRPVFFTG-QCQLLMRKAAKA  124 (165)
T ss_pred             HCC-CHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc--ccCCCCccchHH-HHHHHhCCHHHH
Confidence            556 9999999999999988888999999999999999999999999999763  233443333221 222345888888


Q ss_pred             HHHHHHHhhHHH
Q 008442          274 DHSVQKVTPRLE  285 (565)
Q Consensus       274 ~~~~~k~~~~~~  285 (565)
                      +.++..++.+.+
T Consensus       125 ~~~f~~a~~~~~  136 (165)
T PRK15331        125 RQCFELVNERTE  136 (165)
T ss_pred             HHHHHHHHhCcc
Confidence            888888776543

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=87.03  E-value=1.6  Score=26.50  Aligned_cols=32  Identities=13%  Similarity=0.071  Sum_probs=20.1

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHhcCCCC
Q 008442           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVS   56 (565)
Q Consensus        25 ~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~   56 (565)
                      .|..........|+.+.++..|+++|..+|.+
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~al~l~p~~   34 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKALELDPNN   34 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTS
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHHCcCC
Confidence            45555666666677777777777777766653

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=86.42  E-value=0.52  Score=49.54  Aligned_cols=68  Identities=18%  Similarity=0.142  Sum_probs=57.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ...+|||+|+...+..+-++.+...||.|.++....         |||.+|..+.....|+. +....++|..+.+..
T Consensus        39 ~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   39 PRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             CCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            457999999999999999999999999887754321         99999999999999987 577778888776655

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=86.20  E-value=3.5  Score=39.24  Aligned_cols=72  Identities=14%  Similarity=0.157  Sum_probs=54.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeE-EEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKK-LSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~-l~v~~a~~  469 (565)
                      ..-|-|-++|+.-. .-|-..|++||.|.+....   .+|   .+-+|-|.+..+|++||..||..|+|.. |-|..+.-
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~---~ng---NwMhirYssr~~A~KALskng~ii~g~vmiGVkpCtD  269 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP---SNG---NWMHIRYSSRTHAQKALSKNGTIIDGDVMIGVKPCTD  269 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecC---CCC---ceEEEEecchhHHHHhhhhcCeeeccceEEeeeecCC
Confidence            45666668887644 5677789999998875433   133   3899999999999999999999999874 55766543

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=85.82  E-value=18  Score=30.47  Aligned_cols=84  Identities=14%  Similarity=0.186  Sum_probs=64.4

Q ss_pred             HcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHH---HHHHhCCH
Q 008442          194 SMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLR---FEREYGTL  270 (565)
Q Consensus       194 ~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~---fE~~~G~~  270 (565)
                      ..+ +.+.|.+.|.++|...|.....+..-++-.+..|+.+.|-.-+++|++-  ..+....-+++|++   +-+..|+.
T Consensus        55 E~g-~Ld~AlE~F~qal~l~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleL--ag~~trtacqa~vQRg~lyRl~g~d  131 (175)
T KOG4555|consen   55 EAG-DLDGALELFGQALCLAPERASAYNNRAQALRLQGDDEEALDDLNKALEL--AGDQTRTACQAFVQRGLLYRLLGND  131 (175)
T ss_pred             hcc-chHHHHHHHHHHHHhcccchHhhccHHHHHHHcCChHHHHHHHHHHHHh--cCccchHHHHHHHHHHHHHHHhCch
Confidence            345 8889999999999988888888888888888889999999999999862  33334456677765   56667888


Q ss_pred             HHHHHHHHHH
Q 008442          271 EDFDHSVQKV  280 (565)
Q Consensus       271 ~~~~~~~~k~  280 (565)
                      +.++.-+..+
T Consensus       132 d~AR~DFe~A  141 (175)
T KOG4555|consen  132 DAARADFEAA  141 (175)
T ss_pred             HHHHHhHHHH
Confidence            8777666554

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=85.72  E-value=2.2  Score=38.48  Aligned_cols=69  Identities=20%  Similarity=0.231  Sum_probs=43.4

Q ss_pred             hcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhc
Q 008442           35 SSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSR  106 (565)
Q Consensus        35 ~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~  106 (565)
                      ++|++..+..-|.+||..||..+.- ..-+-|..+.  ..-.-+.-++-||..|...-+||-.|...|++..
T Consensus       107 ~ngdyeeA~skY~~Ale~cp~~~~e-~rsIly~Nra--aa~iKl~k~e~aI~dcsKaiel~pty~kAl~RRA  175 (271)
T KOG4234|consen  107 KNGDYEEANSKYQEALESCPSTSTE-ERSILYSNRA--AALIKLRKWESAIEDCSKAIELNPTYEKALERRA  175 (271)
T ss_pred             hcccHHHHHHHHHHHHHhCccccHH-HHHHHHhhhH--HHHHHhhhHHHHHHHHHhhHhcCchhHHHHHHHH
Confidence            4678889999999999999877651 1111121110  0011234566777777777778888888787643

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=85.34  E-value=2.8  Score=25.41  Aligned_cols=27  Identities=19%  Similarity=0.305  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          219 AWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       219 lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      +|..........|+++.|+..|++++.
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            344444444445555555555555543

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

>PF06552 TOM20_plant: Plant specific mitochondrial import receptor subunit TOM20; InterPro: IPR010547 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins

Probab=84.86  E-value=12  Score=33.26  Aligned_cols=81  Identities=20%  Similarity=0.150  Sum_probs=48.0

Q ss_pred             hhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh--c-------chhhHHHHHHHHHHHcCCCCH-HHHHH---HHHHHHHhc
Q 008442           40 GRVQLLYERAITDFPVSSDLWLDYTQYLDKT--L-------KVGNVVRDVYSRATKNCPWVG-ELWVR---SLLSLERSR  106 (565)
Q Consensus        40 ~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~--~-------~~~~~~~~v~erAl~~~p~~~-~lW~~---yi~~le~~~  106 (565)
                      +.++..||.....+|.+.+.+..+.-.|...  .       +..+.+..-|+.||+.+|..+ .+|+-   |.. +-...
T Consensus         8 E~ark~aea~y~~nP~DadnL~~WG~ALLELAqfk~g~es~~miedAisK~eeAL~I~P~~hdAlw~lGnA~ts-~A~l~   86 (186)
T PF06552_consen    8 EHARKKAEAAYAKNPLDADNLTNWGGALLELAQFKQGPESKKMIEDAISKFEEALKINPNKHDALWCLGNAYTS-LAFLT   86 (186)
T ss_dssp             HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHH-HHHH-
T ss_pred             HHHHHHHHHHHHhCcHhHHHHHHHHHHHHHHHhccCcchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHH-HHhhc
Confidence            3577889999999999999888876554332  1       123457788999999999875 46643   222 22223


Q ss_pred             CCHHHHHHHHHHHHh
Q 008442          107 ASEEEISTVFEKSLL  121 (565)
Q Consensus       107 ~~~~~~~~if~ral~  121 (565)
                      .+..++...|++|..
T Consensus        87 ~d~~~A~~~F~kA~~  101 (186)
T PF06552_consen   87 PDTAEAEEYFEKATE  101 (186)
T ss_dssp             --HHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHH
Confidence            444566666666654

Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [].; GO: 0045040 protein import into mitochondrial outer membrane, 0005742 mitochondrial outer membrane translocase complex; PDB: 1ZU2_A.

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=84.62  E-value=5.8  Score=29.72  Aligned_cols=70  Identities=16%  Similarity=0.115  Sum_probs=45.9

Q ss_pred             cchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCC--CcHHHHHHHH---HHHHHhCCHHHHHHHHHHHhhHH
Q 008442          214 GAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGT--GSEDICHAWL---RFEREYGTLEDFDHSVQKVTPRL  284 (565)
Q Consensus       214 ~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~--~~~~i~~~~~---~fE~~~G~~~~~~~~~~k~~~~~  284 (565)
                      |+...++...+......|+++.|...|++++.. ....  ....+...+.   ..-...|+.+.+...+++++...
T Consensus         2 ~~~a~~~~~la~~~~~~~~~~~A~~~~~~al~~-~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~i~   76 (78)
T PF13424_consen    2 PDTANAYNNLARVYRELGRYDEALDYYEKALDI-EEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALDIF   76 (78)
T ss_dssp             HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-HHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhh
Confidence            455667888888889999999999999999864 2211  2223333333   34555677777777777765443

...

>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=84.57  E-value=12  Score=30.50  Aligned_cols=66  Identities=20%  Similarity=0.166  Sum_probs=46.3

Q ss_pred             CeEEEcCCCCC-CCHHHHHHHhccC-CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCC
Q 008442          392 CTAFLSNINLK-ATYEDLRRFFSDV-GGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLG  459 (565)
Q Consensus       392 ~~l~V~nl~~~-~~~~~l~~~f~~~-G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g  459 (565)
                      +++.|--.|+. ++.++|..+.+.+ ..|..++|+++.  ..++-.+.+.|.+.++|..-.. .||+.+..
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            44544444555 5556676555555 457888998874  3466788999999999998887 79988653

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=84.54  E-value=38  Score=32.28  Aligned_cols=180  Identities=13%  Similarity=0.121  Sum_probs=99.7

Q ss_pred             HHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHH
Q 008442           59 LWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRI  138 (565)
Q Consensus        59 lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~  138 (565)
                      --..++.|++......+.+.+++|........+..+|..-...+-.+.++++++....++...........++.+-+.+ 
T Consensus        74 Avr~~a~~~~~e~~~~~~~~~l~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~~~lE~~Al~VqI~lk~~r-  152 (299)
T KOG3081|consen   74 AVRLLAEYLELESNKKSILASLYELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLGENLEAAALNVQILLKMHR-  152 (299)
T ss_pred             HHHHHHHHhhCcchhHHHHHHHHHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhccchHHHHHHHHHHHHHHHH-
Confidence            4455666655444334456667777666555555677665444445567788887777662210000011111111111 


Q ss_pred             HHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhc--CCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccch
Q 008442          139 DGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMK--NTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM  216 (565)
Q Consensus       139 ~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~--~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~  216 (565)
                                               ++-|...+.....  +.....+|-..|+.+-.--. .+..|--||+.+-.+++..
T Consensus       153 -------------------------~d~A~~~lk~mq~ided~tLtQLA~awv~la~gge-k~qdAfyifeE~s~k~~~T  206 (299)
T KOG3081|consen  153 -------------------------FDLAEKELKKMQQIDEDATLTQLAQAWVKLATGGE-KIQDAFYIFEELSEKTPPT  206 (299)
T ss_pred             -------------------------HHHHHHHHHHHHccchHHHHHHHHHHHHHHhccch-hhhhHHHHHHHHhcccCCC
Confidence                                     1112222222111  11222346666777765444 5778888899888876666


Q ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhC
Q 008442          217 LEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYG  268 (565)
Q Consensus       217 ~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G  268 (565)
                      +.+-.--+-.-...++++.|-.+++.+|.+  ...+|+.+. -.+-.-...|
T Consensus       207 ~~llnG~Av~~l~~~~~eeAe~lL~eaL~k--d~~dpetL~-Nliv~a~~~G  255 (299)
T KOG3081|consen  207 PLLLNGQAVCHLQLGRYEEAESLLEEALDK--DAKDPETLA-NLIVLALHLG  255 (299)
T ss_pred             hHHHccHHHHHHHhcCHHHHHHHHHHHHhc--cCCCHHHHH-HHHHHHHHhC
Confidence            776666666777788999999999999875  334454443 3444455556

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=84.47  E-value=57  Score=34.21  Aligned_cols=64  Identities=14%  Similarity=0.165  Sum_probs=34.3

Q ss_pred             hHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       181 ~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ..+++...+--+..++ .+..|.+-.+.+++.+|+....|+.=...+....+++.|-+.|..++.
T Consensus       391 Da~lYsNRAac~~kL~-~~~~aL~Da~~~ieL~p~~~kgy~RKg~al~~mk~ydkAleay~eale  454 (539)
T KOG0548|consen  391 DARLYSNRAACYLKLG-EYPEALKDAKKCIELDPNFIKAYLRKGAALRAMKEYDKALEAYQEALE  454 (539)
T ss_pred             hhHHHHHHHHHHHHHh-hHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3444444444444455 555555555555555555555555555555555555555555555554

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=83.99  E-value=90  Score=36.16  Aligned_cols=35  Identities=14%  Similarity=0.209  Sum_probs=19.3

Q ss_pred             HHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccc
Q 008442          115 VFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSG  149 (565)
Q Consensus       115 if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~  149 (565)
                      +|..||..-......+..++.+|.+.+++...+.+
T Consensus       923 Ly~~aL~ly~~~~e~~k~i~~~ya~hL~~~~~~~~  957 (1265)
T KOG1920|consen  923 LYDEALALYKPDSEKQKVIYEAYADHLREELMSDE  957 (1265)
T ss_pred             cchhhhheeccCHHHHHHHHHHHHHHHHHhccccH
Confidence            34444443333445566677777777766555443

>KOG1166 consensus Mitotic checkpoint serine/threonine protein kinase [Cell cycle control, cell division, chromosome partitioning]

Probab=83.94  E-value=9.8  Score=43.35  Aligned_cols=70  Identities=10%  Similarity=0.201  Sum_probs=53.9

Q ss_pred             ChHHHHHHHHHHHHH--ccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCC
Q 008442          198 DMVSARGVWERLLKI--SGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGT  269 (565)
Q Consensus       198 ~~~~ar~i~e~~l~~--~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~  269 (565)
                      ....++.+|..+...  -.....++..|+.++...+.+.+|.++|..++++.  .-....+-.++..|..+.|-
T Consensus        93 ~~~d~~d~f~~m~~kgIg~~lalfYe~~a~~lE~k~~~keA~~v~q~Giq~~--aeP~~rL~~~~~~F~~r~~r  164 (974)
T KOG1166|consen   93 ELQDAEDFFSYLENKGIGTTLALFYEAYAKHLERKEYFKEAKEVFQLGIQNK--AEPLERLLRQYSNFQQRLMR  164 (974)
T ss_pred             HHhhHHHHHHHHHhccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--cCCHHHHHHHHHHHHHHHhh
Confidence            456788888888876  34456678888888888888999999999999853  23356778888889888764

>PRK15331 chaperone protein SicA; Provisional

Probab=83.18  E-value=25  Score=30.93  Aligned_cols=99  Identities=9%  Similarity=-0.085  Sum_probs=69.4

Q ss_pred             hHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCH--HHHHH
Q 008442           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVG--ELWVR   97 (565)
Q Consensus        20 ~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~--~lW~~   97 (565)
                      .+.++.--.|.--.-..|+.+.+..+|.-.+...|.+++.|+..+.- ....+..+.+...|..|...-+.++  -++..
T Consensus        34 ~~~le~iY~~Ay~~y~~Gk~~eA~~~F~~L~~~d~~n~~Y~~GLaa~-~Q~~k~y~~Ai~~Y~~A~~l~~~dp~p~f~ag  112 (165)
T PRK15331         34 QDMMDGLYAHAYEFYNQGRLDEAETFFRFLCIYDFYNPDYTMGLAAV-CQLKKQFQKACDLYAVAFTLLKNDYRPVFFTG  112 (165)
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHcccCCCCccchHH
Confidence            33444444444445567899999999999999999999999998873 4445577889999999988654433  23222


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhc
Q 008442           98 SLLSLERSRASEEEISTVFEKSLLC  122 (565)
Q Consensus        98 yi~~le~~~~~~~~~~~if~ral~~  122 (565)
                      -.. +  ..++.+.++..|+-++..
T Consensus       113 qC~-l--~l~~~~~A~~~f~~a~~~  134 (165)
T PRK15331        113 QCQ-L--LMRKAAKARQCFELVNER  134 (165)
T ss_pred             HHH-H--HhCCHHHHHHHHHHHHhC
Confidence            111 2  247788899999988874

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=83.11  E-value=3  Score=43.11  Aligned_cols=69  Identities=22%  Similarity=0.314  Sum_probs=53.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhcc--CCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-c--CCcccCCeEE
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSD--VGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-K--NKQMFLGKKL  462 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~--~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~--~~~~~~g~~l  462 (565)
                      ....|.|+++-+|..+..++++.+|..  |-.+.+|.+-.+.       -=||+|++..+|+.|-+ +  .-+.|.|++|
T Consensus       172 ~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpI  244 (684)
T KOG2591|consen  172 NHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPI  244 (684)
T ss_pred             CcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcch
Confidence            345688999999999999999999964  7788888875542       35999999999999976 4  2345777765


Q ss_pred             E
Q 008442          463 S  463 (565)
Q Consensus       463 ~  463 (565)
                      .
T Consensus       245 m  245 (684)
T KOG2591|consen  245 M  245 (684)
T ss_pred             h
Confidence            3

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=82.88  E-value=27  Score=29.37  Aligned_cols=87  Identities=15%  Similarity=0.065  Sum_probs=64.8

Q ss_pred             cCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCC-CCHHHHHHHHH--HHHHhcCCHHHH
Q 008442           36 SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCP-WVGELWVRSLL--SLERSRASEEEI  112 (565)
Q Consensus        36 ~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p-~~~~lW~~yi~--~le~~~~~~~~~  112 (565)
                      .|+.+.+.+.|.++|..+|...+.+..-+.-+.-.+ +.+.+++-+++|+..-. ....--..|+.  .+-+..++.+.+
T Consensus        56 ~g~Ld~AlE~F~qal~l~P~raSayNNRAQa~RLq~-~~e~ALdDLn~AleLag~~trtacqa~vQRg~lyRl~g~dd~A  134 (175)
T KOG4555|consen   56 AGDLDGALELFGQALCLAPERASAYNNRAQALRLQG-DDEEALDDLNKALELAGDQTRTACQAFVQRGLLYRLLGNDDAA  134 (175)
T ss_pred             ccchHHHHHHHHHHHHhcccchHhhccHHHHHHHcC-ChHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHhCchHHH
Confidence            578899999999999999999999998888665444 66779999999998653 32222222321  244557888999


Q ss_pred             HHHHHHHHhcc
Q 008442          113 STVFEKSLLCA  123 (565)
Q Consensus       113 ~~if~ral~~~  123 (565)
                      +.-|++|-+.+
T Consensus       135 R~DFe~AA~LG  145 (175)
T KOG4555|consen  135 RADFEAAAQLG  145 (175)
T ss_pred             HHhHHHHHHhC
Confidence            99999988644

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A

Probab=82.62  E-value=3.8  Score=24.86  Aligned_cols=29  Identities=21%  Similarity=0.382  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHcCCChHHHHHHHHHHHHHcc
Q 008442          185 YAYWAHLEQSMGKDMVSARGVWERLLKISG  214 (565)
Q Consensus       185 ~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~  214 (565)
                      |...+.++...+ +++.|...|+++++..|
T Consensus         4 ~~~lg~~y~~~~-~~~~A~~~~~~a~~~~~   32 (34)
T PF13181_consen    4 YYNLGKIYEQLG-DYEEALEYFEKALELNP   32 (34)
T ss_dssp             HHHHHHHHHHTT-SHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcC-CHHHHHHHHHHHHhhCC
Confidence            334444444444 55555555555554433

...

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=82.59  E-value=14  Score=35.15  Aligned_cols=56  Identities=16%  Similarity=0.070  Sum_probs=40.3

Q ss_pred             HHHHHHcCCChHHHHHHHHHHHHHccch---HHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          189 AHLEQSMGKDMVSARGVWERLLKISGAM---LEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       189 a~~e~~~~~~~~~ar~i~e~~l~~~~~~---~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      .+.....+ +++.|-.+|..+++.+|++   .+..+.........|+.+.|+.+|...+.
T Consensus       185 Ge~~y~qg-~y~~Aa~~f~~~~k~~P~s~KApdallKlg~~~~~l~~~d~A~atl~qv~k  243 (262)
T COG1729         185 GESLYAQG-DYEDAAYIFARVVKDYPKSPKAPDALLKLGVSLGRLGNTDEACATLQQVIK  243 (262)
T ss_pred             HHHHHhcc-cchHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            44445556 7777888888888775543   56777777777777888888888888776

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=82.52  E-value=6.8  Score=29.37  Aligned_cols=58  Identities=19%  Similarity=0.327  Sum_probs=34.1

Q ss_pred             CCCCHHHHHHHhccCCC-----eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          401 LKATYEDLRRFFSDVGG-----VSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       401 ~~~~~~~l~~~f~~~G~-----i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ..++..+|-.++...+.     |-.|+|..        .|+||+-... .+..++. +++..+.|+++.|+.|
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~--------~~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFD--------NFSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-S--------S-EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEee--------eEEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            35788889888876643     55677743        2899998764 5777887 7999999999999875

; PDB: 2G0C_A 3MOJ_B.

>PF15297 CKAP2_C: Cytoskeleton-associated protein 2 C-terminus

Probab=81.77  E-value=8.1  Score=38.12  Aligned_cols=48  Identities=15%  Similarity=0.195  Sum_probs=42.0

Q ss_pred             ChHHHHHHHHHHHHHccc---hHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          198 DMVSARGVWERLLKISGA---MLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       198 ~~~~ar~i~e~~l~~~~~---~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ..+++..+++.+++..|+   .+.+|+..+.++...|.++++..||+.||.
T Consensus       118 p~eei~~~L~~li~~IP~A~K~aKYWIC~Arl~~~~~~~e~vi~iyEeAi~  168 (353)
T PF15297_consen  118 PKEEILATLSDLIKNIPDAKKLAKYWICLARLEPRTGPIEDVIAIYEEAIL  168 (353)
T ss_pred             CHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHH
Confidence            566788888888888765   367999999999999999999999999986

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=80.60  E-value=1e+02  Score=34.40  Aligned_cols=97  Identities=16%  Similarity=0.158  Sum_probs=62.6

Q ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHHHc---------------------cchHHHHHHHHHHHHHcCChHHHHHHHH
Q 008442          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKIS---------------------GAMLEAWQSYISMEIELDHINEARSIYK  241 (565)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~---------------------~~~~~lw~~yi~~e~~~~~~~~aR~i~~  241 (565)
                      .||..|+++.+..| +++.|..+|..+-..+                     ..+.......+..+...|++.+|...|.
T Consensus       913 ~L~~WWgqYlES~G-emdaAl~~Y~~A~D~fs~VrI~C~qGk~~kAa~iA~esgd~AAcYhlaR~YEn~g~v~~Av~FfT  991 (1416)
T KOG3617|consen  913 SLYSWWGQYLESVG-EMDAALSFYSSAKDYFSMVRIKCIQGKTDKAARIAEESGDKAACYHLARMYENDGDVVKAVKFFT  991 (1416)
T ss_pred             HHHHHHHHHHhccc-chHHHHHHHHHhhhhhhheeeEeeccCchHHHHHHHhcccHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence            68889999888888 9999999998876542                     1122356666777778899999998888


Q ss_pred             HHHh------cccCCCCcH------------HHHHHHHHHHHHhCCHHHHHHHHHHH
Q 008442          242 RCYS------KRFTGTGSE------------DICHAWLRFEREYGTLEDFDHSVQKV  280 (565)
Q Consensus       242 ~al~------~~~~~~~~~------------~i~~~~~~fE~~~G~~~~~~~~~~k~  280 (565)
                      ||-.      .....+-.+            ++..+-.-||+.=|....+-...+|+
T Consensus       992 rAqafsnAIRlcKEnd~~d~L~nlal~s~~~d~v~aArYyEe~g~~~~~AVmLYHkA 1048 (1416)
T KOG3617|consen  992 RAQAFSNAIRLCKENDMKDRLANLALMSGGSDLVSAARYYEELGGYAHKAVMLYHKA 1048 (1416)
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHhhcCchhHHHHHHHHHHcchhhhHHHHHHHhh
Confidence            8722      111222223            33344445666655666555455554

>PF15297 CKAP2_C: Cytoskeleton-associated protein 2 C-terminus

Probab=80.56  E-value=13  Score=36.64  Aligned_cols=52  Identities=19%  Similarity=0.316  Sum_probs=42.4

Q ss_pred             hhhHHHHHHHHHHHcCCCC---HHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc
Q 008442           73 VGNVVRDVYSRATKNCPWV---GELWVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (565)
Q Consensus        73 ~~~~~~~v~erAl~~~p~~---~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~  125 (565)
                      ..+.++.+++--+.++|..   ...|+..++ |+...++++.|..||+.|+..+-.
T Consensus       118 p~eei~~~L~~li~~IP~A~K~aKYWIC~Ar-l~~~~~~~e~vi~iyEeAi~agAq  172 (353)
T PF15297_consen  118 PKEEILATLSDLIKNIPDAKKLAKYWICLAR-LEPRTGPIEDVIAIYEEAILAGAQ  172 (353)
T ss_pred             CHHHHHHHHHHHHhcCchHHHHHHHHHHHHH-HHhhcCCHHHHHHHHHHHHHcCCC
Confidence            4567888999999999964   468999988 666688899999999999986644

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=80.07  E-value=3.5  Score=25.13  Aligned_cols=31  Identities=23%  Similarity=0.116  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHhcCCC
Q 008442           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPV   55 (565)
Q Consensus        25 ~W~~yi~~e~~~~~~~~~~~lyERal~~~p~   55 (565)
                      .|..-.......++.+.+...|++||..+|.
T Consensus         3 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~   33 (34)
T PF00515_consen    3 AYYNLGNAYFQLGDYEEALEYYQRALELDPD   33 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHHHCcC
Confidence            4555555555666777777777777776664

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	565
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		4e-08
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		7e-08
3ucg_A	89	Crystal Structure Of A Rna Binding Domain Of Hypoth		9e-08
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		4e-07
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		6e-07
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		4e-06
2cq4_A	114	Solution Structure Of Rna Binding Domain In Rna Bin		4e-06
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		1e-05
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		3e-05
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		9e-05
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		2e-04
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		4e-04
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		5e-04
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		5e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		6e-04
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		6e-04
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		7e-04

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score = 56.2 bits (134), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 28/90 (31%), Positives = 51/90 (56%)
Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           D+ + ++ N++  +T +DL   FS  G ++ I IL DKF+G  +G AY++F +   + AA
Sbjct: 35  DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA 94
Query: 450 VAKNKQMFLGKKLSIARSNPKQRKDSSGER 479
           VA ++ +F G+ + +          SS +R
Sbjct: 95  VAMDETVFRGRTIKVLPKRTNMPGISSTDR 124

>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm Length = 96

Iteration: 1
 Score = 55.8 bits (133), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 46/76 (60%)
Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAA 448
            D  + ++ N++  AT E+L   F   G V+ + IL DKF+G  +G AY++F D E +  
Sbjct: 3   ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 62
Query: 449 AVAKNKQMFLGKKLSI 464
           ++A ++ +F G+++ +
Sbjct: 63  SLALDESLFRGRQIKV 78

>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 = 55.1 bits (131), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 24/75 (32%), Positives = 46/75 (61%)
Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           D  + ++ N++  AT E+L   F   G V+ + IL DKF+G  +G AY++F D E +  +
Sbjct: 5   DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64
Query: 450 VAKNKQMFLGKKLSI 464
           +A ++ +F G+++ +
Sbjct: 65  LALDESLFRGRQIKV 79

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 25/87 (28%), Positives = 46/87 (52%), Gaps = 1/87 (1%)
Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
           C  F+  +N   T ++LR +F   G V+ ++I+ D  TG+SRG  ++ F +       V 
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSF-EKPSSVDEVV 62
Query: 452 KNKQMFLGKKLSIARSNPKQRKDSSGE 478
           K + +  GK +   R+ P+  +D +G+
Sbjct: 63  KTQHILDGKVIDPKRAIPRDEQDKTGK 89

>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 = 52.8 bits (125), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 32/94 (34%), Positives = 53/94 (56%), Gaps = 4/94 (4%)
Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDE-HLAAAVA 451
           + F+ NI  +AT E L+  FS+VG V S R+++D+ TGK +G  + ++ D E  L+A   
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 452 KNKQMFLGKKLSIARSNPKQRKD---SSGERAPT 482
            N + F G+ L +  +  ++ K+   S G  AP 
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEELKSLGTGAPV 103

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 45/84 (53%), Gaps = 1/84 (1%)
Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+ N++  ++ EDL + FS  G +S +    D  T K +G A+V F+  EH   A A+ +
Sbjct: 12  FVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVD 71
Query: 454 KQMFLGKKLSIARSNPKQRKDSSG 477
            Q+F G+ L +  S  K+    SG
Sbjct: 72  GQVFQGRMLHVLPSTIKKEASQSG 95

>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 23 Length = 114

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 28/100 (28%), Positives = 51/100 (51%)
Query: 376 PIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGL 435
           P+++ V   +    D  T F   +  +    DL  FFS VG V  +RI+ D+ + +S+G+
Sbjct: 10  PVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGI 69
Query: 436 AYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKDS 475
           AYV+F + + +  A+    Q  LG  + +  S  ++ + S
Sbjct: 70  AYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRLS 109

>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 = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 49/78 (62%), Gaps = 2/78 (2%)
Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           ++ N+   AT E ++  FS  G V ++++++D+ T K +G  +V+ + +E ++ A+AK +
Sbjct: 5   YVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIAKLD 63
Query: 454 KQMFLGKKLSIARSNPKQ 471
              F+G+ + +  +NPK+
Sbjct: 64  NTDFMGRTIRVTEANPKK 81

>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 = 47.0 bits (110), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/67 (37%), Positives = 37/67 (55%), Gaps = 2/67 (2%)
Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHL--AAAV 450
           T ++SN+    T  DL R FS  G V  + I+ DK T KS+G+A++ F+D +        
Sbjct: 18  TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 451 AKNKQMF 457
             NKQ+F
Sbjct: 78  INNKQLF 84

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 45.4 bits (106), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 18/64 (28%), Positives = 33/64 (51%)
Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
           C  F+  ++ + T E LR +F   G V    ++ D  T +SRG  +V F+D   +   +A
Sbjct: 26  CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 85
Query: 452 KNKQ 455
           +++ 
Sbjct: 86  QSRH 89

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/64 (28%), Positives = 33/64 (51%)
Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
           C  F+  ++ + T E LR +F   G V    ++ D  T +SRG  +V F+D   +   +A
Sbjct: 1   CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
Query: 452 KNKQ 455
           +++ 
Sbjct: 61  QSRH 64

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 21/81 (25%), Positives = 41/81 (50%)
Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  I       +LR +F   G V+ + +++D    + RG  ++ F D++ +  AV  + 
Sbjct: 14  FVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHF 73
Query: 455 QMFLGKKLSIARSNPKQRKDS 475
              +GKK+ + R+ P+  K S
Sbjct: 74  HDIMGKKVEVKRAEPRDSKSS 94

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 25/79 (31%), Positives = 45/79 (56%), Gaps = 2/79 (2%)
Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T F+  I+++    ++R FF+  G V  ++I+ D+ TG S+G  +V F +D  +   V +
Sbjct: 12  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV-E 69
Query: 453 NKQMFLGKKLSIARSNPKQ 471
           ++  F GKKL +  +  KQ
Sbjct: 70  SQINFHGKKLKLGPAIRKQ 88

>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 = 42.7 bits (99), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 25/79 (31%), Positives = 45/79 (56%), Gaps = 2/79 (2%)
Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T F+  I+++    ++R FF+  G V  ++I+ D+ TG S+G  +V F +D  +   V +
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV-E 68
Query: 453 NKQMFLGKKLSIARSNPKQ 471
           ++  F GKKL +  +  KQ
Sbjct: 69  SQINFHGKKLKLGPAIRKQ 87

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 23/81 (28%), Positives = 36/81 (44%)
Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  ++   T E LR +FS  G V    I+ DK T +SRG  +V F D   +   +A   
Sbjct: 20  FVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRP 79
Query: 455 QMFLGKKLSIARSNPKQRKDS 475
               G+ +      P+  + S
Sbjct: 80  HTLDGRNIDPKPCTPRGMQPS 100

>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 = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/79 (26%), Positives = 42/79 (53%)
Query: 383 GRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFID 442
           G+ K  ++    F+ +++ + T ED++  F+  G +S  R++ D  TGKS+G  +V F +
Sbjct: 7   GQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 66
Query: 443 DEHLAAAVAKNKQMFLGKK 461
                 A+ +    +LG +
Sbjct: 67  KWDAENAIQQMGGQWLGGR 85

>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 = 42.4 bits (98), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 25/79 (31%), Positives = 45/79 (56%), Gaps = 2/79 (2%)
Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T F+  I+++    ++R FF+  G V  ++I+ D+ TG S+G  +V F +D  +   V +
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV-E 68
Query: 453 NKQMFLGKKLSIARSNPKQ 471
           ++  F GKKL +  +  KQ
Sbjct: 69  SQINFHGKKLKLGPAIRKQ 87

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	565
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	1e-30
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	8e-08
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	4e-29
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	1e-10
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	4e-08
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	2e-04
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	6e-27
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	6e-26
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	2e-14
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	2e-05
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	6e-25
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	9e-23
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-20
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	6e-18
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-17
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-17
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	6e-17
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-16
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-16
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-16
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	5e-16
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	6e-16
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-15
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-15
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	8e-12
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-15
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	4e-15
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	4e-15
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	4e-15
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	4e-15
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	5e-15
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	6e-15
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	8e-15
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-10
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	9e-15
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-14
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-14
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-14
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-14
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-14
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	8e-14
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	8e-14
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	8e-14
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	8e-14
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-13
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-10
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-13
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	5e-12
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-13
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-13
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-13
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-13
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	3e-13
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-13
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-13
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-11
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	5e-13
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	6e-13
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	6e-13
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	7e-13
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	7e-13
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-12
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-08
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-12
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-12
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-12
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-12
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-12
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-12
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-12
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-12
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-12
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-09
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	3e-12
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	5e-12
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-12
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	6e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-11
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	9e-11
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	7e-12
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	7e-12
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	8e-12
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-11
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-09
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-08
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-06
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-11
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-11
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-11
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	3e-11
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-11
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	4e-11
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	5e-11
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	6e-11
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	6e-11
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	7e-11
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	7e-11
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	8e-11
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	8e-11
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	9e-11
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-10
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-10
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-10
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-08
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-10
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-10
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-10
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-08
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	3e-10
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-10
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	4e-10
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	4e-10
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	5e-10
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	5e-10
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	5e-10
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	7e-10
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	8e-10
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-09
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-09
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-09
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-09
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-07
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-09
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	4e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-07
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	6e-09
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	7e-09
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	7e-09
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	9e-09
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	9e-09
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-08
2div_A	99	TRNA selenocysteine associated protein; structural	1e-08
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-08
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-08
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-08
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-08
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	3e-08
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-08
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-08
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	6e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-05
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	4e-08
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-08
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-08
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-07
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	5e-08
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	6e-08
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	8e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	8e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-06
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	8e-08
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-07
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-07
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-07
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-07
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-07
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	3e-07
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-07
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-07
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-07
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-07
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	6e-07
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-06
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-06
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	4e-06
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-06
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	5e-06
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	7e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	8e-06
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-05
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-05
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-05
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-05
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-05
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-05
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-05
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-05
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	3e-05
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	4e-05
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	6e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-04
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-04
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-04
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	5e-04

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A Length = 679

 Score =  125 bits (315), Expect = 1e-30
 Identities = 42/351 (11%), Positives = 109/351 (31%), Gaps = 20/351 (5%)

Query: 9   EEQISRQDLSDSEKFQQYMIYLKYE-------QSSGDPGRVQLLYERAITDFPVSSDLWL 61
           E  + + +  D ++   ++ ++++E              R+  +Y +A      + ++W 
Sbjct: 288 ESNLPKPNEYDVQQLLIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQHVCFAPEIWF 347

Query: 62  DYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEE--EISTVFEKS 119
           +   Y  +      V+        +  P    L        E +    E           
Sbjct: 348 NMANYQGEKNTDSTVITKYLKLGQQCIPNSAVLAFSLSEQYELNTKIPEIETTILSCIDR 407

Query: 120 LLCAFSTFEEYLDLFLTRIDGLRRR-----ILFSGEVEGVLDYSLIRETFQRASDYLSEQ 174
           +    +   E      + I+ L+ +      ++   ++ +   +  R+ F +        
Sbjct: 408 IHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRLKKLV 467

Query: 175 MKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHIN 234
             +       Y   A++E  + KD  +A  V E  LK      E    Y+   I ++  +
Sbjct: 468 TPDI------YLENAYIEYHISKDTKTACKVLELGLKYFATDGEYINKYLDFLIYVNEES 521

Query: 235 EARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQ 294
           + +S+++    K       + I    + FE + G+L       ++   +  E+       
Sbjct: 522 QVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEKFPEVNKLEEFT 581

Query: 295 ESKSLPESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVH 345
               + +    +   +    R+       +    +  KR     +  +   
Sbjct: 582 NKYKVLDVNYLQRLELDYMVRDVMPEAIALDRGSNNLKRTMREEEDGQAFK 632

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A Length = 679

 Score = 54.3 bits (129), Expect = 8e-08
 Identities = 35/281 (12%), Positives = 83/281 (29%), Gaps = 33/281 (11%)

Query: 3   NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLD 62
           +    L + I  Q          Y+  LK+  S     +V   +++    FP+ +++W  
Sbjct: 50  DVIGKLNDMIEEQPTD----IFLYVKLLKHHVSLKQWKQVYETFDKLHDRFPLMANIWCM 105

Query: 63  YTQYLDKTLKVGNV--VRDVYSRATKNCPWVG--ELWVRSLLSLER-------SRASEEE 111
                   ++  +   +  V +R            LW+  +  + +          +   
Sbjct: 106 RLSLEFDKMEELDAAVIEPVLARCLSKELGNNDLSLWLSYITYVRKKNDIITGGEEARNI 165

Query: 112 ISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYL 171
           +   F+  +        + +  +   +  L      +   E       IR+ ++     L
Sbjct: 166 VIQAFQVVVDKCAIFEPKSIQFWNEYLHFLEHWKPVNKFEEQ-QRVQYIRKLYKTL---L 221

Query: 172 SEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELD 231
            + M   + + + Y  W          + + R + E     S   + A   Y        
Sbjct: 222 CQPMDCLESMWQRYTQWEQ----DVNQLTARRHIGEL----SAQYMNARSLYQDWLNITK 273

Query: 232 HINEARSIYKRCYSKRFTGTGSE------DICHAWLRFERE 266
            +     I     ++      +E       I   W+R+E +
Sbjct: 274 GLKRNLPITLNQATESNLPKPNEYDVQQLLIWLEWIRWESD 314

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7 Length = 530

 Score =  120 bits (301), Expect = 4e-29
 Identities = 59/324 (18%), Positives = 110/324 (33%), Gaps = 52/324 (16%)

Query: 1   MCNARAHLEEQISRQDLSDSEKFQQ----YMIYLKYEQSSGD--------PGRVQLLYER 48
                  L+         ++ +  Q    +  Y+++E+S+            RV   YE+
Sbjct: 204 YETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQ 263

Query: 49  AITDFPVSSDLWLDYTQYLDKTLKV-------------GNVVRDVYSRATKNCPWVGELW 95
            +       D+W +  QYL+++ K+              +   ++Y RA         L 
Sbjct: 264 CLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLL 323

Query: 96  VRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVL 155
             +    E SR   E++ +++ + L            +++  +   RR            
Sbjct: 324 YFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTL---VYIQYMKFARRA----------- 369

Query: 156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA 215
                 E  +       +  ++      +Y   A +E    KD   A  ++E  LK  G 
Sbjct: 370 ------EGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGD 423

Query: 216 MLEAWQSYISMEIELDHINEARSIYKRCYSK-RFTGTGSEDICHAWLRFEREYGTLEDFD 274
           + E   +YI     L+  N  R +++R  +        S +I   +L FE   G L    
Sbjct: 424 IPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLA--- 480

Query: 275 HSVQKVTPRLEELRLFRSQQESKS 298
            S+ KV  R      FR + E K 
Sbjct: 481 -SILKVEKRRFT--AFREEYEGKE 501

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7 Length = 530

 Score = 62.6 bits (151), Expect = 1e-10
 Identities = 42/288 (14%), Positives = 96/288 (33%), Gaps = 35/288 (12%)

Query: 8   LEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYL 67
            E+++             + I ++  Q+     + +  YER +  FP S   W  Y +  
Sbjct: 2   AEKKLEENPYD----LDAWSILIREAQN-QPIDKARKTYERLVAQFPSSGRFWKLYIEAE 56

Query: 68  DKTLKVGNV--VRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS 125
              +K  N   V  ++ R       + +LW   L  +  ++           +    A+ 
Sbjct: 57  ---IKAKNYDKVEKLFQRCLMKVLHI-DLWKCYLSYVRETKGKLPSYKEKMAQ----AYD 108

Query: 126 TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYS------LIRETFQRASDYLSEQMKNTD 179
              + + + +         I F   VE V  Y+       +R  +QR        M N +
Sbjct: 109 FALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRG---CVNPMINIE 165

Query: 180 GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSI 239
              +L+  +   E+ +    ++ + + +R        + A +     E  +  ++  R+ 
Sbjct: 166 ---QLWRDYNKYEEGINI-HLAKKMIEDRSRDY----MNARRVAKEYETVMKGLD--RNA 215

Query: 240 YKRCYSKRFTGTGSEDICHAWLRFEREYGT-LEDFDHSVQKVTPRLEE 286
                          D+   ++++E+      ED     ++V    E+
Sbjct: 216 PSVPPQNTPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQ 263

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7 Length = 530

 Score = 54.9 bits (131), Expect = 4e-08
 Identities = 40/338 (11%), Positives = 105/338 (31%), Gaps = 23/338 (6%)

Query: 45  LYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER 104
           + E+ + + P   D W    +         +  R  Y R     P  G  W    +  E 
Sbjct: 1   MAEKKLEENPYDLDAWSILIREAQNQPI--DKARKTYERLVAQFPSSGRFWKL-YIEAEI 57

Query: 105 SRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETF 164
              + +++  +F++ L+         +DL+   +  +R         +       + + +
Sbjct: 58  KAKNYDKVEKLFQRCLMKVLH-----IDLWKCYLSYVRETKGKLPSYK-----EKMAQAY 107

Query: 165 QRASDYLSEQMKNTDGLLRLYAYW-----AHLEQSMGKDMVSARGVWERLLKISGAMLEA 219
             A D +      +  +   Y  +     A    +  + + + R V++R        +E 
Sbjct: 108 DFALDKI-GMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINIEQ 166

Query: 220 -WQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQ 278
            W+ Y   E  ++     + I  R          +++        +R   ++   +   +
Sbjct: 167 LWRDYNKYEEGINIHLAKKMIEDRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQNTPQE 226

Query: 279 KVTPRLEELRLFRSQQESKSLPESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAP 338
               +  ++     Q E  +   + DQ   + +     ++       +     +  ++  
Sbjct: 227 ---AQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVLGHHPDIWYEAAQYLE 283

Query: 339 QKPKKVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQP 376
           Q  K + +K       L  +      ++ +    KK  
Sbjct: 284 QSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNM 321

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7 Length = 530

 Score = 43.3 bits (101), Expect = 2e-04
 Identities = 18/120 (15%), Positives = 44/120 (36%), Gaps = 14/120 (11%)

Query: 4   ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSD----L 59
           A    E  + +    D  ++   + Y+ Y     +    ++L+ER +T   +  +    +
Sbjct: 410 AFKIFELGLKK--YGDIPEY--VLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEI 465

Query: 60  WLDYTQYLDKTLKVGNV--VRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFE 117
           W  +  +      +G++  +  V  R         E    +LL ++R +  +    +  E
Sbjct: 466 WARFLAFE---SNIGDLASILKVEKRRFTAFREEYEGKETALL-VDRYKFMDLYPCSASE 521

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7 Length = 308

 Score =  110 bits (275), Expect = 6e-27
 Identities = 54/311 (17%), Positives = 108/311 (34%), Gaps = 48/311 (15%)

Query: 18  SDSEKFQQYMIYLKYEQS--------SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDK 69
            ++++   +  Y+++E+S        +    RV   YE+ +       D+W +  QYL++
Sbjct: 3   QEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVLGHHPDIWYEAAQYLEQ 62

Query: 70  TLKV-------------GNVVRDVYSRATKN-CPWVGELWVRSLLSLERSRASEEEISTV 115
           + K+              +   ++Y RA          L+       E SR   E++ ++
Sbjct: 63  SSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFA-YADYEESRMKYEKVHSI 121

Query: 116 FEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQM 175
           + + L            +++  +   RR                  E  +       +  
Sbjct: 122 YNRLLAIEDIDPTL---VYIQYMKFARRA-----------------EGIKSGRMIFKKAR 161

Query: 176 KNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINE 235
           ++      +Y   A +E    KD   A  ++E  LK  G + E   +YI     L+  N 
Sbjct: 162 EDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNN 221

Query: 236 ARSIYKRCYSK-RFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQ 294
            R +++R  +        S +I   +L FE   G L     S+ KV  R         + 
Sbjct: 222 TRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLA----SILKVEKRRFTAFREEYEG 277

Query: 295 ESKSLPESADQ 305
           +  +L     +
Sbjct: 278 KETALLVDRYK 288

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B Length = 493

 Score =  110 bits (275), Expect = 6e-26
 Identities = 37/373 (9%), Positives = 103/373 (27%), Gaps = 53/373 (14%)

Query: 7   HLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDP-------GRVQLLYERAITDFPVSSDL 59
             +     Q L      +     +  E  +G          R+  ++   +  F  + ++
Sbjct: 156 SFQRYQQIQPLIRGWSVKNAARLIDLEMENGMKLGGRPHESRMHFIHNYILDSFYYAEEV 215

Query: 60  WLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKS 119
           +  Y++YL    +     + V  R  +    +       L+  E +   + +      ++
Sbjct: 216 YFFYSEYLIGIGQK-EKAKKVVERGIEMSDGMFLSLYYGLVMDEEAVYGDLKRKYSMGEA 274

Query: 120 LLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTD 179
                   +E   L +  ++ + ++              L R+ F    +          
Sbjct: 275 ESAEKVFSKELDLLRINHLNYVLKK----------RGLELFRKLFIELGNEGVGPHV--- 321

Query: 180 GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSI 239
                + Y A +E        +   ++   L          + +    + +     AR++
Sbjct: 322 -----FIYCAFIEYYATGSRATPYNIFSSGLLKHPDSTLLKEEFFLFLLRIGDEENARAL 376

Query: 240 YKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSL 299
           +KR          +  +  + + +E   G++E      +++  +  +     +       
Sbjct: 377 FKRL-------EKTSRMWDSMIEYEFMVGSME----LFRELVDQKMDAIKADAILPPLPP 425

Query: 300 PESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNL--AE 357
            E   Q E  + +                           K +         ++NL    
Sbjct: 426 REHNVQMEGILGR--------------YHCFLDSFNFLDLKIRDNSRLLDEFMENLPKIS 471

Query: 358 ENEGRETKQTVEE 370
           +     +   VE+
Sbjct: 472 QQNNVLSNLRVEK 484

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B Length = 493

 Score = 74.9 bits (183), Expect = 2e-14
 Identities = 29/226 (12%), Positives = 69/226 (30%), Gaps = 7/226 (3%)

Query: 24  QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR 83
              M + +    S D   ++ L+ R +     + DLW+ Y +Y+ K  +    + +VY  
Sbjct: 15  SAIMEHARRLYMSKDYRSLESLFGRCLKKSY-NLDLWMLYIEYVRKVSQKKFKLYEVYEF 73

Query: 84  ATKNCPW---VGELW---VRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTR 137
                        L+   +     +E  +   E+I   + ++L     +  E    F   
Sbjct: 74  TLGQFENYWDSYGLYKEYIEEEGKIEDEQTRIEKIRNGYMRALQTPMGSLSELWKDFENF 133

Query: 138 IDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGK 197
              L +        + +  +    + +Q+    +          L        ++     
Sbjct: 134 ELELNKITGKKIVGDTLPIFQSSFQRYQQIQPLIRGWSVKNAARLIDLEMENGMKLGGRP 193

Query: 198 DMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRC 243
                  +   +L       E +  Y    I +    +A+ + +R 
Sbjct: 194 HESRMHFIHNYILDSFYYAEEVYFFYSEYLIGIGQKEKAKKVVERG 239

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B Length = 493

 Score = 46.4 bits (109), Expect = 2e-05
 Identities = 33/243 (13%), Positives = 79/243 (32%), Gaps = 30/243 (12%)

Query: 46  YERAITDFPVSSDLWLDYTQYLDKTLKVGNV--VRDVYSRATKNCPWVGELWVRSLLSLE 103
            E  +     S    +++ + L       +   +  ++ R  K    + +LW+  +  + 
Sbjct: 3   AEEKMGVELSSPSAIMEHARRL---YMSKDYRSLESLFGRCLKKSYNL-DLWMLYIEYVR 58

Query: 104 RSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRET 163
           +    + ++  V+E +L    + ++ Y  L+   I+   +       +E       IR  
Sbjct: 59  KVSQKKFKLYEVYEFTLGQFENYWDSY-GLYKEYIEEEGKIEDEQTRIE------KIRNG 111

Query: 164 FQRASDYLSEQMKNTDGLLRLYAYWAH-LEQSMGKDMVSARGVWERLLKISGAMLEA--- 219
           + RA   L   M +   L + +  +   L +  GK +V       +        ++    
Sbjct: 112 YMRA---LQTPMGSLSELWKDFENFELELNKITGKKIVGDTLPIFQSSFQRYQQIQPLIR 168

Query: 220 ------WQSYISMEIELDHINEARSIYKR---CYSKRFTGTG-SEDICHAWLRFEREYGT 269
                     I +E+E       R    R    ++        +E++   +  +    G 
Sbjct: 169 GWSVKNAARLIDLEMENGMKLGGRPHESRMHFIHNYILDSFYYAEEVYFFYSEYLIGIGQ 228

Query: 270 LED 272
            E 
Sbjct: 229 KEK 231

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 98.5 bits (246), Expect = 6e-25
 Identities = 29/107 (27%), Positives = 52/107 (48%)

Query: 374 KQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           K P+++ V   +    D  T F   +  +    DL  FFS VG V  +RI+ D+ + +S+
Sbjct: 8   KSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 67

Query: 434 GLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKDSSGERA 480
           G+AYV+F + + +  A+    Q  LG  + +  S  ++ + S     
Sbjct: 68  GIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRLSGPSSG 114

>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 = 92.9 bits (231), Expect = 9e-23
 Identities = 31/124 (25%), Positives = 58/124 (46%)

Query: 356 AEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDV 415
           A     + T   +      +     +    K   D+ + ++ N++  +T +DL   FS  
Sbjct: 1   AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC 60

Query: 416 GGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKDS 475
           G ++ I IL DKF+G  +G AY++F +   + AAVA ++ +F G+ + +          S
Sbjct: 61  GSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRTNMPGIS 120

Query: 476 SGER 479
           S +R
Sbjct: 121 STDR 124

>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 = 84.9 bits (211), Expect = 2e-20
 Identities = 24/82 (29%), Positives = 47/82 (57%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           D  + ++ N++  AT E+L   F   G V+ + IL DKF+G  +G AY++F D E +  +
Sbjct: 5   DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64

Query: 450 VAKNKQMFLGKKLSIARSNPKQ 471
           +A ++ +F G+++ +      +
Sbjct: 65  LALDESLFRGRQIKVIPKRTNR 86

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 78.5 bits (194), Expect = 6e-18
 Identities = 20/85 (23%), Positives = 41/85 (48%), Gaps = 1/85 (1%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           TA++ N+       D+   F D   + S+R++ DK T K +G  YV+F + + L  A+  
Sbjct: 17  TAYVGNLPFNTVQGDIDAIFKD-LSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY 75

Query: 453 NKQMFLGKKLSIARSNPKQRKDSSG 477
           +  +   + L +  +  +++  S  
Sbjct: 76  DGALLGDRSLRVDIAEGRKQDKSGP 100

>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 = 76.5 bits (189), Expect = 3e-17
 Identities = 23/89 (25%), Positives = 46/89 (51%), Gaps = 2/89 (2%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKF-TGKSRGLAYVDFIDDEHLAAAVA 451
           TAFL N+    T E ++ FF  +  +S++R+  +     + +G  Y +F D + L +A++
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 452 KNKQMFLGKKLSIARSNPKQRKDSSGERA 480
            N++    K++ +  ++  Q KDS     
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKDSGPSSG 104

>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 = 75.7 bits (187), Expect = 4e-17
 Identities = 29/96 (30%), Positives = 48/96 (50%), Gaps = 1/96 (1%)

Query: 386 KGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEH 445
            G +     F+ N++  ++ EDL + FS  G +S +    D  T K +G A+V F+  EH
Sbjct: 3   SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62

Query: 446 LAAAVAK-NKQMFLGKKLSIARSNPKQRKDSSGERA 480
              A A+ + Q+F G+ L +  S  K+    SG  +
Sbjct: 63  AVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98

>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 = 79.4 bits (195), Expect = 6e-17
 Identities = 35/174 (20%), Positives = 60/174 (34%), Gaps = 5/174 (2%)

Query: 345 HDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTA-FLSNINLKA 403
           +D       N  +  E R+   T+         K A P     +T +  A ++ N+    
Sbjct: 21  YDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWT 80

Query: 404 TYEDLRRFFSDVGG--VSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NKQMFLGK 460
           T EDL      +G   +  I+   ++  G+S+G A V    +      +    K+   G+
Sbjct: 81  TDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQ 140

Query: 461 KLSIARSNPKQRKDSSGERAPTEQAQSHQQTGNAGTSASKESSIETSKQSRGRG 514
              +   N +       +   T Q+      G AG      S     +  RGRG
Sbjct: 141 NPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAG-PPGGSSRAAFPQGGRGRG 193

>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 = 74.8 bits (184), Expect = 1e-16
 Identities = 20/111 (18%), Positives = 48/111 (43%), Gaps = 4/111 (3%)

Query: 383 GRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGV-SSIRILHDKFTGKSRGLAYVDFI 441
           G     + +  A ++NI    T  D+ +F   +    +++ +L D   G+  G A V F 
Sbjct: 7   GEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFK 65

Query: 442 DDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKDSSGERAPTEQAQSHQQTG 492
           +++    +   +++   G++  +     +  ++   E+ P  Q +S   +G
Sbjct: 66  NEDDARKSERLHRKKLNGREAFVHVVTLEDMREI--EKNPPAQGKSGPSSG 114

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 76.0 bits (187), Expect = 2e-16
 Identities = 27/139 (19%), Positives = 55/139 (39%), Gaps = 3/139 (2%)

Query: 341 PKKVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKG--FTDECTAFLSN 398
            + V      +V      + G + + T ++  K   + +               +  + N
Sbjct: 18  TEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDN 77

Query: 399 INLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NKQMF 457
           +  + + + LRR F   G V  + I  D++T +SRG A+V F D      A+   +  + 
Sbjct: 78  LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL 137

Query: 458 LGKKLSIARSNPKQRKDSS 476
            G++L +  +   +  DS 
Sbjct: 138 DGRELRVQMARYGRPPDSH 156

>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 = 73.8 bits (182), Expect = 3e-16
 Identities = 18/85 (21%), Positives = 36/85 (42%), Gaps = 1/85 (1%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAA 448
           T     F+ N+N   +  +L+   S++   + + ++ D  TG +R   YVDF   E L  
Sbjct: 15  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEK 73

Query: 449 AVAKNKQMFLGKKLSIARSNPKQRK 473
           A+        G ++ + +   +   
Sbjct: 74  ALELTGLKVFGNEIKLEKPKGRDGT 98

>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 = 73.2 bits (180), Expect = 5e-16
 Identities = 17/92 (18%), Positives = 41/92 (44%), Gaps = 2/92 (2%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           D+    +  +   A   D+R FF  +  V ++ +L D   G++ G   V F+  +    A
Sbjct: 15  DDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEA 72

Query: 450 VAKNKQMFLGKKLSIARSNPKQRKDSSGERAP 481
           + +N+ + + + + ++ +  +Q   + G    
Sbjct: 73  LKRNRMLMIQRYVEVSPATERQWVAAGGHITS 104

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 72.7 bits (179), Expect = 6e-16
 Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 2/93 (2%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFI 441
             R     ++   F+S +    T E+L       G V  +R++ ++  GK +GLAYV++ 
Sbjct: 8   VFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYE 66

Query: 442 DDEHLAAAVAK-NKQMFLGKKLSIARSNPKQRK 473
           ++   + AV K +        + +A SN     
Sbjct: 67  NESQASQAVMKMDGMTIKENIIKVAISNSGPSS 99

>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 = 71.9 bits (177), Expect = 1e-15
 Identities = 16/90 (17%), Positives = 30/90 (33%), Gaps = 1/90 (1%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFI 441
            G + G        + N+    + +++  FF     +     L     G   G A V F 
Sbjct: 6   SGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFE 65

Query: 442 DDEHLAAAVAK-NKQMFLGKKLSIARSNPK 470
             +   AAV   N +    +K+ +   +  
Sbjct: 66  SRDEATAAVIDLNDRPIGSRKVKLVLGSGP 95

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 75.0 bits (185), Expect = 1e-15
 Identities = 21/116 (18%), Positives = 48/116 (41%), Gaps = 1/116 (0%)

Query: 374 KQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           +Q  + +   R          ++ +I  +   + +R+ F+  G + SI +  D  T K +
Sbjct: 11  QQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHK 70

Query: 434 GLAYVDFIDDEHLAAAVAK-NKQMFLGKKLSIARSNPKQRKDSSGERAPTEQAQSH 488
           G A+V++   E    A+ + N  M  G+ + + R +   +     ++   E    +
Sbjct: 71  GFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFN 126

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 63.9 bits (156), Expect = 8e-12
 Identities = 19/100 (19%), Positives = 45/100 (45%), Gaps = 4/100 (4%)

Query: 372 PKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGK 431
            + QPI D +    + F      ++++++   + +D++  F   G + S  +  D  TGK
Sbjct: 109 GQAQPIIDQLAEEARAFN---RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGK 165

Query: 432 SRGLAYVDFIDDEHLAAAVAK-NKQMFLGKKLSIARSNPK 470
            +G  ++++   +    AV+  N     G+ L + ++   
Sbjct: 166 HKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205

>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 = 70.7 bits (174), Expect = 3e-15
 Identities = 27/88 (30%), Positives = 48/88 (54%), Gaps = 1/88 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+ NI  +AT E L+  FS+VG V S R+++D+ TGK +G  + ++ D E   +A+   N
Sbjct: 12  FVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLN 71

Query: 454 KQMFLGKKLSIARSNPKQRKDSSGERAP 481
            + F G+ L +  +  ++ K+       
Sbjct: 72  GREFSGRALRVDNAASEKNKEELKSLGT 99

>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 = 70.3 bits (173), Expect = 4e-15
 Identities = 19/80 (23%), Positives = 42/80 (52%), Gaps = 2/80 (2%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFT-GKSRGLAYVDFIDDEHLAAAVA 451
           TAFL N+    T E ++ FF     +S++R+  +     + +G  Y +F D + L +A++
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRG-LNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79

Query: 452 KNKQMFLGKKLSIARSNPKQ 471
            N++    +++ +  ++  Q
Sbjct: 80  LNEESLGNRRIRVDVADQAQ 99

>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 = 70.0 bits (172), Expect = 4e-15
 Identities = 25/86 (29%), Positives = 42/86 (48%), Gaps = 1/86 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           +L +I    T E +    S+VG V +++++ D  TG+S+G A+++F D E  A+AV   N
Sbjct: 6   YLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLN 65

Query: 454 KQMFLGKKLSIARSNPKQRKDSSGER 479
                 + L    S+       S E 
Sbjct: 66  GYQLGSRFLKCGYSSNSDISGVSLEH 91

>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 = 70.3 bits (173), Expect = 4e-15
 Identities = 25/97 (25%), Positives = 43/97 (44%), Gaps = 1/97 (1%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFI 441
            G  +   D  T  ++N++      DL+  F   G +S I +  DK TG+S+G A++ F 
Sbjct: 6   SGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFH 65

Query: 442 DDEHLAAAVAK-NKQMFLGKKLSIARSNPKQRKDSSG 477
             E  A A+A  +   +    L++  + P      S 
Sbjct: 66  RREDAARAIAGVSGFGYDHLILNVEWAKPSTNSGPSS 102

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 70.0 bits (172), Expect = 4e-15
 Identities = 16/88 (18%), Positives = 31/88 (35%), Gaps = 1/88 (1%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFI 441
            G + G        + N+    + +++  FF     +     L     G   G A V F 
Sbjct: 6   SGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFE 65

Query: 442 DDEHLAAAVAK-NKQMFLGKKLSIARSN 468
             +   AAV   N +    +K+ ++  +
Sbjct: 66  SRDEATAAVIDLNDRPIGSRKVKLSGPS 93

>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 = 69.5 bits (171), Expect = 5e-15
 Identities = 19/85 (22%), Positives = 44/85 (51%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           ++ N+   AT E ++  FS  G V ++++++D+ T K +G  +V+  ++    A    + 
Sbjct: 5   YVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKLDN 64

Query: 455 QMFLGKKLSIARSNPKQRKDSSGER 479
             F+G+ + +  +NPK+  +     
Sbjct: 65  TDFMGRTIRVTEANPKKSLEHHHHH 89

>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 = 69.9 bits (172), Expect = 6e-15
 Identities = 24/92 (26%), Positives = 39/92 (42%), Gaps = 2/92 (2%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
              T  + N+  + + + LRR F   G V  + I  +  T   RG A+V F D      A
Sbjct: 12  GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDA 71

Query: 450 VAK-NKQMFLGKKLSIARSNPKQRKDSSGERA 480
            A  +     G++L +  +    R+D SG  +
Sbjct: 72  EAAMDGAELDGRELRVQVARYG-RRDLSGPSS 102

>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 = 71.9 bits (177), Expect = 8e-15
 Identities = 19/91 (20%), Positives = 38/91 (41%), Gaps = 1/91 (1%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAA 448
           T     F+ N+N   +  +L+   S++   + + ++  + TG +R   YVDF   E L  
Sbjct: 11  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEK 69

Query: 449 AVAKNKQMFLGKKLSIARSNPKQRKDSSGER 479
           A+        G ++ + +   +  K     R
Sbjct: 70  ALELTGLKVFGNEIKLEKPKGRDSKKVRAAR 100

>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 = 58.4 bits (142), Expect = 3e-10
 Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 6/95 (6%)

Query: 377 IKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLA 436
           ++      +K      T    N++   T ++L+  F D        I      GKS+G+A
Sbjct: 85  LEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIA 139

Query: 437 YVDFIDDEHLAAAV-AKNKQMFLGKKLSIARSNPK 470
           Y++F  +      +  K      G+ +S+  +  K
Sbjct: 140 YIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 69.7 bits (171), Expect = 9e-15
 Identities = 17/87 (19%), Positives = 26/87 (29%), Gaps = 1/87 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
             + +N       L+      G V  + IL    T K  GLA V F         V   +
Sbjct: 10  TFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLH 69

Query: 454 KQMFLGKKLSIARSNPKQRKDSSGERA 480
               +G  +        Q++    E  
Sbjct: 70  LTSVMGNIIHAQLDIKGQQRMKYYELI 96

>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 = 69.0 bits (169), Expect = 1e-14
 Identities = 24/99 (24%), Positives = 44/99 (44%), Gaps = 3/99 (3%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFI 441
            G +    ++    L  +    + E++ +FFS +  V +   L   F G+S G A+V F 
Sbjct: 6   SGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFA 65

Query: 442 DDEHLAAAVAKNKQMFLGKKLSIARSNP---KQRKDSSG 477
             E    A+ K+K+    + + I +S+    +    SSG
Sbjct: 66  SQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTSGPSSG 104

>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 = 68.9 bits (169), Expect = 2e-14
 Identities = 19/100 (19%), Positives = 37/100 (37%), Gaps = 7/100 (7%)

Query: 383 GRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFID 442
           G     T+  T F+ N++  +  E L       G +  +R++    T  S+G A+  F+ 
Sbjct: 7   GLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMT 66

Query: 443 DEHLAAAVA-------KNKQMFLGKKLSIARSNPKQRKDS 475
            E     +A              G++L +  +  +    S
Sbjct: 67  QEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 69.1 bits (169), Expect = 2e-14
 Identities = 17/98 (17%), Positives = 35/98 (35%)

Query: 374 KQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           K P                  +L  +  +A  + +  FF  +  V     +     GK+ 
Sbjct: 8   KSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKAT 67

Query: 434 GLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQ 471
           G  +V+F ++    AA+ ++KQ    + + +     K 
Sbjct: 68  GEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITKKG 105

>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 = 68.4 bits (168), Expect = 2e-14
 Identities = 20/89 (22%), Positives = 42/89 (47%), Gaps = 1/89 (1%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           DE   F+  ++     + L + FS  G +S + ++ D+ T +SRG  +V F + +    A
Sbjct: 11  DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70

Query: 450 V-AKNKQMFLGKKLSIARSNPKQRKDSSG 477
           + A N +   G+++ + ++       S  
Sbjct: 71  MMAMNGKSVDGRQIRVDQAGKSSDNRSGP 99

>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 = 68.8 bits (168), Expect = 3e-14
 Identities = 19/83 (22%), Positives = 38/83 (45%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAA 448
            ++    L  +    T E++ +FFS +  V +   L     GK  G A+V F   E    
Sbjct: 40  ANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEK 99

Query: 449 AVAKNKQMFLGKKLSIARSNPKQ 471
           A+ K+K+    + + + +S+ ++
Sbjct: 100 ALGKHKERIGHRYIEVFKSSQEE 122

>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 = 66.9 bits (164), Expect = 8e-14
 Identities = 21/103 (20%), Positives = 39/103 (37%), Gaps = 3/103 (2%)

Query: 378 KDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDK-FTGKSRGLA 436
                G+           + NI  +A   ++R  FS  G + ++R+      TG  RG  
Sbjct: 2   SSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFG 61

Query: 437 YVDFIDDEHLAAAVA--KNKQMFLGKKLSIARSNPKQRKDSSG 477
           +VDFI  +    A     +     G++L +  ++ +    S  
Sbjct: 62  FVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGP 104

>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 = 66.4 bits (163), Expect = 8e-14
 Identities = 19/92 (20%), Positives = 40/92 (43%), Gaps = 1/92 (1%)

Query: 387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHL 446
           G +     ++ +++   T + LR  F   G + +I ++ D  TG+S+G  ++ F D E  
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 447 AAAVAK-NKQMFLGKKLSIARSNPKQRKDSSG 477
             A+ + N     G+ + +     +    S  
Sbjct: 61  RRALEQLNGFELAGRPMRVGHVTERLDGGSGP 92

>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 = 66.5 bits (163), Expect = 8e-14
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
            + T ++SN+    T  DL R FS  G V  + I+ DK T KS+G+A++ F+D +     
Sbjct: 15  SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74

Query: 450 VAK-NKQMFLGKKL 462
               N +   G+ +
Sbjct: 75  TRAINNKQLFGRVI 88

>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 = 68.7 bits (168), Expect = 8e-14
 Identities = 27/145 (18%), Positives = 59/145 (40%), Gaps = 2/145 (1%)

Query: 336 HAPQKPKKVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAF 395
              Q   ++ +K K +       +          E+ + +   +  PG  +   +    F
Sbjct: 18  DGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRS-VEGWILF 76

Query: 396 LSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV-AKNK 454
           +++I+ +A  ++++  F D G + +I +  D+ TG S+G A V++   +   AA  A N 
Sbjct: 77  VTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNG 136

Query: 455 QMFLGKKLSIARSNPKQRKDSSGER 479
              +G+ + +     K  K      
Sbjct: 137 AEIMGQTIQVDWCFVKGPKRVKKSE 161

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 68.3 bits (168), Expect = 1e-13
 Identities = 19/77 (24%), Positives = 35/77 (45%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  I      ++   FFS  G +   +++ DK TG+SRG  +V +   + +        
Sbjct: 91  FVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKF 150

Query: 455 QMFLGKKLSIARSNPKQ 471
             F  +K+ I R+ P+ 
Sbjct: 151 IDFKDRKIEIKRAEPRH 167

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 59.5 bits (145), Expect = 1e-10
 Identities = 25/88 (28%), Positives = 45/88 (51%), Gaps = 1/88 (1%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           + C  F+  +N   T ++LR +F   G V+ ++I+ D  TG+SRG  ++ F         
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSS-VDE 60

Query: 450 VAKNKQMFLGKKLSIARSNPKQRKDSSG 477
           V K + +  GK +   R+ P+  +D +G
Sbjct: 61  VVKTQHILDGKVIDPKRAIPRDEQDKTG 88

>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 = 68.9 bits (169), Expect = 1e-13
 Identities = 26/108 (24%), Positives = 40/108 (37%), Gaps = 4/108 (3%)

Query: 377 IKDAVP----GRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKS 432
            K AV      R          F+  I        LR +F   G +  I I+ D+ +GK 
Sbjct: 86  PKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK 145

Query: 433 RGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKDSSGERA 480
           RG A+V F D + +   V +      G    + ++  KQ   S+    
Sbjct: 146 RGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQ 193

>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 = 64.2 bits (157), Expect = 5e-12
 Identities = 19/88 (21%), Positives = 37/88 (42%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  ++ + T E LR  F   G ++   ++ D  T +SRG  +V +   E + AA+    
Sbjct: 17  FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 76

Query: 455 QMFLGKKLSIARSNPKQRKDSSGERAPT 482
               G+ +   R+  ++     G     
Sbjct: 77  HKVDGRVVEPKRAVSREDSQRPGAHLTV 104

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 65.9 bits (161), Expect = 1e-13
 Identities = 23/98 (23%), Positives = 39/98 (39%), Gaps = 5/98 (5%)

Query: 383 GRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFID 442
           G +   T      +  +  +AT  D+  FFS +     + I      G+  G A V+F  
Sbjct: 7   GSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFAT 64

Query: 443 DEHLAAAVAKNKQMFLGKKLSIARSNPK---QRKDSSG 477
            E   AA+AK+K     + + +  ++         SSG
Sbjct: 65  HEDAVAAMAKDKANMQHRYVELFLNSTAGTSGSGPSSG 102

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 66.2 bits (162), Expect = 1e-13
 Identities = 20/103 (19%), Positives = 40/103 (38%), Gaps = 1/103 (0%)

Query: 370 EQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFT 429
                           KG       ++ +++   T + LR  F   G + SI+++ D  T
Sbjct: 5   HHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSET 64

Query: 430 GKSRGLAYVDFIDDEHLAAAVAK-NKQMFLGKKLSIARSNPKQ 471
           G+S+G  ++ F D E    A+ + N     G+ + +     + 
Sbjct: 65  GRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERT 107

>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 = 66.2 bits (162), Expect = 1e-13
 Identities = 23/107 (21%), Positives = 47/107 (43%), Gaps = 3/107 (2%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
                F+  +N +   + L+  F   G +S + ++ D+ T KSRG A++ F +      A
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNA 64

Query: 450 V-AKNKQMFLGKKLSIARSNPKQRKDSSGERAPTEQAQSHQQTGNAG 495
               N +   GK + + ++     + S G R P   +++   +G+  
Sbjct: 65  AKDMNGKSLHGKAIKVEQAKKPSFQ-SGGRRRPPASSRNRSPSGSLE 110

>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 = 66.4 bits (162), Expect = 2e-13
 Identities = 19/98 (19%), Positives = 37/98 (37%), Gaps = 2/98 (2%)

Query: 373 KKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKS 432
           ++          T   T      +  +  KAT  D+  FFS +     + I      G+ 
Sbjct: 28  QQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRV 85

Query: 433 RGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPK 470
            G A V+F   E   AA++K++     + + +  ++  
Sbjct: 86  TGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTT 123

>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 = 64.6 bits (158), Expect = 3e-13
 Identities = 17/77 (22%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           T  L       T +++  F + +    +IRI+ +   G   G  +VDF ++E +  A+  
Sbjct: 12  TVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNA-HGNKTGYIFVDFSNEEEVKQALKC 69

Query: 453 NKQMFLGKKLSIARSNP 469
           N++   G+ + + R   
Sbjct: 70  NREYMGGRYIEVFREKS 86

>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 = 64.9 bits (159), Expect = 3e-13
 Identities = 24/96 (25%), Positives = 44/96 (45%), Gaps = 1/96 (1%)

Query: 383 GRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFID 442
           G +   T +   ++  +  +   + L   F   G ++ I+I  D  T K RG A+V+F  
Sbjct: 4   GSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 63

Query: 443 DEHLAAAVAK-NKQMFLGKKLSIARSNPKQRKDSSG 477
            E  AAA+   N+    G+ + +  + P + K+S  
Sbjct: 64  AEDAAAAIDNMNESELFGRTIRVNLAKPMRIKESGP 99

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 67.0 bits (164), Expect = 5e-13
 Identities = 17/105 (16%), Positives = 35/105 (33%), Gaps = 5/105 (4%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSI-----RILHDKFTGKSRGLAYVDFIDDEHL 446
              ++ NI    T E +  FF+    +  +       +      + +  A+++F   +  
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 447 AAAVAKNKQMFLGKKLSIARSNPKQRKDSSGERAPTEQAQSHQQT 491
             A+A +  +F G+ L I R +  Q      E             
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTV 109

>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 = 63.1 bits (154), Expect = 1e-11
 Identities = 16/79 (20%), Positives = 36/79 (45%), Gaps = 1/79 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+  +      + ++   +  G + +  ++ D  TG S+G A+ +++D      A+A  N
Sbjct: 118 FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 177

Query: 454 KQMFLGKKLSIARSNPKQR 472
                 KKL + R++   +
Sbjct: 178 GMQLGDKKLLVQRASVGAK 196

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 65.5 bits (160), Expect = 5e-13
 Identities = 22/94 (23%), Positives = 41/94 (43%), Gaps = 1/94 (1%)

Query: 383 GRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFID 442
                     +  + N+  + + + LRR F   G V  + I  D++T +SRG A+V F D
Sbjct: 39  RPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 98

Query: 443 DEHLAAAVAK-NKQMFLGKKLSIARSNPKQRKDS 475
                 A+   +  +  G++L +  +   +  DS
Sbjct: 99  KRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDS 132

>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 = 64.7 bits (158), Expect = 6e-13
 Identities = 25/103 (24%), Positives = 50/103 (48%), Gaps = 1/103 (0%)

Query: 383 GRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFID 442
           G+ K  ++    F+ +++ + T ED++  F+  G +S  R++ D  TGKS+G  +V F +
Sbjct: 7   GQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 66

Query: 443 DEHLAAAVAK-NKQMFLGKKLSIARSNPKQRKDSSGERAPTEQ 484
                 A+ +   Q   G+++    +  K     S   + T+Q
Sbjct: 67  KWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQ 109

>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 = 64.6 bits (157), Expect = 6e-13
 Identities = 16/107 (14%), Positives = 43/107 (40%), Gaps = 4/107 (3%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSD---VGGVSSIRILHDKFTGKSRGLAYV 438
                   +     L  +    + ED++ F SD     GV+ +  ++ +  G+  G A+V
Sbjct: 8   MMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFV 66

Query: 439 DFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKDSSGERAPTEQA 485
           +   ++ +  A+ K+++    + + + +S+  +         P   +
Sbjct: 67  ELESEDDVKLALKKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSAS 113

>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 = 63.8 bits (156), Expect = 7e-13
 Identities = 22/87 (25%), Positives = 45/87 (51%), Gaps = 2/87 (2%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  I+++    ++R FF+  G V  ++I+ D+ TG S+G  +V F  ++     + +++
Sbjct: 13  FVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF-YNDVDVQKIVESQ 70

Query: 455 QMFLGKKLSIARSNPKQRKDSSGERAP 481
             F GKKL +  +  KQ   +   +  
Sbjct: 71  INFHGKKLKLGPAIRKQNLSTYHVQPR 97

>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 = 64.7 bits (158), Expect = 7e-13
 Identities = 19/88 (21%), Positives = 41/88 (46%), Gaps = 1/88 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV-AKN 453
           F++ ++ +AT ED+   F++ G + +I +  D+ TG  +G   V++   +   AA+   N
Sbjct: 26  FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 85

Query: 454 KQMFLGKKLSIARSNPKQRKDSSGERAP 481
            Q  +G+ +S+     +           
Sbjct: 86  GQDLMGQPISVDWCFVRGPPKGKRRGGR 113

>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 = 65.3 bits (160), Expect = 1e-12
 Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 1/84 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
            ++ +    T E+ R  F  +G + S +++ DK TG+S G  +V++ID +    A+   N
Sbjct: 6   IVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLN 65

Query: 454 KQMFLGKKLSIARSNPKQRKDSSG 477
                 K + ++ + P        
Sbjct: 66  GLRLQTKTIKVSYARPSSASIRDA 89

>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 = 52.2 bits (126), Expect = 3e-08
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 1/66 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           ++S +    T ++L + FS  G + + RIL D+ TG SRG+ ++ F        A+   N
Sbjct: 92  YVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN 151

Query: 454 KQMFLG 459
            Q   G
Sbjct: 152 GQKPSG 157

>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 = 64.4 bits (157), Expect = 1e-12
 Identities = 22/112 (19%), Positives = 43/112 (38%), Gaps = 1/112 (0%)

Query: 367 TVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHD 426
            +++  ++Q                    ++ I        LR+ F   G + S++I+ D
Sbjct: 18  QLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCD 77

Query: 427 KFTGKSRGLAYVDFIDDEHLAAAVAK-NKQMFLGKKLSIARSNPKQRKDSSG 477
           + T +SRG  +V F        A+A  N    L K+L +A +    ++    
Sbjct: 78  RETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIA 129

>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 = 63.0 bits (154), Expect = 1e-12
 Identities = 26/90 (28%), Positives = 39/90 (43%), Gaps = 4/90 (4%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV- 450
            T F+  ++   T E L+  F    G    RI+ D+ TG S+G  +VDF  +E   AA  
Sbjct: 16  KTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72

Query: 451 AKNKQMFLGKKLSIARSNPKQRKDSSGERA 480
           A       G K+++  + PK    S     
Sbjct: 73  AMEDGEIDGNKVTLDWAKPKGEGGSGPSSG 102

>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 = 63.1 bits (154), Expect = 1e-12
 Identities = 19/78 (24%), Positives = 40/78 (51%), Gaps = 1/78 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+++I+ +A  ++++  F D G + +I +  D+ TG S+G A V++   +   AA    N
Sbjct: 30  FVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALN 89

Query: 454 KQMFLGKKLSIARSNPKQ 471
               +G+ + +     K 
Sbjct: 90  GAEIMGQTIQVDWCFVKG 107

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 63.0 bits (154), Expect = 2e-12
 Identities = 19/91 (20%), Positives = 42/91 (46%), Gaps = 2/91 (2%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
            + T ++  ++ K +   L   F   G V +  +  D+ TG+ +G  +V+F+ +E    A
Sbjct: 14  QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 73

Query: 450 VAK-NKQMFLGKKLSIARSNPKQRKDSSGER 479
           +   +     GK + + +++    K+ SG  
Sbjct: 74  IKIMDMIKLYGKPIRVNKASAH-NKNLSGPS 103

>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 = 63.2 bits (154), Expect = 2e-12
 Identities = 30/105 (28%), Positives = 43/105 (40%), Gaps = 9/105 (8%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSS--------IRILHDKFTGKSR 433
            G     +D    ++  +N   T +DL  FF   G V          I I  DK TGK +
Sbjct: 6   SGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPK 65

Query: 434 GLAYVDFIDDEHLAAAVAK-NKQMFLGKKLSIARSNPKQRKDSSG 477
           G A V + D     AAV   + + F G KL ++ +  K   +S  
Sbjct: 66  GDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGP 110

>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 = 62.2 bits (152), Expect = 2e-12
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 3/82 (3%)

Query: 395 FLSNINLKATYEDLRRFFSDVGG--VSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           ++ N+    T EDL      +G   +  I+   ++  G+S+G A V    +      +  
Sbjct: 5   YIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDL 64

Query: 453 -NKQMFLGKKLSIARSNPKQRK 473
             K+   G+   +  SN  +  
Sbjct: 65  LPKRELHGQNPVVTPSNKLEHH 86

>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 = 62.6 bits (153), Expect = 2e-12
 Identities = 21/83 (25%), Positives = 41/83 (49%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  I       +LR +F   G V+ + +++D    + RG  ++ F D++ +  AV  + 
Sbjct: 14  FVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHF 73

Query: 455 QMFLGKKLSIARSNPKQRKDSSG 477
              +GKK+ + R+ P+  K S  
Sbjct: 74  HDIMGKKVEVKRAEPRDSKSSGP 96

>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 = 62.3 bits (152), Expect = 2e-12
 Identities = 24/95 (25%), Positives = 36/95 (37%), Gaps = 4/95 (4%)

Query: 387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGK---SRGLAYVDFIDD 443
           G +     F+ N+N   T E L+  FS VG + S  I   K       S G  +V++   
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 444 EHLAAAVAK-NKQMFLGKKLSIARSNPKQRKDSSG 477
           E    A+ +       G KL +  S    +  S  
Sbjct: 61  EQAQKALKQLQGHTVDGHKLEVRISERATKPASGP 95

>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 = 64.1 bits (157), Expect = 3e-12
 Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 1/84 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
            ++ +    T  +L   F  +G +++ RI+ D  TG S G A+VDF  +     A+   N
Sbjct: 7   IVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLN 66

Query: 454 KQMFLGKKLSIARSNPKQRKDSSG 477
                 K+L ++ + P        
Sbjct: 67  GITVRNKRLKVSYARPGGESIKDT 90

>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 = 54.9 bits (133), Expect = 4e-09
 Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 3/75 (4%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           +++N+    T + L   F   G +    IL DK TG+ RG+A+V +   E    A++  N
Sbjct: 93  YVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152

Query: 454 KQMFLG--KKLSIAR 466
             +  G  + LS+  
Sbjct: 153 NVIPEGGSQPLSVRL 167

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 62.3 bits (152), Expect = 3e-12
 Identities = 19/82 (23%), Positives = 42/82 (51%), Gaps = 1/82 (1%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           +    F++ ++ +AT ED+   F++ G + +I +  D+ TG  +G   V++   +   AA
Sbjct: 22  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81

Query: 450 VAK-NKQMFLGKKLSIARSNPK 470
           +   N Q  +G+ +S+     +
Sbjct: 82  MEGLNGQDLMGQPISVDWCFVR 103

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 62.2 bits (151), Expect = 5e-12
 Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 5/87 (5%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSD----VGGVSSIRILHDKFTGKSRGLAYVDFIDDE 444
            ++    +  +   AT E++  FF       GG   I  +     G+  G A+V F  +E
Sbjct: 21  ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEE 79

Query: 445 HLAAAVAKNKQMFLGKKLSIARSNPKQ 471
           +   A+ K+K +   + + + RS   +
Sbjct: 80  YAQNALRKHKDLLGKRYIELFRSTAAE 106

>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 = 61.0 bits (149), Expect = 5e-12
 Identities = 17/81 (20%), Positives = 30/81 (37%), Gaps = 1/81 (1%)

Query: 387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHL 446
           G +     ++  +    T +DL +     G + S + + DK T K +G  +VDF      
Sbjct: 1   GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60

Query: 447 AAAV-AKNKQMFLGKKLSIAR 466
             AV A        +    + 
Sbjct: 61  QKAVTALKASGVQAQMAKQSG 81

>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 = 62.1 bits (151), Expect = 6e-12
 Identities = 22/83 (26%), Positives = 42/83 (50%), Gaps = 1/83 (1%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
             C   +  ++L  T  DLR  FS  G ++ + I++D+ + +SRG A+V F + +    A
Sbjct: 45  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104

Query: 450 VAK-NKQMFLGKKLSIARSNPKQ 471
             + N     G+++ +  S  K+
Sbjct: 105 KERANGMELDGRRIRVDFSITKR 127

>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 = 65.4 bits (160), Expect = 7e-12
 Identities = 23/88 (26%), Positives = 34/88 (38%), Gaps = 1/88 (1%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
            ECT +++N     T  ++R    D+  V+    L       SR  AY+D    E     
Sbjct: 116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYC 175

Query: 450 VAK-NKQMFLGKKLSIARSNPKQRKDSS 476
           V K N     G  L    SNP ++   +
Sbjct: 176 VEKLNGLKIEGYTLVTKVSNPLEKSKRT 203

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 62.7 bits (153), Expect = 5e-11
 Identities = 15/78 (19%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 395 FLSNINLKATYED-LRRFFSDVGGVSSIRILHD-KFTGKSRGLAYVDFIDDEHLAAAVAK 452
            + N++ +   E+ LR  F   G +  I I    K    +   A++ F + +    A+  
Sbjct: 214 MIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQM 273

Query: 453 NKQMFLGKKLSIARSNPK 470
           N+ +   +++S++ ++ K
Sbjct: 274 NRSLLGNREISVSLADKK 291

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 61.9 bits (151), Expect = 9e-11
 Identities = 10/78 (12%), Positives = 30/78 (38%), Gaps = 2/78 (2%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAA 448
            +  T  + N+        + ++F   G +  + +       K+   A ++F   +   A
Sbjct: 39  RELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALA 96

Query: 449 AVAKNKQMFLGKKLSIAR 466
           A+ K  ++    ++ ++ 
Sbjct: 97  AITKTHKVVGQNEIIVSH 114

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 62.6 bits (152), Expect = 7e-12
 Identities = 20/140 (14%), Positives = 50/140 (35%), Gaps = 4/140 (2%)

Query: 354 NLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTA-FLSNINLKATYEDLRRFF 412
           NL  ++         E  PK      A+     G  +   A ++ + +   T + L +  
Sbjct: 17  NLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVI 76

Query: 413 SDVGG--VSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NKQMFLGKKLSIARSNP 469
             +G   V  ++   ++  G+S+G A V    +  +   +     ++  G+K+ +  +  
Sbjct: 77  RSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATR 136

Query: 470 KQRKDSSGERAPTEQAQSHQ 489
           +       +    E  +  +
Sbjct: 137 QNLSQFEAQARKRECVRVPR 156

>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 = 61.4 bits (149), Expect = 7e-12
 Identities = 19/85 (22%), Positives = 36/85 (42%), Gaps = 4/85 (4%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSD---VGGVSSIRILHDKFTGKSRGLAYVDFIDDEH 445
            D        +    T ED+  FFSD     G + I  L ++  GK RG A ++   ++ 
Sbjct: 9   DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNR-DGKRRGDALIEMESEQD 67

Query: 446 LAAAVAKNKQMFLGKKLSIARSNPK 470
           +  A+ K++     + + +   N +
Sbjct: 68  VQKALEKHRMYMGQRYVEVYEINNE 92

>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 = 61.2 bits (149), Expect = 8e-12
 Identities = 22/85 (25%), Positives = 35/85 (41%), Gaps = 1/85 (1%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
              +L N++ + T  DL   F+         I     TG+ RG A++ F + E    A+ 
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

Query: 452 K-NKQMFLGKKLSIARSNPKQRKDS 475
             N     GK L I     K+++ S
Sbjct: 86  LVNGYKLYGKILVIEFGKNKKQRSS 110

>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 = 62.6 bits (153), Expect = 1e-11
 Identities = 16/88 (18%), Positives = 35/88 (39%), Gaps = 5/88 (5%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSI-----RILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           ++ NI    T E +  FF+    +  +       +      + +  A+++F   +    A
Sbjct: 8   YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 67

Query: 450 VAKNKQMFLGKKLSIARSNPKQRKDSSG 477
           +A +  +F G+ L I R +  Q    + 
Sbjct: 68  MAFDGIIFQGQSLKIRRPHDYQPLPGAH 95

>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 = 55.3 bits (134), Expect = 4e-09
 Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+  +      + ++   +  G + +  ++ D  TG S+G A+ +++D      A+A  N
Sbjct: 98  FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 157

Query: 454 KQMFLGKKLSIARSN 468
                 KKL + R++
Sbjct: 158 GMQLGDKKLLVQRAS 172

>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 = 59.8 bits (146), Expect = 1e-11
 Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 1/78 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV-AKN 453
           F+ ++N+    E LR  F D     S  ++ D  TG SRG  +V F   +    A+ +  
Sbjct: 5   FVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQ 64

Query: 454 KQMFLGKKLSIARSNPKQ 471
            Q   G+ L I  +   +
Sbjct: 65  GQDLNGRPLRINWAAKLE 82

>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 = 64.6 bits (158), Expect = 1e-11
 Identities = 11/87 (12%), Positives = 34/87 (39%), Gaps = 1/87 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
            ++N+    T +         G +    +++ + TG+S+G  + +++  +  A A +   
Sbjct: 99  CVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLL 158

Query: 454 KQMFLGKKLSIARSNPKQRKDSSGERA 480
            +    + L +  ++  Q   +     
Sbjct: 159 GKPLGPRTLYVHWTDAGQLTPALLHSR 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 = 55.0 bits (133), Expect = 2e-08
 Identities = 15/86 (17%), Positives = 31/86 (36%), Gaps = 2/86 (2%)

Query: 406 EDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NKQMFLGKKLSI 464
           + L R  S V   +  ++   +  G+ +G A +++   E    A  + +     G  L +
Sbjct: 200 DALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 258

Query: 465 ARSNPKQRKDSSGERAPTEQAQSHQQ 490
           +   P     S        QA +  +
Sbjct: 259 SFCAPGPPGRSMLAALIAAQATALNR 284

>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 = 49.2 bits (118), Expect = 1e-06
 Identities = 15/99 (15%), Positives = 36/99 (36%), Gaps = 8/99 (8%)

Query: 373 KKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKS 432
             + I+  +    + F +     +  +    T +++    SD   +         F  K 
Sbjct: 4   DPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYC------FVDKY 56

Query: 433 RGLAYVDFIDDEHLAAAVAK-NKQMFLGKKLSIARSNPK 470
           +G A+V  ++ E   AA+   ++     ++LS+      
Sbjct: 57  KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD 95

>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 = 60.5 bits (147), Expect = 2e-11
 Identities = 18/130 (13%), Positives = 45/130 (34%), Gaps = 8/130 (6%)

Query: 358 ENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGG 417
            +     +   +    +  + D+  G  +G        +SN++   +  D++  F++ G 
Sbjct: 2   ASMTGGQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGT 61

Query: 418 VSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NKQMFLGKKLSIARSNPKQRKDSS 476
           +    + +D+ +G+S G A V F        A+ +       G+ + I     +      
Sbjct: 62  LKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI----- 115

Query: 477 GERAPTEQAQ 486
            +        
Sbjct: 116 -DLEHHHHHH 124

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 60.1 bits (146), Expect = 2e-11
 Identities = 22/100 (22%), Positives = 42/100 (42%), Gaps = 9/100 (9%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSS--------IRILHDKFTGKSRGLAYVDF 440
           +D  T F+  +    T E +  +F  +G + +        I +  D+ TGK +G A V F
Sbjct: 5   SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 64

Query: 441 IDDEHLAAAVAK-NKQMFLGKKLSIARSNPKQRKDSSGER 479
            D     AA+   + + F G  + ++ +  +   +  G  
Sbjct: 65  DDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGN 104

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 60.4 bits (146), Expect = 2e-11
 Identities = 14/93 (15%), Positives = 40/93 (43%), Gaps = 4/93 (4%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSD---VGGVSSIRILHDKFTGKSRGLAYV 438
                   +     L  +    + ED++ F SD     G + +  ++ +  G+  G A+V
Sbjct: 35  MMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR-EGRQSGEAFV 93

Query: 439 DFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQ 471
           +   ++ +  A+ K+++    + + + +S+  +
Sbjct: 94  ELGSEDDVKMALKKDRESMGHRYIEVFKSHRTE 126

>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 = 59.3 bits (144), Expect = 3e-11
 Identities = 20/91 (21%), Positives = 39/91 (42%), Gaps = 4/91 (4%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAA 448
            D    F+  I      +DL+  F + G +  + +L D+FTG  +G A++ + + E    
Sbjct: 11  HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALK 70

Query: 449 AVAK--NKQMFLGKKLSIA--RSNPKQRKDS 475
           A +    ++   G    I    ++ + R  S
Sbjct: 71  AQSALHEQKTLPGMNRPIQVKPADSESRGGS 101

>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 = 59.3 bits (144), Expect = 4e-11
 Identities = 21/97 (21%), Positives = 39/97 (40%), Gaps = 4/97 (4%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           ++ N+  K T E++   F   G +  IR+     T ++RG AYV + D      AV   +
Sbjct: 12  YIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKNAVDHLS 68

Query: 454 KQMFLGKKLSIARSNPKQRKDSSGERAPTEQAQSHQQ 490
                 + L +   N  +       +   EQ +  ++
Sbjct: 69  GFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKE 105

>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 = 59.3 bits (144), Expect = 4e-11
 Identities = 19/82 (23%), Positives = 34/82 (41%), Gaps = 1/82 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+ ++  +   +DL + F   G V S ++  DK T  S+   +V + +     AA+   N
Sbjct: 29  FIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMN 88

Query: 454 KQMFLGKKLSIARSNPKQRKDS 475
                 K+L +     K    S
Sbjct: 89  GFQIGMKRLKVQLKRSKNDSKS 110

>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 = 59.8 bits (145), Expect = 5e-11
 Identities = 22/139 (15%), Positives = 53/139 (38%), Gaps = 14/139 (10%)

Query: 346 DKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATY 405
           D+   +  +  E  +GR +++ +E     +  +   P            ++ N+      
Sbjct: 8   DEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRI--------YVKNLAKHVQE 59

Query: 406 EDLRRFFSDVGGVSS-----IRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NKQMFLG 459
           +DL+  F      SS     +  +     G+ +G A++   +++  A A+ + N  +  G
Sbjct: 60  KDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFG 119

Query: 460 KKLSIARSNPKQRKDSSGE 478
           K + +  +   + K    E
Sbjct: 120 KPMVVQFARSARPKQDPKE 138

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 58.4 bits (142), Expect = 6e-11
 Identities = 18/80 (22%), Positives = 37/80 (46%), Gaps = 2/80 (2%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
            + T F+ N+  +   E L   F   G ++ + I  D+  GK +   +V F   E ++ A
Sbjct: 15  ADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYA 73

Query: 450 VAK-NKQMFLGKKLSIARSN 468
           +A  N     G+ ++++  +
Sbjct: 74  IALLNGIRLYGRPINVSGPS 93

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 58.6 bits (142), Expect = 6e-11
 Identities = 15/75 (20%), Positives = 28/75 (37%), Gaps = 1/75 (1%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
              + ++      AT +D++ +  D G V +I++         +G  +V F   E     
Sbjct: 10  KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKF 68

Query: 450 VAKNKQMFLGKKLSI 464
           V    Q +    L I
Sbjct: 69  VETPGQKYKETDLLI 83

>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 = 58.0 bits (141), Expect = 7e-11
 Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 3/76 (3%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
            +  ++L  T  DLR  FS  G ++ + I++D+ + +SRG A+V F + +    A  + N
Sbjct: 19  GVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERAN 78

Query: 454 KQMFLGKKLSI--ARS 467
                G+++ +    S
Sbjct: 79  GMELDGRRIRVSGPSS 94

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 58.1 bits (141), Expect = 7e-11
 Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 5/92 (5%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAA 448
            +  T  LSN++  AT E L+  F     +     +     GKS+G A+++F   E    
Sbjct: 13  GESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEFASFEDAKE 68

Query: 449 AVAK-NKQMFLGKKLSIARSNPKQRKDSSGER 479
           A+   NK+   G+ + +    P+   +S    
Sbjct: 69  ALNSCNKREIEGRAIRLELQGPRGSPNSGPSS 100

>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 = 58.5 bits (142), Expect = 8e-11
 Identities = 27/115 (23%), Positives = 46/115 (40%), Gaps = 8/115 (6%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFI 441
            G  +      T F++N++ K  ++ L+  FS  G V    IL DK  GKSRG+  V F 
Sbjct: 6   SGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFE 64

Query: 442 DDEHLAAAVAK-NKQMFLGKKLSIARSNPKQRKDSSGERAPTEQAQSHQQTGNAG 495
                  A++  N Q+   + + +              +      +  QQ+G + 
Sbjct: 65  QSIEAVQAISMFNGQLLFDRPMHVKMDERAL------PKGDFFPPERPQQSGPSS 113

>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 = 58.0 bits (141), Expect = 8e-11
 Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 3/82 (3%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           ++ N++     E LR+ FS  G ++S +++ +   G+S+G  +V F   E    AV + N
Sbjct: 19  YVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMN 76

Query: 454 KQMFLGKKLSIARSNPKQRKDS 475
            ++   K L +A +  K+ + S
Sbjct: 77  GRIVATKPLYVALAQRKEERQS 98

>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 = 59.4 bits (144), Expect = 9e-11
 Identities = 19/108 (17%), Positives = 37/108 (34%), Gaps = 1/108 (0%)

Query: 371 QPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTG 430
           Q + Q  +     + K     CT ++ N++   T E +   FS  G +  I +  DK   
Sbjct: 19  QYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKK 78

Query: 431 KSRGLAYVDFIDDEHLAAAVAK-NKQMFLGKKLSIARSNPKQRKDSSG 477
            + G  +V++        A+   N      + +        +     G
Sbjct: 79  TACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYG 126

>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 = 57.2 bits (139), Expect = 1e-10
 Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+ +++ + T   +   F+  G +S  R++ D  TGKS+G  +V F +      A+ +  
Sbjct: 10  FVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMG 69

Query: 454 KQMFLGKKLSIARSNPK 470
            Q   G+++    +  K
Sbjct: 70  GQWLGGRQIRTNWATRK 86

>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 = 56.4 bits (137), Expect = 2e-10
 Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
            +   ++  +  +   + L   F   G ++ I+I  D  T K RG A+V+F   E  AAA
Sbjct: 6   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65

Query: 450 VAK-NKQMFLGKKL 462
           +   N+    G+ +
Sbjct: 66  IDNMNESELFGRTI 79

>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 = 58.3 bits (142), Expect = 2e-10
 Identities = 17/87 (19%), Positives = 39/87 (44%), Gaps = 2/87 (2%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
             ++ N++   T + L+++F   G +++I+I+ DK   K+   A+V++        A+  
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQT 60

Query: 453 -NKQMFLGKKLSIARSNPKQRKDSSGE 478
            N +      + I  +   Q+  S   
Sbjct: 61  LNGKQIENNIVKINWAFQSQQSSSDDT 87

>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 = 52.1 bits (126), Expect = 4e-08
 Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 1/89 (1%)

Query: 380 AVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVD 439
           A   +     D    F+ ++N+    E LR  F D     S  ++ D  TG SRG  +V 
Sbjct: 76  AFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVS 135

Query: 440 FIDDEHLAAAVAK-NKQMFLGKKLSIARS 467
           F   +    A+     Q   G+ L I  +
Sbjct: 136 FTSQDDAQNAMDSMQGQDLNGRPLRINWA 164

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 57.0 bits (138), Expect = 3e-10
 Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 3/75 (4%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+ ++  + T  DL   F   G V S ++  DK T  S+   +V F + +    A+   N
Sbjct: 44  FIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMN 103

Query: 454 KQMFLGKKL--SIAR 466
                 K+L   + +
Sbjct: 104 GFQVGTKRLKVQLKK 118

>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 = 56.7 bits (137), Expect = 3e-10
 Identities = 18/93 (19%), Positives = 36/93 (38%), Gaps = 5/93 (5%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVG-GVSSIRILHD-KFTGKSRGLAYVDFIDDEHL 446
           +  C  F+  I      E++    + V  GV  + +        K+RG A+V++      
Sbjct: 6   SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 65

Query: 447 AAAVAK---NKQMFLGKKLSIARSNPKQRKDSS 476
           A A  K    +    G ++++  + P+   D  
Sbjct: 66  AMARRKLMPGRIQLWGHQIAVDWAEPEIDVDED 98

>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 = 59.2 bits (144), Expect = 3e-10
 Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 3/92 (3%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAA 448
               + ++ +++   T   L   FS  G + SIR+  D  T +S G AYV+F        
Sbjct: 13  YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 72

Query: 449 AVAK-NKQMFLGK--KLSIARSNPKQRKDSSG 477
           A+   N  +  GK  ++  ++ +P  RK   G
Sbjct: 73  ALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVG 104

>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 = 53.1 bits (128), Expect = 4e-08
 Identities = 21/104 (20%), Positives = 43/104 (41%), Gaps = 5/104 (4%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+ N++     + L   FS  G + S +++ D     S+G  +V F   E    A+ K N
Sbjct: 107 FIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMN 164

Query: 454 KQMFLGKKLSIARSNPKQRKDSSGERAPTE--QAQSHQQTGNAG 495
             +   +K+ + R   ++ +++       E          G++G
Sbjct: 165 GMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPDYAGSSG 208

>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 = 56.1 bits (136), Expect = 3e-10
 Identities = 24/96 (25%), Positives = 39/96 (40%), Gaps = 1/96 (1%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFI 441
            G  +         +  +  K T +DL+ +FS  G V  +++  D  TG S+G  +V F 
Sbjct: 6   SGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF- 64

Query: 442 DDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKDSSG 477
            +      V   + M  G+       N KQ +DS  
Sbjct: 65  TEYETQVKVMSQRHMIDGRWCDCKLPNSKQSQDSGP 100

>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 = 56.5 bits (137), Expect = 4e-10
 Identities = 22/84 (26%), Positives = 33/84 (39%), Gaps = 2/84 (2%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           ++SN+ L    ++L       G V S RIL D  +G SRG+ +      E   A +   N
Sbjct: 29  YISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFN 87

Query: 454 KQMFLGKKLSIARSNPKQRKDSSG 477
            +         A + P   K S  
Sbjct: 88  GKFIKTPPGVSAPTEPLLCKFSGP 111

>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 = 56.1 bits (136), Expect = 4e-10
 Identities = 19/96 (19%), Positives = 41/96 (42%), Gaps = 3/96 (3%)

Query: 383 GRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFID 442
           G ++  +      +SNI  +    DLR+ F   G +  + I+ ++    S+G  +V F +
Sbjct: 7   GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFEN 64

Query: 443 DEHLAAAVAK-NKQMFLGKKLSIARSNPKQRKDSSG 477
                 A  K +  +  G+K+ +  +  +   +S  
Sbjct: 65  SADADRAREKLHGTVVEGRKIEVNNATARVMTNSGP 100

>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 = 55.8 bits (135), Expect = 4e-10
 Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 9/85 (10%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSS--------IRILHDKFTGKSRGLAYVDF 440
           +D  T F+  +    T E +  +F  +G + +        I +  D+ TGK +G A V F
Sbjct: 11  SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 70

Query: 441 IDDEHLAAAVAK-NKQMFLGKKLSI 464
            D     AA+   + + F G  + +
Sbjct: 71  DDPPSAKAAIDWFDGKEFSGNPIKV 95

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 55.7 bits (135), Expect = 5e-10
 Identities = 19/93 (20%), Positives = 37/93 (39%), Gaps = 6/93 (6%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFI 441
           P  +K      T    N++   T ++L+  F D   +  +        GKS+G+AY++F 
Sbjct: 7   PCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFK 61

Query: 442 DDEHLAAAV-AKNKQMFLGKKLSIARSNPKQRK 473
            +      +  K      G+ +S+  +  K   
Sbjct: 62  SEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGT 94

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 55.4 bits (134), Expect = 5e-10
 Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 2/60 (3%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVG--GVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV 450
           T  L NI      + +    S      V++IR++ DK T ++RG A+V        +  +
Sbjct: 11  TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70

>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 = 55.7 bits (135), Expect = 5e-10
 Identities = 22/97 (22%), Positives = 44/97 (45%)

Query: 378 KDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAY 437
              VP  +   +  C  F+  ++ + T E LR +F   G V    ++ D  T +SRG  +
Sbjct: 12  SGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGF 71

Query: 438 VDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKD 474
           V F+D   +   +A+++     K +    + P++ + 
Sbjct: 72  VTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQP 108

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 56.3 bits (136), Expect = 7e-10
 Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFI 441
            G     T +   ++  +  +   + L   F   G ++ I+I  D  T K RG A+V+F 
Sbjct: 54  GGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 113

Query: 442 DDEHLAAAVAK-NKQMFLGKKL 462
             E  AAA+   N+    G+ +
Sbjct: 114 LAEDAAAAIDNMNESELFGRTI 135

>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 = 54.9 bits (133), Expect = 8e-10
 Identities = 13/81 (16%), Positives = 32/81 (39%), Gaps = 2/81 (2%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKF-TGKSRGLAYVDFIDDEHLAAAVAK- 452
            +  +    T + +   FS  G +  I +  ++     S+G AYV+F + +    A+   
Sbjct: 8   HIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHM 67

Query: 453 NKQMFLGKKLSIARSNPKQRK 473
           +     G++++         +
Sbjct: 68  DGGQIDGQEITATAVLAPWPR 88

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 54.5 bits (132), Expect = 1e-09
 Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 3/92 (3%)

Query: 385 TKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDE 444
           + G +  C  F+ N+    T++ L+  F++ G V    I  +   GKS+G   V F   E
Sbjct: 2   SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPE 59

Query: 445 HLAAAVAK-NKQMFLGKKLSIARSNPKQRKDS 475
               A    N     G+++ +          S
Sbjct: 60  VAERACRMMNGMKLSGREIDVRIDRNASGPSS 91

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 56.8 bits (137), Expect = 1e-09
 Identities = 18/111 (16%), Positives = 43/111 (38%), Gaps = 2/111 (1%)

Query: 361 GRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSS 420
              ++        +  + D+  G  +G        +SN++   +  D++  F++ G +  
Sbjct: 58  APYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKK 117

Query: 421 IRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NKQMFLGKKLSIARSNPK 470
             + +D+ +G+S G A V F        A+ +       G+ + I     +
Sbjct: 118 AAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ 167

>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 = 55.0 bits (133), Expect = 1e-09
 Identities = 16/72 (22%), Positives = 35/72 (48%), Gaps = 2/72 (2%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
            +SN++   +  D++  F++ G +    + +D+ +G+S G A V F        A+ + N
Sbjct: 33  LVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYN 91

Query: 454 KQMFLGKKLSIA 465
                G+ ++I 
Sbjct: 92  GVPLDGRPMNIQ 103

>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 = 54.5 bits (132), Expect = 1e-09
 Identities = 22/92 (23%), Positives = 44/92 (47%), Gaps = 2/92 (2%)

Query: 387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGV-SSIRILHDKFTGKSRGLAYVDFIDDEH 445
           G +     F+ N++ +   + L   FS  G +  + +I+ D  TG S+G A+++F   + 
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60

Query: 446 LAAAVAK-NKQMFLGKKLSIARSNPKQRKDSS 476
             AA+   N Q    + ++++ +  K  K S 
Sbjct: 61  SDAAIEAMNGQYLCNRPITVSYAFKKDSKGSG 92

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 60.3 bits (145), Expect = 1e-09
 Identities = 49/301 (16%), Positives = 95/301 (31%), Gaps = 62/301 (20%)

Query: 30  LKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQY-LDKTLKVG------NVVRDVYS 82
           L  E  + +P R+ ++ E  I D   + D W       L   ++           R ++ 
Sbjct: 318 LPREVLTTNPRRLSIIAES-IRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFD 376

Query: 83  -----RATKNCPW--VGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFL 135
                  + + P   +  +W       +  ++    +     K  L      E+      
Sbjct: 377 RLSVFPPSAHIPTILLSLIW------FDVIKSDVMVVVNKLHKYSLV-----EKQPKEST 425

Query: 136 TRIDGLRRRILFSGEVEGVLDYSLIRE-TFQRASDYLSEQMKNTDGLLRLYAYWA---HL 191
             I  +   +    E E  L  S++      +  D         D     Y Y     HL
Sbjct: 426 ISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQ----YFYSHIGHHL 481

Query: 192 EQ-SMGKDMVSARGV-----W-ERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCY 244
           +     + M   R V     + E+ ++       AW +  S+   L+ + + +  YK  Y
Sbjct: 482 KNIEHPERMTLFRMVFLDFRFLEQKIRHDST---AWNASGSI---LNTLQQLK-FYKP-Y 533

Query: 245 SKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRS--QQESKSLPES 302
                      IC    ++ER    + DF   +++     +   L R     E +++ E 
Sbjct: 534 -----------ICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEE 582

Query: 303 A 303
           A
Sbjct: 583 A 583

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 49.9 bits (118), Expect = 2e-06
 Identities = 59/518 (11%), Positives = 141/518 (27%), Gaps = 130/518 (25%)

Query: 38  DPGRVQLLYERAITDF--PVSSDL----WLDYTQY------LDKTLKVGNVVRDVY---- 81
           + G  Q  Y+  ++ F      +       D  +       +D  +   + V        
Sbjct: 10  ETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFW 69

Query: 82  ------SRATKNCPWVGEL------WVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEE 129
                     +   +V E+      ++ S +  E+ + S      + ++  L  ++  + 
Sbjct: 70  TLLSKQEEMVQK--FVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRL--YNDNQV 125

Query: 130 YLDLFLTR---IDGLRRRILFSGEVEGVLDY--------SLIRETFQRASDYLSEQMKNT 178
           +    ++R      LR+ +L     + VL           +  +       Y   Q K  
Sbjct: 126 FAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDV---CLSY-KVQCKMD 181

Query: 179 DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDH-INEAR 237
             +     +W     ++     S   V E L K+   +   W S       +   I+  +
Sbjct: 182 FKI-----FWL----NLKNCN-SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQ 231

Query: 238 SIYKRCYSKRFTGTGS----EDICHAWLRFEREYGTLEDFDHSVQK-VTPRLEELRLFRS 292
           +  +R    +           ++ +A             F+ S +  +T R +++  F S
Sbjct: 232 AELRRLLKSK-PYENCLLVLLNVQNAK--------AWNAFNLSCKILLTTRFKQVTDFLS 282

Query: 293 QQESKSLPESADQKEHSVKKTGREKRKSDS------NISYEQSPAKRQKHAPQK----PK 342
              +  +       +H          +  S      +   +  P +     P++     +
Sbjct: 283 AATTTHISL-----DHHSM--TLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAE 335

Query: 343 KVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLK 402
            + D       N               +      +   +        +     L     +
Sbjct: 336 SIRDGLAT-WDNW--------------KHVNCDKLTTII--------ESSLNVLEPAEYR 372

Query: 403 ATYEDLRRFFSDV---GGVSSI----------RILHDKFTGKS----RGLAYVDFIDDEH 445
             ++ L  F         + S+           ++ +K    S    +       I   +
Sbjct: 373 KMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIY 432

Query: 446 LAAAVAKNKQMFLGKKLSIARSNPKQRKDSSGERAPTE 483
           L   V    +  L + + +   N  +  DS     P  
Sbjct: 433 LELKVKLENEYALHRSI-VDHYNIPKTFDSDDLIPPYL 469

>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 = 56.5 bits (137), Expect = 1e-09
 Identities = 21/94 (22%), Positives = 37/94 (39%), Gaps = 8/94 (8%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTG--KSRGLAYVDFIDDEHL 446
           +D    F+  +    + +DLR  F   G V  I +L D+     +S+G  +V F   +  
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 447 AAAVAK-NKQMFLGKKLSIARSNPKQRKDSSGER 479
             A    +       K+     +P Q K +  E+
Sbjct: 61  LEAQNALH-----NMKVLPGMHHPIQMKPADSEK 89

>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 = 50.7 bits (122), Expect = 1e-07
 Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 5/78 (6%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+  I+ K T  D+R  FS  G +   RIL     G SRG A+V F        A+   +
Sbjct: 99  FIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMH 157

Query: 454 KQMFL---GKKLSIARSN 468
           +   +      + +  ++
Sbjct: 158 QAQTMEGCSSPMVVKFAD 175

>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 = 53.8 bits (130), Expect = 3e-09
 Identities = 19/97 (19%), Positives = 33/97 (34%), Gaps = 7/97 (7%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFI 441
            G  K FT     F+ N+    T E++R+ F   G    + I       K +G  ++   
Sbjct: 6   SGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRLE 59

Query: 442 DDEHLAAAVAK-NKQMFLGKKLSIARSNPKQRKDSSG 477
                  A  + +     GK+L +  +       S  
Sbjct: 60  TRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGP 96

>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 = 52.1 bits (126), Expect = 4e-09
 Identities = 17/67 (25%), Positives = 29/67 (43%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  ++     E +R +F   G V SI +  D  T K RG  ++ F ++E +   + K  
Sbjct: 3   FVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKY 62

Query: 455 QMFLGKK 461
                 K
Sbjct: 63  HNVGLSK 69

>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 = 55.9 bits (134), Expect = 4e-09
 Identities = 9/128 (7%), Positives = 30/128 (23%), Gaps = 7/128 (5%)

Query: 338 PQKPKKVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLS 397
             K   +   +   +++ +   +     +       +Q  K+      +           
Sbjct: 76  VSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKN------RIQHPSNVLHFF 129

Query: 398 NINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NKQM 456
           N  L+ T E+      ++G      +       +      +++         +   N   
Sbjct: 130 NAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQ 189

Query: 457 FLGKKLSI 464
                   
Sbjct: 190 MKNPNGPY 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 = 49.7 bits (118), Expect = 5e-07
 Identities = 14/106 (13%), Positives = 31/106 (29%), Gaps = 7/106 (6%)

Query: 390 DECTAFLSNINLKA-TYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAA 448
           D     +  ++      + +   F   G V  ++ +  K      G A V+  D   +  
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDR 57

Query: 449 AVAK-NKQMFLGKKLSIARSNPKQRKDSSGERAPTEQAQSHQQTGN 493
           A+   N     G+K+++  S                       + +
Sbjct: 58  AITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSES 103

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 52.7 bits (127), Expect = 6e-09
 Identities = 21/114 (18%), Positives = 39/114 (34%), Gaps = 10/114 (8%)

Query: 361 GRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSS 420
           G              P    +  R +G       F+    L     +L   F   G +  
Sbjct: 2   GSSHHHH-HHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKE 60

Query: 421 IRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NKQMFLGKKLSIARSNPKQRK 473
           ++IL         G A+V+F + E  A A+ + + + F  + L +  S    ++
Sbjct: 61  VKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKR 106

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 52.7 bits (127), Expect = 7e-09
 Identities = 23/97 (23%), Positives = 40/97 (41%), Gaps = 4/97 (4%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGG-VSSIRILHDKFTGKSRGLAYVDFID-DEHL 446
             E + F+ ++        L  FF  V       +++ D+ TG S+G  +V F D  E  
Sbjct: 7   GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQK 65

Query: 447 AAAVAKNKQMFLG-KKLSIARSNPKQRKDSSGERAPT 482
            A       + LG K + ++ + PK  +    E  P+
Sbjct: 66  RALTECQGAVGLGSKPVRLSVAIPKASRVKPVESGPS 102

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 52.7 bits (127), Expect = 7e-09
 Identities = 20/111 (18%), Positives = 40/111 (36%), Gaps = 6/111 (5%)

Query: 361 GRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSS 420
           G              P    +    K  +      +SNI  +    DLR+ F   G +  
Sbjct: 2   GSSHHH-HHHSSGLVPRGSHMNTENK--SQPKRLHVSNIPFRFRDPDLRQMFGQFGKILD 58

Query: 421 IRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NKQMFLGKKLSIARSNPK 470
           + I+ ++    S+G  +V F +      A  K +  +  G+K+ +  +  +
Sbjct: 59  VEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>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 = 52.3 bits (126), Expect = 9e-09
 Identities = 24/89 (26%), Positives = 36/89 (40%), Gaps = 8/89 (8%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-- 452
           F+  +N + + ED+ R F   G +    +L     G S+G A+V F       AA+    
Sbjct: 19  FVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALH 77

Query: 453 NKQMFLGKKLSI----ARSNPKQRKDSSG 477
             Q   G   S+    A    K+   SSG
Sbjct: 78  GSQTMPGASSSLVVKFAD-TDKESGPSSG 105

>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 = 52.7 bits (127), Expect = 9e-09
 Identities = 19/82 (23%), Positives = 34/82 (41%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  +    T   LR++F   G +    ++ D+ TGKSRG  +V   D      A     
Sbjct: 21  FVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN 80

Query: 455 QMFLGKKLSIARSNPKQRKDSS 476
            +  G+K ++  +    +  S 
Sbjct: 81  PIIDGRKANVNLAYLGAKPRSL 102

>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 = 51.9 bits (125), Expect = 1e-08
 Identities = 24/94 (25%), Positives = 38/94 (40%)

Query: 386 KGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEH 445
            G  +    F+  ++   T E LR +FS  G V    I+ DK T +SRG  +V F D   
Sbjct: 11  SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNC 70

Query: 446 LAAAVAKNKQMFLGKKLSIARSNPKQRKDSSGER 479
           +   +A       G+ +      P+  + S    
Sbjct: 71  VGTVLASRPHTLDGRNIDPKPCTPRGMQPSGPSS 104

>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 = 51.9 bits (125), Expect = 1e-08
 Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 12/80 (15%)

Query: 406 EDLRRFFSDVG-GVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NKQMFLGK--- 460
             + R F+ +G  V S++I+ ++ TG   G  +V+F D       + K N +   G    
Sbjct: 24  NFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPA 83

Query: 461 ---KLSIARSNPKQRKDSSG 477
              KL+ A         SSG
Sbjct: 84  KRFKLNYA----TYSGPSSG 99

>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 = 51.9 bits (125), Expect = 1e-08
 Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 5/82 (6%)

Query: 398 NINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NKQM 456
           N++   T   + + FS +G   S +++ +  +       +V+F +    AAA+A  N + 
Sbjct: 22  NLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRK 79

Query: 457 FLGK--KLSIARSNPKQRKDSS 476
            LGK  K++ A +   Q+   S
Sbjct: 80  ILGKEVKVNWATTPSSQKSGPS 101

>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 = 51.5 bits (124), Expect = 1e-08
 Identities = 19/85 (22%), Positives = 32/85 (37%), Gaps = 8/85 (9%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-- 452
           ++ N++   T +DLR+ F D                   G A+VD+ D      A+    
Sbjct: 12  YIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFVDYPDQNWAIRAIETLS 65

Query: 453 NKQMFLGKKLSIARSNPKQRKDSSG 477
            K    GK + +  S  K+ + S  
Sbjct: 66  GKVELHGKIMEVDYSVSKKLRSSGP 90

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 50.5 bits (122), Expect = 2e-08
 Identities = 14/58 (24%), Positives = 25/58 (43%)

Query: 404 TYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKK 461
           T ED++ +F   G V    ++ DK T + RG  +V F  ++ +      +      K 
Sbjct: 12  TVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKM 69

>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 = 51.5 bits (124), Expect = 2e-08
 Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 4/89 (4%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+ N++     + L   FS  G + S +++ D     S+G  +V F   E    A+ K N
Sbjct: 9   FIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMN 66

Query: 454 KQMFLGKKLSIARSNPKQ-RKDSSGERAP 481
             +   +K+ + R   ++ R+   G RA 
Sbjct: 67  GMLLNDRKVFVGRFKSRKEREAELGARAK 95

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 53.3 bits (127), Expect = 3e-08
 Identities = 15/73 (20%), Positives = 28/73 (38%), Gaps = 1/73 (1%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
            + ++      AT +D++ +  D G V +I++         +G  +V F   E     V 
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE 168

Query: 452 KNKQMFLGKKLSI 464
              Q +    L I
Sbjct: 169 TPGQKYKETDLLI 181

>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 = 50.8 bits (122), Expect = 3e-08
 Identities = 27/113 (23%), Positives = 42/113 (37%), Gaps = 12/113 (10%)

Query: 369 EEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKF 428
                KQ   + V  ++      CT +   I    T + +R+ FS  G +  IR+  +K 
Sbjct: 5   SSGNTKQLRFEDVVNQS--SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK- 61

Query: 429 TGKSRGLAYVDFIDDEHLAAAVAK-NKQMFLGK--KLSIARSNP-KQRKDSSG 477
                G ++V F   E  A A+   N     G   K    + +P      SSG
Sbjct: 62  -----GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPSSG 109

>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 = 53.9 bits (130), Expect = 3e-08
 Identities = 17/101 (16%), Positives = 35/101 (34%), Gaps = 3/101 (2%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-- 452
            + N++   + E L + FS  G V    ++ D   G++ G  +V+F        A+ +  
Sbjct: 100 TVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERCG 158

Query: 453 NKQMFLGKKLSIARSNPKQRKDSSGERAPTEQAQSHQQTGN 493
           +    L          P ++ D           ++ Q    
Sbjct: 159 DGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKE 199

>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 = 50.1 bits (120), Expect = 6e-07
 Identities = 21/98 (21%), Positives = 35/98 (35%), Gaps = 7/98 (7%)

Query: 373 KKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKS 432
               IK  +    K +T  C  F+ N+    T ED +R F   G  S + I       + 
Sbjct: 4   FTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN------RD 57

Query: 433 RGLAYVDFIDDEHLAAAVAK-NKQMFLGKKLSIARSNP 469
           RG  ++          A A+ +  +   + L I  +  
Sbjct: 58  RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH 95

>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 = 54.1 bits (129), Expect = 4e-08
 Identities = 22/108 (20%), Positives = 43/108 (39%), Gaps = 10/108 (9%)

Query: 392 CTAFLSNINLKATYEDLRR----FFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLA 447
            T +++N+N K   ++L++     FS  G +  I +     + K RG A+V F +     
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 66

Query: 448 AAV-AKNKQMFLGKKLSIARSNPKQRKDSSGERAPTEQAQSHQQTGNA 494
            A+ +     F  K + I  +  K   D   +   T   +  ++    
Sbjct: 67  NALRSMQGFPFYDKPMRIQYA--KTDSDIIAKMKGTFVERDRKREKRK 112

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 44.9 bits (105), Expect = 3e-05
 Identities = 25/191 (13%), Positives = 60/191 (31%), Gaps = 13/191 (6%)

Query: 283 RLEELRLFRSQQESKSLPESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPK 342
            + +++    +++ K        +E    K   +   +   +   Q P        Q P+
Sbjct: 93  IIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPR 152

Query: 343 KVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDE------CTAFL 396
            +H    +                  +  P   P +  +PG+                FL
Sbjct: 153 IMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFL 212

Query: 397 SNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK--NK 454
           +N+  +     L   F+   G   +R++  +       +A+V+F ++    AA       
Sbjct: 213 TNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGF 267

Query: 455 QMFLGKKLSIA 465
           ++     + I+
Sbjct: 268 KITQNNAMKIS 278

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 50.4 bits (121), Expect = 4e-08
 Identities = 18/84 (21%), Positives = 35/84 (41%), Gaps = 6/84 (7%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV-AKN 453
           ++ N+   A   +L R FS  G + ++ I  +       G A+V+F D      AV   +
Sbjct: 4   YVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLD 58

Query: 454 KQMFLGKKLSIARSNPKQRKDSSG 477
            ++  G ++ +  S    R+    
Sbjct: 59  GKVICGSRVRVELSTGMPRRSRFD 82

>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 = 50.8 bits (122), Expect = 4e-08
 Identities = 16/91 (17%), Positives = 33/91 (36%), Gaps = 4/91 (4%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           ++C  ++ N+      +D+   F   G +  I +   K        A+V+F D      A
Sbjct: 21  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPRDAEDA 77

Query: 450 V-AKNKQMFLGKKLSIARSNPKQRKDSSGER 479
           V  ++   + G +L +      +   S    
Sbjct: 78  VYGRDGYDYDGYRLRVEFPRSGRGTGSGPSS 108

>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 = 53.1 bits (127), Expect = 5e-08
 Identities = 31/133 (23%), Positives = 46/133 (34%), Gaps = 6/133 (4%)

Query: 340 KPKKVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNI 399
           KP ++   + + VQ   E  E +   +     P  +  K         F    T  LSNI
Sbjct: 100 KPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNI 159

Query: 400 NLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK--NKQMF 457
               + EDL+  FS  GGV         F  K R +A +     E    A+    N  + 
Sbjct: 160 PPSVSEEDLKVLFSSNGGVVKGFK----FFQKDRKMALIQMGSVEEAVQALIDLHNHDLG 215

Query: 458 LGKKLSIARSNPK 470
               L ++ S   
Sbjct: 216 ENHHLRVSFSKST 228

>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 = 49.6 bits (118), Expect = 7e-07
 Identities = 26/132 (19%), Positives = 45/132 (34%), Gaps = 15/132 (11%)

Query: 380 AVPGRTKGFTDECTAFLSNINLKA-TYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYV 438
           A+PG            +SN+N +  T + L   F   G V  ++IL +K     +  A V
Sbjct: 25  AIPGLAG--AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALV 77

Query: 439 DFIDDEHLAAAVAK-NKQMFLGKKLSIARS------NPKQRKDSSGERAPTEQAQSHQQT 491
              D      A++  N     GK + I  S       P++ ++  G       +  H+  
Sbjct: 78  QMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFK 137

Query: 492 GNAGTSASKESS 503
                +      
Sbjct: 138 KPGSKNFQNIFP 149

>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 = 49.7 bits (119), Expect = 5e-08
 Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 5/77 (6%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRI-----LHDKFTGKSRGLAYVDFIDDEHLAAA 449
           ++ NI    T E +  FF+    +  +       +      + +  A+++F   +    A
Sbjct: 10  YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 69

Query: 450 VAKNKQMFLGKKLSIAR 466
           +A +  +F G+ L I R
Sbjct: 70  MAFDGIIFQGQSLKIRR 86

>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 = 49.5 bits (119), Expect = 6e-08
 Identities = 18/78 (23%), Positives = 35/78 (44%)

Query: 384 RTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDD 443
            +K   D    F+  ++   + +DL+ +F+  G V    I  D  TG+SRG  ++ F D 
Sbjct: 4   ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDA 63

Query: 444 EHLAAAVAKNKQMFLGKK 461
             +   + + +    G+ 
Sbjct: 64  ASVEKVLDQKEHRLDGRV 81

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 50.0 bits (120), Expect = 8e-08
 Identities = 19/110 (17%), Positives = 43/110 (39%), Gaps = 3/110 (2%)

Query: 370 EQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFT 429
           E+  +    +      +        F+  ++ + T E LR ++   G ++   ++ D  +
Sbjct: 9   EKTLETVPLERKK---REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPAS 65

Query: 430 GKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKDSSGER 479
            +SRG  +V F     + AA+A       G+ +   R+  ++   S    
Sbjct: 66  KRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESGSGPSS 115

>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 = 51.8 bits (124), Expect = 8e-08
 Identities = 32/133 (24%), Positives = 47/133 (35%), Gaps = 6/133 (4%)

Query: 340 KPKKVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNI 399
           KP ++   + + VQ   E  E +   +     P  +  K         F    T  LSNI
Sbjct: 69  KPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNI 128

Query: 400 NLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK--NKQMF 457
               + EDL+  FS  GGV        KF  K R +A +     E    A+    N  + 
Sbjct: 129 PPSVSEEDLKVLFSSNGGVVK----GFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLG 184

Query: 458 LGKKLSIARSNPK 470
               L ++ S   
Sbjct: 185 ENHHLRVSFSKST 197

>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 = 48.4 bits (115), Expect = 1e-06
 Identities = 24/123 (19%), Positives = 41/123 (33%), Gaps = 11/123 (8%)

Query: 392 CTAFLSNINLKA-TYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV 450
               +SN+N +  T + L   F   G V  ++IL +K     +  A V   D      A+
Sbjct: 4   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAM 58

Query: 451 AK-NKQMFLGKKLSIARSN----PKQRKDSSGERAPTEQAQSHQQTGNAGTSASKESSIE 505
           +  N     GK + I  S        R+    +    +   S         S + ++   
Sbjct: 59  SHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFP 118

Query: 506 TSK 508
            S 
Sbjct: 119 PSA 121

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 48.6 bits (117), Expect = 8e-08
 Identities = 19/70 (27%), Positives = 34/70 (48%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
           C  F+  ++ + T E LR +F   G V    ++ D  T +SRG  +V F+D   +   +A
Sbjct: 1   CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

Query: 452 KNKQMFLGKK 461
           +++     K 
Sbjct: 61  QSRHELDSKT 70

>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 = 48.8 bits (117), Expect = 1e-07
 Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 6/83 (7%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+       T ++LR FFS  G V  + I         R  A+V F  D+ +A ++    
Sbjct: 9   FVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTF-ADDQIAQSLCGED 62

Query: 455 QMFLGKKLSIARSNPKQRKDSSG 477
            +  G  + I+ + PK   +S  
Sbjct: 63  LIIKGISVHISNAEPKHNSNSGP 85

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 48.6 bits (116), Expect = 1e-07
 Identities = 13/78 (16%), Positives = 22/78 (28%), Gaps = 4/78 (5%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
            + NI     +E L       G V S   ++            V +   +    A+ K N
Sbjct: 19  QIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV---VNVTYSSKDQARQALDKLN 75

Query: 454 KQMFLGKKLSIARSNPKQ 471
                   L +A    + 
Sbjct: 76  GFQLENFTLKVAYIPDEM 93

>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 = 48.0 bits (115), Expect = 2e-07
 Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 6/81 (7%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+       T E+L++FF   G V  + I         R  A+V F  D+ +A ++    
Sbjct: 15  FVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTF-ADDKVAQSLCGED 68

Query: 455 QMFLGKKLSIARSNPKQRKDS 475
            +  G  + I+ + PK  K +
Sbjct: 69  LIIKGISVHISNAEPKHNKLN 89

>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 = 48.4 bits (116), Expect = 2e-07
 Identities = 18/89 (20%), Positives = 38/89 (42%), Gaps = 10/89 (11%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
             ++ N+ L  + E + + F+++   +  R+       K R  A+V F + E    A+  
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEAMKA 70

Query: 453 -NKQMFLGKKLSIARSNPKQRK---DSSG 477
            N ++  G  + +  + P  +     SSG
Sbjct: 71  LNGKVLDGSPIEVTLAKPVDKDSSGPSSG 99

>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 = 48.0 bits (115), Expect = 2e-07
 Identities = 23/99 (23%), Positives = 42/99 (42%), Gaps = 11/99 (11%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+ N+    T E L + FS  G +  ++ L        +  A++ F + +    A+ + N
Sbjct: 15  FVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMN 66

Query: 454 KQMFLGKKLSIARSNPKQRKDSSGERAPTEQAQSHQQTG 492
            +   G+ + I  + P  +K    ER    QA S   +G
Sbjct: 67  GKDLEGENIEIVFAKPPDQK--RKERKAQRQAASGPSSG 103

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 17/83 (20%), Positives = 33/83 (39%), Gaps = 5/83 (6%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+S          L  +F   G V+S+ +  DK  G     A V+  D     A +++++
Sbjct: 12  FVSGFPRGVDSAQLSEYFLAFGPVASVVM--DKDKGV---FAIVEMGDVGAREAVLSQSQ 66

Query: 455 QMFLGKKLSIARSNPKQRKDSSG 477
               G +L +     K+ +  + 
Sbjct: 67  HSLGGHRLRVRPREQKEFQSPAS 89

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 48.2 bits (115), Expect = 3e-07
 Identities = 12/64 (18%), Positives = 25/64 (39%), Gaps = 1/64 (1%)

Query: 398 NINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NKQM 456
           +  +    + L   FS  G V ++    D+ TGK++G  +V+          +   + + 
Sbjct: 19  SAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKR 78

Query: 457 FLGK 460
              K
Sbjct: 79  LDLK 82

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 48.7 bits (116), Expect = 3e-07
 Identities = 30/130 (23%), Positives = 47/130 (36%), Gaps = 11/130 (8%)

Query: 365 KQTVEEQPKKQPIKDAVPGRTKGFTDE-CTAFLSNINLKATYEDLRR----FFSDVGGVS 419
           K+T   + ++Q +     G T   T+      ++NIN +   E L+       S  G + 
Sbjct: 2   KETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDIL 61

Query: 420 SIRILHDKFTGKSRGLAYVDFIDDEHLAAAV-AKNKQMFLGKKLSIARSNPKQRKDSSGE 478
            I +     +  + G AY+ F   E   A V A     F G  L I  S  +  +    E
Sbjct: 62  DIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFS--ETPQSQVAE 116

Query: 479 RAPTEQAQSH 488
               E    H
Sbjct: 117 DGSLEHHHHH 126

>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 = 47.6 bits (114), Expect = 3e-07
 Identities = 19/84 (22%), Positives = 35/84 (41%), Gaps = 8/84 (9%)

Query: 392 CTAFLSNINLKATYEDLRR----FFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLA 447
            T +++N+N K   ++L++     FS  G +  I +     + K RG A+V F +     
Sbjct: 9   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 65

Query: 448 AAVAK-NKQMFLGKKLSIARSNPK 470
            A+       F  K + I  +   
Sbjct: 66  NALRSMQGFPFYDKPMRIQYAKTD 89

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 9/88 (10%)

Query: 391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV 450
                + NI+   T ++LR  F + G V    I+        +  A+V     E    A+
Sbjct: 10  STKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAI 61

Query: 451 AK-NKQMFLGKKLSIARSNPKQRKDSSG 477
              +   F GK++ +  S  + R  S  
Sbjct: 62  RGLDNTEFQGKRMHVQLSTSRLRTASGP 89

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 47.7 bits (114), Expect = 3e-07
 Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 9/79 (11%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
            TA++ NI   AT  DL   F + G +   +   +K      G  ++ +   E  A  + 
Sbjct: 28  TTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK------GCCFIKYDTHEQAAVCIV 81

Query: 452 K-NKQMFLGK--KLSIARS 467
                 F G+  +    + 
Sbjct: 82  ALANFPFQGRNLRTGWGKE 100

>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 = 46.8 bits (112), Expect = 6e-07
 Identities = 16/82 (19%), Positives = 31/82 (37%), Gaps = 9/82 (10%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+ N+  +AT +++R  F   G V    I+        +   +V   D      A+   +
Sbjct: 12  FIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLH 63

Query: 454 KQMFLGKKLSIARSNPKQRKDS 475
                G  +++  S  K +  S
Sbjct: 64  HYKLHGVNINVEASKNKSKASS 85

>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 = 45.7 bits (109), Expect = 1e-06
 Identities = 16/75 (21%), Positives = 34/75 (45%), Gaps = 8/75 (10%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEH--LAAA 449
            T ++  +    T  DLR  F   G + +I ++  +        A++ F   +   +AA 
Sbjct: 13  TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQFATRQAAEVAAE 66

Query: 450 VAKNKQMFLGKKLSI 464
            + NK +  G++L++
Sbjct: 67  KSFNKLIVNGRRLNV 81

>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 = 45.7 bits (109), Expect = 1e-06
 Identities = 20/92 (21%), Positives = 40/92 (43%), Gaps = 11/92 (11%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAA 448
            +    F+ N++   T ++LR  F   G V    ++        +  A+V    +    A
Sbjct: 7   GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKA 58

Query: 449 AVAK-NKQMFLGKKLSI--ARSNPKQRKDSSG 477
           A+A+ N +   GK++++  +    K+   SSG
Sbjct: 59  AIAQLNGKEVKGKRINVELSTKGQKKSGPSSG 90

>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 = 46.0 bits (109), Expect = 4e-06
 Identities = 21/116 (18%), Positives = 41/116 (35%), Gaps = 6/116 (5%)

Query: 358 ENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGG 417
           + E      T      +                +C  ++ N+       +L R F   G 
Sbjct: 40  DGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGP 99

Query: 418 VSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV-AKNKQMFLGKKLSIARSNPKQR 472
           + S+ +  +       G A+V+F D    A AV   + +   G ++ +  SN ++R
Sbjct: 100 LRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEKR 150

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 44.1 bits (105), Expect = 5e-06
 Identities = 23/94 (24%), Positives = 41/94 (43%), Gaps = 12/94 (12%)

Query: 388 FTDECTAFLSNINLK-ATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHL 446
              +   F+ N+ LK  + EDL R FS  G +  I I             ++ F + + +
Sbjct: 7   IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSV 58

Query: 447 AAAVAK-NKQMFLGKKLSI--ARSNPKQRKDSSG 477
             A+   +++M  GKKL +  + SN + + D   
Sbjct: 59  RDAIECESQEMNFGKKLILEVSSSNARPQFDHGD 92

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 44.1 bits (104), Expect = 7e-06
 Identities = 15/85 (17%), Positives = 33/85 (38%), Gaps = 9/85 (10%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA--- 451
            +  + +  T  ++       G V+++ +L      K +  A+++   +E     V    
Sbjct: 20  HIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVNYYT 73

Query: 452 KNKQMFLGKKLSIARSNPKQRKDSS 476
               +  G+ + I  SN K+ K  S
Sbjct: 74  SVTPVLRGQPIYIQFSNHKELKTDS 98

>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 = 47.5 bits (112), Expect = 8e-06
 Identities = 22/138 (15%), Positives = 50/138 (36%), Gaps = 8/138 (5%)

Query: 338 PQKPKKVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLS 397
           P + +   ++ +R+ +   E  +     +     P   P                T F++
Sbjct: 57  PTRAETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDA--------FKTLFVA 108

Query: 398 NINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMF 457
            +N   T   LRR F   G +  I +++ K +GK RG A++++  +  + +A        
Sbjct: 109 RVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKK 168

Query: 458 LGKKLSIARSNPKQRKDS 475
           +  +  +      +    
Sbjct: 169 IDGRRVLVDVERGRTVKG 186

>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 = 43.6 bits (103), Expect = 1e-05
 Identities = 14/92 (15%), Positives = 25/92 (27%), Gaps = 15/92 (16%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-- 452
            +  +       DL       G +  + ++  K        A V+F + +     V    
Sbjct: 19  HVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQALVEFENIDSAKECVTFAA 72

Query: 453 -NKQMFLGKKLSIARSN------PKQRKDSSG 477
                  G++     S       P     SSG
Sbjct: 73  DVPVYIAGQQAFFNYSTSKRITRPGNSGPSSG 104

>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 = 43.8 bits (103), Expect = 1e-05
 Identities = 15/85 (17%), Positives = 33/85 (38%), Gaps = 9/85 (10%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV---A 451
            +  + +  T  ++       G V+++ +L      K +  A+++   +E     V    
Sbjct: 35  HIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVNYYT 88

Query: 452 KNKQMFLGKKLSIARSNPKQRKDSS 476
               +  G+ + I  SN K+ K  S
Sbjct: 89  SVTPVLRGQPIYIQFSNHKELKTDS 113

>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 = 43.5 bits (103), Expect = 1e-05
 Identities = 22/101 (21%), Positives = 39/101 (38%), Gaps = 12/101 (11%)

Query: 381 VPGRTKGFTDECTAFLSNINL-KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVD 439
           V  +    +     F+ N+N       D+   FS  G V+   +         +G A+V 
Sbjct: 17  VTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQ 68

Query: 440 FIDDEHLAAAVAK-NKQMFLGKKL--SIARSNPKQRKDSSG 477
           + ++ H  AAV   N ++  G+ L  ++A      R   S 
Sbjct: 69  YSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSGPSS 109

>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 = 43.0 bits (102), Expect = 1e-05
 Identities = 21/88 (23%), Positives = 33/88 (37%), Gaps = 11/88 (12%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
            T ++   ++  T   LR  FS  G +  + +         R  A+V +   E    AVA
Sbjct: 16  NTLYVYGEDM--TPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVA 67

Query: 452 K-NKQMFLGK--KLSIARSNPKQRKDSS 476
           + N         K++IAR  P      S
Sbjct: 68  ELNGTQVESVQLKVNIARKQPMLDSGPS 95

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 42.9 bits (101), Expect = 1e-05
 Identities = 18/95 (18%), Positives = 32/95 (33%), Gaps = 8/95 (8%)

Query: 382 PGRTKGFTD--ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVD 439
           PG   G         ++ N+   A   DL+R   ++G V              R  A++ 
Sbjct: 8   PGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-----LRLTWQGPRRRAFLH 62

Query: 440 FIDDEHLAAAVAK-NKQMFLGKKLSIARSNPKQRK 473
           + D      AV+           L +A +  ++ K
Sbjct: 63  YPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRDK 97

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 22/91 (24%), Positives = 39/91 (42%), Gaps = 10/91 (10%)

Query: 384 RTKGFTDECTAFLSNINL-KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFID 442
             +G   +   F+ N+ L   + EDL R FS  G +  I I             ++ F +
Sbjct: 15  VPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDN 66

Query: 443 DEHLAAAVAK-NKQMFLGKKLSIARSNPKQR 472
            + +  A+   +++M  GKKL +  S+   R
Sbjct: 67  PQSVRDAIEXESQEMNFGKKLILEVSSSNAR 97

>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 = 42.5 bits (100), Expect = 3e-05
 Identities = 18/90 (20%), Positives = 31/90 (34%), Gaps = 8/90 (8%)

Query: 391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV 450
           E    +S +    +++DL+    + G V    +  D       G   V+F+  E +  AV
Sbjct: 15  ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAV 67

Query: 451 AK-NKQMFLGKKLSIARSNPKQRKDSSGER 479
            K +   F   +   A    K     S   
Sbjct: 68  RKLDNTKFRSHEGETAYIRVKVDGPRSPSY 97

>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 = 42.5 bits (100), Expect = 3e-05
 Identities = 13/110 (11%), Positives = 37/110 (33%), Gaps = 8/110 (7%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
            +      N+       +++  FS  G +  + +       +    A V+F++      A
Sbjct: 9   SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKA 62

Query: 450 VAK-NKQMFLGKKLSIARSNPKQRKDSSGERAPTEQAQSHQQTGNAGTSA 498
                   F    L +  + P     ++ ++  ++  Q  ++  +  +S 
Sbjct: 63  FRHLAYSKFHHVPLYLEWA-PIGVFGAAPQKKDSQHEQPAEKAESGPSSG 111

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 42.5 bits (100), Expect = 3e-05
 Identities = 13/92 (14%), Positives = 32/92 (34%), Gaps = 11/92 (11%)

Query: 391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV 450
                + N+    +++DL+    +    ++        T    G   ++F  +E L  A+
Sbjct: 28  RYRITMKNLPEGCSWQDLKDLARENSLETTFS---SVNTRDFDGTGALEFPSEEILVEAL 84

Query: 451 AK-NKQMFLGKKLSIARSNPKQRKDSSGERAP 481
            + N   F G  +++        +D +     
Sbjct: 85  ERLNNIEFRGSVITV-------ERDDNPPPIR 109

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 42.1 bits (99), Expect = 4e-05
 Identities = 18/91 (19%), Positives = 31/91 (34%), Gaps = 8/91 (8%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
            E    +S +    +++DL+    + G V    +  D       G   V+F+  E +  A
Sbjct: 15  SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYA 67

Query: 450 VAK-NKQMFLGKKLSIARSNPKQRKDSSGER 479
           V K +   F   +   A    K     S   
Sbjct: 68  VRKLDNTKFRSHEGETAYIRVKVDGPRSPSY 98

>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 = 40.9 bits (96), Expect = 6e-05
 Identities = 15/92 (16%), Positives = 33/92 (35%), Gaps = 9/92 (9%)

Query: 387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHL 446
           G +      + N+   +  +++     D         L   +  +++  A+V  ++ E  
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQA 53

Query: 447 AAAVAK-NKQMFLGKKLSIARSNPKQRKDSSG 477
             A+   ++  F GK L +    P      SG
Sbjct: 54  QNAIQMFHQYSFRGKDLIVQLQ-PTDALLCSG 84

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 40.1 bits (94), Expect = 2e-04
 Identities = 14/80 (17%), Positives = 27/80 (33%), Gaps = 9/80 (11%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV---A 451
            +  +       DL     + G +S + ++        +  A V+F D      AV   A
Sbjct: 25  HIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNAVNYAA 78

Query: 452 KNKQMFLGKKLSIARSNPKQ 471
            N+    G    +  S  ++
Sbjct: 79  DNQIYIAGHPAFVNYSTSQK 98

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 9/56 (16%), Positives = 23/56 (41%), Gaps = 3/56 (5%)

Query: 406 EDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NKQMFLGK 460
             + + FS  G +++      +  GK++G  ++++    H   AV   +      +
Sbjct: 36  NVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 89

>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 = 39.1 bits (92), Expect = 3e-04
 Identities = 15/80 (18%), Positives = 28/80 (35%), Gaps = 11/80 (13%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           ++  +    +   L R F   G + +I  +           AY+ +   +   AA AK  
Sbjct: 21  WVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMR 74

Query: 454 KQMFLGK----KLSIARSNP 469
                G     ++  A+S P
Sbjct: 75  GFPLGGPDRRLRVDFAKSGP 94

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 11/56 (19%), Positives = 24/56 (42%), Gaps = 2/56 (3%)

Query: 406 EDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKK 461
             + + FS  G +++      +  GK++G  ++++    H   AV       L K+
Sbjct: 22  NVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 75

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	565
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.96
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.94
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	99.92
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.91
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.88
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	99.88
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.86
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.82
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.8
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.78
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.77
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.76
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.76
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.75
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.75
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.75
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.74
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.74
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.74
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.74
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.74
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.74
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.74
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.74
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.74
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.73
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.73
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.73
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.73
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.73
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.73
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.73
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.73
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.73
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.73
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.73
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.73
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.72
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.72
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.72
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.72
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.72
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.72
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.72
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.72
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.72
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.72
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.72
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.72
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.72
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.71
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.71
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.71
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.71
2div_A	99	TRNA selenocysteine associated protein; structural	99.71
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.71
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.71
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.71
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.71
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.71
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.71
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.7
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.7
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.7
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.7
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.7
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.7
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.7
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.7
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.69
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.69
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.69
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.69
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.69
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.69
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.68
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.68
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.68
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.68
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.68
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.68
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.68
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.68
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.68
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.67
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.67
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.67
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.67
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.67
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.67
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.67
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.67
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.48
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.66
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.66
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.66
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.66
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.66
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.66
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.66
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.66
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.66
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.66
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.66
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.66
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.65
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.65
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.65
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.65
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.65
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.65
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.65
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.65
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.64
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.64
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.64
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.64
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.64
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.64
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.64
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.64
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.63
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.63
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.63
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.63
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.62
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.62
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.62
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.62
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.61
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.61
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.61
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.61
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.61
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.61
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.6
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.6
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.6
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.6
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.59
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.59
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.59
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.59
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.59
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.59
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.58
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.58
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.58
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.58
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.58
1x5p_A	97	Negative elongation factor E; structure genomics,	99.57
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.57
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.56
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.56
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.56
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.56
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.56
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.55
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.55
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.55
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.54
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.54
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.54
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.54
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.54
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.54
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.53
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.52
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.51
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.51
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.51
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.51
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.51
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.5
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.49
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.48
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.48
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.48
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.47
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.47
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.46
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.46
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.46
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.45
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.45
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.45
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	99.45
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.45
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.44
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.44
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.44
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.44
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.42
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.42
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.4
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.4
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.38
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	99.37
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.37
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.37
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.37
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.37
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.36
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.36
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.36
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.36
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.36
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.35
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.35
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.35
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.34
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.34
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.31
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.31
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.31
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.3
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.3
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.29
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.28
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.27
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.26
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.26
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.25
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.25
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.25
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.25
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.24
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.24
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.23
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.23
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.23
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.22
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.21
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.21
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.19
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.17
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.13
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.13
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.12
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.12
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.11
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.1
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.09
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.09
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.07
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.07
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.03
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.03
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.02
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.0
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.0
4g1t_A	472	Interferon-induced protein with tetratricopeptide	98.99
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	98.98
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.97
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.94
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.89
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	98.88
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	98.86
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.85
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	98.85
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.84
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	98.83
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.79
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.77
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.77
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.73
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.72
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	98.69
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.68
4g1t_A	472	Interferon-induced protein with tetratricopeptide	98.67
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	98.64
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.62
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	98.6
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.6
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.56
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.53
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.52
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.51
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.51
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.5
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.46
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.44
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.43
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.43
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.43
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.41
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.4
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.4
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.38
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.36
3esl_A	202	Checkpoint serine/threonine-protein kinase BUB1; m	98.33
2wvi_A	164	Mitotic checkpoint serine/threonine-protein kinase	98.31
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.27
4a1g_A	152	Mitotic checkpoint serine/threonine-protein kinas;	98.27
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.25
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.24
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.23
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.23
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.21
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.2
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.19
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.18
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.18
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.17
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.16
4a1g_A	152	Mitotic checkpoint serine/threonine-protein kinas;	98.15
3esl_A	202	Checkpoint serine/threonine-protein kinase BUB1; m	98.14
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.13
4aez_C	223	MAD3, mitotic spindle checkpoint component MAD3; c	98.12
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	98.07
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.05
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.05
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.05
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.05
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.04
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.03
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.02
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.02
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.01
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.0
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	97.97
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	97.97
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	97.96
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	97.96
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	97.95
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.95
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	97.92
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	97.92
4aez_C	223	MAD3, mitotic spindle checkpoint component MAD3; c	97.9
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.9
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	97.89
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	97.87
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.87
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.87
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	97.83
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	97.81
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	97.81
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	97.8
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	97.79
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	97.78
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	97.77
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	97.73
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.73
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	97.71
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	97.69
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.66
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	97.66
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.66
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	97.65
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.64
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	97.63
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.62
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.6
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.6
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	97.59
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.59
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	97.58
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	97.58
2wvi_A	164	Mitotic checkpoint serine/threonine-protein kinase	97.57
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	97.57
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.56
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.53
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	97.52
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	97.48
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	97.45
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.45
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.45
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.43
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.42
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	97.4
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.33
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.31
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.3
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.3
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.28
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	97.28
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.27
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.27
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.22
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	97.21
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	97.2
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.17
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	97.14
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.13
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	97.13
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.1
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.09
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.06
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.03
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	97.02
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.01
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.01
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	97.0
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	96.99
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	96.96
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	96.93
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	96.91
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.91
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	96.89
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	96.86
2l6j_A	111	TPR repeat-containing protein associated with HSP;	96.84
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	96.84
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	96.81
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	96.8
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	96.78
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	96.75
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.75
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	96.73
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	96.72
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	96.72
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	96.63
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	96.58
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.54
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	96.52
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	96.47
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	96.44
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	96.43
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.36
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.35
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	96.3
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.26
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	96.25
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	96.21
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	96.14
2l6j_A	111	TPR repeat-containing protein associated with HSP;	96.14
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.1
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	96.09
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	95.79
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	95.76
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	95.75
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	95.57
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.43
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	95.18
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	94.87
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	94.69
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	94.62
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	94.43
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	94.32
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	94.12
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	93.91
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	92.55
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	92.44
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	91.02
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	89.97
1pc2_A	152	Mitochondria fission protein; unknown function; NM	87.36
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	87.13
1klx_A	138	Cysteine rich protein B; structural genomics, heli	86.44
1klx_A	138	Cysteine rich protein B; structural genomics, heli	86.15
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	86.12
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	86.0
1pc2_A	152	Mitochondria fission protein; unknown function; NM	82.0

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=99.96  E-value=1e-27  Score=259.20  Aligned_cols=243  Identities=15%  Similarity=0.183  Sum_probs=200.5

Q ss_pred             HhHHHHHHHHHHHHhcC-------CchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHH-HHHHHHHHcCCCCH
Q 008442           21 EKFQQYMIYLKYEQSSG-------DPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVR-DVYSRATKNCPWVG   92 (565)
Q Consensus        21 ~~~~~W~~yi~~e~~~~-------~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~-~v~erAl~~~p~~~   92 (565)
                      ..+..|+.||+||+..+       ...+++.+||+||..+|+++++|++|+.|++.++. .+.++ .||+||+..||.+.
T Consensus       300 ~ql~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~~p~~~~lW~~ya~~~~~~~~-~~~a~r~il~rAi~~~P~s~  378 (679)
T 4e6h_A          300 QQLLIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQHVCFAPEIWFNMANYQGEKNT-DSTVITKYLKLGQQCIPNSA  378 (679)
T ss_dssp             HHHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHSC-CTTHHHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCc-HHHHHHHHHHHHHHhCCCCH
Confidence            55789999999999764       23578899999999999999999999999988764 45575 99999999999999


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccH------------------HHHHHHHHHHHHHHHHHhhccccchhh
Q 008442           93 ELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTF------------------EEYLDLFLTRIDGLRRRILFSGEVEGV  154 (565)
Q Consensus        93 ~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~------------------~~~~~~~~~~~~~~~r~~~~~~~~e~~  154 (565)
                      .||+.|+.+.+. .+.++.++.+|++++...+...                  .....+|..+..+.+|..         
T Consensus       379 ~Lwl~~a~~ee~-~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~---------  448 (679)
T 4e6h_A          379 VLAFSLSEQYEL-NTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQ---------  448 (679)
T ss_dssp             HHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHH---------
T ss_pred             HHHHHHHHHHHH-hCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcC---------
Confidence            999999995555 6789999999999997532100                  123457888887776532         


Q ss_pred             hhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChH
Q 008442          155 LDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHIN  234 (565)
Q Consensus       155 ~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~  234 (565)
                       +.+.+|.+|.+|++.+      ......+|..++.+|...+++++.||.||+++|+.+|+...+|+.|++||...|+.+
T Consensus       449 -~l~~AR~vf~~A~~~~------~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~~fe~~~~~~~  521 (679)
T 4e6h_A          449 -GLAASRKIFGKCRRLK------KLVTPDIYLENAYIEYHISKDTKTACKVLELGLKYFATDGEYINKYLDFLIYVNEES  521 (679)
T ss_dssp             -CHHHHHHHHHHHHHTG------GGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCHH
T ss_pred             -CHHHHHHHHHHHHHhc------CCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHhCCCHH
Confidence             4567888999887752      112356889999999998867999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          235 EARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       235 ~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      +||.+|++|+....+......||..|++||..+|+.++++++..++.
T Consensus       522 ~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~  568 (679)
T 4e6h_A          522 QVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFF  568 (679)
T ss_dssp             HHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            99999999998432223467899999999999999999998877764

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=99.94  E-value=6.8e-25  Score=237.20  Aligned_cols=269  Identities=12%  Similarity=0.102  Sum_probs=197.3

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCC---chhHHHHHHHHHhcCC--CCHHHHHHHHHHHHHhcch----
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGD---PGRVQLLYERAITDFP--VSSDLWLDYTQYLDKTLKV----   73 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~---~~~~~~lyERal~~~p--~~~~lW~~Y~~~l~~~~~~----   73 (565)
                      .+|.+||.+|...|.    ...+|..|+++|.+.++   .+.+..+|+|||..+|  .+++||..|+.|+......    
T Consensus        84 ~aR~vyEraL~~fP~----~~~lW~~Yi~~E~~~~~~~~~~~v~~lfeRal~~~~~~~sv~LW~~Yl~f~~~~~~~~~~~  159 (679)
T 4e6h_A           84 QVYETFDKLHDRFPL----MANIWCMRLSLEFDKMEELDAAVIEPVLARCLSKELGNNDLSLWLSYITYVRKKNDIITGG  159 (679)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHTC--CCCHHHHHHHHHHHTCSSSCCCCHHHHHHHHHHHHHHSCSTTTH
T ss_pred             HHHHHHHHHHHHCCC----CHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHhccccccc
Confidence            579999999999998    78899999999999988   9999999999999994  7899999999998875532    


Q ss_pred             ---hhHHHHHHHHHHHcCCC----CHHHHHHHHHHHHH--------hcCCHHHHHHHHHHHHhccccc----HHHHHHHH
Q 008442           74 ---GNVVRDVYSRATKNCPW----VGELWVRSLLSLER--------SRASEEEISTVFEKSLLCAFST----FEEYLDLF  134 (565)
Q Consensus        74 ---~~~~~~v~erAl~~~p~----~~~lW~~yi~~le~--------~~~~~~~~~~if~ral~~~~~~----~~~~~~~~  134 (565)
                         .+.++.+|++|+..++.    ++.||..|+.++..        .+..++.++.||+++|..|...    |..|..+.
T Consensus       160 ~~~r~~vr~~FErAl~~vG~~d~~s~~iW~~Yi~f~~~~~~~~~~eeq~~~~~~R~iy~raL~iP~~~~~~~w~~Y~~fe  239 (679)
T 4e6h_A          160 EEARNIVIQAFQVVVDKCAIFEPKSIQFWNEYLHFLEHWKPVNKFEEQQRVQYIRKLYKTLLCQPMDCLESMWQRYTQWE  239 (679)
T ss_dssp             HHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHTCCCCSHHHHHHHHHHHHHHHHHHTTSCCSSHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHhccccCcHHHHhHHHHHHHHHHHHHhCccHHHHHHHHHHHHHH
Confidence               24578999999997654    78899999986543        1234678999999999876432    22233222


Q ss_pred             HHH-------------HHHHHHHhhc--------------cc----------------------cchhhhhH--------
Q 008442          135 LTR-------------IDGLRRRILF--------------SG----------------------EVEGVLDY--------  157 (565)
Q Consensus       135 ~~~-------------~~~~~r~~~~--------------~~----------------------~~e~~~~~--------  157 (565)
                      ...             -+|...+..+              ..                      .+..++++        
T Consensus       240 ~~~~~~~a~~~~~e~~~~y~~Ar~~~~e~~~~~~~l~r~~p~~~~~~~~~~~p~~~~~~~~ql~lW~~yi~fEk~~~~~l  319 (679)
T 4e6h_A          240 QDVNQLTARRHIGELSAQYMNARSLYQDWLNITKGLKRNLPITLNQATESNLPKPNEYDVQQLLIWLEWIRWESDNKLEL  319 (679)
T ss_dssp             HHHCTTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCCSSSTTCCTTTSCCTTCCCHHHHHHHHHHHHHHHTCTTCC
T ss_pred             HhcCcchHHHHHHHhhHHHHHHHHHHHHHHHHHHhHhhccccccccchhccCCCCchhHHHHHHHHHHHHHHHHhCCccc
Confidence            110             0011000000              00                      00011111        


Q ss_pred             ------HHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHH-HHHHHHHHHccchHHHHHHHHHHHHHc
Q 008442          158 ------SLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSAR-GVWERLLKISGAMLEAWQSYISMEIEL  230 (565)
Q Consensus       158 ------~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar-~i~e~~l~~~~~~~~lw~~yi~~e~~~  230 (565)
                            .+++.+|++|+..       ++....+|..|++++...+ +.+.|+ .+|++|+..+|.+..+|+.|+.+|...
T Consensus       320 ~~~~~~~Rv~~~Ye~aL~~-------~p~~~~lW~~ya~~~~~~~-~~~~a~r~il~rAi~~~P~s~~Lwl~~a~~ee~~  391 (679)
T 4e6h_A          320 SDDLHKARMTYVYMQAAQH-------VCFAPEIWFNMANYQGEKN-TDSTVITKYLKLGQQCIPNSAVLAFSLSEQYELN  391 (679)
T ss_dssp             CHHHHHHHHHHHHHHHHHH-------TTTCHHHHHHHHHHHHHHS-CCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT
T ss_pred             cchhhHHHHHHHHHHHHHH-------cCCCHHHHHHHHHHHHhcC-cHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHh
Confidence                  2233445555543       4556789999999999998 788886 999999999999999999999999999


Q ss_pred             CChHHHHHHHHHHHhcc----------cCCC---------CcHHHHHHHHHHHHHhCCHHHHHHHHHHHhhH
Q 008442          231 DHINEARSIYKRCYSKR----------FTGT---------GSEDICHAWLRFEREYGTLEDFDHSVQKVTPR  283 (565)
Q Consensus       231 ~~~~~aR~i~~~al~~~----------~~~~---------~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~~  283 (565)
                      |+++.||++|++++...          .+.+         ....+|..|+.||++.|+++.++.++.++...
T Consensus       392 ~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~  463 (679)
T 4e6h_A          392 TKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRL  463 (679)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            99999999999998631          0110         13458999999999999999999999888654

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=99.92  E-value=1.4e-23  Score=220.72  Aligned_cols=258  Identities=13%  Similarity=0.083  Sum_probs=184.1

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHh----cCCchhHHHHHHHHHhcCCCC-----------------------
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQS----SGDPGRVQLLYERAITDFPVS-----------------------   56 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~----~~~~~~~~~lyERal~~~p~~-----------------------   56 (565)
                      .|..||.+|.... .++.+..+|..|++|+..    +++.++++.+|+|||. .|..                       
T Consensus        67 i~~~fe~al~~vg-~d~~s~~iW~~Yi~f~~~~~~~~~~~~~vR~iy~rAL~-~P~~~~~~lw~~Y~~fE~~~~~~~~~~  144 (493)
T 2uy1_A           67 LYEVYEFTLGQFE-NYWDSYGLYKEYIEEEGKIEDEQTRIEKIRNGYMRALQ-TPMGSLSELWKDFENFELELNKITGKK  144 (493)
T ss_dssp             THHHHHHHHHHST-TCTTCHHHHHHHHHHTSSCSSHHHHHHHHHHHHHHHHT-SCCTTHHHHHHHHHHHHHHHCHHHHHH
T ss_pred             HHHHHHHHHHHcC-CCcccHHHHHHHHHHHHhchhhhHHHHHHHHHHHHHHh-ChhhhHHHHHHHHHHHHHHhccccHHH
Confidence            5778888887642 123366889999988653    3556788899999987 3432                       


Q ss_pred             ---------------------------HHHHHHHHHHHHHhcc---h---hhHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Q 008442           57 ---------------------------SDLWLDYTQYLDKTLK---V---GNVVRDVYSRATKNCPWVGELWVRSLLSLE  103 (565)
Q Consensus        57 ---------------------------~~lW~~Y~~~l~~~~~---~---~~~~~~v~erAl~~~p~~~~lW~~yi~~le  103 (565)
                                                 .++|..|++|...+..   +   ..++..+|++||..||..+.+|+.|+.+++
T Consensus       145 ~~~~~~~~y~~ar~~y~~~~~~~~~~s~~~W~~y~~~E~~~~~~~~~~~~~~Rv~~~ye~al~~~p~~~~lW~~ya~~~~  224 (493)
T 2uy1_A          145 IVGDTLPIFQSSFQRYQQIQPLIRGWSVKNAARLIDLEMENGMKLGGRPHESRMHFIHNYILDSFYYAEEVYFFYSEYLI  224 (493)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTCSHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHhcCCccCcchhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence                                       2367777777553311   1   345788999999999999999999998665


Q ss_pred             HhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHH---------HHHHh-hcc-------------ccchhh------
Q 008442          104 RSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDG---------LRRRI-LFS-------------GEVEGV------  154 (565)
Q Consensus       104 ~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~---------~~r~~-~~~-------------~~~e~~------  154 (565)
                      . .++.+.++.+|++|+.. +.....+    ..+..+         +..+. ...             ..+-.+      
T Consensus       225 ~-~~~~~~ar~i~erAi~~-P~~~~l~----~~y~~~~e~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~y~~~~~r  298 (493)
T 2uy1_A          225 G-IGQKEKAKKVVERGIEM-SDGMFLS----LYYGLVMDEEAVYGDLKRKYSMGEAESAEKVFSKELDLLRINHLNYVLK  298 (493)
T ss_dssp             H-TTCHHHHHHHHHHHHHH-CCSSHHH----HHHHHHTTCTHHHHHHHHHTC----------CHHHHHHHHHHHHHHHHH
T ss_pred             H-cCCHHHHHHHHHHHHhC-CCcHHHH----HHHHhhcchhHHHHHHHHHHHhhccchhhhhcccccHHHHHHHHHHHHH
Confidence            4 67889999999999987 4432211    111111         11000 000             000001      


Q ss_pred             -hhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCCh
Q 008442          155 -LDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHI  233 (565)
Q Consensus       155 -~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~  233 (565)
                       .+.+.+|.+|++|        ........+|..++.+|..++++++.||.||+.+++.+|+...+|+.|++||...|+.
T Consensus       299 ~~~~~~AR~i~~~A--------~~~~~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~~~~~~~~~~~yid~e~~~~~~  370 (493)
T 2uy1_A          299 KRGLELFRKLFIEL--------GNEGVGPHVFIYCAFIEYYATGSRATPYNIFSSGLLKHPDSTLLKEEFFLFLLRIGDE  370 (493)
T ss_dssp             HHCHHHHHHHHHHH--------TTSCCCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCH
T ss_pred             cCCHHHHHHHHHHh--------hCCCCChHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCH
Confidence             1233444555544        1112245689999999998887899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhhHH
Q 008442          234 NEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRL  284 (565)
Q Consensus       234 ~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~~~  284 (565)
                      ++||.+|+++..       ...+|..|++||..+|+.++++.+++++++.+
T Consensus       371 ~~aR~l~er~~k-------~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~~~  414 (493)
T 2uy1_A          371 ENARALFKRLEK-------TSRMWDSMIEYEFMVGSMELFRELVDQKMDAI  414 (493)
T ss_dssp             HHHHHHHHHSCC-------BHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH-------HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence            999999999942       57999999999999999999998888876655

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.91  E-value=2.1e-22  Score=199.61  Aligned_cols=242  Identities=21%  Similarity=0.269  Sum_probs=189.1

Q ss_pred             ChHhHHHHHHHHHHHHhc----CCc----hhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh------cchh-------hHH
Q 008442           19 DSEKFQQYMIYLKYEQSS----GDP----GRVQLLYERAITDFPVSSDLWLDYTQYLDKT------LKVG-------NVV   77 (565)
Q Consensus        19 ~~~~~~~W~~yi~~e~~~----~~~----~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~------~~~~-------~~~   77 (565)
                      ++.....|+.|++||++.    ++.    .++..+|++||..+|.++++|..|+.++...      .++.       +.+
T Consensus         4 ~~~~~~~W~~yi~~E~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A   83 (308)
T 2ond_A            4 EAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEA   83 (308)
T ss_dssp             HHHHHHHHHHHHHHHHTCTTCCCCHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCcccCCchHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHH
Confidence            345778999999999985    233    5788999999999999999999999988643      2343       789


Q ss_pred             HHHHHHHHH-cCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhh
Q 008442           78 RDVYSRATK-NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLD  156 (565)
Q Consensus        78 ~~v~erAl~-~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~  156 (565)
                      +.+|+||+. ..|.+..+|..|+.+++. .+..++++.+|++++...+....   .+|..+..++.+.          .+
T Consensus        84 ~~~~~rAl~~~~p~~~~~~~~~~~~~~~-~~~~~~A~~~~~~al~~~p~~~~---~~~~~~~~~~~~~----------~~  149 (308)
T 2ond_A           84 ANIYERAISTLLKKNMLLYFAYADYEES-RMKYEKVHSIYNRLLAIEDIDPT---LVYIQYMKFARRA----------EG  149 (308)
T ss_dssp             HHHHHHHHTTTTTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTSSSSCTH---HHHHHHHHHHHHH----------HC
T ss_pred             HHHHHHHHHHhCcccHHHHHHHHHHHHh-cCCHHHHHHHHHHHHhccccCcc---HHHHHHHHHHHHh----------cC
Confidence            999999999 579999999999985554 68899999999999997665332   1344444333221          13


Q ss_pred             HHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHH
Q 008442          157 YSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEA  236 (565)
Q Consensus       157 ~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~a  236 (565)
                      ++.++..|.+++..       .+....+|..++.++....++++.|+.+|+++++.+|++..+|..|+.++...|+++.|
T Consensus       150 ~~~A~~~~~~a~~~-------~p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~A  222 (308)
T 2ond_A          150 IKSGRMIFKKARED-------ARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNT  222 (308)
T ss_dssp             HHHHHHHHHHHHTS-------TTCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHH
T ss_pred             HHHHHHHHHHHHhc-------CCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHH
Confidence            44555666655543       33445678788888766434999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcc-cCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          237 RSIYKRCYSKR-FTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       237 R~i~~~al~~~-~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      +.+|++++... ++.+....+|..|+.||..+|+.+.+..++.+++
T Consensus       223 ~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a~  268 (308)
T 2ond_A          223 RVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRF  268 (308)
T ss_dssp             HHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            99999999831 2222467899999999999999998887766653

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.88  E-value=1.2e-20  Score=201.46  Aligned_cols=241  Identities=21%  Similarity=0.254  Sum_probs=185.3

Q ss_pred             hHHHHHHHHHHHHhcC----Cc----hhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh------cchhh-------HHHHH
Q 008442           22 KFQQYMIYLKYEQSSG----DP----GRVQLLYERAITDFPVSSDLWLDYTQYLDKT------LKVGN-------VVRDV   80 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~----~~----~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~------~~~~~-------~~~~v   80 (565)
                      ....|..|+.|+....    +.    .++..+|++||..+|.++++|..|+.++...      .++.+       .++.+
T Consensus       229 ~~~~w~~~~~~e~~~~~~~~~~~~~~~~a~~~y~~al~~~p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~  308 (530)
T 2ooe_A          229 QVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANI  308 (530)
T ss_dssp             HHHHHHHHHHHHHHCSSCCSCSHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCccCCcchhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHH
Confidence            4679999999998642    32    3778899999999999999999999998863      34444       79999


Q ss_pred             HHHHHH-cCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHH
Q 008442           81 YSRATK-NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSL  159 (565)
Q Consensus        81 ~erAl~-~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~  159 (565)
                      |+||+. .+|.+..+|..|+.++ ...+..++++.+|++++..++....   .+|..+..++++.          .+++.
T Consensus       309 ~~~Al~~~~p~~~~l~~~~~~~~-~~~g~~~~A~~~~~~al~~~p~~~~---~~~~~~~~~~~~~----------~~~~~  374 (530)
T 2ooe_A          309 YERAISTLLKKNMLLYFAYADYE-ESRMKYEKVHSIYNRLLAIEDIDPT---LVYIQYMKFARRA----------EGIKS  374 (530)
T ss_dssp             HHHHTTTTCSSCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHSSSSCHH---HHHHHHHHHHHHH----------HHHHH
T ss_pred             HHHHHHHhCcccHHHHHHHHHHH-HhcCCHHHHHHHHHHHhCccccCch---HHHHHHHHHHHHh----------cCHHH
Confidence            999998 7899999999999844 4478999999999999997765321   2455444443321          13445


Q ss_pred             HHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHH
Q 008442          160 IRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSI  239 (565)
Q Consensus       160 ~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i  239 (565)
                      ++.+|.+|+..       .+....++...+.++....++++.|+.+|+++++.+|++..+|+.|++++...|++++||.+
T Consensus       375 A~~~~~~Al~~-------~~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~p~~~~~~~~~~~~~~~~g~~~~Ar~~  447 (530)
T 2ooe_A          375 GRMIFKKARED-------ARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVL  447 (530)
T ss_dssp             HHHHHHHHHTC-------TTCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTTCHHHHHHH
T ss_pred             HHHHHHHHHhc-------cCCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHCCCCHHHHHHHHHHHHhCCCHhhHHHH
Confidence            55666665542       22334455555556544334999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcccCC--CCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhhHH
Q 008442          240 YKRCYSKRFTG--TGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRL  284 (565)
Q Consensus       240 ~~~al~~~~~~--~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~~~  284 (565)
                      |++++.. .+.  .....+|..|+.||..+|+.+++..+..++....
T Consensus       448 ~~~al~~-~~~~~~~~~~lw~~~~~~e~~~G~~~~~~~~~~r~~~~~  493 (530)
T 2ooe_A          448 FERVLTS-GSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAF  493 (530)
T ss_dssp             HHHHHHS-CCSCGGGCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHT
T ss_pred             HHHHHhc-cCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            9999974 222  1345699999999999999999988777765433

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=99.88  E-value=7.3e-22  Score=207.71  Aligned_cols=241  Identities=12%  Similarity=0.046  Sum_probs=171.0

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcC--C-----chhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSG--D-----PGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNV   76 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~--~-----~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~   76 (565)
                      +|..|+.++...+..   +.+.|..|++||+.+.  .     ..++..+|++||..+|+++.+|+.|+.|+...+ +.+.
T Consensus       156 ar~~y~~~~~~~~~~---s~~~W~~y~~~E~~~~~~~~~~~~~~Rv~~~ye~al~~~p~~~~lW~~ya~~~~~~~-~~~~  231 (493)
T 2uy1_A          156 SFQRYQQIQPLIRGW---SVKNAARLIDLEMENGMKLGGRPHESRMHFIHNYILDSFYYAEEVYFFYSEYLIGIG-QKEK  231 (493)
T ss_dssp             HHHHHHHHHHHHHTC---SHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHTT-CHHH
T ss_pred             HHHHHHHHHHHHhhc---cHHHHHHHHHHHhcCCccCcchhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcC-CHHH
Confidence            466666665433211   4579999999998642  1     357889999999999999999999999987654 7788


Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHH---------------------------------------HhcCCHHHHHHHHH
Q 008442           77 VRDVYSRATKNCPWVGELWVRSLLSLE---------------------------------------RSRASEEEISTVFE  117 (565)
Q Consensus        77 ~~~v~erAl~~~p~~~~lW~~yi~~le---------------------------------------~~~~~~~~~~~if~  117 (565)
                      ++.||+||+.. |++..||..|+.+++                                       +..+..+.++.+|+
T Consensus       232 ar~i~erAi~~-P~~~~l~~~y~~~~e~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~  310 (493)
T 2uy1_A          232 AKKVVERGIEM-SDGMFLSLYYGLVMDEEAVYGDLKRKYSMGEAESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFI  310 (493)
T ss_dssp             HHHHHHHHHHH-CCSSHHHHHHHHHTTCTHHHHHHHHHTC----------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHH
T ss_pred             HHHHHHHHHhC-CCcHHHHHHHHhhcchhHHHHHHHHHHHhhccchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            99999999999 988777776665321                                       11223455556666


Q ss_pred             HHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCC
Q 008442          118 KSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGK  197 (565)
Q Consensus       118 ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~  197 (565)
                      +| ..+...+..|+.  .+.+++.   ..        .+.+.+|.+|+.++..+       +....+|..|+++|...+ 
T Consensus       311 ~A-~~~~~~~~v~i~--~A~lE~~---~~--------~d~~~ar~ife~al~~~-------~~~~~~~~~yid~e~~~~-  368 (493)
T 2uy1_A          311 EL-GNEGVGPHVFIY--CAFIEYY---AT--------GSRATPYNIFSSGLLKH-------PDSTLLKEEFFLFLLRIG-  368 (493)
T ss_dssp             HH-TTSCCCHHHHHH--HHHHHHH---HH--------CCSHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHHT-
T ss_pred             Hh-hCCCCChHHHHH--HHHHHHH---HC--------CChHHHHHHHHHHHHHC-------CCCHHHHHHHHHHHHHcC-
Confidence            65 322222221111  1111111   00        13556777888777643       123457888999999998 


Q ss_pred             ChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccC--CCCcHHHHHHHHHHHHHhCCHHHHHH
Q 008442          198 DMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFT--GTGSEDICHAWLRFEREYGTLEDFDH  275 (565)
Q Consensus       198 ~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~--~~~~~~i~~~~~~fE~~~G~~~~~~~  275 (565)
                      ++++||.+|+++    .....+|..|++||..+|+.+.+|++|++++.....  .++|..++++|++||+.+|+++++-.
T Consensus       369 ~~~~aR~l~er~----~k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~~~~~~~~~~~~~~~~~~~~fe~~~g~l~~~~~  444 (493)
T 2uy1_A          369 DEENARALFKRL----EKTSRMWDSMIEYEFMVGSMELFRELVDQKMDAIKADAILPPLPPREHNVQMEGILGRYHCFLD  444 (493)
T ss_dssp             CHHHHHHHHHHS----CCBHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTCCBCCCCCC--CCCCCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHH----HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhcccccCCcccccccHHHHHHHhhhHHHHHH
Confidence            999999999998    346899999999999999999999999999863211  25677889999999999999887653

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.86  E-value=2.6e-20  Score=198.95  Aligned_cols=272  Identities=15%  Similarity=0.190  Sum_probs=184.2

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhH----HH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNV----VR   78 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~----~~   78 (565)
                      .+|..|+.+|...|.    +...|..|++++...|+++.++.+|+|||..+| +.++|..|+.|+....++.+.    ++
T Consensus        30 ~a~~~~e~al~~~P~----~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~p-~~~lw~~~~~~~~~~~~~~~~a~~~~~  104 (530)
T 2ooe_A           30 KARKTYERLVAQFPS----SGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKVL-HIDLWKCYLSYVRETKGKLPSYKEKMA  104 (530)
T ss_dssp             HHHHHHHHHHTTCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTCC-CHHHHHHHHHHHHHHTTTSTTHHHHHH
T ss_pred             HHHHHHHHHHHHCCC----CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC-ChHHHHHHHHHHHHHccchhhHHHHHH
Confidence            578999999999988    889999999999999999999999999999999 788999999988766554443    45


Q ss_pred             HHHHHHHHcCC---CCHHHHHHHHHHHHHh--------cCCHHHHHHHHHHHHhccccc----HHHHHHHHHHHH-----
Q 008442           79 DVYSRATKNCP---WVGELWVRSLLSLERS--------RASEEEISTVFEKSLLCAFST----FEEYLDLFLTRI-----  138 (565)
Q Consensus        79 ~v~erAl~~~p---~~~~lW~~yi~~le~~--------~~~~~~~~~if~ral~~~~~~----~~~~~~~~~~~~-----  138 (565)
                      .+|++|+..++   .+..+|..|+.++...        .+..+.++.+|++++..|...    |..|..+.....     
T Consensus       105 ~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~P~~~~~~~~~~~~~~e~~~~~~~~~  184 (530)
T 2ooe_A          105 QAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINIEQLWRDYNKYEEGINIHLAK  184 (530)
T ss_dssp             HHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTSCCTTHHHHHHHHHHHHHHHCHHHHH
T ss_pred             HHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhchhhhHHHHHHHHHHHHHhhchhHHH
Confidence            69999998764   5789999999855431        456889999999999865332    112222111000     


Q ss_pred             --------HHHHHHh----------hcccc------------------chhhhhHHHHH--------HHHHHHHHHHHhh
Q 008442          139 --------DGLRRRI----------LFSGE------------------VEGVLDYSLIR--------ETFQRASDYLSEQ  174 (565)
Q Consensus       139 --------~~~~r~~----------~~~~~------------------~e~~~~~~~~~--------~~~~~a~~~l~~~  174 (565)
                              .+...+.          .....                  +..+++++.-.        ....+++..+...
T Consensus       185 ~~l~~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~w~~~~~~e~~~~~~~~~~~~~~~~a~~~y~~a  264 (530)
T 2ooe_A          185 KMIEDRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQC  264 (530)
T ss_dssp             HHHHTTHHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC--CCHHHHHHHHHHHHHHHHHCSSCCSCSHHHHHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHhccccccCCCCCChhHHHHHHHHHHHHHHHHcCCccCCcchhHHHHHHHHHHHH
Confidence                    0000000          00000                  00001110000        0011222333333


Q ss_pred             hcCCchhHHHHHHHHHHHHH-------cCCChH-------HHHHHHHHHHH-HccchHHHHHHHHHHHHHcCChHHHHHH
Q 008442          175 MKNTDGLLRLYAYWAHLEQS-------MGKDMV-------SARGVWERLLK-ISGAMLEAWQSYISMEIELDHINEARSI  239 (565)
Q Consensus       175 ~~~~~~~~~l~~~~a~~e~~-------~~~~~~-------~ar~i~e~~l~-~~~~~~~lw~~yi~~e~~~~~~~~aR~i  239 (565)
                      +...+....+|..|+.++..       .| +++       .|+.+|++++. .+|++..+|..|+.++...|+++.|+.+
T Consensus       265 l~~~p~~~~~w~~~~~~~~~~~~~~~~~g-~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~  343 (530)
T 2ooe_A          265 LLVLGHHPDIWYEAAQYLEQSSKLLAEKG-DMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSI  343 (530)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHHHTTT-CCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHhCCCCHHHHHHHHHHHHHhchhhhhcc-chhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHH
Confidence            33334456788888888765       45 765       78888888887 5788888888888888888888888888


Q ss_pred             HHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhh
Q 008442          240 YKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTP  282 (565)
Q Consensus       240 ~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~  282 (565)
                      |++++..  +...+..+|..|..|+...|+.+.++.++.+++.
T Consensus       344 ~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~  384 (530)
T 2ooe_A          344 YNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARE  384 (530)
T ss_dssp             HHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHh
Confidence            8888863  3333446888888888888888888877777753

>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=99.82  E-value=7e-20  Score=147.75  Aligned_cols=83  Identities=22%  Similarity=0.467  Sum_probs=78.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ..++++|||+|||+++++++|+++|++||.|.+++++.++.+|.++|||||+|.++++|.+|+. +||..|+|++|.|.+
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~   95 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY   95 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3567899999999999999999999999999999999999899999999999999999999997 899999999999999


Q ss_pred             cCCC
Q 008442          467 SNPK  470 (565)
Q Consensus       467 a~~~  470 (565)
                      |+|.
T Consensus        96 AkPS   99 (99)
T 4fxv_A           96 ARPS   99 (99)
T ss_dssp             CCBC
T ss_pred             eeCC
Confidence            9873

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.80  E-value=1.2e-17  Score=165.14  Aligned_cols=215  Identities=16%  Similarity=0.195  Sum_probs=175.2

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHh-------cCCc-------hhHHHHHHHHHh-cCCCCHHHHHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQS-------SGDP-------GRVQLLYERAIT-DFPVSSDLWLDYTQYLD   68 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~-------~~~~-------~~~~~lyERal~-~~p~~~~lW~~Y~~~l~   68 (565)
                      +...|+.+|..+|.    +..+|..|+.++..       .|+.       +.++.+|+|||. ..|.+..+|..|+.++.
T Consensus        35 a~~~~~~al~~~p~----~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~  110 (308)
T 2ond_A           35 VMFAYEQCLLVLGH----HPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEE  110 (308)
T ss_dssp             HHHHHHHHHHHHTT----CHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCC----CHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHH
Confidence            45799999999988    89999999999864       4776       899999999999 69999999999999877


Q ss_pred             HhcchhhHHHHHHHHHHHcCCCCHH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhc
Q 008442           69 KTLKVGNVVRDVYSRATKNCPWVGE-LWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILF  147 (565)
Q Consensus        69 ~~~~~~~~~~~v~erAl~~~p~~~~-lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~  147 (565)
                      ..+ ..+.++.+|++|+...|.... +|..|+.++ ...+.+++++.+|++|+...+..+..++......  +   .  .
T Consensus       111 ~~~-~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~-~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~a~~~--~---~--~  181 (308)
T 2ond_A          111 SRM-KYEKVHSIYNRLLAIEDIDPTLVYIQYMKFA-RRAEGIKSGRMIFKKAREDARTRHHVYVTAALME--Y---Y--C  181 (308)
T ss_dssp             HTT-CHHHHHHHHHHHHTSSSSCTHHHHHHHHHHH-HHHHCHHHHHHHHHHHHTSTTCCTHHHHHHHHHH--H---H--T
T ss_pred             hcC-CHHHHHHHHHHHHhccccCccHHHHHHHHHH-HHhcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHH--H---H--H
Confidence            655 778899999999998888776 999999855 4467899999999999987665444333221110  0   0  0


Q ss_pred             cccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH---cc-chHHHHHHH
Q 008442          148 SGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI---SG-AMLEAWQSY  223 (565)
Q Consensus       148 ~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~---~~-~~~~lw~~y  223 (565)
                      .      .++..++..|++++...       +....+|..|+.++...+ ++++|+.+|++++..   .| ....+|..|
T Consensus       182 ~------~~~~~A~~~~~~al~~~-------p~~~~~~~~~~~~~~~~g-~~~~A~~~~~~al~~~~l~p~~~~~l~~~~  247 (308)
T 2ond_A          182 S------KDKSVAFKIFELGLKKY-------GDIPEYVLAYIDYLSHLN-EDNNTRVLFERVLTSGSLPPEKSGEIWARF  247 (308)
T ss_dssp             S------CCHHHHHHHHHHHHHHH-------TTCHHHHHHHHHHHHTTC-CHHHHHHHHHHHHHSSSSCGGGCHHHHHHH
T ss_pred             c------CCHHHHHHHHHHHHHhC-------CCcHHHHHHHHHHHHHCC-CHHHHHHHHHHHHhccCCCHHHHHHHHHHH
Confidence            0      14566778888877754       234678999999999988 999999999999995   34 468999999


Q ss_pred             HHHHHHcCChHHHHHHHHHHHh
Q 008442          224 ISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       224 i~~e~~~~~~~~aR~i~~~al~  245 (565)
                      +.|+...|+.+.|+.++++++.
T Consensus       248 ~~~~~~~g~~~~a~~~~~~a~~  269 (308)
T 2ond_A          248 LAFESNIGDLASILKVEKRRFT  269 (308)
T ss_dssp             HHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHH
Confidence            9999999999999999999987

>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=99.78  E-value=1.2e-18  Score=153.72  Aligned_cols=84  Identities=18%  Similarity=0.330  Sum_probs=79.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||.++++++|+.+|+.||.|..|.|+.++.++.++|||||+|.+.++|.+||. |++..|.|++|.|.++
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            457899999999999999999999999999999999998889999999999999999999998 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .+...
T Consensus       117 ~~~~~  121 (156)
T 1h2v_Z          117 AGFKE  121 (156)
T ss_dssp             SCCCT
T ss_pred             CCCCC
Confidence            87654

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.77  E-value=3.1e-19  Score=141.69  Aligned_cols=81  Identities=27%  Similarity=0.465  Sum_probs=75.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-c-CCcccCCeEEEEeecC
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVG-GVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-K-NKQMFLGKKLSIARSN  468 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~-~~~~~~g~~l~v~~a~  468 (565)
                      ++|||+|||+++++++|+++|++|| .|.+|+|+.++.+|.++|||||+|.++++|.+|+. + ++..++|++|.|.+|.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            6899999999999999999999999 79999999999899999999999999999999997 5 5667999999999998


Q ss_pred             CCCC
Q 008442          469 PKQR  472 (565)
Q Consensus       469 ~~~~  472 (565)
                      |++.
T Consensus        82 ~~~~   85 (91)
T 2lxi_A           82 PKPK   85 (91)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8754

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=7.3e-18  Score=136.44  Aligned_cols=84  Identities=23%  Similarity=0.491  Sum_probs=79.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecC
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSN  468 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~  468 (565)
                      ...++|||+|||.++++++|+++|+.||.|.+|.|+.++.+|.++|||||+|.+.++|.+|+.+++..|.|++|.|.++.
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~a~   87 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRAE   87 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 008442          469 PKQR  472 (565)
Q Consensus       469 ~~~~  472 (565)
                      ++..
T Consensus        88 ~~~~   91 (99)
T 2dgs_A           88 PRDS   91 (99)
T ss_dssp             CCCC
T ss_pred             CCcc
Confidence            8754

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.76  E-value=4.6e-18  Score=139.78  Aligned_cols=81  Identities=19%  Similarity=0.138  Sum_probs=77.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      +.++|||+|||+++++++|+++|++||.|.+|.|+.++.||+++|||||+|.+.++|.+|+. ||+..|+|++|.|.++.
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            45899999999999999999999999999999999999899999999999999999999998 89999999999999986


Q ss_pred             CC
Q 008442          469 PK  470 (565)
Q Consensus       469 ~~  470 (565)
                      ..
T Consensus        85 ~~   86 (110)
T 3s8s_A           85 KG   86 (110)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.75  E-value=1.1e-17  Score=144.62  Aligned_cols=85  Identities=25%  Similarity=0.340  Sum_probs=80.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ....++|||+|||.++++++|+.+|+.||.|.+|.|+.++.+|+++|||||+|.+.++|.+|+. +++..|.|++|.|.+
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            4557899999999999999999999999999999999998889999999999999999999998 899999999999999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +.+...
T Consensus       119 a~~~~~  124 (139)
T 1u6f_A          119 AASGHQ  124 (139)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            988754

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.75  E-value=1.6e-18  Score=137.94  Aligned_cols=79  Identities=22%  Similarity=0.308  Sum_probs=73.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCC--eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCc----ccCCeEEE
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGG--VSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQ----MFLGKKLS  463 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~--i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~----~~~g~~l~  463 (565)
                      =.||||+|||+++|+++|+++|++||.  |.+|+++.|+.+|++||||||+|.++++|++|+. +|+.    .|+|++|.
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~   88 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIG   88 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEE
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEE
Confidence            369999999999999999999999995  6799999999899999999999999999999998 7775    48999999


Q ss_pred             EeecCC
Q 008442          464 IARSNP  469 (565)
Q Consensus       464 v~~a~~  469 (565)
                      |.+|+.
T Consensus        89 V~~Aks   94 (95)
T 2lkz_A           89 VDFAKS   94 (95)
T ss_dssp             EEECCC
T ss_pred             EEEccC
Confidence            999875

>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=99.75  E-value=1.2e-17  Score=135.31  Aligned_cols=85  Identities=31%  Similarity=0.486  Sum_probs=79.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .+.++|||+|||+++++++|+.+|+.||.|.+|.++.++.+|.++|||||+|.+.++|..|+. +++..|.|++|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            456899999999999999999999999999999999998899999999999999999999996 8999999999999999


Q ss_pred             CCCCCC
Q 008442          468 NPKQRK  473 (565)
Q Consensus       468 ~~~~~~  473 (565)
                      .++...
T Consensus        86 ~~~~~~   91 (99)
T 1whw_A           86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCccc
Confidence            887553

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.5e-17  Score=135.64  Aligned_cols=86  Identities=27%  Similarity=0.409  Sum_probs=80.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ..+.++|||+|||.++++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..|+. +++..|.|++|.|.+
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            4567999999999999999999999999999999999998899999999999999999999998 899999999999999


Q ss_pred             cCCCCCC
Q 008442          467 SNPKQRK  473 (565)
Q Consensus       467 a~~~~~~  473 (565)
                      +.++..+
T Consensus        92 a~~~~~~   98 (103)
T 2cq0_A           92 AKPSTNS   98 (103)
T ss_dssp             SSCCCCS
T ss_pred             CCCCCCC
Confidence            9887543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=1.6e-17  Score=133.34  Aligned_cols=84  Identities=20%  Similarity=0.421  Sum_probs=79.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||.++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|..|+. +++..+.|++|.|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            346899999999999999999999999999999999998889999999999999999999998 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .++..
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            87644

>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=99.74  E-value=1.2e-17  Score=130.45  Aligned_cols=80  Identities=26%  Similarity=0.396  Sum_probs=76.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCCC
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNPK  470 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~~  470 (565)
                      ++|||+|||+++++++|+.+|+.||.|.++.++.++.+|.++|||||+|.++++|..|+. +++..++|++|.|.++.++
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            689999999999999999999999999999999998899999999999999999999998 8999999999999999886


Q ss_pred             C
Q 008442          471 Q  471 (565)
Q Consensus       471 ~  471 (565)
                      .
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.74  E-value=2.2e-17  Score=134.63  Aligned_cols=84  Identities=23%  Similarity=0.449  Sum_probs=78.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      ....++|||+|||+++++++|+.+|+.|| |.+|+|+.++.+|+++|||||+|.+.++|..|+.+++..|.|++|.|.++
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            34578999999999999999999999997 99999999988899999999999999999999988999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .++..
T Consensus        91 ~~~~~   95 (103)
T 2dng_A           91 EGRKQ   95 (103)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            88654

>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=99.74  E-value=2.1e-18  Score=136.83  Aligned_cols=81  Identities=20%  Similarity=0.332  Sum_probs=71.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCC--CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVG--GVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G--~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      .+|||+|||+++++++|+++|+.||  .|.+++++.++.+|+++|||||+|.+.++|.+|+. +||..++|++|.|..+.
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            5899999999999999999999999  99999999998899999999999999999999997 89999999999999998


Q ss_pred             CCCC
Q 008442          469 PKQR  472 (565)
Q Consensus       469 ~~~~  472 (565)
                      |+..
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            8754

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=3.4e-17  Score=136.69  Aligned_cols=85  Identities=24%  Similarity=0.391  Sum_probs=78.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      .....++|||+|||+++++++|+++|+.||.|.+|+|+.++.+++++|||||+|.+.++|++|+. +++ .|.|++|.|.
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            34567999999999999999999999999999999999998899999999999999999999998 677 8999999999


Q ss_pred             ecCCCCC
Q 008442          466 RSNPKQR  472 (565)
Q Consensus       466 ~a~~~~~  472 (565)
                      ++.+...
T Consensus        92 ~a~~~~~   98 (116)
T 2cqd_A           92 LAYLGAK   98 (116)
T ss_dssp             ESTTTCC
T ss_pred             EcccCCC
Confidence            9987644

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=2.4e-17  Score=133.61  Aligned_cols=85  Identities=24%  Similarity=0.427  Sum_probs=79.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      ...+.++|||+|||+++++++|+.+|+.||.|.+++++.++ +|.++|||||+|.+.++|..|+. +++..+.|++|.|.
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   91 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998 99999999999999999999997 89999999999999


Q ss_pred             ecCCCCC
Q 008442          466 RSNPKQR  472 (565)
Q Consensus       466 ~a~~~~~  472 (565)
                      ++.|+..
T Consensus        92 ~a~~~~~   98 (100)
T 2do4_A           92 ISNSGPS   98 (100)
T ss_dssp             ECCCCSC
T ss_pred             ECCCCCC
Confidence            9988754

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.74  E-value=4.3e-17  Score=135.84  Aligned_cols=87  Identities=23%  Similarity=0.420  Sum_probs=81.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      ...+.++|||+|||.++++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|+.|+. +++..|.|++|.|.
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            34567999999999999999999999999999999999998899999999999999999999997 89999999999999


Q ss_pred             ecCCCCCC
Q 008442          466 RSNPKQRK  473 (565)
Q Consensus       466 ~a~~~~~~  473 (565)
                      ++.++...
T Consensus        91 ~a~~~~~~   98 (115)
T 2dgo_A           91 WATRKPPA   98 (115)
T ss_dssp             ESSCCCCC
T ss_pred             EccCCCCC
Confidence            99887553

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=2.1e-17  Score=135.31  Aligned_cols=85  Identities=19%  Similarity=0.429  Sum_probs=80.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ....++|||+|||+++++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|..|+. +++..|.|++|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   91 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   91 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            4567899999999999999999999999999999999998899999999999999999999998 899999999999999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +.++..
T Consensus        92 a~~~~~   97 (105)
T 1x5u_A           92 ASAHNK   97 (105)
T ss_dssp             TTTTSC
T ss_pred             CCCCCc
Confidence            988754

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.2e-17  Score=136.06  Aligned_cols=85  Identities=26%  Similarity=0.393  Sum_probs=80.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .+.++|||+|||+++++++|+++|+.||.|.+|.|+.++.+|.++|||||+|.+.++|..|+. +++..|.|++|.|.++
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   89 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeC
Confidence            457899999999999999999999999999999999998899999999999999999999997 8999999999999999


Q ss_pred             CCCCCC
Q 008442          468 NPKQRK  473 (565)
Q Consensus       468 ~~~~~~  473 (565)
                      .++..+
T Consensus        90 ~~~~~~   95 (102)
T 2cqb_A           90 KPMRIK   95 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            887654

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.73  E-value=1.7e-17  Score=130.81  Aligned_cols=80  Identities=21%  Similarity=0.432  Sum_probs=75.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      ..+.++|||+|||+++++++|+++|++||.|.++.++.++.+|+++|||||+|.+.++|.+|+.+++..|+|++|.|..|
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            35678999999999999999999999999999999999988999999999999999999999998888999999999875

>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=2.6e-17  Score=136.95  Aligned_cols=83  Identities=22%  Similarity=0.408  Sum_probs=78.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .+.++|||+|||.++++++|+++|+.||.|.+|.|+.++ +|.++|||||+|.+.++|+.|+. +++..|.|++|.|.++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            446899999999999999999999999999999999998 99999999999999999999998 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .++..
T Consensus        84 ~~~~~   88 (116)
T 2fy1_A           84 KKPSF   88 (116)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            87643

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.4e-17  Score=135.88  Aligned_cols=86  Identities=24%  Similarity=0.372  Sum_probs=80.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      ...+.++|||+|||+++++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|+. +++..|+|++|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34567999999999999999999999999999999999998889999999999999999999998 89999999999999


Q ss_pred             ecCCCCC
Q 008442          466 RSNPKQR  472 (565)
Q Consensus       466 ~a~~~~~  472 (565)
                      ++.+...
T Consensus        89 ~a~~~~~   95 (103)
T 2dnm_A           89 VARYGRR   95 (103)
T ss_dssp             ECSSCCS
T ss_pred             ECCcCCC
Confidence            9987654

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.3e-17  Score=134.09  Aligned_cols=84  Identities=23%  Similarity=0.368  Sum_probs=79.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEE-EEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSI-RILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~-~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      .+.++|||+|||+++++++|+.+|+.||.|..+ +|+.++.+|.++|||||+|.++++|..|+. +++..|.|++|.|.+
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            356899999999999999999999999999999 999997899999999999999999999998 899999999999999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +.++..
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            988754

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.73  E-value=2.5e-17  Score=137.26  Aligned_cols=86  Identities=21%  Similarity=0.259  Sum_probs=80.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      ...+.++|||+|||+++++++|+++|+.||.|.+|+|+.++.+|.++|||||+|.+.++|..|+. +|+..|.|++|.|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34566899999999999999999999999999999999998899999999999999999999997 89999999999999


Q ss_pred             ecCCCCC
Q 008442          466 RSNPKQR  472 (565)
Q Consensus       466 ~a~~~~~  472 (565)
                      ++.++..
T Consensus       101 ~a~~~~~  107 (115)
T 2cpz_A          101 LKRSKND  107 (115)
T ss_dssp             CCCCSCC
T ss_pred             EcCCCCc
Confidence            9988755

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.73  E-value=1.3e-17  Score=131.58  Aligned_cols=82  Identities=22%  Similarity=0.395  Sum_probs=75.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .+.++|||+|||.++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|..|+. +++..++|++|.|.++
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            346899999999999999999999999999999999998899999999999999999999998 8999999999999999


Q ss_pred             CCC
Q 008442          468 NPK  470 (565)
Q Consensus       468 ~~~  470 (565)
                      .++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            875

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.5e-17  Score=136.54  Aligned_cols=85  Identities=22%  Similarity=0.347  Sum_probs=79.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      ...++++|||+|||.++++++|+.+|+.||.|.+|.++.++.+|.++|||||+|.+.++|..|+. +++..|.|++|.|.
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   98 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999998889999999999999999999998 89999999999999


Q ss_pred             ecCCCC
Q 008442          466 RSNPKQ  471 (565)
Q Consensus       466 ~a~~~~  471 (565)
                      ++.+++
T Consensus        99 ~a~~~~  104 (106)
T 1p27_B           99 WCFVRG  104 (106)
T ss_dssp             ESEESS
T ss_pred             eecCCC
Confidence            997764

>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=99.73  E-value=9.8e-18  Score=142.27  Aligned_cols=86  Identities=22%  Similarity=0.339  Sum_probs=80.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      ...+.++|||+|||+++++++|+.+|+.||.|.+|.|+.++.+|.++|||||+|.+.++|.+|+. |++..|.|++|.|.
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999997 89999999999999


Q ss_pred             ecCCCCC
Q 008442          466 RSNPKQR  472 (565)
Q Consensus       466 ~a~~~~~  472 (565)
                      ++.++..
T Consensus        98 ~a~~~~~  104 (126)
T 3ex7_B           98 WCFVRGP  104 (126)
T ss_dssp             ESEESSS
T ss_pred             EecCCCC
Confidence            9987644

>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=99.73  E-value=3.6e-17  Score=135.43  Aligned_cols=86  Identities=20%  Similarity=0.369  Sum_probs=80.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cC------CcccCC
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KN------KQMFLG  459 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~------~~~~~g  459 (565)
                      ...+.++|||+|||+++++++|+.+|+.||.|.+|+|+.++.+|.++|||||+|.+.++|..|+. ++      +..|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            34567899999999999999999999999999999999998899999999999999999999998 78      999999


Q ss_pred             eEEEEeecCCCCC
Q 008442          460 KKLSIARSNPKQR  472 (565)
Q Consensus       460 ~~l~v~~a~~~~~  472 (565)
                      ++|.|.++.++..
T Consensus        91 ~~l~v~~a~~~~~  103 (111)
T 1x4h_A           91 RQLKVDLAVTRDE  103 (111)
T ss_dssp             CEEEEECCCCCCC
T ss_pred             EEEEEEECCCCcc
Confidence            9999999988754

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=2.2e-17  Score=133.36  Aligned_cols=85  Identities=26%  Similarity=0.377  Sum_probs=78.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCC---CCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEE
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKF---TGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSI  464 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~---~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v  464 (565)
                      .+.++|||+|||+++++++|+++|+.||.|..|.++.++.   ++.++|||||+|.+.++|..|+. |++..|.|++|.|
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            3568999999999999999999999999999999998875   56899999999999999999998 8999999999999


Q ss_pred             eecCCCCCC
Q 008442          465 ARSNPKQRK  473 (565)
Q Consensus       465 ~~a~~~~~~  473 (565)
                      .++.++...
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999887543

>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=3.2e-17  Score=133.92  Aligned_cols=83  Identities=24%  Similarity=0.474  Sum_probs=77.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCC-CCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFT-GKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~-g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||+++++++|+.+|+.|| |.+|.|+.++.+ |.++|||||+|.+.++|.+|+.+++..|.|++|.|.++
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            4568999999999999999999999999 999999999877 99999999999999999999988999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .++..
T Consensus        92 ~~~~~   96 (104)
T 1wi8_A           92 DQAQD   96 (104)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            88754

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=2.1e-17  Score=134.58  Aligned_cols=85  Identities=21%  Similarity=0.427  Sum_probs=79.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ..+.++|||+|||+++++++|+++|+.||.|..+.|+.++.++.++|||||+|.++++|..|+. +|+..|.|++|.|.+
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3457899999999999999999999999999999999998899999999999999999999996 899999999999999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +.++..
T Consensus        89 a~~~~~   94 (102)
T 1x5s_A           89 AGKSSD   94 (102)
T ss_dssp             EECCCC
T ss_pred             CCCCCC
Confidence            987654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=2.9e-17  Score=134.25  Aligned_cols=84  Identities=20%  Similarity=0.317  Sum_probs=78.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhcc-CCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcc-cCCeEEEE
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSD-VGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQM-FLGKKLSI  464 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~-~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~-~~g~~l~v  464 (565)
                      ....++|||+|||+++++++|+.+|+. ||.|.+|.|+.++ +|.++|||||+|.+.++|..|+. +++.. |+|++|.|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            355789999999999999999999999 9999999999998 99999999999999999999998 89999 99999999


Q ss_pred             eecCCCCC
Q 008442          465 ARSNPKQR  472 (565)
Q Consensus       465 ~~a~~~~~  472 (565)
                      .++.++..
T Consensus        85 ~~a~~~~~   92 (104)
T 2dhg_A           85 SVAIPKAS   92 (104)
T ss_dssp             CBCCCCCS
T ss_pred             EEccCCCc
Confidence            99987654

>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=99.72  E-value=2.8e-17  Score=134.89  Aligned_cols=86  Identities=23%  Similarity=0.454  Sum_probs=80.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEE
Q 008442          386 KGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSI  464 (565)
Q Consensus       386 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v  464 (565)
                      +.....++|||+|||+.+++++|+.+|+.||.|.++.++.++.+|.++|||||+|.+.++|..|+. +++..|+|++|.|
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            344567899999999999999999999999999999999998899999999999999999999997 8999999999999


Q ss_pred             eecCCCC
Q 008442          465 ARSNPKQ  471 (565)
Q Consensus       465 ~~a~~~~  471 (565)
                      .++.++.
T Consensus       101 ~~a~~k~  107 (108)
T 2jrs_A          101 GHVTERT  107 (108)
T ss_dssp             ECSCSSC
T ss_pred             EEcccCC
Confidence            9998763

>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=99.72  E-value=6.5e-17  Score=132.40  Aligned_cols=84  Identities=20%  Similarity=0.354  Sum_probs=78.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCC---eEEEE
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLG---KKLSI  464 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g---~~l~v  464 (565)
                      ...++|||+|||+++++++|+.+|+.||.|..|.|+.++ +|.++|||||+|.+.++|..|+. +++..+.|   ++|.|
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            457999999999999999999999999999999999998 89999999999999999999998 89999988   99999


Q ss_pred             eecCCCCCC
Q 008442          465 ARSNPKQRK  473 (565)
Q Consensus       465 ~~a~~~~~~  473 (565)
                      .++.++..+
T Consensus        92 ~~a~~~~~~  100 (105)
T 2dnh_A           92 KFADTDKES  100 (105)
T ss_dssp             EESCSSCCC
T ss_pred             EECccCccc
Confidence            999887654

>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=99.72  E-value=4.1e-17  Score=167.24  Aligned_cols=85  Identities=22%  Similarity=0.396  Sum_probs=79.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||+.+++++|..+|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||. ||+..|.|++|.|.++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            345899999999999999999999999999999999998899999999999999999999997 8999999999999999


Q ss_pred             CCCCCC
Q 008442          468 NPKQRK  473 (565)
Q Consensus       468 ~~~~~~  473 (565)
                      .+....
T Consensus       180 ~~~~~~  185 (437)
T 3pgw_S          180 RGRTVK  185 (437)
T ss_pred             CCCCCC
Confidence            876553

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=6.7e-17  Score=131.80  Aligned_cols=84  Identities=25%  Similarity=0.417  Sum_probs=78.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ..+.++|||+|||+++++++|+.+|+.||.|..|.|+.+  +|.++|||||+|.+.++|..|+. +++..|.|++|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            346789999999999999999999999999999999997  89999999999999999999998 899999999999999


Q ss_pred             cCCCCCC
Q 008442          467 SNPKQRK  473 (565)
Q Consensus       467 a~~~~~~  473 (565)
                      +.++..+
T Consensus        90 a~~~~~~   96 (103)
T 2d9p_A           90 AQRKEER   96 (103)
T ss_dssp             CSSCCCC
T ss_pred             ecccccC
Confidence            9887553

>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=99.72  E-value=1.1e-17  Score=156.53  Aligned_cols=81  Identities=19%  Similarity=0.328  Sum_probs=76.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCC--CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVG--GVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G--~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ..++|||+|||+++++++|+++|+.||  .|.+|+|+.++.+|+++|||||+|.+.++|.+||. ||+..|.|++|.|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            568999999999999999999999999  99999999998899999999999999999999998 899999999999999


Q ss_pred             cCCC
Q 008442          467 SNPK  470 (565)
Q Consensus       467 a~~~  470 (565)
                      +.+.
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8654

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.72  E-value=2.6e-17  Score=135.00  Aligned_cols=85  Identities=21%  Similarity=0.450  Sum_probs=79.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCccc---CCeEEE
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMF---LGKKLS  463 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~---~g~~l~  463 (565)
                      ..+.++|||+|||.++++++|+.+|+.||.|.+|+|+.++.+|.++|||||+|.+.++|..|+. +++..+   .|++|.
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            4567899999999999999999999999999999999998889999999999999999999998 899887   899999


Q ss_pred             EeecCCCCC
Q 008442          464 IARSNPKQR  472 (565)
Q Consensus       464 v~~a~~~~~  472 (565)
                      |.++.++..
T Consensus        90 v~~a~~~~~   98 (106)
T 2dgp_A           90 VKPADSESR   98 (106)
T ss_dssp             EEECCCCSC
T ss_pred             EEECCcccc
Confidence            999988654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=3.9e-17  Score=135.65  Aligned_cols=86  Identities=33%  Similarity=0.432  Sum_probs=80.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCee--------EEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCccc
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVS--------SIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMF  457 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--------~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~  457 (565)
                      ...+.++|||+|||+++++++|+++|+.||.|.        .|+|+.++.+|.++|||||+|.+.++|..|+. +++..|
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            345679999999999999999999999999999        69999998899999999999999999999998 899999


Q ss_pred             CCeEEEEeecCCCCC
Q 008442          458 LGKKLSIARSNPKQR  472 (565)
Q Consensus       458 ~g~~l~v~~a~~~~~  472 (565)
                      .|++|.|.++.++..
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            999999999988654

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.3e-17  Score=135.12  Aligned_cols=80  Identities=19%  Similarity=0.264  Sum_probs=75.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecC
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSN  468 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~  468 (565)
                      ...++|||+|||+++++++|+++|++||.|.+|+|+.++. |.++|||||+|.++++|..|+.+++..++|++|.|..+.
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   87 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEch
Confidence            4568999999999999999999999999999999999985 999999999999999999999999999999999998864


Q ss_pred             C
Q 008442          469 P  469 (565)
Q Consensus       469 ~  469 (565)
                      .
T Consensus        88 ~   88 (103)
T 1s79_A           88 D   88 (103)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.72  E-value=1.9e-17  Score=136.90  Aligned_cols=86  Identities=22%  Similarity=0.337  Sum_probs=80.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      ...+.++|||+|||.++++++|+.+|+.||.|.++.++.++.+|.++|||||+|.+.++|..|+. +++..|+|++|.|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999998 89999999999999


Q ss_pred             ecCCCCC
Q 008442          466 RSNPKQR  472 (565)
Q Consensus       466 ~a~~~~~  472 (565)
                      ++.++..
T Consensus       102 ~a~~~~~  108 (110)
T 1oo0_B          102 WCFVKGP  108 (110)
T ss_dssp             ESEESSC
T ss_pred             EcccCCC
Confidence            9987654

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=3.6e-17  Score=132.57  Aligned_cols=82  Identities=23%  Similarity=0.297  Sum_probs=75.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      ....++|||+|||+++++++|+++|++||. .+|+|+.++ +|+++|||||+|.++++|++||.+++..|+|+.|.|..+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEEC
Confidence            355689999999999999999999999995 599999998 999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 008442          468 NPKQ  471 (565)
Q Consensus       468 ~~~~  471 (565)
                      .+..
T Consensus        90 ~~~~   93 (102)
T 1wez_A           90 STAG   93 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=5.8e-17  Score=133.21  Aligned_cols=85  Identities=22%  Similarity=0.454  Sum_probs=79.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeec-CCCCCcceEEEEEecCHHHHHHHHH-c-CCcccCCeEEEE
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHD-KFTGKSRGLAYVDFIDDEHLAAAVA-K-NKQMFLGKKLSI  464 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~-~~~g~~~g~afv~f~~~~~a~~a~~-~-~~~~~~g~~l~v  464 (565)
                      ....++|||+|||+++++++|+.+|+.||.|..|+|+.+ +.+|.++|||||+|.+.++|.+|+. + ++..|.|++|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            456789999999999999999999999999999999998 7799999999999999999999998 8 999999999999


Q ss_pred             eecCCCCC
Q 008442          465 ARSNPKQR  472 (565)
Q Consensus       465 ~~a~~~~~  472 (565)
                      .++.++..
T Consensus        92 ~~a~~~~~   99 (107)
T 2cph_A           92 EWADSEVT   99 (107)
T ss_dssp             EECCCCCC
T ss_pred             EeCCCCCC
Confidence            99988754

>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=99.71  E-value=3e-17  Score=131.95  Aligned_cols=82  Identities=28%  Similarity=0.387  Sum_probs=77.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      .++|||+|||.++++++|+.+|+.||.|.+++++.++.+|.++|||||+|.+.++|..|+. ++|..++|++|.|.++.+
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            5799999999999999999999999999999999998889999999999999999999997 899999999999999988


Q ss_pred             CCC
Q 008442          470 KQR  472 (565)
Q Consensus       470 ~~~  472 (565)
                      +..
T Consensus        82 ~~~   84 (96)
T 2x1f_A           82 SDI   84 (96)
T ss_dssp             SSG
T ss_pred             CCC
Confidence            653

>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=99.71  E-value=4e-17  Score=129.31  Aligned_cols=81  Identities=30%  Similarity=0.644  Sum_probs=77.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecCC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~~  469 (565)
                      +.++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|+.+++..+.|++|.|.++.+
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            35799999999999999999999999999999999998899999999999999999999998899999999999999987


Q ss_pred             C
Q 008442          470 K  470 (565)
Q Consensus       470 ~  470 (565)
                      +
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            5

>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=99.71  E-value=2.9e-17  Score=128.87  Aligned_cols=80  Identities=25%  Similarity=0.382  Sum_probs=75.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .+.++|||+|||+++++++|+++|++||.|.++.++.++.+|.++|||||+|.+.++|..|+. +++..++|++|.|.++
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            456899999999999999999999999999999999998899999999999999999999997 8999999999999987


Q ss_pred             C
Q 008442          468 N  468 (565)
Q Consensus       468 ~  468 (565)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=1.7e-16  Score=131.96  Aligned_cols=85  Identities=28%  Similarity=0.416  Sum_probs=78.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ....++|||+|||.++++++|+++|+.||.|.+|.|+.++ +|.++|||||+|.+.++|..|+. +++..|.|++|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEE
Confidence            3457899999999999999999999999999999999997 79999999999999999999998 899999999999999


Q ss_pred             cCCCCCC
Q 008442          467 SNPKQRK  473 (565)
Q Consensus       467 a~~~~~~  473 (565)
                      +.+...+
T Consensus        91 a~~~~~~   97 (114)
T 2do0_A           91 DERALPK   97 (114)
T ss_dssp             CSCCCCC
T ss_pred             cccCCCC
Confidence            9765443

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=3.9e-17  Score=132.13  Aligned_cols=83  Identities=16%  Similarity=0.313  Sum_probs=78.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCee-EEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeE----E
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVS-SIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKK----L  462 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~-~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~----l  462 (565)
                      ...++|||+|||+++++++|+.+|++||.|. +++++.++.+|.++|||||+|.+.++|+.|+. +|+..+.|+.    |
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l   86 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF   86 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeE
Confidence            4568999999999999999999999999999 99999998899999999999999999999998 8999999999    9


Q ss_pred             EEeecCCCC
Q 008442          463 SIARSNPKQ  471 (565)
Q Consensus       463 ~v~~a~~~~  471 (565)
                      .|.++.+..
T Consensus        87 ~v~~a~~~~   95 (99)
T 2div_A           87 KLNYATYSG   95 (99)
T ss_dssp             CEEETTCCS
T ss_pred             EEeecCCCC
Confidence            999998764

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.71  E-value=5.2e-18  Score=137.29  Aligned_cols=82  Identities=15%  Similarity=0.185  Sum_probs=77.3

Q ss_pred             CCCCeEEEcCCCC------CCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCC-e
Q 008442          389 TDECTAFLSNINL------KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLG-K  460 (565)
Q Consensus       389 ~~~~~l~V~nl~~------~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g-~  460 (565)
                      ..+++|||+|||+      ++++++|+++|++||.|.+|+|+.++.||+++|||||+|.++++|.+|+. +||..|.| +
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            3468999999999      99999999999999999999999999889999999999999999999997 89999999 9


Q ss_pred             EEEEeecCCC
Q 008442          461 KLSIARSNPK  470 (565)
Q Consensus       461 ~l~v~~a~~~  470 (565)
                      +|.|.++.|.
T Consensus        84 ~l~V~~a~~~   93 (100)
T 3ns6_A           84 RLFLYTMKDV   93 (100)
T ss_dssp             BCEEEESHHH
T ss_pred             EEEEEECchh
Confidence            9999998764

>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=99.71  E-value=3.6e-17  Score=136.05  Aligned_cols=80  Identities=21%  Similarity=0.391  Sum_probs=74.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      ..+|||+|||+++++++|+++|+.||.|.+|+|+.++  +.++|||||+|.+.++|+.||. |++..|+|++|.|.++.+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999999985  5589999999999999999997 899999999999999987


Q ss_pred             CCC
Q 008442          470 KQR  472 (565)
Q Consensus       470 ~~~  472 (565)
                      +..
T Consensus        83 ~~~   85 (115)
T 4f25_A           83 RKE   85 (115)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            643

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.71  E-value=6e-17  Score=131.00  Aligned_cols=81  Identities=26%  Similarity=0.436  Sum_probs=76.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeE--------EEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccC
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSS--------IRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFL  458 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~--------~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~  458 (565)
                      ....++|||+|||.++++++|+++|+.||.|..        ++++.++.+|+++|||||+|.+.++|+.|+. +++..+.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~   89 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   89 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            455799999999999999999999999999999        9999998899999999999999999999998 8999999


Q ss_pred             CeEEEEeecC
Q 008442          459 GKKLSIARSN  468 (565)
Q Consensus       459 g~~l~v~~a~  468 (565)
                      |++|.|.+|+
T Consensus        90 g~~l~V~~A~   99 (99)
T 2la6_A           90 GNPIKVSFAT   99 (99)
T ss_dssp             SSBCEEEECC
T ss_pred             CcEEEEEecC
Confidence            9999999874

>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=99.71  E-value=1.2e-16  Score=130.18  Aligned_cols=84  Identities=25%  Similarity=0.414  Sum_probs=78.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      ..+.++|||+|||+++++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..|+. ++..|+|++|.|.++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~l~v~~a   90 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCKLP   90 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEECC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH-cCCeeCCeEEEEEec
Confidence            3556899999999999999999999999999999999998889999999999999999999998 577899999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .++..
T Consensus        91 ~~~~~   95 (103)
T 2cqg_A           91 NSKQS   95 (103)
T ss_dssp             CTTCC
T ss_pred             CCCCc
Confidence            88654

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=4.2e-17  Score=133.51  Aligned_cols=86  Identities=27%  Similarity=0.477  Sum_probs=80.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEee
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIAR  466 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~  466 (565)
                      ...+.++|||+|||+++++++|+.+|+.||.|.+|.|+.++.+|.++|||||+|.+.++|..|+..++..|+|++|.|.+
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            34567999999999999999999999999999999999998899999999999999999999998899999999999999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +.++..
T Consensus        92 a~~~~~   97 (105)
T 2dh8_A           92 CTPRGM   97 (105)
T ss_dssp             SCCSSC
T ss_pred             ccCCCC
Confidence            987654

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.71  E-value=5.2e-17  Score=133.57  Aligned_cols=85  Identities=24%  Similarity=0.509  Sum_probs=76.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      ..+.++|||+|||+++++++|+.+|+.||.|.+|+|+.++.+|.++|||||+|.+.++|..|+...+..|+|+.|.|.++
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~~a  101 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA  101 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEc
Confidence            35678999999999999999999999999999999999988899999999999999999999996668999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .++..
T Consensus       102 ~~~~~  106 (109)
T 2rs2_A          102 FPRRA  106 (109)
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=99.70  E-value=3.5e-17  Score=129.30  Aligned_cols=83  Identities=16%  Similarity=0.293  Sum_probs=77.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCC-cceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGK-SRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~-~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ..++|||+|||.++++++|+.+|++||.|.++.++.++.++. ++|||||+|.+.++|.+|+. +|+..++|++|.|.++
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            458999999999999999999999999999999999876666 89999999999999999998 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .|+..
T Consensus        83 ~~~~~   87 (88)
T 4a8x_A           83 LAPWP   87 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=7.3e-17  Score=129.48  Aligned_cols=82  Identities=24%  Similarity=0.402  Sum_probs=77.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ....++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|+. +++..++|++|.|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            3456899999999999999999999999999999999998889999999999999999999998 899999999999999


Q ss_pred             cCC
Q 008442          467 SNP  469 (565)
Q Consensus       467 a~~  469 (565)
                      +++
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            864

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=5.2e-17  Score=135.54  Aligned_cols=84  Identities=20%  Similarity=0.399  Sum_probs=79.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecC
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSN  468 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~  468 (565)
                      ...++|||+|||+++++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..++..|+|++|.|.++.
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            45689999999999999999999999999999999999888999999999999999999999889999999999999998


Q ss_pred             CCCC
Q 008442          469 PKQR  472 (565)
Q Consensus       469 ~~~~  472 (565)
                      ++..
T Consensus       105 ~~~~  108 (116)
T 1x4b_A          105 AREE  108 (116)
T ss_dssp             SCCC
T ss_pred             CCcc
Confidence            8754

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=8.2e-17  Score=128.89  Aligned_cols=81  Identities=28%  Similarity=0.482  Sum_probs=76.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ..+.++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+. +++..|.|++|.|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            3457899999999999999999999999999999999998889999999999999999999997 899999999999998


Q ss_pred             cC
Q 008442          467 SN  468 (565)
Q Consensus       467 a~  468 (565)
                      |+
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>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=99.70  E-value=7.4e-17  Score=129.53  Aligned_cols=82  Identities=17%  Similarity=0.164  Sum_probs=75.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----HHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEE
Q 008442          388 FTDECTAFLSNINLKATYEDLR----RFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKL  462 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~----~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l  462 (565)
                      ..+.++|||+|||+++++++|+    .+|++||.|.+|+|+.++.+   +|||||+|.+.++|..|+. +|+..|+|++|
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l   82 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKI   82 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            3567899999999999999999    99999999999999998744   8999999999999999998 89999999999


Q ss_pred             EEeecCCCCC
Q 008442          463 SIARSNPKQR  472 (565)
Q Consensus       463 ~v~~a~~~~~  472 (565)
                      .|.++.+...
T Consensus        83 ~V~~a~~~~~   92 (96)
T 2dgx_A           83 LVSLATGASG   92 (96)
T ss_dssp             EEEECCCSSC
T ss_pred             EEEEcCCCCC
Confidence            9999987654

>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=99.70  E-value=2.4e-16  Score=128.51  Aligned_cols=84  Identities=19%  Similarity=0.369  Sum_probs=77.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|.|+.++ . .++|||||+|.+.++|..|+. +++..|+|++|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~-~-~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   89 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-R-GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT-T-TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-C-CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567999999999999999999999999999999999885 3 389999999999999999998 899999999999999


Q ss_pred             cCCCCCC
Q 008442          467 SNPKQRK  473 (565)
Q Consensus       467 a~~~~~~  473 (565)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cq3_A           90 ATARVMT   96 (103)
T ss_dssp             CCSSCCC
T ss_pred             cccCCCC
Confidence            9887553

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.70  E-value=2.2e-17  Score=126.10  Aligned_cols=75  Identities=20%  Similarity=0.442  Sum_probs=72.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       393 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      +|||+|||+++++++|+.+|++||.|.++.++.++.+|.++|||||+|.++++|++|+.+++..++|++|.|.+|
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            589999999999999999999999999999999988999999999999999999999999999999999999875

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=1.6e-16  Score=126.35  Aligned_cols=83  Identities=22%  Similarity=0.354  Sum_probs=77.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      ....++|||+|||+++++++|+++|+.| .|.+++|+.+ .+|+++|||||+|.+.++|..|+.+++..|+|++|.|.++
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEEC
Confidence            3557899999999999999999999999 8999999999 5999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .+++.
T Consensus        85 ~~~~~   89 (91)
T 2dgw_A           85 KSGPS   89 (91)
T ss_dssp             SSCCC
T ss_pred             CcCCC
Confidence            87643

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.69  E-value=6.7e-17  Score=137.02  Aligned_cols=84  Identities=26%  Similarity=0.388  Sum_probs=79.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ....++|||+|||+++++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|++|+. +++..|+|++|.|.+
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567899999999999999999999999999999999998899999999999999999999998 899999999999999


Q ss_pred             cCCCC
Q 008442          467 SNPKQ  471 (565)
Q Consensus       467 a~~~~  471 (565)
                      +.+++
T Consensus       123 a~~~~  127 (129)
T 2kxn_B          123 SITKR  127 (129)
T ss_dssp             CSSSS
T ss_pred             ecCCC
Confidence            98764

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.69  E-value=6.3e-17  Score=141.75  Aligned_cols=81  Identities=14%  Similarity=0.311  Sum_probs=76.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCC--CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVG--GVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G--~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      +.++|||+|||+++++++|+++|+.||  .|.+|+|+.|+.+|+++|||||+|.+.++|.+||. |||..|+|++|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            568999999999999999999999999  99999999999899999999999999999999998 799999999999999


Q ss_pred             cCCC
Q 008442          467 SNPK  470 (565)
Q Consensus       467 a~~~  470 (565)
                      +.++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            9765

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=2.5e-16  Score=128.41  Aligned_cols=84  Identities=20%  Similarity=0.348  Sum_probs=76.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      .....++|||+|||+++++++|+.+|+.||.|.+|.|+.++  +.++|||||+|.+.++|..|+. +++..|.|++|.|.
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 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCC--CSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecC--CCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEE
Confidence            34567999999999999999999999999999999999985  3378999999999999999998 89999999999999


Q ss_pred             ecCCCCC
Q 008442          466 RSNPKQR  472 (565)
Q Consensus       466 ~a~~~~~  472 (565)
                      ++.++..
T Consensus        89 ~a~~~~~   95 (103)
T 2cqi_A           89 WATTPSS   95 (103)
T ss_dssp             ECCCTTC
T ss_pred             ECCCCcc
Confidence            9988654

>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=99.69  E-value=1.4e-16  Score=129.86  Aligned_cols=83  Identities=24%  Similarity=0.378  Sum_probs=76.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeE-EEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSS-IRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~-~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~  466 (565)
                      ....++|||+|||+++++++|+++|++||.|.. |+|+.+ .+|+++|||||+|.++++|..||..++..|+|+.|.|..
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEE
Confidence            356789999999999999999999999999987 899888 599999999999999999999998899999999999999


Q ss_pred             cCCCC
Q 008442          467 SNPKQ  471 (565)
Q Consensus       467 a~~~~  471 (565)
                      +.+..
T Consensus        91 ~~~~~   95 (104)
T 1wg5_A           91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            87654

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.69  E-value=1.4e-16  Score=126.92  Aligned_cols=82  Identities=23%  Similarity=0.378  Sum_probs=76.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .+.++|||+|||.++++++|+.+|++||.|..+.++.+  +|.++|||||+|.+.++|..|+. +++..++|++|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45789999999999999999999999999999999984  89999999999999999999998 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .++..
T Consensus        84 ~~~~~   88 (92)
T 2dgv_A           84 RNASG   88 (92)
T ss_dssp             SCCSS
T ss_pred             CCCCC
Confidence            87644

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.69  E-value=1.1e-16  Score=135.28  Aligned_cols=83  Identities=30%  Similarity=0.622  Sum_probs=78.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecCC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~~  469 (565)
                      +.++|||+|||.++++++|+++|+.||.|.+|.++.++.+|.++|||||+|.+.++|..|+.+++..|+|++|.|.++.+
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            45899999999999999999999999999999999998899999999999999999999998899999999999999987


Q ss_pred             CCC
Q 008442          470 KQR  472 (565)
Q Consensus       470 ~~~  472 (565)
                      ...
T Consensus       115 ~~~  117 (124)
T 2jwn_A          115 NMP  117 (124)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            543

>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=99.68  E-value=3.6e-17  Score=132.45  Aligned_cols=83  Identities=23%  Similarity=0.458  Sum_probs=75.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDK-FTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~-~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~  466 (565)
                      ....++|||+|||+++++++|+.+|+.|| |.+++|+.++ .+|+++|||||+|.+.++|..|+.+++..|+|+.|.|.+
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            35579999999999999999999999999 9999999987 589999999999999999999998899999999999999


Q ss_pred             cCCCC
Q 008442          467 SNPKQ  471 (565)
Q Consensus       467 a~~~~  471 (565)
                      +.++.
T Consensus        95 a~~~~   99 (100)
T 2j76_E           95 ADQAQ   99 (100)
T ss_dssp             CCCSC
T ss_pred             ccCCC
Confidence            98763

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.68  E-value=5.2e-17  Score=138.56  Aligned_cols=85  Identities=21%  Similarity=0.293  Sum_probs=78.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeE--EEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCc----ccCC
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSS--IRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQ----MFLG  459 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~--~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~----~~~g  459 (565)
                      .....++|||+|||+++++++|+++|++||.|..  |+|+.++.+|+++|||||+|.+. +|..|+. +++.    .|+|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            3456789999999999999999999999999976  99999998999999999999999 9999998 8999    9999


Q ss_pred             eEEEEeecCCCCC
Q 008442          460 KKLSIARSNPKQR  472 (565)
Q Consensus       460 ~~l~v~~a~~~~~  472 (565)
                      ++|.|.++.+...
T Consensus        98 r~l~V~~a~~~~~  110 (131)
T 2m2b_A           98 KTINVEFAKGSKR  110 (131)
T ss_dssp             CCCCCEECCCSCC
T ss_pred             EEEEEEECCCCCC
Confidence            9999999988644

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.68  E-value=1.5e-16  Score=133.26  Aligned_cols=83  Identities=23%  Similarity=0.297  Sum_probs=77.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEE
Q 008442          386 KGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSI  464 (565)
Q Consensus       386 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v  464 (565)
                      ....+.++|||+|||+++++++|+++|+.||.|.+|+++.++.+|+++|||||+|.+.++|..|+. +|+..|+|++|.|
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V  114 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV  114 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            344667999999999999999999999999999999999998899999999999999999999998 8999999999999


Q ss_pred             eecC
Q 008442          465 ARSN  468 (565)
Q Consensus       465 ~~a~  468 (565)
                      .+++
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            9864

>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=99.68  E-value=1.3e-16  Score=127.92  Aligned_cols=81  Identities=22%  Similarity=0.413  Sum_probs=75.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|+.++ +|.++|||||+|.++++|.+|+. +++..+.|++|.|.+
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            3456899999999999999999999999999999999998 59999999999999999999998 899999999999998


Q ss_pred             cCC
Q 008442          467 SNP  469 (565)
Q Consensus       467 a~~  469 (565)
                      +..
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            753

>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=99.68  E-value=1.9e-17  Score=137.52  Aligned_cols=83  Identities=17%  Similarity=0.297  Sum_probs=77.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCe-eEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGV-SSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i-~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~  466 (565)
                      ..+.++|||+|||+++++++|+++|+.||.| ..|+|+.++ +|+++|||||+|.+.++|..||.+++..|+|++|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHV   90 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEEE
Confidence            3557899999999999999999999999999 899999998 99999999999999999999998899999999999999


Q ss_pred             cCCCC
Q 008442          467 SNPKQ  471 (565)
Q Consensus       467 a~~~~  471 (565)
                      +.++.
T Consensus        91 a~~~~   95 (114)
T 2cpy_A           91 VTLED   95 (114)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            97654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1e-16  Score=128.65  Aligned_cols=80  Identities=16%  Similarity=0.227  Sum_probs=71.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cC--CcccCCeEEEE
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KN--KQMFLGKKLSI  464 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~--~~~~~g~~l~v  464 (565)
                      ..+.++|||+|||+++++++|+++|++||.|.+|+|+.+      ||||||+|.+.++|..|+. ++  +..|.|++|.|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            456789999999999999999999999999999999864      5999999999999999998 65  47899999999


Q ss_pred             eecCCCCCC
Q 008442          465 ARSNPKQRK  473 (565)
Q Consensus       465 ~~a~~~~~~  473 (565)
                      .++.++...
T Consensus        87 ~~A~~~~~~   95 (105)
T 1sjq_A           87 QFSNHKELK   95 (105)
T ss_dssp             CCCSSSSCC
T ss_pred             EEcCCCCCC
Confidence            999876543

>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=99.68  E-value=5e-17  Score=132.87  Aligned_cols=84  Identities=31%  Similarity=0.534  Sum_probs=79.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||+++++++|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+. +++..+.|++|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            345899999999999999999999999999999999998899999999999999999999997 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .++..
T Consensus        86 ~~~~~   90 (104)
T 1p1t_A           86 ASEKN   90 (104)
T ss_dssp             TCTTH
T ss_pred             CCccc
Confidence            88654

>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=99.68  E-value=2.2e-16  Score=130.41  Aligned_cols=85  Identities=16%  Similarity=0.276  Sum_probs=77.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH---HHhccCCCeeEEEEeecCCCC---CcceEEEEEecCHHHHHHHHH-cCCcccCCe
Q 008442          388 FTDECTAFLSNINLKATYEDLR---RFFSDVGGVSSIRILHDKFTG---KSRGLAYVDFIDDEHLAAAVA-KNKQMFLGK  460 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~---~~f~~~G~i~~~~~~~~~~~g---~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~  460 (565)
                      ....++|||+|||+++++++|+   ++|++||.|.+|.|+.++.++   .++|||||+|.++++|++|+. ||+..|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            4557899999999999999999   999999999999999887644   566999999999999999998 899999999


Q ss_pred             EEEEeecCCCCC
Q 008442          461 KLSIARSNPKQR  472 (565)
Q Consensus       461 ~l~v~~a~~~~~  472 (565)
                      +|.|.++.++..
T Consensus        92 ~l~V~~a~~k~~  103 (111)
T 2cpi_A           92 TLKASLGTTKYC  103 (111)
T ss_dssp             EEEEESCCCCSC
T ss_pred             EEEEEecccccc
Confidence            999999988753

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=7.6e-17  Score=131.69  Aligned_cols=81  Identities=19%  Similarity=0.435  Sum_probs=75.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      ..+.++|||+|||+++++++|+++|+.| .|.+|+|+.++ +|+++|||||+|.++++|++||.+++..|+|+.|.|..+
T Consensus        13 ~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a   90 (109)
T 2dnn_A           13 NPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPA   90 (109)
T ss_dssp             CHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEEC
Confidence            3456899999999999999999999999 89999999997 699999999999999999999999999999999999888


Q ss_pred             CCC
Q 008442          468 NPK  470 (565)
Q Consensus       468 ~~~  470 (565)
                      .+.
T Consensus        91 ~~~   93 (109)
T 2dnn_A           91 TER   93 (109)
T ss_dssp             CHH
T ss_pred             Ccc
Confidence            653

>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=99.67  E-value=2.3e-16  Score=130.05  Aligned_cols=85  Identities=18%  Similarity=0.302  Sum_probs=77.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCC-eeEEEEe-ecCCCCCcceEEEEEecCHHHHHHHHH-cC--CcccCCeEEE
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGG-VSSIRIL-HDKFTGKSRGLAYVDFIDDEHLAAAVA-KN--KQMFLGKKLS  463 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~-i~~~~~~-~~~~~g~~~g~afv~f~~~~~a~~a~~-~~--~~~~~g~~l~  463 (565)
                      .+.++|||+|||+++++++|+.+|..||. |.++.++ .++.+|.++|||||+|.+.++|..|+. ++  +..+.|++|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            35689999999999999999999999998 9999998 788889999999999999999999998 75  5899999999


Q ss_pred             EeecCCCCCC
Q 008442          464 IARSNPKQRK  473 (565)
Q Consensus       464 v~~a~~~~~~  473 (565)
                      |.++.|+...
T Consensus        86 V~~a~~~~~~   95 (109)
T 2dis_A           86 VDWAEPEIDV   95 (109)
T ss_dssp             EEESCSSCST
T ss_pred             EEEcCCCCCc
Confidence            9999887653

>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=99.67  E-value=6.4e-17  Score=134.54  Aligned_cols=85  Identities=29%  Similarity=0.500  Sum_probs=79.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      ..+.++|||+|||.++++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..|+.+++..|.|+.|.|.++
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEH
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEec
Confidence            34568999999999999999999999999999999999998899999999999999999999988999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .++..
T Consensus       102 ~~~~~  106 (114)
T 2cq4_A          102 QAEKN  106 (114)
T ss_dssp             HHHHH
T ss_pred             CCCcc
Confidence            77543

>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=99.67  E-value=1.4e-16  Score=128.58  Aligned_cols=82  Identities=17%  Similarity=0.205  Sum_probs=76.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||+++++++|+.+|..||.|..+.++.++.+|+++|||||+|.+.++|++|+. +++..|.|++|.|.++
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            345899999999999999999999999999988888888899999999999999999999996 8999999999999998


Q ss_pred             CCC
Q 008442          468 NPK  470 (565)
Q Consensus       468 ~~~  470 (565)
                      .++
T Consensus        93 ~~~   95 (98)
T 2cqp_A           93 SGP   95 (98)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            764

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=3.8e-16  Score=126.80  Aligned_cols=82  Identities=26%  Similarity=0.389  Sum_probs=74.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      ...+.++|||+|||+++++++|+++|++||.|   +++.+ .+|+++|||||+|.+.++|+.|+. +++..|.|++|.|.
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            34567999999999999999999999999976   56666 489999999999999999999998 89999999999999


Q ss_pred             ecCCCCC
Q 008442          466 RSNPKQR  472 (565)
Q Consensus       466 ~a~~~~~  472 (565)
                      ++.++..
T Consensus        87 ~a~~~~~   93 (101)
T 2fc9_A           87 LQGPRGS   93 (101)
T ss_dssp             ECSSCCC
T ss_pred             EcCCCCC
Confidence            9988744

>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=99.67  E-value=4.8e-16  Score=128.07  Aligned_cols=83  Identities=17%  Similarity=0.335  Sum_probs=75.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      .....++|||+|||+++++++|+++|+.||.|..|.|+.   ++.++|||||+|.+.++|..|+. +++..|.|++|.|.
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 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   94 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            345678999999999999999999999999999999965   45689999999999999999996 89999999999999


Q ss_pred             ecCCCCC
Q 008442          466 RSNPKQR  472 (565)
Q Consensus       466 ~a~~~~~  472 (565)
                      ++.++..
T Consensus        95 ~a~~~~~  101 (109)
T 1x4a_A           95 FPRSGRG  101 (109)
T ss_dssp             CCCCCCC
T ss_pred             EcccCCC
Confidence            9987643

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.67  E-value=2.9e-16  Score=128.96  Aligned_cols=80  Identities=20%  Similarity=0.330  Sum_probs=76.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ....++|||+|||+.+++++|+++|+.||.|.+|.|+.++ +|.++|||||+|.+.++|.+|+. |++..|.|++|.|.+
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3567899999999999999999999999999999999998 99999999999999999999998 899999999999998


Q ss_pred             cC
Q 008442          467 SN  468 (565)
Q Consensus       467 a~  468 (565)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>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=99.67  E-value=2.6e-16  Score=139.18  Aligned_cols=85  Identities=24%  Similarity=0.424  Sum_probs=79.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||+++++++|+.+|+.||.|.+|+|+.++.+|.++|||||+|.+.++|..|+. ||+..|.|++|.|.++
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            456899999999999999999999999999999999998899999999999999999999997 8999999999999999


Q ss_pred             CCCCCC
Q 008442          468 NPKQRK  473 (565)
Q Consensus       468 ~~~~~~  473 (565)
                      .++..+
T Consensus       148 ~~~~~~  153 (158)
T 2kn4_A          148 RYGRPP  153 (158)
T ss_dssp             CCSSCC
T ss_pred             CCCCCC
Confidence            886543

>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=99.67  E-value=3.5e-17  Score=139.65  Aligned_cols=81  Identities=22%  Similarity=0.313  Sum_probs=74.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecC
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSN  468 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~  468 (565)
                      ...++|||+|||+++++++|+++|++|| |.+|+|+.++ +|+++|||||+|.++++|.+||.+++..|+|+.|.|..+.
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~-~g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a~  121 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNS  121 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSS-SSCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECC-CCCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEECC
Confidence            4568999999999999999999999999 7799999998 5999999999999999999999889999999999999987


Q ss_pred             CCC
Q 008442          469 PKQ  471 (565)
Q Consensus       469 ~~~  471 (565)
                      ++.
T Consensus       122 ~~~  124 (139)
T 2hgn_A          122 TTG  124 (139)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            654

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.48  E-value=5.2e-18  Score=141.63  Aligned_cols=84  Identities=25%  Similarity=0.426  Sum_probs=78.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeE--------EEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCC
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSS--------IRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLG  459 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~--------~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g  459 (565)
                      .+.++|||+|||.++++++|+.+|+.||.|..        |.|+.++.+|.++|||||+|.+.++|..|+. +++..|.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            45689999999999999999999999999998        9999998789999999999999999999998 89999999


Q ss_pred             eEEEEeecCCCCC
Q 008442          460 KKLSIARSNPKQR  472 (565)
Q Consensus       460 ~~l~v~~a~~~~~  472 (565)
                      ++|.|.++.++..
T Consensus        85 ~~l~V~~a~~~~~   97 (116)
T 2lcw_A           85 NPIKVSFATRRAD   97 (116)
Confidence            9999999987643

>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=99.66  E-value=7.7e-16  Score=125.36  Aligned_cols=77  Identities=22%  Similarity=0.374  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||+++++++|+++|++||.|..|.++        +|||||+|.+.++|..|+. |++..|.|++|.|.++
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            456899999999999999999999999999999986        3699999999999999998 8999999999999999


Q ss_pred             CCCCCC
Q 008442          468 NPKQRK  473 (565)
Q Consensus       468 ~~~~~~  473 (565)
                      .++..+
T Consensus        81 ~~~~~~   86 (103)
T 2dgu_A           81 KPPDQK   86 (103)
T ss_dssp             CCCCCC
T ss_pred             CCCccc
Confidence            887654

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=6.3e-17  Score=126.89  Aligned_cols=79  Identities=19%  Similarity=0.273  Sum_probs=73.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .+.++|||+|||+++++++|+.+|+.||.|.++.++.++.+|.++|||||+|.+.++|..|+. +|+..+.|+.|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            356899999999999999999999999999999999998899999999999999999999998 8999999998877654

>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=99.66  E-value=1.3e-16  Score=135.66  Aligned_cols=82  Identities=16%  Similarity=0.306  Sum_probs=76.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCC---eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEE
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGG---VSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSI  464 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~---i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v  464 (565)
                      ..+.++|||+|||+++++++|+++|++||.   |.+|+|+.++. |+++|||||+|.++++|++||.+++..|+|+.|.|
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~V  119 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEV  119 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEEE
Confidence            356789999999999999999999999999   89999999984 99999999999999999999999999999999999


Q ss_pred             eecCCC
Q 008442          465 ARSNPK  470 (565)
Q Consensus       465 ~~a~~~  470 (565)
                      ..+.+.
T Consensus       120 ~~a~~~  125 (136)
T 2hgl_A          120 FKSHRT  125 (136)
T ss_dssp             EECCHH
T ss_pred             EECChH
Confidence            998654

>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=99.66  E-value=8.9e-16  Score=126.11  Aligned_cols=78  Identities=19%  Similarity=0.382  Sum_probs=72.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCC-----eE
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLG-----KK  461 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g-----~~  461 (565)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+       |||||+|.+.++|+.||. ||+..|.|     ++
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            356799999999999999999999999999999999875       899999999999999998 89999999     99


Q ss_pred             EEEeecCCCCC
Q 008442          462 LSIARSNPKQR  472 (565)
Q Consensus       462 l~v~~a~~~~~  472 (565)
                      |.|.++.++..
T Consensus        85 i~V~~a~~~~~   95 (108)
T 1x4c_A           85 IRVKVDGPRSP   95 (108)
T ss_dssp             EEEEESSCCSC
T ss_pred             EEEEeCCCCCC
Confidence            99999988644

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.66  E-value=1.8e-16  Score=132.25  Aligned_cols=82  Identities=17%  Similarity=0.342  Sum_probs=76.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCC---eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEE
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGG---VSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSI  464 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~---i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v  464 (565)
                      ..+.++|||+|||+++++++|+++|+.||.   |..|+|+.++ .|+++|||||+|.+.++|.+||.+++..|+|+.|.|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~-~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V   92 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFVELESEDDVKLALKKDRESMGHRYIEV   92 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECS-SSCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECC-CCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEE
Confidence            456789999999999999999999999998   8999999998 599999999999999999999999999999999999


Q ss_pred             eecCCC
Q 008442          465 ARSNPK  470 (565)
Q Consensus       465 ~~a~~~  470 (565)
                      ..+.+.
T Consensus        93 ~~a~~~   98 (118)
T 2db1_A           93 FKSHRT   98 (118)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            998654

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.66  E-value=1.3e-16  Score=136.58  Aligned_cols=87  Identities=23%  Similarity=0.415  Sum_probs=80.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      ...+.++|||+|||+++++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|+.|+. +++..|.|++|.|.
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            34567899999999999999999999999999999999998899999999999999999999998 89999999999999


Q ss_pred             ecCCCCCC
Q 008442          466 RSNPKQRK  473 (565)
Q Consensus       466 ~a~~~~~~  473 (565)
                      ++.+...+
T Consensus       123 ~a~~~~~~  130 (135)
T 2lea_A          123 MARYGRPP  130 (135)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCCCC
Confidence            99876543

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.66  E-value=2.4e-16  Score=128.72  Aligned_cols=81  Identities=12%  Similarity=0.178  Sum_probs=74.2

Q ss_pred             CCCCCeEEEcCCCCCC------CHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCe
Q 008442          388 FTDECTAFLSNINLKA------TYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGK  460 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~------~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~  460 (565)
                      ....++|||+|||+.+      ++++|+.+|++||.|.+|.|+.  .+|+++|||||+|.+.++|..|+. +||..|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~--~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC--BTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC--CCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            3456899999999999      7899999999999999999983  589999999999999999999998 899999998


Q ss_pred             -EEEEeecCCC
Q 008442          461 -KLSIARSNPK  470 (565)
Q Consensus       461 -~l~v~~a~~~  470 (565)
                       +|.|.++...
T Consensus        90 ~~l~V~~a~~~  100 (105)
T 2nlw_A           90 HTFRVNLFTDF  100 (105)
T ss_dssp             CEEEEECSCCC
T ss_pred             ceEEEEEcchH
Confidence             9999998754

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.66  E-value=8.4e-17  Score=123.60  Aligned_cols=75  Identities=25%  Similarity=0.538  Sum_probs=71.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ++|||+|||+++++++|+++|++||.|.++.++.++.+|.++|||||+|.++++|..|+. ++ ..++|++|.|.+|
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            589999999999999999999999999999999998889999999999999999999998 57 8999999999876

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.66  E-value=5.1e-17  Score=124.10  Aligned_cols=75  Identities=24%  Similarity=0.402  Sum_probs=71.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       393 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      +|||+|||+++++++|+.+|++||.|.++.++.++.+|.++|||||+|.++++|..|+.+++..++|++|.|..|
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            699999999999999999999999999999999988899999999999999999999998899999999999875

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.66  E-value=5.1e-16  Score=131.13  Aligned_cols=85  Identities=19%  Similarity=0.317  Sum_probs=79.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      .....++|||+|||.++++++|+.+|+.||.|.+|.|+.++ +|.++|||||+|.+.++|..|+. +++..|+|++|.|.
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            44667899999999999999999999999999999999998 99999999999999999999998 89999999999999


Q ss_pred             ecCCCCC
Q 008442          466 RSNPKQR  472 (565)
Q Consensus       466 ~a~~~~~  472 (565)
                      +|.+...
T Consensus       110 ~a~~~~~  116 (124)
T 2kt5_A          110 LVASQID  116 (124)
T ss_dssp             EECCTTC
T ss_pred             EeCCCCC
Confidence            9987654

>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=99.66  E-value=7e-16  Score=128.25  Aligned_cols=82  Identities=27%  Similarity=0.408  Sum_probs=76.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCccc--------C
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMF--------L  458 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~--------~  458 (565)
                      ..+.++|||+|||+++++++|+.+|+.||.|.+++|+.++ +|.++|||||+|.+.++|..|+. +|+..|        .
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            3567899999999999999999999999999999999998 99999999999999999999998 899998        5


Q ss_pred             CeEEEEeecCCC
Q 008442          459 GKKLSIARSNPK  470 (565)
Q Consensus       459 g~~l~v~~a~~~  470 (565)
                      |++|.|.++.|+
T Consensus       101 ~~~l~v~~a~p~  112 (114)
T 1x5o_A          101 TEPLLCKFSGPS  112 (114)
T ss_dssp             SSCBEEEECCCS
T ss_pred             CCceeEEccCCC
Confidence            788999999875

>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=99.66  E-value=3.4e-16  Score=139.21  Aligned_cols=86  Identities=22%  Similarity=0.337  Sum_probs=79.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      ...+.++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||. |++..|.|++|.|.
T Consensus        68 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  147 (165)
T 1rk8_A           68 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  147 (165)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999998 89999999999999


Q ss_pred             ecCCCCC
Q 008442          466 RSNPKQR  472 (565)
Q Consensus       466 ~a~~~~~  472 (565)
                      ++.++..
T Consensus       148 ~a~~~~~  154 (165)
T 1rk8_A          148 WCFVKGP  154 (165)
T ss_dssp             ESEECC-
T ss_pred             EecCCCC
Confidence            9977654

>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=99.65  E-value=5.7e-16  Score=127.67  Aligned_cols=80  Identities=16%  Similarity=0.249  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cC--CcccCCeEEEEe
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KN--KQMFLGKKLSIA  465 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~--~~~~~g~~l~v~  465 (565)
                      .+.++|||+|||+++++++|+++|++||.|.+|.|+.+      ||||||+|.+.++|.+|+. ++  +..|.|++|.|.
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~  102 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ  102 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEE
Confidence            45689999999999999999999999999999999865      6999999999999999998 65  468999999999


Q ss_pred             ecCCCCCCC
Q 008442          466 RSNPKQRKD  474 (565)
Q Consensus       466 ~a~~~~~~~  474 (565)
                      ++.++..+.
T Consensus       103 ~a~~k~~~~  111 (119)
T 2ad9_A          103 FSNHKELKT  111 (119)
T ss_dssp             ECSSSSCCC
T ss_pred             EccCCCCCc
Confidence            998776543

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=1.3e-15  Score=122.41  Aligned_cols=79  Identities=16%  Similarity=0.190  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-c--CCcccCCeEEEEe
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-K--NKQMFLGKKLSIA  465 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~--~~~~~~g~~l~v~  465 (565)
                      .+.++|||+|||+++++++|+.+|++||.|.+|.++.+      ||||||+|.+.++|..|+. +  ++..+.|++|.|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   86 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   86 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEE
Confidence            45689999999999999999999999999999998754      6999999999999999997 5  5678999999999


Q ss_pred             ecCCCCCC
Q 008442          466 RSNPKQRK  473 (565)
Q Consensus       466 ~a~~~~~~  473 (565)
                      ++.++...
T Consensus        87 ~a~~~~~~   94 (101)
T 2cq1_A           87 YSNHKELK   94 (101)
T ss_dssp             ECSCSSCC
T ss_pred             EcCcccCc
Confidence            99876553

>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=1e-15  Score=124.43  Aligned_cols=82  Identities=28%  Similarity=0.409  Sum_probs=74.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ....++|||+|||+++++++|+++|+.|+   .+.++.++.++.++|||||+|.+.++|..|+. |++..|.|++|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            45679999999999999999999999774   67788887799999999999999999999998 899999999999999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +.++..
T Consensus        89 a~~~~~   94 (102)
T 2fc8_A           89 AKPKGE   94 (102)
T ss_dssp             CCCCCS
T ss_pred             ecCCCC
Confidence            988644

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.65  E-value=4.9e-17  Score=129.04  Aligned_cols=80  Identities=25%  Similarity=0.578  Sum_probs=72.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCCC
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNPK  470 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~~  470 (565)
                      ++|||+|||.++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.+ |..|+. +++..++|++|.|.+|.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            58999999999999999999999999999999999888999999999999999 999998 8999999999999999876


Q ss_pred             CC
Q 008442          471 QR  472 (565)
Q Consensus       471 ~~  472 (565)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            54

>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=99.65  E-value=1.7e-16  Score=127.31  Aligned_cols=80  Identities=18%  Similarity=0.232  Sum_probs=74.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      ..++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.++++|++|+. +|+..|.|++|.|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            35899999999999999999999999999999898888899999999999999999999998 89999999999999876


Q ss_pred             C
Q 008442          469 P  469 (565)
Q Consensus       469 ~  469 (565)
                      +
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            4

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=4e-16  Score=128.31  Aligned_cols=82  Identities=20%  Similarity=0.392  Sum_probs=75.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      .....++|||+|||.++++++|+.+|+.||.|.++.++.++  +.++|||||+|.+.++|..|+. +++..++|++|.|.
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            34567999999999999999999999999999999999885  4589999999999999999998 89999999999999


Q ss_pred             ecCCC
Q 008442          466 RSNPK  470 (565)
Q Consensus       466 ~a~~~  470 (565)
                      ++.++
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            99875

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.65  E-value=2.6e-16  Score=119.95  Aligned_cols=72  Identities=15%  Similarity=0.190  Sum_probs=67.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      ...|||+||++.+++++|+++|.+||+|.+++++.      ++|||||+|.++++|..|+. ||+..+.|++|.|..|.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            57899999999999999999999999999999865      57999999999999999998 89999999999999883

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.65  E-value=5.2e-16  Score=123.17  Aligned_cols=77  Identities=16%  Similarity=0.177  Sum_probs=69.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcc--cCCeEEEEe
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQM--FLGKKLSIA  465 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~--~~g~~l~v~  465 (565)
                      .++++|||+|||+++++++|+.+|++||.|.++.++.      +||||||+|.+.++|.+|+. +++..  +.|++|.|.
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~   92 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            3468999999999999999999999999999999875      36899999999999999998 77664  889999999


Q ss_pred             ecCCCC
Q 008442          466 RSNPKQ  471 (565)
Q Consensus       466 ~a~~~~  471 (565)
                      +|+++.
T Consensus        93 ~S~~k~   98 (100)
T 3r27_A           93 YSTSQK   98 (100)
T ss_dssp             ECSCSC
T ss_pred             eccccc
Confidence            998753

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.64  E-value=5.9e-16  Score=124.28  Aligned_cols=78  Identities=19%  Similarity=0.255  Sum_probs=69.7

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCC--cccCCeEEEE
Q 008442          389 TDECTAFLSNINL-KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNK--QMFLGKKLSI  464 (565)
Q Consensus       389 ~~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~--~~~~g~~l~v  464 (565)
                      .+.++|||+|||+ ++++++|+.+|++||.|.+|.|+.+      +|||||+|.+.++|..|+. +++  ..|.|++|.|
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   86 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   86 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEE
Confidence            3578999999999 9999999999999999999999865      3899999999999999997 764  4599999999


Q ss_pred             eecCCCCC
Q 008442          465 ARSNPKQR  472 (565)
Q Consensus       465 ~~a~~~~~  472 (565)
                      .+|.+.+.
T Consensus        87 ~~a~~~~~   94 (102)
T 1x4d_A           87 HLSQKYKR   94 (102)
T ss_dssp             EEECCCTT
T ss_pred             EECCCCCC
Confidence            99986543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.64  E-value=5.7e-16  Score=130.19  Aligned_cols=81  Identities=26%  Similarity=0.304  Sum_probs=72.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEE
Q 008442          389 TDECTAFLSNINLKATYEDLR----RFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLS  463 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~----~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~  463 (565)
                      ..+++|||+|||+.+++++|+    .+|++||.|.+|.+..   +|+++|||||+|.+.++|..|+. |||..|.|++|.
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            446899999999999999876    6999999999988753   78899999999999999999997 899999999999


Q ss_pred             EeecCCCCC
Q 008442          464 IARSNPKQR  472 (565)
Q Consensus       464 v~~a~~~~~  472 (565)
                      |.++.++..
T Consensus       104 V~~a~~~~~  112 (127)
T 2a3j_A          104 ITFSETPQS  112 (127)
T ss_dssp             EEECCCCCH
T ss_pred             EEEccCcch
Confidence            999987643

>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=99.64  E-value=2e-16  Score=133.52  Aligned_cols=83  Identities=18%  Similarity=0.302  Sum_probs=75.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      ..+.++|||+|||+++++++|+.+|+.||.|..+.++.+..+|+++|||||+|.+.++|..||.+|+..|+|++|.|.++
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            34668999999999999999999999999998865566556999999999999999999999999999999999999998


Q ss_pred             CCC
Q 008442          468 NPK  470 (565)
Q Consensus       468 ~~~  470 (565)
                      .++
T Consensus       102 ~~~  104 (124)
T 1wel_A          102 TKK  104 (124)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            764

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=1.4e-15  Score=120.58  Aligned_cols=76  Identities=20%  Similarity=0.370  Sum_probs=70.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||.++++++|+.+|++||.|.++.++        +|||||+|.+.++|..|+. +++..+.|++|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   77 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS   77 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECS
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEEC
Confidence            456899999999999999999999999999999986        5899999999999999997 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .++..
T Consensus        78 ~~~~~   82 (90)
T 2dnq_A           78 KNKSK   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            88754

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.64  E-value=2e-16  Score=122.65  Aligned_cols=73  Identities=14%  Similarity=0.279  Sum_probs=67.2

Q ss_pred             CCeEEEcCCCCCC------CHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCe-EE
Q 008442          391 ECTAFLSNINLKA------TYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGK-KL  462 (565)
Q Consensus       391 ~~~l~V~nl~~~~------~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~-~l  462 (565)
                      +++|||+|||..+      ++++|+.+|++||.|.++.++.  .+|+++|||||+|.+.++|..|+. +||..++|+ +|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~--~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC--BTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC--CCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            3799999999999      6799999999999999999883  489999999999999999999998 899999999 88


Q ss_pred             EEe
Q 008442          463 SIA  465 (565)
Q Consensus       463 ~v~  465 (565)
                      .|.
T Consensus        79 ~V~   81 (81)
T 2krb_A           79 RVN   81 (81)
T ss_dssp             CCC
T ss_pred             EeC
Confidence            763

>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=99.64  E-value=1.5e-16  Score=130.52  Aligned_cols=82  Identities=22%  Similarity=0.304  Sum_probs=76.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCC---eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEE
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGG---VSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSI  464 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~---i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v  464 (565)
                      ..+.++|||+|||+++++++|+.+|+.||.   |.+|+|+.++. |+++|||||+|.+.++|..||.+++..|+|+.|.|
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V   86 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEV   86 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEEE
Confidence            356789999999999999999999999988   89999999984 99999999999999999999999999999999999


Q ss_pred             eecCCC
Q 008442          465 ARSNPK  470 (565)
Q Consensus       465 ~~a~~~  470 (565)
                      ..+.+.
T Consensus        87 ~~a~~~   92 (107)
T 2lmi_A           87 YEINNE   92 (107)
T ss_dssp             EECCHH
T ss_pred             EECCHH
Confidence            998764

>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=3.1e-16  Score=130.65  Aligned_cols=85  Identities=25%  Similarity=0.330  Sum_probs=72.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||.++++++|+.+|+.||.|..+.+..+..+|.++|||||+|.+.++|..|+. |++..|.|++|.|.++
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            457899999999999999999999999998433222222278999999999999999999998 8999999999999999


Q ss_pred             CCCCCC
Q 008442          468 NPKQRK  473 (565)
Q Consensus       468 ~~~~~~  473 (565)
                      .++..+
T Consensus       103 ~~~~~~  108 (115)
T 2cpx_A          103 KNKKQR  108 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCC
Confidence            887553

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.64  E-value=6.3e-17  Score=131.42  Aligned_cols=83  Identities=22%  Similarity=0.355  Sum_probs=75.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecC
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSN  468 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~  468 (565)
                      ...++|||+|||+++++++|+.+|+.||.|.. .++.++.+|.++|||||+|.+.++|.+|+.+++..|.|++|.|.++.
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~   93 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK   93 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEcC
Confidence            45689999999999999999999999999887 66666668999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 008442          469 PKQR  472 (565)
Q Consensus       469 ~~~~  472 (565)
                      ++..
T Consensus        94 ~~~~   97 (101)
T 1fj7_A           94 GRDG   97 (101)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.63  E-value=5e-16  Score=127.05  Aligned_cols=78  Identities=15%  Similarity=0.262  Sum_probs=70.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVG-GVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ...++|||+|||+++++++|+++|+.|| .|..+.++.    +.++|||||+|.+.++|+.|+. +|+..|+|++|.|..
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~  101 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVER  101 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3468999999999999999999999999 899998853    3578999999999999999997 899999999999999


Q ss_pred             cCCC
Q 008442          467 SNPK  470 (565)
Q Consensus       467 a~~~  470 (565)
                      +.++
T Consensus       102 a~~~  105 (111)
T 2jvr_A          102 DDNP  105 (111)
T ss_dssp             SCC-
T ss_pred             CCCC
Confidence            8754

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=2.6e-16  Score=131.32  Aligned_cols=81  Identities=21%  Similarity=0.317  Sum_probs=74.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCe----eEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEE
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGV----SSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSI  464 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i----~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v  464 (565)
                      .+.++|||+|||+++++++|+++|++||.|    ..|+|+.++ +|+++|||||+|.++++|.+||..++..|+|+.|.|
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            456899999999999999999999999875    689999986 999999999999999999999998999999999999


Q ss_pred             eecCCC
Q 008442          465 ARSNPK  470 (565)
Q Consensus       465 ~~a~~~  470 (565)
                      ..+.+.
T Consensus       100 ~~a~~~  105 (123)
T 2dha_A          100 FRSTAA  105 (123)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            988654

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.63  E-value=1.8e-15  Score=122.46  Aligned_cols=78  Identities=13%  Similarity=0.145  Sum_probs=69.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCC--cccCCeEEEEe
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNK--QMFLGKKLSIA  465 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~--~~~~g~~l~v~  465 (565)
                      ...++|||+|||+++++++|+.+|++||.|.+|.++.+      ||||||+|.+.++|..|+. +++  ..|.|++|.|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~   86 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            44689999999999999999999999999999998753      6899999999999999997 654  46999999999


Q ss_pred             ecCCCCC
Q 008442          466 RSNPKQR  472 (565)
Q Consensus       466 ~a~~~~~  472 (565)
                      ++.++..
T Consensus        87 ~a~~~~~   93 (104)
T 1wex_A           87 YSTSKRI   93 (104)
T ss_dssp             ECSSSSC
T ss_pred             EccCccc
Confidence            9987654

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.63  E-value=3.7e-16  Score=130.61  Aligned_cols=80  Identities=24%  Similarity=0.379  Sum_probs=73.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCee--EEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEee
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVS--SIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIAR  466 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~  466 (565)
                      ...++|||+|||+++++++|+++|++| .|.  +|+|+.++ .|+++|||||+|.++++|.+||.+++..|+|+.|.|..
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~-~GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDP-EGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFK  117 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCS-SSSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECC-CCCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEEE
Confidence            456899999999999999999999999 577  99999998 49999999999999999999999888999999999988


Q ss_pred             cCCC
Q 008442          467 SNPK  470 (565)
Q Consensus       467 a~~~  470 (565)
                      +.++
T Consensus       118 a~~~  121 (126)
T 2hgm_A          118 SSQE  121 (126)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8653

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.62  E-value=1.3e-15  Score=131.75  Aligned_cols=81  Identities=25%  Similarity=0.366  Sum_probs=75.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      .....++|||+|||+++++++|+.+|++||.|..++++.++.+|.++|||||+|.+.++|.+|+. +++..|.|++|.|.
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            34567899999999999999999999999999999999998899999999999999999999997 89999999999998


Q ss_pred             ec
Q 008442          466 RS  467 (565)
Q Consensus       466 ~a  467 (565)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            75

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.62  E-value=3.4e-16  Score=127.29  Aligned_cols=82  Identities=30%  Similarity=0.562  Sum_probs=76.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecC
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSN  468 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~  468 (565)
                      ...++|||+|||+++++++|+.+|+.||.|.+++++.++ +|.++|||||+|.+.++|..|+. ++..++|++|.|..+.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~-~~~~~~g~~l~v~~a~   84 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT-CCCEETTEECEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh-CCCeECCEEEEEEECC
Confidence            346899999999999999999999999999999999998 99999999999999999999999 9999999999999987


Q ss_pred             CCCC
Q 008442          469 PKQR  472 (565)
Q Consensus       469 ~~~~  472 (565)
                      ++..
T Consensus        85 ~~~~   88 (102)
T 2xs2_A           85 RKQN   88 (102)
T ss_dssp             ECC-
T ss_pred             cCcc
Confidence            6543

>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=7.8e-16  Score=123.66  Aligned_cols=80  Identities=21%  Similarity=0.380  Sum_probs=72.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ....++|||+|||+++++++|+.+|+.||.|..+    . .+|.++|||||+|.+.++|..|+. +++..|+|++|.|.+
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----S-QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----E-ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----C-CCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3457899999999999999999999999988766    2 388999999999999999999998 899999999999999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +.++..
T Consensus        88 a~~~~~   93 (96)
T 1fjc_A           88 TGEKGG   93 (96)
T ss_dssp             CSSSCC
T ss_pred             cCCCCC
Confidence            987654

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.62  E-value=1.6e-15  Score=123.02  Aligned_cols=76  Identities=24%  Similarity=0.404  Sum_probs=71.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCCC
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNPK  470 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~~  470 (565)
                      ++|||+|||+++++++|+++|++||.|.++.++.+     ++|||||+|.+.++|.+|+. +++..+.|++|.|.++.++
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            58999999999999999999999999999999875     67999999999999999998 8999999999999999886


Q ss_pred             CC
Q 008442          471 QR  472 (565)
Q Consensus       471 ~~  472 (565)
                      ..
T Consensus        76 ~~   77 (101)
T 2hvz_A           76 PR   77 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=2.4e-15  Score=123.80  Aligned_cols=78  Identities=23%  Similarity=0.386  Sum_probs=72.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||.++++++|+.+|+.||.|.+|.++.+      +|||||+|.+.++|..|+. +++..|.|++|.|.++
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   96 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            34689999999999999999999999999999999875      6899999999999999997 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .++..
T Consensus        97 ~~~~~  101 (109)
T 1x4g_A           97 KESPD  101 (109)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            88754

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=2.7e-15  Score=120.68  Aligned_cols=80  Identities=19%  Similarity=0.294  Sum_probs=71.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ....++|||+|||+++++++|+.+|+.||.|. +.++.    +.++|||||+|.+.++|+.|+. +|+..|+|++|.|.+
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            34568999999999999999999999999997 66664    4678999999999999999997 899999999999999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +.+++.
T Consensus        91 a~~~~~   96 (97)
T 2e5j_A           91 ARQQRD   96 (97)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            988643

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=4.3e-15  Score=118.18  Aligned_cols=77  Identities=23%  Similarity=0.346  Sum_probs=70.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ....++|||+|||+++++++|+.+|++||.|..+.++.        +||||+|.+.++|.+|+. +|+..+.|++|.|.+
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   78 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            35578999999999999999999999999999999863        499999999999999997 899999999999999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +.++..
T Consensus        79 a~~~~~   84 (92)
T 2dgt_A           79 STSRLR   84 (92)
T ss_dssp             SSCCCS
T ss_pred             ccCCCC
Confidence            988754

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.61  E-value=4.3e-15  Score=119.97  Aligned_cols=79  Identities=20%  Similarity=0.361  Sum_probs=72.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ..+.++|||+|||+++++++|+.+|+.||.|..+.++.+      +|||||+|.+.++|..|+. +++..|.|++|.|.+
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            456789999999999999999999999999999999754      5899999999999999997 899999999999999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +.++..
T Consensus        86 a~~~~~   91 (99)
T 2cpj_A           86 ACHSAS   91 (99)
T ss_dssp             SSCCSC
T ss_pred             cCCCCC
Confidence            988644

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=3.5e-15  Score=118.18  Aligned_cols=76  Identities=24%  Similarity=0.402  Sum_probs=70.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||+++++++|+.+|++||.|.++.++.        +||||+|.+.++|..|+. +++..+.|++|.|.++
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   78 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS   78 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            4568999999999999999999999999999999863        499999999999999998 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .+...
T Consensus        79 ~~~~~   83 (90)
T 2dnp_A           79 TKGQK   83 (90)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87643

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.61  E-value=2.9e-15  Score=120.54  Aligned_cols=78  Identities=14%  Similarity=0.247  Sum_probs=71.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccC--CeEEEEe
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFL--GKKLSIA  465 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~--g~~l~v~  465 (565)
                      ...++|||+|||+++++++|+++|++||.|.++.++.+      +|||||+|.+.++|+.|+. +|+..+.  |++|.|.
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            45689999999999999999999999999999998653      6899999999999999998 8999999  9999999


Q ss_pred             ecCCCCC
Q 008442          466 RSNPKQR  472 (565)
Q Consensus       466 ~a~~~~~  472 (565)
                      ++.+++.
T Consensus        89 ~a~~~~~   95 (97)
T 1why_A           89 FAKSGPS   95 (97)
T ss_dssp             ECCCCCC
T ss_pred             ECCCCCC
Confidence            9988754

>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=99.60  E-value=9.7e-16  Score=123.38  Aligned_cols=81  Identities=23%  Similarity=0.340  Sum_probs=74.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEE
Q 008442          389 TDECTAFLSNINLKATYEDLR----RFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLS  463 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~----~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~  463 (565)
                      ...++|||+|||.++++++|+    .+|++||.|.+|.++.   +|.++|||||+|.+.++|..|+. ++|..++|++|.
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            456899999999999999999    9999999999999873   67889999999999999999998 899999999999


Q ss_pred             EeecCCCCC
Q 008442          464 IARSNPKQR  472 (565)
Q Consensus       464 v~~a~~~~~  472 (565)
                      |.++.++..
T Consensus        83 v~~a~~~~~   91 (97)
T 1nu4_A           83 IQYAKTDSD   91 (97)
T ss_dssp             EEECSSCCT
T ss_pred             EEEccCCCc
Confidence            999988643

>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=99.60  E-value=2.8e-15  Score=122.11  Aligned_cols=79  Identities=14%  Similarity=0.163  Sum_probs=70.0

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cC--CcccCCeEEE
Q 008442          388 FTDECTAFLSNINLK-ATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KN--KQMFLGKKLS  463 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~--~~~~~g~~l~  463 (565)
                      ....++|||+|||++ +++++|+.+|++||.|.+|.|+.      +||||||+|.+.++|..|+. ++  +..|.|++|.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            345789999999998 99999999999999999999974      36999999999999999997 64  5679999999


Q ss_pred             EeecCCCCC
Q 008442          464 IARSNPKQR  472 (565)
Q Consensus       464 v~~a~~~~~  472 (565)
                      |.++.+...
T Consensus        96 V~~a~~~~~  104 (112)
T 1x4f_A           96 VDLSEKYKK  104 (112)
T ss_dssp             EEEECSCSS
T ss_pred             EEECccccc
Confidence            999987644

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.60  E-value=2.9e-15  Score=122.76  Aligned_cols=77  Identities=22%  Similarity=0.403  Sum_probs=71.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ....++|||+|||.++++++|+.+|++||.|..+.++        +|||||+|.+.++|..|+. ++|..++|++|.|.+
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   99 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY   99 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            4567999999999999999999999999999999987        5899999999999999998 899999999999999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +.++..
T Consensus       100 a~~~~~  105 (108)
T 2jvo_A          100 SKLPAK  105 (108)
T ss_dssp             CSCCC-
T ss_pred             ecCCCC
Confidence            988754

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.60  E-value=1.6e-15  Score=121.64  Aligned_cols=76  Identities=28%  Similarity=0.498  Sum_probs=69.8

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          389 TDECTAFLSNINL-KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       389 ~~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      .+.++|||+|||+ ++++++|+.+|++||.|.++.+.        +|||||+|.+.++|..|+. +++..+.|++|.|.+
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   79 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            4578999999998 99999999999999999999983        6899999999999999998 899999999999999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +.++..
T Consensus        80 a~~~~~   85 (96)
T 2kvi_A           80 SSSNAR   85 (96)
T ss_dssp             EECCCC
T ss_pred             cCcCCC
Confidence            987644

>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=99.59  E-value=5e-15  Score=118.86  Aligned_cols=76  Identities=26%  Similarity=0.453  Sum_probs=70.2

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          388 FTDECTAFLSNINL-KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       388 ~~~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      ..+.++|||+|||+ ++++++|+.+|+.||.|.++.+.        +|||||+|.+.++|..|+. +++..++|++|.|.
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   90 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45679999999998 99999999999999999999983        6899999999999999998 89999999999999


Q ss_pred             ecCCCC
Q 008442          466 RSNPKQ  471 (565)
Q Consensus       466 ~a~~~~  471 (565)
                      ++.++.
T Consensus        91 ~a~~~~   96 (97)
T 2xnq_A           91 VSSSNA   96 (97)
T ss_dssp             ECCCCC
T ss_pred             ecCCCC
Confidence            987753

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.59  E-value=2e-15  Score=122.90  Aligned_cols=77  Identities=12%  Similarity=0.238  Sum_probs=69.1

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecC----HHH----HHHHHH---cCCcc
Q 008442          392 CTAFLSNI----NLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFID----DEH----LAAAVA---KNKQM  456 (565)
Q Consensus       392 ~~l~V~nl----~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~----~~~----a~~a~~---~~~~~  456 (565)
                      ..|||+||    |+.+++.+|+.+|+.||.|.++.++.|+.||.++|||||+|.+    +++    |..|+.   +++..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    9999999999999999999999999999999999999999996    333    777775   49999


Q ss_pred             cCCeEEEEeecC
Q 008442          457 FLGKKLSIARSN  468 (565)
Q Consensus       457 ~~g~~l~v~~a~  468 (565)
                      |+|++|+|.+.+
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999854

>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=1.2e-14  Score=117.42  Aligned_cols=76  Identities=20%  Similarity=0.423  Sum_probs=69.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccC--CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDV--GGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~--G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      ...++|||+|||+++++++|+.+|+.|  |.|..+.++        +|||||+|.+.++|..|+. +++..|.|++|.|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVT   84 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            456899999999999999999999999  899988764        5799999999999999998 89999999999999


Q ss_pred             ecCCCCC
Q 008442          466 RSNPKQR  472 (565)
Q Consensus       466 ~a~~~~~  472 (565)
                      ++.++..
T Consensus        85 ~a~~~~~   91 (99)
T 2cpd_A           85 LAKPVDK   91 (99)
T ss_dssp             CCCCCCC
T ss_pred             ECCCCCC
Confidence            9987654

>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=99.59  E-value=6.6e-15  Score=121.39  Aligned_cols=76  Identities=25%  Similarity=0.477  Sum_probs=69.8

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          389 TDECTAFLSNINLK-ATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       389 ~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ...++|||+|||++ +++++|+.+|++||.|..|.+        ++|||||+|.+.++|..|+. +++..|+|++|.|.+
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   96 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM   96 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34689999999999 999999999999999999988        46899999999999999996 899999999999999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +.+++.
T Consensus        97 a~~~~~  102 (110)
T 1wf1_A           97 AGEPKP  102 (110)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            986543

>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=99.59  E-value=2.1e-15  Score=125.27  Aligned_cols=75  Identities=20%  Similarity=0.434  Sum_probs=65.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeE-----E
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKK-----L  462 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~-----l  462 (565)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.+       |||||+|.+.++|+.||. ||+..|+|++     |
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEE
Confidence            45789999999999999999999999999999999764       899999999999999998 8999999998     7


Q ss_pred             EEeecCCC
Q 008442          463 SIARSNPK  470 (565)
Q Consensus       463 ~v~~a~~~  470 (565)
                      .|..+.+.
T Consensus        87 ~v~~~~~~   94 (115)
T 3beg_B           87 RVKVDGPR   94 (115)
T ss_dssp             EEEECC--
T ss_pred             EeccCCCC
Confidence            77776664

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=2.9e-15  Score=119.52  Aligned_cols=77  Identities=23%  Similarity=0.359  Sum_probs=68.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCC-eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCC-cccCCeEEEEe
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGG-VSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNK-QMFLGKKLSIA  465 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~-i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~-~~~~g~~l~v~  465 (565)
                      ...++|||+|||+++++++|+.+|++||. |..+.+.       ++|||||+|.+.++|..|+. +|+ ..++|++|.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            44689999999999999999999999999 6655552       46899999999999999998 899 99999999999


Q ss_pred             ecCCCCC
Q 008442          466 RSNPKQR  472 (565)
Q Consensus       466 ~a~~~~~  472 (565)
                      ++.++..
T Consensus        79 ~a~~~~~   85 (93)
T 2cqh_A           79 YSVSKKL   85 (93)
T ss_dssp             ECCCCCC
T ss_pred             EccCccc
Confidence            9988654

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=6.4e-15  Score=115.32  Aligned_cols=76  Identities=20%  Similarity=0.356  Sum_probs=69.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-c-CCcccCCeEEEE
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-K-NKQMFLGKKLSI  464 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~-~~~~~~g~~l~v  464 (565)
                      .....++|||+|||.++++++|+.+|++||.|.++.++.+      +|||||+|.+.++|..|+. + ++..++|++|.|
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v   81 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV   81 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCE
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEE
Confidence            3456789999999999999999999999999999999863      6899999999999999998 8 999999999999


Q ss_pred             eecC
Q 008442          465 ARSN  468 (565)
Q Consensus       465 ~~a~  468 (565)
                      .+++
T Consensus        82 ~~ak   85 (85)
T 2ytc_A           82 KWGR   85 (85)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9874

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.58  E-value=3.1e-15  Score=121.31  Aligned_cols=75  Identities=21%  Similarity=0.349  Sum_probs=69.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      ..++|||+|||.++++++|+.+|+.||.|.+++++      +++|||||+|.+.++|..|+. +++..++|++|.|.+++
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            46899999999999999999999999999999987      356999999999999999997 89999999999999987


Q ss_pred             CC
Q 008442          469 PK  470 (565)
Q Consensus       469 ~~  470 (565)
                      ++
T Consensus       100 ~~  101 (101)
T 2la4_A          100 ER  101 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=1.1e-14  Score=116.21  Aligned_cols=78  Identities=22%  Similarity=0.304  Sum_probs=69.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecCC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~~  469 (565)
                      ..++|||+|||+++++++|+.+|+.||.|.+|  +.++.+|+   ||||+|.+.++|.+|+.+++..|+|++|.|..+.+
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~l~g~~~~g~~l~V~~a~~   81 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPREQ   81 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHTCSCCEETTEECCCBCSCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHhcCCeEECCEEEEEEECCc
Confidence            45799999999999999999999999999987  55555665   99999999999999999999999999999998866


Q ss_pred             CCC
Q 008442          470 KQR  472 (565)
Q Consensus       470 ~~~  472 (565)
                      +..
T Consensus        82 ~~~   84 (94)
T 2e5g_A           82 KEF   84 (94)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            543

>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=99.58  E-value=4.6e-15  Score=123.49  Aligned_cols=80  Identities=23%  Similarity=0.275  Sum_probs=73.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      ..++|||+|||+++++++|+.+|+.||.|.+|.++.+   +.++|||||+|.+.++|..|+. +||..++|+.|.|.++.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            4689999999999999999999999999999999864   5568999999999999999998 89999999999999998


Q ss_pred             CCCC
Q 008442          469 PKQR  472 (565)
Q Consensus       469 ~~~~  472 (565)
                      ++..
T Consensus        84 ~~~~   87 (115)
T 3lqv_A           84 ANRA   87 (115)
T ss_dssp             HHHH
T ss_pred             CChh
Confidence            7543

>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=99.58  E-value=4.3e-15  Score=117.04  Aligned_cols=76  Identities=25%  Similarity=0.427  Sum_probs=62.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCc--ccCCeEEEEee
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQ--MFLGKKLSIAR  466 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~--~~~g~~l~v~~  466 (565)
                      ...++|||+|||+++++++|+++|++||.|.+++|+.+     +||||||+|.++++|.+   +++.  .+.|++|.|..
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~---~~~~~~~~~g~~v~v~~   80 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS---LCGEDLIIKGISVHISN   80 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH---HTTCEEEETTEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH---HcCCCcccCCEEEEEEE
Confidence            45689999999999999999999999999999999764     68999999999999884   3444  45799999999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +.|+..
T Consensus        81 a~~k~~   86 (89)
T 3d2w_A           81 AEPKHN   86 (89)
T ss_dssp             CC----
T ss_pred             cCCCCc
Confidence            988654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=2.6e-14  Score=114.79  Aligned_cols=77  Identities=21%  Similarity=0.188  Sum_probs=69.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ....++|||+||  ++++++|+.+|++||.|.+|.|.      .++|||||+|.+.++|..|+. |++..|.|++|.|.+
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            346789999996  89999999999999999999984      457999999999999999997 899999999999999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +.++..
T Consensus        84 a~~~~~   89 (97)
T 1x5p_A           84 ARKQPM   89 (97)
T ss_dssp             CSSCCC
T ss_pred             CCCCCC
Confidence            988654

>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=99.57  E-value=6.2e-15  Score=128.94  Aligned_cols=79  Identities=23%  Similarity=0.431  Sum_probs=73.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ....++|||+|||+++++++|+.+|++||.|.+|+++.+     ++|||||+|.+.++|..|+. +++..|+|++|.|.+
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            355789999999999999999999999999999999875     57999999999999999998 899999999999999


Q ss_pred             cCCCC
Q 008442          467 SNPKQ  471 (565)
Q Consensus       467 a~~~~  471 (565)
                      +.|++
T Consensus       145 a~~~~  149 (150)
T 2i2y_A          145 SNGEK  149 (150)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98864

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.56  E-value=7e-15  Score=131.73  Aligned_cols=84  Identities=19%  Similarity=0.322  Sum_probs=78.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      .....++|||+|||+.+++++|+++|+.||.|..|.|+.++ +|.++|||||+|.+.++|..|+. +++..|+|++|.|.
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~  162 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998 99999999999999999999998 89999999999999


Q ss_pred             ecCCCC
Q 008442          466 RSNPKQ  471 (565)
Q Consensus       466 ~a~~~~  471 (565)
                      ++.+..
T Consensus       163 ~a~~~~  168 (177)
T 2f3j_A          163 LVASQI  168 (177)
T ss_dssp             EESSGG
T ss_pred             EecCCC
Confidence            987653

>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=99.56  E-value=8.9e-15  Score=134.30  Aligned_cols=85  Identities=21%  Similarity=0.360  Sum_probs=78.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEee
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIAR  466 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~  466 (565)
                      ...+.++|||+|||+++++++|+++|+.||.|.+|.++.++.+|.++|||||+|.+.++|..|+..++..+.|+.|.|..
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            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 008442          467 SNPKQ  471 (565)
Q Consensus       467 a~~~~  471 (565)
                      +.+..
T Consensus        89 ~~~~~   93 (196)
T 1l3k_A           89 AVSRE   93 (196)
T ss_dssp             CCC--
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=99.56  E-value=1.4e-14  Score=133.05  Aligned_cols=84  Identities=25%  Similarity=0.435  Sum_probs=76.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecC
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSN  468 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~  468 (565)
                      ...++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|.+|+..++..|+|+.|.|.++.
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~~~~~~~G~~i~v~~a~  181 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKAL  181 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEECC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHhCCcEECCEEEEEEecC
Confidence            34589999999999999999999999999999999999889999999999999999999999988999999999999998


Q ss_pred             CCCC
Q 008442          469 PKQR  472 (565)
Q Consensus       469 ~~~~  472 (565)
                      |+..
T Consensus       182 ~k~~  185 (196)
T 1l3k_A          182 SKQE  185 (196)
T ss_dssp             ----
T ss_pred             ChhH
Confidence            8755

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.56  E-value=1.3e-14  Score=134.97  Aligned_cols=82  Identities=27%  Similarity=0.358  Sum_probs=76.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      +.+||||+|||+++++++|+++|++||.|.+|+|+.++.+|+++|||||+|.+.++|..|+. +++..+.|+.|.|..+.
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~   93 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   93 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccc
Confidence            45799999999999999999999999999999999999899999999999999999999998 79999999999999886


Q ss_pred             CCC
Q 008442          469 PKQ  471 (565)
Q Consensus       469 ~~~  471 (565)
                      +..
T Consensus        94 ~~~   96 (213)
T 4f02_A           94 RDP   96 (213)
T ss_dssp             CCT
T ss_pred             ccc
Confidence            543

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=6.8e-15  Score=115.96  Aligned_cols=77  Identities=26%  Similarity=0.440  Sum_probs=66.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecCC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~~  469 (565)
                      ..++|||+|||+++++++|+.+|++||.|.+++++.+     ++|||||+|.+.++|++++.. ...+.|++|.|.++.|
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l~v~~a~~   77 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE-DLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC-EEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC-CceeCCEEEEEEecCC
Confidence            4689999999999999999999999999999998754     689999999999998765332 3456899999999987


Q ss_pred             CCC
Q 008442          470 KQR  472 (565)
Q Consensus       470 ~~~  472 (565)
                      +..
T Consensus        78 ~~~   80 (88)
T 1wf0_A           78 KHN   80 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=2.1e-14  Score=119.02  Aligned_cols=77  Identities=14%  Similarity=0.178  Sum_probs=66.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCC---CCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEE
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFT---GKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSI  464 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~---g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v  464 (565)
                      ...++|||+|||+++++++|+++|++||.|. +.++.++.+   |+++|||||+|.++++|++|+. ++  .++|+.+.|
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            4568999999999999999999999999999 888887766   7999999999999999999997 63  366776666


Q ss_pred             eecC
Q 008442          465 ARSN  468 (565)
Q Consensus       465 ~~a~  468 (565)
                      ..+.
T Consensus        83 ~~~~   86 (114)
T 2dnl_A           83 VSSP   86 (114)
T ss_dssp             ECCS
T ss_pred             ccCC
Confidence            5544

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.55  E-value=2.8e-14  Score=127.05  Aligned_cols=82  Identities=27%  Similarity=0.395  Sum_probs=77.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ....++|||+|||.++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|+. ++|..++|++|.|.+
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            3457899999999999999999999999999999999998899999999999999999999998 899999999999999


Q ss_pred             cCC
Q 008442          467 SNP  469 (565)
Q Consensus       467 a~~  469 (565)
                      |.+
T Consensus       164 a~~  166 (166)
T 3md3_A          164 AAK  166 (166)
T ss_dssp             SCC
T ss_pred             cCC
Confidence            864

>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=99.55  E-value=2.2e-14  Score=127.87  Aligned_cols=81  Identities=23%  Similarity=0.484  Sum_probs=77.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      .++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.++++|..|+. +++..+.|++|.|.++.|
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            5899999999999999999999999999999999998899999999999999999999998 899999999999999876


Q ss_pred             CC
Q 008442          470 KQ  471 (565)
Q Consensus       470 ~~  471 (565)
                      ..
T Consensus        82 ~~   83 (167)
T 1fxl_A           82 SS   83 (167)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>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=99.54  E-value=1.2e-14  Score=125.88  Aligned_cols=81  Identities=20%  Similarity=0.403  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEE--------EEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCC
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSI--------RILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLG  459 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~--------~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g  459 (565)
                      ...++|||+|||+++++++|+.+|+.||.|..+        .+.   .+|+++|||||+|.+.++|..|+. +|+..|.|
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~---~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g  119 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLM---KEGRMKGQAFIGLPNEKAAAKALKEANGYVLFG  119 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEE---EETTTEEEEEEECSSHHHHHHHHHHHTTBEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEec---cCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCC
Confidence            456899999999999999999999999998763        332   378999999999999999999998 89999999


Q ss_pred             eEEEEeecCCCCC
Q 008442          460 KKLSIARSNPKQR  472 (565)
Q Consensus       460 ~~l~v~~a~~~~~  472 (565)
                      ++|.|.++.+...
T Consensus       120 ~~l~V~~a~~~~~  132 (143)
T 3egn_A          120 KPMVVQFARSARP  132 (143)
T ss_dssp             EECEEEECCCSCC
T ss_pred             cEEEEEECCCCCC
Confidence            9999999987644

>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=99.54  E-value=9.4e-15  Score=120.40  Aligned_cols=77  Identities=13%  Similarity=0.137  Sum_probs=70.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      +..++|||+|||+++++++|+.+|++||.|..|.|+.      ++|||||+|.+.++|..|+. ||+..+.|++|.|.++
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            3468999999999999999999999999999998864      46899999999999999998 8999999999999998


Q ss_pred             CCCC
Q 008442          468 NPKQ  471 (565)
Q Consensus       468 ~~~~  471 (565)
                      ....
T Consensus        82 ~~~~   85 (111)
T 1whx_A           82 PIGV   85 (111)
T ss_dssp             ETTT
T ss_pred             CCCc
Confidence            7643

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=1.9e-14  Score=110.64  Aligned_cols=72  Identities=22%  Similarity=0.336  Sum_probs=64.2

Q ss_pred             CCe-EEEcCCCCCCCHHH----HHHHhccCC-CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEE
Q 008442          391 ECT-AFLSNINLKATYED----LRRFFSDVG-GVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLS  463 (565)
Q Consensus       391 ~~~-l~V~nl~~~~~~~~----l~~~f~~~G-~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~  463 (565)
                      ..| |||+|||+.+++++    |+++|++|| .|.+|       +|   |||||.|.+.++|++|+. |+|..|.||+|+
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~   77 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRII   77 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEE
Confidence            455 99999999999987    558999994 99987       34   999999999999999998 999999999999


Q ss_pred             EeecCCCCC
Q 008442          464 IARSNPKQR  472 (565)
Q Consensus       464 v~~a~~~~~  472 (565)
                      |.+|..+..
T Consensus        78 v~~A~~~sd   86 (96)
T 2diu_A           78 VSFTPKNRE   86 (96)
T ss_dssp             EESSCCSCC
T ss_pred             EEecCCCcc
Confidence            999987644

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.54  E-value=1.7e-14  Score=128.80  Aligned_cols=82  Identities=24%  Similarity=0.387  Sum_probs=77.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      .+++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.++++|..|+. +++..+.|++|.|.++.
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            46899999999999999999999999999999999998899999999999999999999997 89999999999999988


Q ss_pred             CCC
Q 008442          469 PKQ  471 (565)
Q Consensus       469 ~~~  471 (565)
                      +..
T Consensus        82 ~~~   84 (168)
T 1b7f_A           82 PGG   84 (168)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            754

>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=99.54  E-value=1.8e-14  Score=113.46  Aligned_cols=75  Identities=13%  Similarity=0.289  Sum_probs=69.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      +..++|||+|||+++++++|+++|++| .|.++++.      +++|||||+|.++++|..|+. +++..++|++|.|.++
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            346899999999999999999999999 99999884      578999999999999999998 8999999999999998


Q ss_pred             CCC
Q 008442          468 NPK  470 (565)
Q Consensus       468 ~~~  470 (565)
                      ...
T Consensus        76 ~~~   78 (88)
T 1wg1_A           76 PTD   78 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.54  E-value=8.8e-15  Score=130.60  Aligned_cols=80  Identities=24%  Similarity=0.458  Sum_probs=76.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecCCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPK  470 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~~~  470 (565)
                      .++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|+.+++..++|++|.|.++.|+
T Consensus        87 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A           87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHHCSEECSSSSCEEEEECCCC
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHhCCCEEeCCeEEEEeecCCC
Confidence            56999999999999999999999999999999999988999999999999999999999999999999999999999886

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=1.8e-14  Score=115.55  Aligned_cols=78  Identities=18%  Similarity=0.147  Sum_probs=70.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEE-EeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIR-ILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~-~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ...++|||+|||+++++++|+.+|+.||.|.+++ ++.++.+    |.|||+|.+.++|..|+. +|+..|+|++|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~----~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET----AVVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSS----EEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCC----CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            4568999999999999999999999999999995 8777544    349999999999999998 899999999999999


Q ss_pred             cCCC
Q 008442          467 SNPK  470 (565)
Q Consensus       467 a~~~  470 (565)
                      +.|+
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            9886

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.52  E-value=5.7e-14  Score=131.00  Aligned_cols=84  Identities=17%  Similarity=0.326  Sum_probs=79.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      ..++|||+|||.++++++|+++|+.||.|..++++.++.+|.++|||||+|.+.++|.+|+. +++..|+|++|.|.++.
T Consensus       124 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~  203 (216)
T 2qfj_A          124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV  203 (216)
T ss_dssp             TSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECS
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEec
Confidence            45799999999999999999999999999999999998899999999999999999999998 89999999999999998


Q ss_pred             CCCCC
Q 008442          469 PKQRK  473 (565)
Q Consensus       469 ~~~~~  473 (565)
                      ++...
T Consensus       204 ~~~~~  208 (216)
T 2qfj_A          204 TPPMP  208 (216)
T ss_dssp             SCSST
T ss_pred             CCCCC
Confidence            87543

>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=99.51  E-value=3.3e-14  Score=115.77  Aligned_cols=77  Identities=10%  Similarity=0.089  Sum_probs=68.0

Q ss_pred             CCCeEEE--cCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCccc-----CCeE
Q 008442          390 DECTAFL--SNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMF-----LGKK  461 (565)
Q Consensus       390 ~~~~l~V--~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~-----~g~~  461 (565)
                      ..++|||  +|||+++++++|+++|++||.|.+|.|+.      .||||||+|.+.++|++|+. |||..+     .|++
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~   97 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   97 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcE
Confidence            3578999  77999999999999999999999988753      26899999999999999998 999988     6899


Q ss_pred             EEEeecCCCCC
Q 008442          462 LSIARSNPKQR  472 (565)
Q Consensus       462 l~v~~a~~~~~  472 (565)
                      |.|.++...+-
T Consensus        98 l~v~~a~~~p~  108 (114)
T 2cq2_A           98 LYLNFVEKVQW  108 (114)
T ss_dssp             CEEEEESCCCC
T ss_pred             EEEEecccCcc
Confidence            99999875443

>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=99.51  E-value=5.3e-14  Score=127.94  Aligned_cols=78  Identities=19%  Similarity=0.267  Sum_probs=72.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~~  469 (565)
                      .++|||+|||+++++++|+.+|++||.|.+|+|+.+. +|.++|||||+|.++++|..|+...+..++|++|.|..+..
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHH
Confidence            4799999999999999999999999999999999987 79999999999999999999999666799999999998654

>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=99.51  E-value=5e-14  Score=122.00  Aligned_cols=79  Identities=19%  Similarity=0.172  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCC--eEEEEe
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLG--KKLSIA  465 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g--~~l~v~  465 (565)
                      ....+|||+|||+.+++++|+++|++||.|.+|.|..+    .++|||||+|.+.++|..|+. |||..|.|  ++|+|.
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~  119 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            34578999999999999999999999999999998653    257999999999999999998 99999965  999999


Q ss_pred             ecCCCC
Q 008442          466 RSNPKQ  471 (565)
Q Consensus       466 ~a~~~~  471 (565)
                      +++++.
T Consensus       120 ~Ak~~~  125 (164)
T 1sjr_A          120 FSKLTS  125 (164)
T ss_dssp             ECSSSS
T ss_pred             EecCCc
Confidence            998864

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.51  E-value=6.6e-14  Score=128.66  Aligned_cols=84  Identities=19%  Similarity=0.359  Sum_probs=79.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||.++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|..|+. +++..|+|++|.|.++
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            456899999999999999999999999999999999998899999999999999999999998 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .|+..
T Consensus       192 ~~~~~  196 (198)
T 2yh0_A          192 SVGAK  196 (198)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            88754

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.51  E-value=8e-14  Score=116.19  Aligned_cols=78  Identities=19%  Similarity=0.198  Sum_probs=70.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceE-EEEEecCHHHHHHHHH-cCCcccCC--eEEEE
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGL-AYVDFIDDEHLAAAVA-KNKQMFLG--KKLSI  464 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~-afv~f~~~~~a~~a~~-~~~~~~~g--~~l~v  464 (565)
                      ..-.+|||+||++.+++++|+++|++||.|.+|.++.+     ++|| |||+|.+.++|..|+. |||..|.|  ++|+|
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI  100 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  100 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEE
Confidence            34468999999999999999999999999999988764     2588 9999999999999998 89999988  89999


Q ss_pred             eecCCCC
Q 008442          465 ARSNPKQ  471 (565)
Q Consensus       465 ~~a~~~~  471 (565)
                      .++++..
T Consensus       101 ~~ak~~~  107 (130)
T 3zzy_A          101 DFSKLTS  107 (130)
T ss_dssp             EECSCSS
T ss_pred             EecCCCc
Confidence            9998764

>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=99.50  E-value=8.4e-14  Score=124.82  Aligned_cols=78  Identities=21%  Similarity=0.383  Sum_probs=74.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ..++|||+|||.++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+. +++..++|++|.|.+|
T Consensus        93 ~~~~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           93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            36899999999999999999999999999999999998899999999999999999999998 8999999999999987

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.49  E-value=7.9e-14  Score=124.12  Aligned_cols=80  Identities=20%  Similarity=0.335  Sum_probs=74.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCCC
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNPK  470 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~~  470 (565)
                      ++|||+|||+++++++|+++|+.||.|.++.++.++ +|+++|||||+|.+.++|..|+. +++..+.|++|.|..+.+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            589999999999999999999999999999999997 78899999999999999999996 8999999999999998765


Q ss_pred             CC
Q 008442          471 QR  472 (565)
Q Consensus       471 ~~  472 (565)
                      ..
T Consensus        80 ~~   81 (166)
T 3md3_A           80 QQ   81 (166)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.48  E-value=8.4e-14  Score=129.47  Aligned_cols=79  Identities=22%  Similarity=0.386  Sum_probs=73.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      .++|||+|||+++++++|+++|+.||.|.+++|+.++  +.++|||||+|.+.++|.+|+. |||..|+|++|.|.++.+
T Consensus       103 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4689999999999999999999999999999999984  5589999999999999999997 899999999999999987


Q ss_pred             CC
Q 008442          470 KQ  471 (565)
Q Consensus       470 ~~  471 (565)
                      +.
T Consensus       181 ~~  182 (213)
T 4f02_A          181 RK  182 (213)
T ss_dssp             HH
T ss_pred             Cc
Confidence            54

>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=99.48  E-value=5.2e-14  Score=125.53  Aligned_cols=80  Identities=28%  Similarity=0.634  Sum_probs=74.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecCC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~~  469 (565)
                      +.++|||+|||+++++++|+++|+.||.|.+|.++.++.+|.++|||||+|.++++|..|+. ++..++|+.|.|..+.+
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 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK-TQHILDGKVIDPKRAIP   80 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH-SCCEETTEECCCEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh-cccccCCeEcccccccc
Confidence            46899999999999999999999999999999999998899999999999999999999998 35789999999988765


Q ss_pred             C
Q 008442          470 K  470 (565)
Q Consensus       470 ~  470 (565)
                      +
T Consensus        81 ~   81 (167)
T 2cjk_A           81 R   81 (167)
T ss_dssp             H
T ss_pred             h
Confidence            4

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.48  E-value=2.3e-13  Score=113.02  Aligned_cols=75  Identities=24%  Similarity=0.213  Sum_probs=67.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceE-EEEEecCHHHHHHHHH-cCCcccCC--eEEEEee
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGL-AYVDFIDDEHLAAAVA-KNKQMFLG--KKLSIAR  466 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~-afv~f~~~~~a~~a~~-~~~~~~~g--~~l~v~~  466 (565)
                      -..|||+|||+.+++++|+++|++||.|.+|.|+. +     .|| |||+|.+.++|..|+. |||..|.|  ++|.|.+
T Consensus        25 vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~   98 (124)
T 2e5i_A           25 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEY   98 (124)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEEC
T ss_pred             EEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEE
Confidence            35678999999999999999999999999999865 2     286 9999999999999998 89999987  6899999


Q ss_pred             cCCCC
Q 008442          467 SNPKQ  471 (565)
Q Consensus       467 a~~~~  471 (565)
                      |+++.
T Consensus        99 Ak~~~  103 (124)
T 2e5i_A           99 ARPTR  103 (124)
T ss_dssp             CSCSC
T ss_pred             ecCCc
Confidence            98874

>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=99.47  E-value=8.1e-14  Score=109.52  Aligned_cols=72  Identities=26%  Similarity=0.455  Sum_probs=66.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccC----C-------CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCccc
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDV----G-------GVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMF  457 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~----G-------~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~  457 (565)
                      ...++|||+|||+++++++|+++|++|    |       .|.++.++.+      +|||||+|.++++|.+|+.+|+..+
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~~l~g~~~   77 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAMAFDGIIF   77 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHGGGTTCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHHhcCCCEE
Confidence            346899999999999999999999999    8       8999998754      6999999999999999998899999


Q ss_pred             CCeEEEEee
Q 008442          458 LGKKLSIAR  466 (565)
Q Consensus       458 ~g~~l~v~~  466 (565)
                      .|++|.|..
T Consensus        78 ~g~~l~V~r   86 (87)
T 2hzc_A           78 QGQSLKIRR   86 (87)
T ss_dssp             TTEECEEEC
T ss_pred             CCeEEEEeC
Confidence            999999974

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.46  E-value=1.5e-12  Score=126.73  Aligned_cols=81  Identities=23%  Similarity=0.337  Sum_probs=73.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----HHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEE
Q 008442          388 FTDECTAFLSNINLKATYEDLR----RFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKL  462 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~----~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l  462 (565)
                      ....++|||+|||+++++++|+    ++|+.||.|.+|.++.   +|+++|||||+|.+.++|..|+. +++..|.|++|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            3557899999999999999977    8999999999999875   78899999999999999999996 89999999999


Q ss_pred             EEeecCCCC
Q 008442          463 SIARSNPKQ  471 (565)
Q Consensus       463 ~v~~a~~~~  471 (565)
                      .|.++.+..
T Consensus        83 ~v~~a~~~~   91 (282)
T 3pgw_A           83 RIQYAKTDS   91 (282)
T ss_pred             EEEEeccCc
Confidence            999986654

>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=99.46  E-value=1.8e-13  Score=125.89  Aligned_cols=76  Identities=18%  Similarity=0.361  Sum_probs=70.5

Q ss_pred             CCCeEEEcCCC-CCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          390 DECTAFLSNIN-LKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       390 ~~~~l~V~nl~-~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ++++|||+||| ..+++++|+.+|+.||.|.+|+++.+     ++|||||+|.++++|+.|+. |||..+.|++|.|.++
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            56899999999 89999999999999999999999765     37999999999999999998 8999999999999998


Q ss_pred             CCC
Q 008442          468 NPK  470 (565)
Q Consensus       468 ~~~  470 (565)
                      +.+
T Consensus        78 ~~~   80 (205)
T 3tyt_A           78 KQP   80 (205)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            754

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.46  E-value=3.4e-11  Score=122.38  Aligned_cols=269  Identities=13%  Similarity=0.059  Sum_probs=153.4

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...++.++...|.    +...|...+......|+.+.+...|++++...|.+...|...+..+... +..+.+...|+
T Consensus        51 ~a~~~~~~a~~~~p~----~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~-g~~~~A~~~~~  125 (388)
T 1w3b_A           51 RSAHFSTLAIKQNPL----LAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAALVAA-GDMEGAVQAYV  125 (388)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-SCSSHHHHHHH
T ss_pred             HHHHHHHHHHhcCCC----chHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHc-CCHHHHHHHHH
Confidence            355667777777776    6777888888777788888888888888888888888888777655443 36667888888


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHH---------HHHHH-hhccccch
Q 008442           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRID---------GLRRR-ILFSGEVE  152 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~---------~~~r~-~~~~~~~e  152 (565)
                      +++...|....+|..... +....+..+++..+|++++...+.....+..+-..+..         ++.+- ........
T Consensus       126 ~al~~~p~~~~~~~~l~~-~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~  204 (388)
T 1w3b_A          126 SALQYNPDLYCVRSDLGN-LLKALGRLEEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLD  204 (388)
T ss_dssp             HHHHHCTTCTHHHHHHHH-HHHTTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHH
T ss_pred             HHHHhCCCcHHHHHHHHH-HHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHH
Confidence            888888877777776655 33446777888888888876544433322222211110         00000 00000000


Q ss_pred             hhhhHHH---HHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHH
Q 008442          153 GVLDYSL---IRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE  229 (565)
Q Consensus       153 ~~~~~~~---~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~  229 (565)
                      .+.....   ....+++++..+...+...+....++...+.+....+ +++.|...|++++...|+...+|...+.....
T Consensus       205 ~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g-~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~  283 (388)
T 1w3b_A          205 AYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQG-LIDLAIDTYRRAIELQPHFPDAYCNLANALKE  283 (388)
T ss_dssp             HHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCcCCHHHHHHHHHHHHHcC-CHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHH
Confidence            0000000   0011223333333333222333344555555555656 66667777777766666666666666666666


Q ss_pred             cCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          230 LDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       230 ~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      .|+++.|..+|++++..   .+.....|..........|+.+.+...+++++
T Consensus       284 ~g~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al  332 (388)
T 1w3b_A          284 KGSVAEAEDCYNTALRL---CPTHADSLNNLANIKREQGNIEEAVRLYRKAL  332 (388)
T ss_dssp             HSCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHT
T ss_pred             cCCHHHHHHHHHHHHhh---CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            66777777777766652   12223444444555555566666555555543

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.45  E-value=5.6e-12  Score=127.04  Aligned_cols=253  Identities=11%  Similarity=-0.006  Sum_probs=150.6

Q ss_pred             HHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHH
Q 008442            6 AHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRAT   85 (565)
Q Consensus         6 ~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl   85 (565)
                      ..++..+...+...+.....|...+......|+++.+..+|++++...|.+..+|..++..... .++.+.+..+|++|+
T Consensus        48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~-~g~~~~A~~~~~~al  126 (365)
T 4eqf_A           48 SASEKGYYFHTENPFKDWPGAFEEGLKRLKEGDLPVTILFMEAAILQDPGDAEAWQFLGITQAE-NENEQAAIVALQRCL  126 (365)
T ss_dssp             -----CCCCCSSCTTTTCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHH
T ss_pred             HHHHHhhhcccCCcccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHH-CCCHHHHHHHHHHHH
Confidence            3444444443321112345688888888888999999999999999999999999988876554 447788999999999


Q ss_pred             HcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccccc---HHHH---HHHHHHHHHHHHHHhhccccchhhhhHHH
Q 008442           86 KNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFST---FEEY---LDLFLTRIDGLRRRILFSGEVEGVLDYSL  159 (565)
Q Consensus        86 ~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~---~~~~---~~~~~~~~~~~~r~~~~~~~~e~~~~~~~  159 (565)
                      ...|.....|......+ ...+..+++...|++++...+..   +...   ..++......+.      .    ..++..
T Consensus       127 ~~~p~~~~~~~~l~~~~-~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~------~----~g~~~~  195 (365)
T 4eqf_A          127 ELQPNNLKALMALAVSY-TNTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPV------D----SSVLEG  195 (365)
T ss_dssp             HHCTTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCHHHHCC-------------------------C----CHHHHH
T ss_pred             hcCCCCHHHHHHHHHHH-HccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHh------h----hhhHHH
Confidence            99998888888877634 44688899999999998754321   1111   001111111110      0    012223


Q ss_pred             HHHHHHHHHHHHHhhhcCCch--hHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHH
Q 008442          160 IRETFQRASDYLSEQMKNTDG--LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEAR  237 (565)
Q Consensus       160 ~~~~~~~a~~~l~~~~~~~~~--~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR  237 (565)
                      +...|.+++..       .+.  ...++...+.++...+ ++++|..+|++++...|++..+|...+......|+++.|.
T Consensus       196 A~~~~~~al~~-------~p~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~  267 (365)
T 4eqf_A          196 VKELYLEAAHQ-------NGDMIDPDLQTGLGVLFHLSG-EFNRAIDAFNAALTVRPEDYSLWNRLGATLANGDRSEEAV  267 (365)
T ss_dssp             HHHHHHHHHHH-------SCSSCCHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHh-------CcCccCHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHH
Confidence            33333333332       122  2345555566666666 6666777777777666666666666666666667777777


Q ss_pred             HHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          238 SIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       238 ~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      .+|++++..   .+....+|..........|+.+.+...+++++
T Consensus       268 ~~~~~al~~---~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al  308 (365)
T 4eqf_A          268 EAYTRALEI---QPGFIRSRYNLGISCINLGAYREAVSNFLTAL  308 (365)
T ss_dssp             HHHHHHHHH---CTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHhc---CCCchHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            777776652   11223444445555555566666655555554

>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=99.45  E-value=3.4e-13  Score=120.34  Aligned_cols=79  Identities=27%  Similarity=0.477  Sum_probs=74.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCC--eEEEEe
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLG--KKLSIA  465 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g--~~l~v~  465 (565)
                      ...++|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|..|+. +++..+.|  ++|.|.
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            346899999999999999999999999999999999998899999999999999999999998 89999988  999998


Q ss_pred             ec
Q 008442          466 RS  467 (565)
Q Consensus       466 ~a  467 (565)
                      +|
T Consensus       167 ~A  168 (168)
T 1b7f_A          167 LA  168 (168)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.45  E-value=3.5e-13  Score=109.16  Aligned_cols=81  Identities=16%  Similarity=0.094  Sum_probs=71.2

Q ss_pred             CCCeEEEcCCCC-----CCCHHHHHHHhccCCCeeEEEEeecCCC-CCcceEEEEEecCHHHHHHHHH-cCCcccCCeEE
Q 008442          390 DECTAFLSNINL-----KATYEDLRRFFSDVGGVSSIRILHDKFT-GKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKL  462 (565)
Q Consensus       390 ~~~~l~V~nl~~-----~~~~~~l~~~f~~~G~i~~~~~~~~~~~-g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l  462 (565)
                      ..++|+|.||..     +-++++|++.|++||.|.++.|+.++.+ +.++|||||+|.++++|.+|+. |||..++|++|
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i   86 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV   86 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEE
Confidence            357999999963     2368999999999999999999998643 6899999999999999999998 89999999999


Q ss_pred             EEeecCCC
Q 008442          463 SIARSNPK  470 (565)
Q Consensus       463 ~v~~a~~~  470 (565)
                      .|.++.+.
T Consensus        87 ~v~~a~~~   94 (105)
T 2pe8_A           87 KACFYNLD   94 (105)
T ss_dssp             EEEECCHH
T ss_pred             EEEEcCHH
Confidence            99998753

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=99.45  E-value=8.2e-13  Score=109.98  Aligned_cols=62  Identities=11%  Similarity=0.192  Sum_probs=53.8

Q ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ..||..||.|+.- . |+++||.+|+.++..+..-..+|+.|++||.++|++..||+|+.+|+.
T Consensus        61 I~LWIrYA~~~ei-~-D~d~aR~vy~~a~~~hKkFAKiwi~~AqFEiRqgnl~kARkILg~AiG  122 (161)
T 4h7y_A           61 ARIQVRFAELKAI-Q-EPDDARDYFQMARANCKKFAFVHISFAQFELSQGNVKKSKQLLQKAVE  122 (161)
T ss_dssp             HHHHHHHHHHHHH-H-CGGGCHHHHHHHHHHCTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh-c-CHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcccHHHHHHHHHHHhc
Confidence            3466677777533 4 999999999999988766689999999999999999999999999998

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.45  E-value=3.1e-11  Score=119.06  Aligned_cols=237  Identities=8%  Similarity=-0.068  Sum_probs=110.2

Q ss_pred             HHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Q 008442           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLE  103 (565)
Q Consensus        24 ~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le  103 (565)
                      ..+...+......|+.+.+..+|++++...|.+...|..++..+... +..+.+..+|++++...|.+..+|......+.
T Consensus        23 ~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~-~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~  101 (330)
T 3hym_B           23 DVVVSLAERHYYNCDFKMCYKLTSVVMEKDPFHASCLPVHIGTLVEL-NKANELFYLSHKLVDLYPSNPVSWFAVGCYYL  101 (330)
T ss_dssp             TTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTTHHHHHHHHHHH-TCHHHHHHHHHHHHHHCTTSTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCChhhHHHHHHHHHHh-hhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHH
Confidence            34444444444445555555555555555555555555444433322 24444555555555555555555554443222


Q ss_pred             HhcC-CHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHH-------------------
Q 008442          104 RSRA-SEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRET-------------------  163 (565)
Q Consensus       104 ~~~~-~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~-------------------  163 (565)
                      . .+ ..+++...|++++...+.....+..+-..+...              .++..+...                   
T Consensus       102 ~-~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~--------------~~~~~A~~~~~~a~~~~~~~~~~~~~l~  166 (330)
T 3hym_B          102 M-VGHKNEHARRYLSKATTLEKTYGPAWIAYGHSFAVE--------------SEHDQAMAAYFTAAQLMKGCHLPMLYIG  166 (330)
T ss_dssp             H-SCSCHHHHHHHHHHHHTTCTTCTHHHHHHHHHHHHH--------------TCHHHHHHHHHHHHHHTTTCSHHHHHHH
T ss_pred             H-hhhhHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHc--------------cCHHHHHHHHHHHHHhccccHHHHHHHH
Confidence            2 23 455555555555543332111111111111100              011111112                   


Q ss_pred             --------HHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHc---------cchHHHHHHHHHH
Q 008442          164 --------FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS---------GAMLEAWQSYISM  226 (565)
Q Consensus       164 --------~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~---------~~~~~lw~~yi~~  226 (565)
                              +++|+.++...+...+....++..++.+....+ +++.|..+|++++...         +....+|...+..
T Consensus       167 ~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~  245 (330)
T 3hym_B          167 LEYGLTNNSKLAERFFSQALSIAPEDPFVMHEVGVVAFQNG-EWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHV  245 (330)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcc-cHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHH
Confidence                    233334443333333333445555555555555 6666666666666553         3334566666666


Q ss_pred             HHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHH
Q 008442          227 EIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (565)
Q Consensus       227 e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~  280 (565)
                      ....|+++.|..+|++++..  .. ....+|......-...|+.+.+...+.++
T Consensus       246 ~~~~g~~~~A~~~~~~a~~~--~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~a  296 (330)
T 3hym_B          246 CRKLKKYAEALDYHRQALVL--IP-QNASTYSAIGYIHSLMGNFENAVDYFHTA  296 (330)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH--ST-TCSHHHHHHHHHHHHHTCHHHHHHHHHTT
T ss_pred             HHHhcCHHHHHHHHHHHHhh--Cc-cchHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence            66666666666666666542  11 12234444444444555555555555444

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.44  E-value=2e-13  Score=122.63  Aligned_cols=82  Identities=21%  Similarity=0.383  Sum_probs=73.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCC--CcceEEEEEecCHHHHHHHHH-cCCcccC---CeEEE
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTG--KSRGLAYVDFIDDEHLAAAVA-KNKQMFL---GKKLS  463 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g--~~~g~afv~f~~~~~a~~a~~-~~~~~~~---g~~l~  463 (565)
                      +.++|||+|||+++++++|+++|++||.|.+++++.++.+|  .++|||||+|.++++|..|+. +++..+.   ++++.
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            56899999999999999999999999999999999998666  899999999999999999998 8887765   56788


Q ss_pred             EeecCCCC
Q 008442          464 IARSNPKQ  471 (565)
Q Consensus       464 v~~a~~~~  471 (565)
                      |..+.+..
T Consensus        82 ~~~~~~~~   89 (175)
T 3nmr_A           82 MKPADSEK   89 (175)
T ss_dssp             EEECGGGC
T ss_pred             Eccccccc
Confidence            88776543

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.44  E-value=2.1e-13  Score=127.09  Aligned_cols=81  Identities=22%  Similarity=0.369  Sum_probs=73.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      +.++|||+|||.++++++|+++|+.||.|.+|.++.++.+|.++|||||+|.+.++|..|+. +++..|.|++|.|..+.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            45799999999999999999999999999999999998899999999999999999999998 89999999999998876


Q ss_pred             CC
Q 008442          469 PK  470 (565)
Q Consensus       469 ~~  470 (565)
                      +.
T Consensus       107 ~~  108 (216)
T 2qfj_A          107 NI  108 (216)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.44  E-value=5.8e-11  Score=120.67  Aligned_cols=269  Identities=13%  Similarity=0.099  Sum_probs=196.6

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...|+.++...|.    ....|...+......|+.+.+...|++++...|.+..+|......+. ..+..+.+..+|+
T Consensus        85 ~A~~~~~~al~~~p~----~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~-~~g~~~~A~~~~~  159 (388)
T 1w3b_A           85 EAIEHYRHALRLKPD----FIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLK-ALGRLEEAKACYL  159 (388)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHH-TTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcc----hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH-HccCHHHHHHHHH
Confidence            467889999988876    77889999998888999999999999999999999999998887655 4457788999999


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHH---------HHHHHH-hhccccch
Q 008442           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRI---------DGLRRR-ILFSGEVE  152 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~---------~~~~r~-~~~~~~~e  152 (565)
                      +++...|.....|..... +....+..+++...|++++...+.....+..+-..+.         ..+.+. ....+...
T Consensus       160 ~al~~~p~~~~~~~~l~~-~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~  238 (388)
T 1w3b_A          160 KAIETQPNFAVAWSNLGC-VFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAV  238 (388)
T ss_dssp             HHHHHCTTCHHHHHHHHH-HHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHH
T ss_pred             HHHHhCCCCHHHHHHHHH-HHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcCCHH
Confidence            999999999999988776 4445788999999999999866554443333222211         011110 11111111


Q ss_pred             hhhhH---HHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHH
Q 008442          153 GVLDY---SLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE  229 (565)
Q Consensus       153 ~~~~~---~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~  229 (565)
                      .+...   ......+++|+..+...+...+.....|...+.+....+ +++.|..+|++++...|++...|...+.....
T Consensus       239 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g-~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~  317 (388)
T 1w3b_A          239 VHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKG-SVAEAEDCYNTALRLCPTHADSLNNLANIKRE  317 (388)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcC-CHHHHHHHHHHHHhhCcccHHHHHHHHHHHHH
Confidence            00011   011123456677766666555555667888888888888 99999999999999999999999999999999


Q ss_pred             cCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          230 LDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       230 ~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      .|+++.|..+|++++..   .+.....+......-...|+.+.+...+++++
T Consensus       318 ~g~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~  366 (388)
T 1w3b_A          318 QGNIEEAVRLYRKALEV---FPEFAAAHSNLASVLQQQGKLQEALMHYKEAI  366 (388)
T ss_dssp             TTCHHHHHHHHHHHTTS---CTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhc---CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            99999999999999873   22234555555666666788777776666654

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.44  E-value=2.8e-13  Score=121.75  Aligned_cols=79  Identities=25%  Similarity=0.429  Sum_probs=72.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccC---CeEEEE
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFL---GKKLSI  464 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~---g~~l~v  464 (565)
                      ...++|||+|||+++++++|+++|++||.|.+++++.++ +|.++|||||+|.+.++|.+|+. +||..+.   |++|.|
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            356899999999999999999999999999999999996 79999999999999999999997 8988765   499999


Q ss_pred             eecC
Q 008442          465 ARSN  468 (565)
Q Consensus       465 ~~a~  468 (565)
                      .+|+
T Consensus       172 ~~ad  175 (175)
T 3nmr_A          172 KFAD  175 (175)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9874

>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=99.42  E-value=5.5e-13  Score=118.71  Aligned_cols=79  Identities=25%  Similarity=0.418  Sum_probs=73.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeE--EEEe
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKK--LSIA  465 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~--l~v~  465 (565)
                      ...++|||+|||..+++++|+.+|++||.|..++++.++.+|.++|||||+|.+.++|.+|+. ++|..+.|+.  |.|.
T Consensus        86 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~  165 (167)
T 1fxl_A           86 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK  165 (167)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEE
Confidence            346799999999999999999999999999999999998899999999999999999999998 8999999974  8887


Q ss_pred             ec
Q 008442          466 RS  467 (565)
Q Consensus       466 ~a  467 (565)
                      +|
T Consensus       166 ~A  167 (167)
T 1fxl_A          166 FA  167 (167)
T ss_dssp             EC
T ss_pred             eC
Confidence            65

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.42  E-value=4.5e-13  Score=120.43  Aligned_cols=77  Identities=22%  Similarity=0.402  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||+++++++|+++|+.||.|..+     ..+|.++|||||+|.+.++|.+|+. ++|..|+|++|.|.++
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            456899999999999999999999999987765     3489999999999999999999998 8999999999999999


Q ss_pred             CCC
Q 008442          468 NPK  470 (565)
Q Consensus       468 ~~~  470 (565)
                      .|+
T Consensus       172 ~~k  174 (175)
T 1fje_B          172 GEK  174 (175)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            876

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.40  E-value=1.2e-10  Score=114.75  Aligned_cols=261  Identities=9%  Similarity=0.033  Sum_probs=159.9

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (565)
                      +...|+.++...|.    +...|..++......|+.+.+..+|++++...|.+..+|...+......+...+.+...|++
T Consensus        41 A~~~~~~~l~~~p~----~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~  116 (330)
T 3hym_B           41 CYKLTSVVMEKDPF----HASCLPVHIGTLVELNKANELFYLSHKLVDLYPSNPVSWFAVGCYYLMVGHKNEHARRYLSK  116 (330)
T ss_dssp             HHHHHHHHHHHCTT----CTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTHHHHHHHHHHHHSCSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCC----ChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhhhhHHHHHHHHHH
Confidence            55667777777665    45556666666666677777777777777777777777777776554443356667777777


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHH---------HHHHHHHhh-ccccchh
Q 008442           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTR---------IDGLRRRIL-FSGEVEG  153 (565)
Q Consensus        84 Al~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~---------~~~~~r~~~-~~~~~e~  153 (565)
                      |+...|.....|......+ ...+..+++...|++++...+.....+..+-..+         ..++.+-.. .......
T Consensus       117 a~~~~~~~~~~~~~l~~~~-~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~  195 (330)
T 3hym_B          117 ATTLEKTYGPAWIAYGHSF-AVESEHDQAMAAYFTAAQLMKGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIAPEDPFV  195 (330)
T ss_dssp             HHTTCTTCTHHHHHHHHHH-HHHTCHHHHHHHHHHHHHHTTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHH
T ss_pred             HHHhCCccHHHHHHHHHHH-HHccCHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCCCChHH
Confidence            7777777777776665533 3356677777777777764332111111111111         001111100 0010000


Q ss_pred             ----------hhhHHHHHHHHHHHHHHHHhhhcC--CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHH
Q 008442          154 ----------VLDYSLIRETFQRASDYLSEQMKN--TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQ  221 (565)
Q Consensus       154 ----------~~~~~~~~~~~~~a~~~l~~~~~~--~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~  221 (565)
                                ..++..+...|++++.........  .+....++...+.+....+ +++.|..+|++++...|+...+|.
T Consensus       196 ~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~a~~~~~~~~~~~~  274 (330)
T 3hym_B          196 MHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLK-KYAEALDYHRQALVLIPQNASTYS  274 (330)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHSTTCSHHHH
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhc-CHHHHHHHHHHHHhhCccchHHHH
Confidence                      013334444455554443221111  1333567788888888888 999999999999999999999999


Q ss_pred             HHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHH-HHHHHhCCHHHH
Q 008442          222 SYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWL-RFEREYGTLEDF  273 (565)
Q Consensus       222 ~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~-~fE~~~G~~~~~  273 (565)
                      ..+.+....|+++.|...|++++..  ..+.+ ..+.... .++...|+.+.+
T Consensus       275 ~la~~~~~~g~~~~A~~~~~~al~~--~p~~~-~~~~~l~~~~~~~~g~~~a~  324 (330)
T 3hym_B          275 AIGYIHSLMGNFENAVDYFHTALGL--RRDDT-FSVTMLGHCIEMYIGDSEAY  324 (330)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHTTTTT--CSCCH-HHHHHHHHHHHTTTTC----
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHcc--CCCch-HHHHHHHHHHHHHhCchhcc
Confidence            9999999999999999999999873  22333 3443333 356677776543

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.40  E-value=5.3e-11  Score=119.68  Aligned_cols=115  Identities=11%  Similarity=0.068  Sum_probs=85.0

Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHH
Q 008442            7 HLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATK   86 (565)
Q Consensus         7 ~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~   86 (565)
                      .|+.++...+.........|..........|+++.+..+|++++...|.+..+|...+..... .+..+.+...|++|+.
T Consensus        48 ~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~-~g~~~~A~~~~~~al~  126 (368)
T 1fch_A           48 TYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAE-NEQELLAISALRRCLE  126 (368)
T ss_dssp             HHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHH
T ss_pred             hhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-CcCHHHHHHHHHHHHh
Confidence            566666554431111245677777777788888999999999999999998888888775544 4467778899999999


Q ss_pred             cCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcc
Q 008442           87 NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA  123 (565)
Q Consensus        87 ~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~  123 (565)
                      ..|....+|......+ ...+..+++...|++++...
T Consensus       127 ~~~~~~~~~~~l~~~~-~~~g~~~~A~~~~~~~~~~~  162 (368)
T 1fch_A          127 LKPDNQTALMALAVSF-TNESLQRQACEILRDWLRYT  162 (368)
T ss_dssp             HCTTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHTS
T ss_pred             cCCCCHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHhC
Confidence            8888888888777633 34678888889999888644

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.38  E-value=5.8e-13  Score=123.52  Aligned_cols=80  Identities=20%  Similarity=0.255  Sum_probs=69.8

Q ss_pred             CCCCCCeEEEcCCCCCC---------CHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcc
Q 008442          387 GFTDECTAFLSNINLKA---------TYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQM  456 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~---------~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~  456 (565)
                      .....++|||+|||..+         ++++|+.+|++||.|.+|+|+.      ++|||||+|.+.++|+.|+. |++..
T Consensus       130 ~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~  203 (240)
T 3u1l_A          130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQT  203 (240)
T ss_dssp             -CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             cccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCE
Confidence            35678999999999998         7999999999999999999985      36999999999999999997 89999


Q ss_pred             c------------CCeEEEEeecCCCCC
Q 008442          457 F------------LGKKLSIARSNPKQR  472 (565)
Q Consensus       457 ~------------~g~~l~v~~a~~~~~  472 (565)
                      |            .|+.|.|.+|.+.+.
T Consensus       204 l~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          204 LLLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             EeccccccccccCCCCEEEEEEccCCCC
Confidence            8            899999999987654

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=99.37  E-value=4.5e-12  Score=105.58  Aligned_cols=103  Identities=14%  Similarity=0.204  Sum_probs=90.0

Q ss_pred             ChHhHHHHHHHHHHHHhcCCc------hhHHHHHHHHHhcCCCCH--------HHHHHHHHHHHHhcchhhHHHHHHHHH
Q 008442           19 DSEKFQQYMIYLKYEQSSGDP------GRVQLLYERAITDFPVSS--------DLWLDYTQYLDKTLKVGNVVRDVYSRA   84 (565)
Q Consensus        19 ~~~~~~~W~~yi~~e~~~~~~------~~~~~lyERal~~~p~~~--------~lW~~Y~~~l~~~~~~~~~~~~v~erA   84 (565)
                      .+.+++.|..|+..+++.|++      ++++.+|+||+...|...        .||+.|+.|.+-  ++.+.++++|+.|
T Consensus         9 ~p~~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~~Pp~k~~~wrrYI~LWIrYA~~~ei--~D~d~aR~vy~~a   86 (161)
T 4h7y_A            9 MANNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEALPPDKYGQNESFARIQVRFAELKAI--QEPDDARDYFQMA   86 (161)
T ss_dssp             -CCSHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHHSCGGGGTTCHHHHHHHHHHHHHHHH--HCGGGCHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHcCCccccccHHHHHHHHHHHHHHHHh--cCHHHHHHHHHHH
Confidence            344899999999999999999      999999999999988653        399999998543  6889999999999


Q ss_pred             HHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccc
Q 008442           85 TKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAF  124 (565)
Q Consensus        85 l~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~  124 (565)
                      +..|.....||+.|.. +|..++++..++.|+.+|+-..+
T Consensus        87 ~~~hKkFAKiwi~~Aq-FEiRqgnl~kARkILg~AiG~~~  125 (161)
T 4h7y_A           87 RANCKKFAFVHISFAQ-FELSQGNVKKSKQLLQKAVERGA  125 (161)
T ss_dssp             HHHCTTBHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHhHHHHHHHHHHHH-HHHHcccHHHHHHHHHHHhccCC
Confidence            9988777999999999 77778999999999999997543

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.37  E-value=5.8e-11  Score=119.55  Aligned_cols=205  Identities=8%  Similarity=-0.075  Sum_probs=125.0

Q ss_pred             HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHH
Q 008442           57 SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLT  136 (565)
Q Consensus        57 ~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~  136 (565)
                      ...|...+......+ +.+.+..+|++++...|....+|......+ ...+..+++...|++++...+.....+..+-..
T Consensus        65 ~~~~~~~~~~~~~~g-~~~~A~~~~~~al~~~p~~~~~~~~lg~~~-~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~  142 (365)
T 4eqf_A           65 WPGAFEEGLKRLKEG-DLPVTILFMEAAILQDPGDAEAWQFLGITQ-AENENEQAAIVALQRCLELQPNNLKALMALAVS  142 (365)
T ss_dssp             CTTHHHHHHHHHHHT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCcCCHHHHHHHHHHH-HHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            344777766554433 667788888888888888877877766533 346778888888888887555444444333333


Q ss_pred             HHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCc---hhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHc
Q 008442          137 RIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTD---GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS  213 (565)
Q Consensus       137 ~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~---~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~  213 (565)
                      +...              .++..+...|.+++...........   ....++...+.++...+ ++++|..+|++++...
T Consensus       143 ~~~~--------------g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~al~~~  207 (365)
T 4eqf_A          143 YTNT--------------SHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSS-VLEGVKELYLEAAHQN  207 (365)
T ss_dssp             HHHT--------------TCHHHHHHHHHHHHHHCHHHHCC-------------------CCH-HHHHHHHHHHHHHHHS
T ss_pred             HHcc--------------ccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhh-hHHHHHHHHHHHHHhC
Confidence            3211              1445556666666665433322211   12334444555666666 7888888888888887


Q ss_pred             cc--hHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          214 GA--MLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       214 ~~--~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      |.  ...+|...+.+....|+++.|..+|++++..   .+....+|..........|+.+.+...+++++
T Consensus       208 p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al  274 (365)
T 4eqf_A          208 GDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTV---RPEDYSLWNRLGATLANGDRSEEAVEAYTRAL  274 (365)
T ss_dssp             CSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            77  6778888888888888888888888888763   12234566666666667788777777777665

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.37  E-value=5.6e-10  Score=115.51  Aligned_cols=253  Identities=11%  Similarity=-0.007  Sum_probs=179.1

Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHH
Q 008442            7 HLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATK   86 (565)
Q Consensus         7 ~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~   86 (565)
                      .+..++...|.    +...|...+......|+++.+..+|++++...|.+..+|...+..... .+..+.+..+|++++.
T Consensus        14 ~~~~~~~~~p~----~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~-~g~~~~A~~~~~~al~   88 (450)
T 2y4t_A           14 GTENLYFQSMA----DVEKHLELGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLA-MGKSKAALPDLTKVIQ   88 (450)
T ss_dssp             ---------CH----HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHH
T ss_pred             cccccccccHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHH-CCCHHHHHHHHHHHHh
Confidence            34444555544    889999999999999999999999999999999999999998876554 4477889999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccH---HHHHHHHHHH---HHHHHHHhhccccchhhhhHHHH
Q 008442           87 NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTF---EEYLDLFLTR---IDGLRRRILFSGEVEGVLDYSLI  160 (565)
Q Consensus        87 ~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~---~~~~~~~~~~---~~~~~r~~~~~~~~e~~~~~~~~  160 (565)
                      ..|.....|......+. ..+..+++...|++++...+...   ..+..+...+   ..+..-.            ....
T Consensus        89 ~~p~~~~~~~~l~~~~~-~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~------------~~~~  155 (450)
T 2y4t_A           89 LKMDFTAARLQRGHLLL-KQGKLDEAEDDFKKVLKSNPSENEEKEAQSQLIKSDEMQRLRSQAL------------NAFG  155 (450)
T ss_dssp             HCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHH------------HHHH
T ss_pred             cCCCcHHHHHHHHHHHH-HcCCHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHH------------HHHH
Confidence            99999999988776444 47889999999999998665433   2222221110   0000000            0011


Q ss_pred             HHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHH
Q 008442          161 RETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIY  240 (565)
Q Consensus       161 ~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~  240 (565)
                      ...+++|+.++...+...+....++...+.++...+ +++.|..+|++++...|.+..+|...+......|+++.|..+|
T Consensus       156 ~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  234 (450)
T 2y4t_A          156 SGDYTAAIAFLDKILEVCVWDAELRELRAECFIKEG-EPRKAISDLKAASKLKNDNTEAFYKISTLYYQLGDHELSLSEV  234 (450)
T ss_dssp             HTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT-CGGGGHHHHHHHHHHHCSCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            122344444444444334445567778888888888 9999999999999999999999999999999999999999999


Q ss_pred             HHHHhcccCCCCcHHHHHHH------------HHHHHHhCCHHHHHHHHHHHh
Q 008442          241 KRCYSKRFTGTGSEDICHAW------------LRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       241 ~~al~~~~~~~~~~~i~~~~------------~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      ++++..  . +....++..+            ...-...|+.+.+...+.+++
T Consensus       235 ~~~~~~--~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l  284 (450)
T 2y4t_A          235 RECLKL--D-QDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVM  284 (450)
T ss_dssp             HHHHHH--C-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHh--C-CChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            999873  2 2233444433            444555688777776666654

>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=99.37  E-value=9.9e-13  Score=128.66  Aligned_cols=82  Identities=16%  Similarity=0.266  Sum_probs=75.4

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEeecCC-CCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEee
Q 008442          389 TDECTAFLSNINLK-ATYEDLRRFFSDVGGVSSIRILHDKF-TGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIAR  466 (565)
Q Consensus       389 ~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~  466 (565)
                      ...++|||+|||+. +++++|+++|+.||.|..|+++.+.. ||.++|||||+|.+.++|.+|+.+||..|+|++|.|.+
T Consensus       208 ~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~~l~g~~~~g~~i~V~~  287 (292)
T 2ghp_A          208 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSL  287 (292)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEE
T ss_pred             CCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHHHhcCCEECCcEEEEEE
Confidence            45689999999999 99999999999999999999999874 49999999999999999999997799999999999999


Q ss_pred             cCCC
Q 008442          467 SNPK  470 (565)
Q Consensus       467 a~~~  470 (565)
                      +.|+
T Consensus       288 a~~k  291 (292)
T 2ghp_A          288 ADKK  291 (292)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            9886

>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=99.37  E-value=2e-12  Score=125.89  Aligned_cols=83  Identities=14%  Similarity=0.179  Sum_probs=77.8

Q ss_pred             CCCCeEEEcCCCCCC-CHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          389 TDECTAFLSNINLKA-TYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~-~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ...++|||+|||+++ ++++|+.+|+.||.|.++.|+.++ +|.++|||||+|.+.++|..|+. ++|..++|++|.|.+
T Consensus       182 ~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  260 (284)
T 3smz_A          182 LHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF  260 (284)
T ss_dssp             TSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEE
Confidence            456899999999995 999999999999999999999987 89999999999999999999998 899999999999999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +.|+..
T Consensus       261 a~~~~~  266 (284)
T 3smz_A          261 CAPGPP  266 (284)
T ss_dssp             CCSSSC
T ss_pred             ecCCCc
Confidence            988754

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.36  E-value=2.9e-12  Score=117.64  Aligned_cols=77  Identities=26%  Similarity=0.374  Sum_probs=71.4

Q ss_pred             CCCeEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          390 DECTAFLSNINL-KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       390 ~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .+++|||+|||+ ++++++|+.+|+.||.|.+|.++.++     +|||||+|.+.++|..|+. +++..+.|++|.|.++
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            358999999999 99999999999999999999998764     6899999999999999998 8999999999999998


Q ss_pred             CCCC
Q 008442          468 NPKQ  471 (565)
Q Consensus       468 ~~~~  471 (565)
                      .+..
T Consensus        77 ~~~~   80 (198)
T 1qm9_A           77 KHQN   80 (198)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            7654

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.36  E-value=7.6e-11  Score=116.12  Aligned_cols=98  Identities=10%  Similarity=-0.006  Sum_probs=68.7

Q ss_pred             HHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Q 008442           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLE  103 (565)
Q Consensus        24 ~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le  103 (565)
                      ..|...+......|+.+.+..+|++++...|.+...|...+..... .++.+.+...|++++...|....+|......+ 
T Consensus        22 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~-   99 (327)
T 3cv0_A           22 ENPMEEGLSMLKLANLAEAALAFEAVCQAAPEREEAWRSLGLTQAE-NEKDGLAIIALNHARMLDPKDIAVHAALAVSH-   99 (327)
T ss_dssp             SCHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-cCCHHHHHHHHHHHHhcCcCCHHHHHHHHHHH-
Confidence            4566666666667777788888888888888888877776664443 34666777888888887777777777666533 


Q ss_pred             HhcCCHHHHHHHHHHHHhcc
Q 008442          104 RSRASEEEISTVFEKSLLCA  123 (565)
Q Consensus       104 ~~~~~~~~~~~if~ral~~~  123 (565)
                      ...+..+++...|++++...
T Consensus       100 ~~~~~~~~A~~~~~~~~~~~  119 (327)
T 3cv0_A          100 TNEHNANAALASLRAWLLSQ  119 (327)
T ss_dssp             HHTTCHHHHHHHHHHHHHTS
T ss_pred             HHcCCHHHHHHHHHHHHHhC
Confidence            34567777778888877643

>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=99.36  E-value=1.8e-13  Score=123.10  Aligned_cols=83  Identities=22%  Similarity=0.368  Sum_probs=72.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      ..+.++|||+|||+++++++|+++|..||.+..+ ++.+..+|.++|||||+|.++++|..|+.+++..+.|++|.|.++
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~-~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~   88 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   88 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-CCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE-EEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecC
Confidence            3567899999999999999999999999876653 333334889999999999999999999999999999999999998


Q ss_pred             CCCC
Q 008442          468 NPKQ  471 (565)
Q Consensus       468 ~~~~  471 (565)
                      .+..
T Consensus        89 ~~~~   92 (175)
T 1fje_B           89 KGRD   92 (175)
T ss_dssp             CCSS
T ss_pred             CCcc
Confidence            7754

>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=99.36  E-value=2.8e-12  Score=124.87  Aligned_cols=83  Identities=13%  Similarity=0.242  Sum_probs=77.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      ..++|||+|||+++++++|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+. +++..++|++|.|.++.
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            45799999999999999999999999999999999998899999999999999999999996 89999999999999997


Q ss_pred             CCCC
Q 008442          469 PKQR  472 (565)
Q Consensus       469 ~~~~  472 (565)
                      +...
T Consensus       174 ~~~~  177 (284)
T 3smz_A          174 AGQL  177 (284)
T ss_dssp             GGGC
T ss_pred             CCCC
Confidence            7543

>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=99.36  E-value=6.4e-12  Score=103.55  Aligned_cols=82  Identities=21%  Similarity=0.308  Sum_probs=69.5

Q ss_pred             CCCCCCeEEEcCCCCCCC-----------HHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCC
Q 008442          387 GFTDECTAFLSNINLKAT-----------YEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNK  454 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~-----------~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~  454 (565)
                      .....++|+|.||.....           +++|+.+|++||.|.+|.| .++   .++|||||+|.+.++|..|+. |||
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            345678999999954432           5799999999999999965 443   379999999999999999997 899


Q ss_pred             cccCCeEEEEeecCCCCC
Q 008442          455 QMFLGKKLSIARSNPKQR  472 (565)
Q Consensus       455 ~~~~g~~l~v~~a~~~~~  472 (565)
                      ..++|++|.|.++.+...
T Consensus        87 ~~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             CEETTEECEEEECCSCCC
T ss_pred             CEECCcEEEEEEeCCCCC
Confidence            999999999999987643

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.35  E-value=2.9e-10  Score=122.33  Aligned_cols=237  Identities=8%  Similarity=-0.043  Sum_probs=167.5

Q ss_pred             HhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHH
Q 008442           21 EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (565)
Q Consensus        21 ~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~  100 (565)
                      .+...|...+......|+++.+..+|++++...|.+...|..++..+...+ ..+.+..+|++++...|....+|...+.
T Consensus       303 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~~~~~~~~~~l~~  381 (597)
T 2xpi_A          303 KSSDLLLCKADTLFVRSRFIDVLAITTKILEIDPYNLDVYPLHLASLHESG-EKNKLYLISNDLVDRHPEKAVTWLAVGI  381 (597)
T ss_dssp             GCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCCTTHHHHHHHHHHHT-CHHHHHHHHHHHHHHCTTSHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHhC-CHHHHHHHHHHHHhhCcccHHHHHHHHH
Confidence            478899999999999999999999999999999999999999988766544 6778999999999999999999988776


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCch
Q 008442          101 SLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG  180 (565)
Q Consensus       101 ~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~  180 (565)
                      .+ ...+..+++..+|++++...+.....+..+-..+...              .+++.+...|++++.       ..+.
T Consensus       382 ~~-~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~--------------g~~~~A~~~~~~~~~-------~~~~  439 (597)
T 2xpi_A          382 YY-LCVNKISEARRYFSKSSTMDPQFGPAWIGFAHSFAIE--------------GEHDQAISAYTTAAR-------LFQG  439 (597)
T ss_dssp             HH-HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH--------------TCHHHHHHHHHHHHH-------TTTT
T ss_pred             HH-HHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc--------------CCHHHHHHHHHHHHH-------hCcc
Confidence            44 4468899999999999975544333333222222110              122333334443332       2223


Q ss_pred             hHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhccc--CCCCc--HHH
Q 008442          181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRF--TGTGS--EDI  256 (565)
Q Consensus       181 ~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~--~~~~~--~~i  256 (565)
                      ....|...+..+...+ ++++|..+|++++...|.+..+|...+......|+++.|..+|++++...-  +.+..  ..+
T Consensus       440 ~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~  518 (597)
T 2xpi_A          440 THLPYLFLGMQHMQLG-NILLANEYLQSSYALFQYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAAT  518 (597)
T ss_dssp             CSHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHH
T ss_pred             chHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHH
Confidence            3445666666666777 788888888888877777777788888887788888888888888775310  11111  356


Q ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          257 CHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       257 ~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      |......-...|+.+.+...+++++
T Consensus       519 ~~~l~~~~~~~g~~~~A~~~~~~~~  543 (597)
T 2xpi_A          519 WANLGHAYRKLKMYDAAIDALNQGL  543 (597)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            6666666777777777776666654

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.35  E-value=3.6e-10  Score=121.61  Aligned_cols=248  Identities=13%  Similarity=0.102  Sum_probs=191.0

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...|+.++...|.    +...|..++......|+.+.+..+|++++...|.+..+|...+...... +..+.+..+|+
T Consensus       323 ~A~~~~~~~~~~~~~----~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~-g~~~~A~~~~~  397 (597)
T 2xpi_A          323 DVLAITTKILEIDPY----NLDVYPLHLASLHESGEKNKLYLISNDLVDRHPEKAVTWLAVGIYYLCV-NKISEARRYFS  397 (597)
T ss_dssp             HHHHHHHHHHHHCTT----CCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHT-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcc----cHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHh-ccHHHHHHHHH
Confidence            466778888877765    6678889999888999999999999999999999999999988765544 47788999999


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHH
Q 008442           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRE  162 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~  162 (565)
                      +++...|.....|...+..+.. .+..+++..+|++++...+.....+..+-..+...              .+++....
T Consensus       398 ~~~~~~~~~~~~~~~l~~~~~~-~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~--------------g~~~~A~~  462 (597)
T 2xpi_A          398 KSSTMDPQFGPAWIGFAHSFAI-EGEHDQAISAYTTAARLFQGTHLPYLFLGMQHMQL--------------GNILLANE  462 (597)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHH-HTCHHHHHHHHHHHHHTTTTCSHHHHHHHHHHHHH--------------TCHHHHHH
T ss_pred             HHHHhCCCCHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHc--------------CCHHHHHH
Confidence            9999999999999988874444 68899999999999976554333333222222110              13444455


Q ss_pred             HHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH------ccch-HHHHHHHHHHHHHcCChHH
Q 008442          163 TFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI------SGAM-LEAWQSYISMEIELDHINE  235 (565)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~------~~~~-~~lw~~yi~~e~~~~~~~~  235 (565)
                      .|.+++..       .+.....|...+.++...+ ++++|..+|++++..      .|+. ..+|...+......|+++.
T Consensus       463 ~~~~~~~~-------~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~  534 (597)
T 2xpi_A          463 YLQSSYAL-------FQYDPLLLNELGVVAFNKS-DMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDA  534 (597)
T ss_dssp             HHHHHHHH-------CCCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHh-------CCCChHHHHHHHHHHHHhC-CHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHH
Confidence            55554442       2334456778888888888 999999999999987      4443 7899999999999999999


Q ss_pred             HHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          236 ARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       236 aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      |..+|++++..  . +....+|......-...|+.+.+...+++++
T Consensus       535 A~~~~~~~~~~--~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l  577 (597)
T 2xpi_A          535 AIDALNQGLLL--S-TNDANVHTAIALVYLHKKIPGLAITHLHESL  577 (597)
T ss_dssp             HHHHHHHHHHH--S-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHh--C-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            99999999873  2 2345777777788888999988887777664

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.35  E-value=8.2e-10  Score=109.99  Aligned_cols=215  Identities=14%  Similarity=0.001  Sum_probs=121.5

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (565)
                      +...|+.++...|.    +...|..........|+++.+...|++++...|.+...|...+......+ +.+.+..+|++
T Consensus        22 A~~~~~~~l~~~p~----~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~   96 (359)
T 3ieg_A           22 ALSQFHAAVDGDPD----NYIAYYRRATVFLAMGKSKAALPDLTKVIALKMDFTAARLQRGHLLLKQG-KLDEAEDDFKK   96 (359)
T ss_dssp             HHHHHHHHHHHCTT----CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHhhCcc----cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHcC-ChHHHHHHHHH
Confidence            55667777776665    56677777777777777788888888888878877777777776554433 56667788888


Q ss_pred             HHHcCC---CCHHHHHHHHH-----------HHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccc
Q 008442           84 ATKNCP---WVGELWVRSLL-----------SLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSG  149 (565)
Q Consensus        84 Al~~~p---~~~~lW~~yi~-----------~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~  149 (565)
                      ++...|   ....+|..+..           .+....+..+++..+|++++...+.....+..+-..+..          
T Consensus        97 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~----------  166 (359)
T 3ieg_A           97 VLKSNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVCVWDAELRELRAECFIK----------  166 (359)
T ss_dssp             HHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH----------
T ss_pred             HHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHH----------
Confidence            887777   66666655420           122335677777777777776544433322222221110          


Q ss_pred             cchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHH------
Q 008442          150 EVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSY------  223 (565)
Q Consensus       150 ~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~y------  223 (565)
                                 ..-+.+|+.++...+...+.....+...+.++...+ +++.|...|++++...|+....|..|      
T Consensus       167 -----------~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~  234 (359)
T 3ieg_A          167 -----------EGEPRKAISDLKAASKLKSDNTEAFYKISTLYYQLG-DHELSLSEVRECLKLDQDHKRCFAHYKQVKKL  234 (359)
T ss_dssp             -----------TTCHHHHHHHHHHHHTTCSCCHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             -----------CCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcC-CHHHHHHHHHHHHhhCccchHHHHHHHHHHHH
Confidence                       011222333333333323333344445555555555 55555555555555555554444333      


Q ss_pred             ------HHHHHHcCChHHHHHHHHHHHh
Q 008442          224 ------ISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       224 ------i~~e~~~~~~~~aR~i~~~al~  245 (565)
                            +......|+++.|..+|++++.
T Consensus       235 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~  262 (359)
T 3ieg_A          235 NKLIESAEELIRDGRYTDATSKYESVMK  262 (359)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence                  3334445555555555555554

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.34  E-value=1.4e-09  Score=108.25  Aligned_cols=249  Identities=9%  Similarity=-0.029  Sum_probs=180.9

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCC---CCHHHHHHHHH-----------HHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFP---VSSDLWLDYTQ-----------YLD   68 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p---~~~~lW~~Y~~-----------~l~   68 (565)
                      ++...|+.++...|.    +...|..........|+.+.+...|++++...|   .+...|..+..           .+.
T Consensus        55 ~A~~~~~~~~~~~~~----~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  130 (359)
T 3ieg_A           55 AALPDLTKVIALKMD----FTAARLQRGHLLLKQGKLDEAEDDFKKVLKSNPSEQEEKEAESQLVKADEMQRLRSQALDA  130 (359)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC----cchHHHHHHHHHHHcCChHHHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356778888888776    678899999999999999999999999999999   88998887731           122


Q ss_pred             HhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhcc
Q 008442           69 KTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFS  148 (565)
Q Consensus        69 ~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~  148 (565)
                      ...+..+.+..+|++++...|....+|......+ ...+..+++...|++++...+.....+..+-..+...        
T Consensus       131 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~--------  201 (359)
T 3ieg_A          131 FDGADYTAAITFLDKILEVCVWDAELRELRAECF-IKEGEPRKAISDLKAASKLKSDNTEAFYKISTLYYQL--------  201 (359)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHTTCSCCHHHHHHHHHHHHHH--------
T ss_pred             HHccCHHHHHHHHHHHHHhCCCchHHHHHHHHHH-HHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc--------
Confidence            3445778899999999999999999988877644 4478899999999999987665544443333332210        


Q ss_pred             ccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHH------------HHHHHHHcCCChHHHHHHHHHHHHHccch
Q 008442          149 GEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAY------------WAHLEQSMGKDMVSARGVWERLLKISGAM  216 (565)
Q Consensus       149 ~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~------------~a~~e~~~~~~~~~ar~i~e~~l~~~~~~  216 (565)
                            .++..+...|.+++...       +.....+..            .+.+....+ +++.|..+|++++...|+.
T Consensus       202 ------~~~~~A~~~~~~a~~~~-------~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~-~~~~A~~~~~~~~~~~~~~  267 (359)
T 3ieg_A          202 ------GDHELSLSEVRECLKLD-------QDHKRCFAHYKQVKKLNKLIESAEELIRDG-RYTDATSKYESVMKTEPSV  267 (359)
T ss_dssp             ------TCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCCSS
T ss_pred             ------CCHHHHHHHHHHHHhhC-------ccchHHHHHHHHHHHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHhcCCCc
Confidence                  13344445555554432       222222222            255566777 9999999999999988876


Q ss_pred             HHH----HHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          217 LEA----WQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       217 ~~l----w~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      ..+    |...+......|+++.|..+|++++..   .+....+|......-...|+.+.+...+++++
T Consensus       268 ~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~  333 (359)
T 3ieg_A          268 AEYTVRSKERICHCFSKDEKPVEAIRICSEVLQM---EPDNVNALKDRAEAYLIEEMYDEAIQDYEAAQ  333 (359)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHh---CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            643    555677788899999999999999873   22334666667777777899888888877765

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.34  E-value=1.8e-12  Score=121.80  Aligned_cols=78  Identities=26%  Similarity=0.371  Sum_probs=72.5

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          389 TDECTAFLSNINL-KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       389 ~~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      .++++|||+|||+ ++++++|+++|+.||.|.+|+++.++     +|||||+|.+.++|..|+. +++..+.|++|.|.+
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~  106 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL  106 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            5678999999999 99999999999999999999998764     7899999999999999997 899999999999999


Q ss_pred             cCCCC
Q 008442          467 SNPKQ  471 (565)
Q Consensus       467 a~~~~  471 (565)
                      +.+..
T Consensus       107 a~~~~  111 (229)
T 2adc_A          107 SKHQN  111 (229)
T ss_dssp             CSCCC
T ss_pred             ecCcc
Confidence            97653

>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=99.31  E-value=6.8e-13  Score=107.42  Aligned_cols=71  Identities=18%  Similarity=0.308  Sum_probs=64.0

Q ss_pred             EcCCCCCCCHHHHHHHh------------ccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEE
Q 008442          396 LSNINLKATYEDLRRFF------------SDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKL  462 (565)
Q Consensus       396 V~nl~~~~~~~~l~~~f------------~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l  462 (565)
                      +.|||..+++++|++.|            ++||.|.+|.|+.++ +|+++|||||+|.++++|.+|+. |||..++|++|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            67788888888877766            999999999999986 68999999999999999999998 89999999999


Q ss_pred             EEeec
Q 008442          463 SIARS  467 (565)
Q Consensus       463 ~v~~a  467 (565)
                      .|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99886

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.31  E-value=1.1e-10  Score=108.58  Aligned_cols=197  Identities=14%  Similarity=-0.005  Sum_probs=117.8

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~  101 (565)
                      +...|..........|+++.+...|+++|...|.+...|...+..+.. .+..+.+...|++|+...|.....|......
T Consensus         4 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~-~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~   82 (217)
T 2pl2_A            4 AEQNPLRLGVQLYALGRYDAALTLFERALKENPQDPEALYWLARTQLK-LGLVNPALENGKTLVARTPRYLGGYMVLSEA   82 (217)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHhCCCcHHHHHHHHHH
Confidence            556888888888889999999999999999999999999998876554 4477889999999999999998888877654


Q ss_pred             HHHhc-----------CCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHH
Q 008442          102 LERSR-----------ASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDY  170 (565)
Q Consensus       102 le~~~-----------~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~  170 (565)
                      +.. .           +..+++...|++++...+.....+..+-..+..              ..+++.....|++++..
T Consensus        83 ~~~-~~~~~~~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~lg~~~~~--------------~g~~~~A~~~~~~al~~  147 (217)
T 2pl2_A           83 YVA-LYRQAEDRERGKGYLEQALSVLKDAERVNPRYAPLHLQRGLVYAL--------------LGERDKAEASLKQALAL  147 (217)
T ss_dssp             HHH-HHHTCSSHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH--------------TTCHHHHHHHHHHHHHH
T ss_pred             HHH-hhhhhhhhcccccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHH--------------cCChHHHHHHHHHHHhc
Confidence            433 3           455666666666665444433222222221110              01223333334433332


Q ss_pred             HHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHH
Q 008442          171 LSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRC  243 (565)
Q Consensus       171 l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~a  243 (565)
                             . ....++...+.+....+ +++.|...|++++...|++..+|..++.+....|+++.|...|+++
T Consensus       148 -------~-~~~~~~~~la~~~~~~g-~~~~A~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~  211 (217)
T 2pl2_A          148 -------E-DTPEIRSALAELYLSMG-RLDEALAQYAKALEQAPKDLDLRVRYASALLLKGKAEEAARAAALE  211 (217)
T ss_dssp             -------C-CCHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTC--------------
T ss_pred             -------c-cchHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence                   1 22334445555555555 6666666666666666666666666666666666666666666555

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.31  E-value=6e-10  Score=111.90  Aligned_cols=240  Identities=10%  Similarity=-0.015  Sum_probs=162.7

Q ss_pred             CCchhHHH-HHHHHHhcCCCCH----HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHH
Q 008442           37 GDPGRVQL-LYERAITDFPVSS----DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEE  111 (565)
Q Consensus        37 ~~~~~~~~-lyERal~~~p~~~----~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~  111 (565)
                      ++++.+.. .|++++...|.++    ..|...+..... .++.+.+..+|++++...|....+|......+ ...+..++
T Consensus        39 ~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~-~~~g~~~~  116 (368)
T 1fch_A           39 SDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQ-EGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQ-AENEQELL  116 (368)
T ss_dssp             -------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHH-TTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHH-HHTTCHHH
T ss_pred             HHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHH-CCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH-HHCcCHHH
Confidence            45667777 8999998887764    457766665544 34778899999999999999888888776633 44688899


Q ss_pred             HHHHHHHHHhcccccHHHHHHHHHHHHH---------HHHHHhh-ccccchh------------------hhhHHHHHHH
Q 008442          112 ISTVFEKSLLCAFSTFEEYLDLFLTRID---------GLRRRIL-FSGEVEG------------------VLDYSLIRET  163 (565)
Q Consensus       112 ~~~if~ral~~~~~~~~~~~~~~~~~~~---------~~~r~~~-~~~~~e~------------------~~~~~~~~~~  163 (565)
                      +...|++++...+.....+..+-..+..         ++.+-.. .......                  ..........
T Consensus       117 A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  196 (368)
T 1fch_A          117 AISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSL  196 (368)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHhhhhcccHHHHHHHHHhhccc
Confidence            9999999997655433333322222111         1111111 1110000                  0111113355


Q ss_pred             HHHHHHHHHhhhcCCch--hHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHH
Q 008442          164 FQRASDYLSEQMKNTDG--LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYK  241 (565)
Q Consensus       164 ~~~a~~~l~~~~~~~~~--~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~  241 (565)
                      +.+|+.++...+...+.  ...++...+.+....+ +++.|..+|++++...|+...+|...+......|+++.|..+|+
T Consensus       197 ~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  275 (368)
T 1fch_A          197 FLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSG-EYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYR  275 (368)
T ss_dssp             HHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            67777777666654444  4667778888888888 99999999999999999999999999999999999999999999


Q ss_pred             HHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhh
Q 008442          242 RCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTP  282 (565)
Q Consensus       242 ~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~  282 (565)
                      +++..  . +....++..........|+.+.+...+.+++.
T Consensus       276 ~al~~--~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  313 (368)
T 1fch_A          276 RALEL--Q-PGYIRSRYNLGISCINLGAHREAVEHFLEALN  313 (368)
T ss_dssp             HHHHH--C-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHh--C-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            99873  2 23345666666777778998888877777653

>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=99.30  E-value=4.6e-12  Score=123.92  Aligned_cols=82  Identities=11%  Similarity=0.208  Sum_probs=71.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEe
Q 008442          386 KGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIA  465 (565)
Q Consensus       386 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~  465 (565)
                      ....+.++|||+|||+++++++|+.+|+.||.|.+|.|+.++ .+ ++|||||+|.++++|..|+.+++..+.|++|.|.
T Consensus        36 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~-~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~  113 (292)
T 2ghp_A           36 TRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL-KK-NFRFARIEFARYDGALAAITKTHKVVGQNEIIVS  113 (292)
T ss_dssp             ------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECT-TS-SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CC-CcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEE
Confidence            345678999999999999999999999999999999999986 33 5899999999999999999999999999999998


Q ss_pred             ecCC
Q 008442          466 RSNP  469 (565)
Q Consensus       466 ~a~~  469 (565)
                      .+..
T Consensus       114 ~~~~  117 (292)
T 2ghp_A          114 HLTE  117 (292)
T ss_dssp             ECCS
T ss_pred             ECCC
Confidence            8754

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.30  E-value=1.2e-09  Score=112.87  Aligned_cols=270  Identities=11%  Similarity=-0.007  Sum_probs=185.2

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...|+.++...|.    +...|...+......|+++.+..+|++++...|.+...|..++...... +..+.+..+|+
T Consensus        44 ~A~~~~~~~l~~~p~----~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~-g~~~~A~~~~~  118 (450)
T 2y4t_A           44 DALSQFHAAVDGDPD----NYIAYYRRATVFLAMGKSKAALPDLTKVIQLKMDFTAARLQRGHLLLKQ-GKLDEAEDDFK  118 (450)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCc----cHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHc-CCHHHHHHHHH
Confidence            467889999988776    6888999999888899999999999999999999999999988765544 47788999999


Q ss_pred             HHHHcCCCCH---HHHHHHHHH-----------HHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHH---------
Q 008442           83 RATKNCPWVG---ELWVRSLLS-----------LERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRID---------  139 (565)
Q Consensus        83 rAl~~~p~~~---~lW~~yi~~-----------le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~---------  139 (565)
                      +++...|...   ..|...+..           .....+..+++..+|++++...+.....+..+-..+..         
T Consensus       119 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  198 (450)
T 2y4t_A          119 KVLKSNPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVCVWDAELRELRAECFIKEGEPRKAIS  198 (450)
T ss_dssp             HHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCGGGGHH
T ss_pred             HHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHCCCHHHHHH
Confidence            9999889877   777654321           12335788999999999987554433333322222211         


Q ss_pred             HHHHHh-hccccchhhhhH---HHHHHHHHHHHHHHHhhhcCCchhHHHHHHH------------HHHHHHcCCChHHHH
Q 008442          140 GLRRRI-LFSGEVEGVLDY---SLIRETFQRASDYLSEQMKNTDGLLRLYAYW------------AHLEQSMGKDMVSAR  203 (565)
Q Consensus       140 ~~~r~~-~~~~~~e~~~~~---~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~------------a~~e~~~~~~~~~ar  203 (565)
                      .+.+.. ........+...   .....-+++|+.++...+...+.....+..+            +......+ +++.|.
T Consensus       199 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g-~~~~A~  277 (450)
T 2y4t_A          199 DLKAASKLKNDNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQDHKRCFAHYKQVKKLNKLIESAEELIRDG-RYTDAT  277 (450)
T ss_dssp             HHHHHHHHHCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHT-CHHHHH
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHHcC-CHHHHH
Confidence            000000 000111100000   0011223455555555444333333334333            66677778 999999


Q ss_pred             HHHHHHHHHccchH----HHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHH
Q 008442          204 GVWERLLKISGAML----EAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQK  279 (565)
Q Consensus       204 ~i~e~~l~~~~~~~----~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k  279 (565)
                      .+|++++...|++.    .+|...+......|+++.|..+|++++..   .+....+|......-...|+.+.+...+++
T Consensus       278 ~~~~~~l~~~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~---~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~  354 (450)
T 2y4t_A          278 SKYESVMKTEPSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQM---EPDNVNALKDRAEAYLIEEMYDEAIQDYET  354 (450)
T ss_dssp             HHHHHHHHHCCSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHhcCCcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh---CcccHHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence            99999999988764    47777888888999999999999999873   223446777777777888999988888887


Q ss_pred             Hh
Q 008442          280 VT  281 (565)
Q Consensus       280 ~~  281 (565)
                      ++
T Consensus       355 al  356 (450)
T 2y4t_A          355 AQ  356 (450)
T ss_dssp             HH
T ss_pred             HH
Confidence            75

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.29  E-value=7.4e-12  Score=120.12  Aligned_cols=79  Identities=25%  Similarity=0.423  Sum_probs=71.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEE
Q 008442          386 KGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSI  464 (565)
Q Consensus       386 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v  464 (565)
                      ....+.++|||+|||+++++++|+.+|+.||.|.+|.+..+      +|||||+|.+.++|..|+. +++..|.|++|.|
T Consensus        17 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v   90 (261)
T 3sde_A           17 KTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRI   90 (261)
T ss_dssp             CSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEe
Confidence            34466789999999999999999999999999999998643      6999999999999999998 8999999999999


Q ss_pred             eecCCC
Q 008442          465 ARSNPK  470 (565)
Q Consensus       465 ~~a~~~  470 (565)
                      .++.+.
T Consensus        91 ~~a~~~   96 (261)
T 3sde_A           91 RFATHG   96 (261)
T ss_dssp             EECCCS
T ss_pred             eecccC
Confidence            998764

>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=99.28  E-value=8.4e-12  Score=119.74  Aligned_cols=82  Identities=17%  Similarity=0.279  Sum_probs=74.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-c-CCcccC---CeEEEE
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-K-NKQMFL---GKKLSI  464 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~-~~~~~~---g~~l~v  464 (565)
                      ..++|||+|||+.+++++|+.+|+.||.|.+|.++.+. +|.++|||||+|.+.++|.+|+. + ++..+.   |++|.|
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            46799999999999999999999999999999999995 99999999999999999999998 7 555554   999999


Q ss_pred             eecCCCCC
Q 008442          465 ARSNPKQR  472 (565)
Q Consensus       465 ~~a~~~~~  472 (565)
                      .++.+...
T Consensus       174 ~~~~~~~~  181 (261)
T 3sde_A          174 EPMEQFDD  181 (261)
T ss_dssp             EECCCEES
T ss_pred             eeccccCc
Confidence            99987543

>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=99.27  E-value=4.5e-12  Score=116.52  Aligned_cols=76  Identities=11%  Similarity=0.172  Sum_probs=67.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCe--eEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCe----EE
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGV--SSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGK----KL  462 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i--~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~----~l  462 (565)
                      ..++|||+|||+++++++|+++|++||.|  .+++++.++  |.++|||||+|.+.++|..||. ||+..|.|+    ++
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~  199 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY  199 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCE
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcce
Confidence            46799999999999999999999999999  899998874  5567999999999999999998 899999887    56


Q ss_pred             EEeec
Q 008442          463 SIARS  467 (565)
Q Consensus       463 ~v~~a  467 (565)
                      .|.+|
T Consensus       200 ~vk~~  204 (205)
T 3tyt_A          200 TLKLC  204 (205)
T ss_dssp             ECEEE
T ss_pred             EEEec
Confidence            66654

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.26  E-value=7.4e-11  Score=94.11  Aligned_cols=66  Identities=20%  Similarity=0.215  Sum_probs=57.5

Q ss_pred             CCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecCCCCC
Q 008442          401 LKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQR  472 (565)
Q Consensus       401 ~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~~~~~  472 (565)
                      .++++++|+.+|++||.|.+|.|+     ++++|||||+|.+.++|..|+.. ...+.|++|.|.++.++..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~-~~~~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQN-EVGLVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHT-CCBCSSSBCEEECSSCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHh-cCCCCCCeEEEEEccCCCC
Confidence            468999999999999999999987     46789999999999999999984 3336799999999987654

>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=99.26  E-value=8.5e-12  Score=101.03  Aligned_cols=81  Identities=21%  Similarity=0.164  Sum_probs=69.0

Q ss_pred             CCCeEEEcCC--CCCCC--------HHHHHHHhccCCCeeEEEEeecCCC--CCcceEEEEEecCHHHHHHHHH-cCCcc
Q 008442          390 DECTAFLSNI--NLKAT--------YEDLRRFFSDVGGVSSIRILHDKFT--GKSRGLAYVDFIDDEHLAAAVA-KNKQM  456 (565)
Q Consensus       390 ~~~~l~V~nl--~~~~~--------~~~l~~~f~~~G~i~~~~~~~~~~~--g~~~g~afv~f~~~~~a~~a~~-~~~~~  456 (565)
                      +.+.|.+.|+  |.++.        +++|++.|++||.|.+|.|+.++.+  +.++|||||+|.++++|.+|+. |||..
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            3568899998  33443        3689999999999999999988643  3689999999999999999997 89999


Q ss_pred             cCCeEEEEeecCCC
Q 008442          457 FLGKKLSIARSNPK  470 (565)
Q Consensus       457 ~~g~~l~v~~a~~~  470 (565)
                      ++||+|.|.++.+.
T Consensus        84 f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           84 FANRVVVTKYCDPD   97 (105)
T ss_dssp             ETTEECEEEEECHH
T ss_pred             eCCCEEEEEEeCHH
Confidence            99999999998653

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.25  E-value=7.6e-09  Score=97.78  Aligned_cols=227  Identities=6%  Similarity=-0.088  Sum_probs=174.2

Q ss_pred             HhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCC-------HH
Q 008442           21 EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV-------GE   93 (565)
Q Consensus        21 ~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~-------~~   93 (565)
                      .....|..........|+.+.+..+|++++... .+..+|...+..... .++.+.+...|++++...|..       ..
T Consensus         3 ~~a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~~~~~-~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~   80 (258)
T 3uq3_A            3 SMADKEKAEGNKFYKARQFDEAIEHYNKAWELH-KDITYLNNRAAAEYE-KGEYETAISTLNDAVEQGREMRADYKVISK   80 (258)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-CCTHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHTTCCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhh-ccHHHHHHHHHHHHH-cccHHHHHHHHHHHHHhCcccccchHHHHH
Confidence            356788888888889999999999999999999 889999888875554 447888999999999977654       46


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHh
Q 008442           94 LWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSE  173 (565)
Q Consensus        94 lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~  173 (565)
                      +|......+ ...+..+++...|++++...+.. .    ++                        .....+++++..+..
T Consensus        81 ~~~~l~~~~-~~~~~~~~A~~~~~~a~~~~~~~-~----~~------------------------~~~~~~~~a~~~~~~  130 (258)
T 3uq3_A           81 SFARIGNAY-HKLGDLKKTIEYYQKSLTEHRTA-D----IL------------------------TKLRNAEKELKKAEA  130 (258)
T ss_dssp             HHHHHHHHH-HHTTCHHHHHHHHHHHHHHCCCH-H----HH------------------------HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHH-HHcccHHHHHHHHHHHHhcCchh-H----HH------------------------HHHhHHHHHHHHHHH
Confidence            666655533 44688999999999999754431 0    00                        111234444555545


Q ss_pred             hhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCc
Q 008442          174 QMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGS  253 (565)
Q Consensus       174 ~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~  253 (565)
                      .+...+....++...+.+....+ +++.|..+|++++...|....+|...+......|+++.|..+|++++..  . +..
T Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~-~~~  206 (258)
T 3uq3_A          131 EAYVNPEKAEEARLEGKEYFTKS-DWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEK--D-PNF  206 (258)
T ss_dssp             HHHCCHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--C-TTC
T ss_pred             HHHcCcchHHHHHHHHHHHHHhc-CHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh--C-HHH
Confidence            44445556677888888888888 9999999999999999999999999999999999999999999999973  2 233


Q ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHhhH
Q 008442          254 EDICHAWLRFEREYGTLEDFDHSVQKVTPR  283 (565)
Q Consensus       254 ~~i~~~~~~fE~~~G~~~~~~~~~~k~~~~  283 (565)
                      ...|......-...|+.+.+...+.+++..
T Consensus       207 ~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~  236 (258)
T 3uq3_A          207 VRAYIRKATAQIAVKEYASALETLDAARTK  236 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHh
Confidence            466666666777789988888777776544

>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=99.25  E-value=1.3e-11  Score=110.33  Aligned_cols=76  Identities=24%  Similarity=0.409  Sum_probs=67.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccC----C-------CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCccc
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDV----G-------GVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMF  457 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~----G-------~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~  457 (565)
                      ++.++|||+|||+++++++|+++|+.|    |       .|.++.+.      .++|||||+|.++++|..|+.+++..+
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~~~~~~~~   75 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAMAFDGIIF   75 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHGGGTTCEE
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHHHhCCcEe
Confidence            456899999999999999999999999    6       66776654      447999999999999999998899999


Q ss_pred             CCeEEEEeecCCC
Q 008442          458 LGKKLSIARSNPK  470 (565)
Q Consensus       458 ~g~~l~v~~a~~~  470 (565)
                      .|++|.|..+.+.
T Consensus        76 ~g~~i~v~~~~~~   88 (172)
T 2g4b_A           76 QGQSLKIRRPHDY   88 (172)
T ss_dssp             TTEECEEECCSSC
T ss_pred             cCceeeecCCccc
Confidence            9999999987654

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=99.25  E-value=2e-09  Score=101.82  Aligned_cols=203  Identities=12%  Similarity=0.027  Sum_probs=148.7

Q ss_pred             ChHh-HHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHH
Q 008442           19 DSEK-FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVR   97 (565)
Q Consensus        19 ~~~~-~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~   97 (565)
                      ++.. ...|...+......|+++.+..+|++++...|.+..+|..++..... .++.+.+..+|++++...|....+|..
T Consensus        32 ~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~-~~~~~~A~~~~~~a~~~~~~~~~~~~~  110 (252)
T 2ho1_A           32 GRDEARDAYIQLGLGYLQRGNTEQAKVPLRKALEIDPSSADAHAALAVVFQT-EMEPKLADEEYRKALASDSRNARVLNN  110 (252)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCTGGGHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCChHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHHCcCcHHHHHH
Confidence            4544 67899999988899999999999999999999999999988876554 447788999999999999999899888


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHh--cccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhh
Q 008442           98 SLLSLERSRASEEEISTVFEKSLL--CAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQM  175 (565)
Q Consensus        98 yi~~le~~~~~~~~~~~if~ral~--~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~  175 (565)
                      +...+ ...+..+++...|++++.  ..+.....+..+-..+..        .      .+++.+...|.+++..     
T Consensus       111 la~~~-~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~--------~------g~~~~A~~~~~~~~~~-----  170 (252)
T 2ho1_A          111 YGGFL-YEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQ--------M------KKPAQAKEYFEKSLRL-----  170 (252)
T ss_dssp             HHHHH-HHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHH--------T------TCHHHHHHHHHHHHHH-----
T ss_pred             HHHHH-HHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHH--------c------CCHHHHHHHHHHHHhc-----
Confidence            77644 447889999999999988  333222222222111110        0      1233334444444332     


Q ss_pred             cCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          176 KNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       176 ~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                        .+.....+..++.++...+ +++.|..+|++++...|.....|...+.+....|+++.|..+|++++.
T Consensus       171 --~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~  237 (252)
T 2ho1_A          171 --NRNQPSVALEMADLLYKER-EYVPARQYYDLFAQGGGQNARSLLLGIRLAKVFEDRDTAASYGLQLKR  237 (252)
T ss_dssp             --CSCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             --CcccHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence              2333456667777777777 888888888888888887788888888888888888888888888876

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.25  E-value=2.8e-09  Score=104.79  Aligned_cols=230  Identities=10%  Similarity=-0.002  Sum_probs=160.7

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...|+.++...|.    +...|...+......|+.+.+...|++++...|.+...|...+..... .++.+.+...|+
T Consensus        39 ~A~~~~~~~~~~~~~----~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~-~~~~~~A~~~~~  113 (327)
T 3cv0_A           39 EAALAFEAVCQAAPE----REEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTN-EHNANAALASLR  113 (327)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC----CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcCCHHHHHHHHHHHHH-cCCHHHHHHHHH
Confidence            366788888888876    778899888888889999999999999999999999999988876554 447788999999


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHH
Q 008442           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRE  162 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~  162 (565)
                      +++...|....+|...+..+..                    . ..   ..+.      ......           ....
T Consensus       114 ~~~~~~~~~~~~~~~~~~~~~~--------------------~-~~---~~~~------~~~~~~-----------~~~~  152 (327)
T 3cv0_A          114 AWLLSQPQYEQLGSVNLQADVD--------------------I-DD---LNVQ------SEDFFF-----------AAPN  152 (327)
T ss_dssp             HHHHTSTTTTTC--------------------------------------------------CCT-----------TSHH
T ss_pred             HHHHhCCccHHHHHHHhHHHHH--------------------H-HH---HHHH------HHhHHH-----------HHcc
Confidence            9999888776666554221100                    0 00   0000      000000           0012


Q ss_pred             HHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHH
Q 008442          163 TFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKR  242 (565)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~  242 (565)
                      .+.+|+.++...+...+....++...+.+....+ +++.|..+|++++...|+...+|...+......|+++.|..+|++
T Consensus       153 ~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~  231 (327)
T 3cv0_A          153 EYRECRTLLHAALEMNPNDAQLHASLGVLYNLSN-NYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNR  231 (327)
T ss_dssp             HHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhc-cHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            2333333333333323334567777788888888 999999999999999999999999999999999999999999999


Q ss_pred             HHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhh
Q 008442          243 CYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTP  282 (565)
Q Consensus       243 al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~  282 (565)
                      ++..  . +....+|..........|+.+.+...+++++.
T Consensus       232 a~~~--~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~  268 (327)
T 3cv0_A          232 ALDI--N-PGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIY  268 (327)
T ss_dssp             HHHH--C-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHc--C-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            9873  1 23345666666677778998888877776653

>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=99.24  E-value=2.3e-11  Score=118.20  Aligned_cols=76  Identities=17%  Similarity=0.277  Sum_probs=70.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccC-CeEEEEe
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFL-GKKLSIA  465 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~-g~~l~v~  465 (565)
                      ....++|||+|||.++++++|+++|+.||.|.+|+++.++     +|||||+|.+.++|..|+. +||..|. |++|.|.
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  278 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS  278 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEE
Confidence            3457899999999999999999999999999999998654     5899999999999999998 8999999 9999999


Q ss_pred             ecC
Q 008442          466 RSN  468 (565)
Q Consensus       466 ~a~  468 (565)
                      +++
T Consensus       279 ~ak  281 (282)
T 3pgw_A          279 FAK  281 (282)
T ss_pred             Eec
Confidence            975

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.24  E-value=5.2e-10  Score=105.08  Aligned_cols=215  Identities=11%  Similarity=0.026  Sum_probs=145.3

Q ss_pred             HHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Q 008442           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLE  103 (565)
Q Consensus        24 ~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le  103 (565)
                      ..|..........|+++.+..+|++++...|.+..+|...+..... .+..+.+..+|++++...|....+|......+ 
T Consensus        24 ~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~-~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~-  101 (243)
T 2q7f_A           24 MTGGQQMGRGSEFGDYEKAAEAFTKAIEENKEDAIPYINFANLLSS-VNELERALAFYDKALELDSSAATAYYGAGNVY-  101 (243)
T ss_dssp             ------------------CCTTHHHHHTTCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHhhCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHcCCcchHHHHHHHHHH-
Confidence            4566666666677899999999999999999999999998876554 44778899999999999999888888877634 


Q ss_pred             HhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHH
Q 008442          104 RSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLR  183 (565)
Q Consensus       104 ~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~  183 (565)
                      ...+..+.+...|++++...+.....+..+-..+..        .      .++..+...|.+++..       .+....
T Consensus       102 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~--------~------~~~~~A~~~~~~~~~~-------~~~~~~  160 (243)
T 2q7f_A          102 VVKEMYKEAKDMFEKALRAGMENGDLFYMLGTVLVK--------L------EQPKLALPYLQRAVEL-------NENDTE  160 (243)
T ss_dssp             HHTTCHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHH--------T------SCHHHHHHHHHHHHHH-------CTTCHH
T ss_pred             HHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH--------h------ccHHHHHHHHHHHHHh-------CCccHH
Confidence            447889999999999998655443332222222110        0      1334444455544443       333455


Q ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHH
Q 008442          184 LYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRF  263 (565)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~f  263 (565)
                      ++..++.+....+ +++.|..+|++++...|....+|...+.+....|+++.|..+|++++..  . +....++..+..+
T Consensus       161 ~~~~l~~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--~-p~~~~~~~~~~~l  236 (243)
T 2q7f_A          161 ARFQFGMCLANEG-MLDEALSQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKAIDI--Q-PDHMLALHAKKLL  236 (243)
T ss_dssp             HHHHHHHHHHHHT-CCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHH--C-TTCHHHHHHHTC-
T ss_pred             HHHHHHHHHHHcC-CHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHcc--C-cchHHHHHHHHHH
Confidence            7777888888888 9999999999999999999999999999999999999999999999873  2 2334455444444


Q ss_pred             HH
Q 008442          264 ER  265 (565)
Q Consensus       264 E~  265 (565)
                      +.
T Consensus       237 ~~  238 (243)
T 2q7f_A          237 GH  238 (243)
T ss_dssp             --
T ss_pred             Hh
Confidence            43

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.23  E-value=1.3e-11  Score=113.23  Aligned_cols=77  Identities=23%  Similarity=0.300  Sum_probs=70.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccC-CeEEEEe
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVG-GVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFL-GKKLSIA  465 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~-g~~l~v~  465 (565)
                      ...++|||+|||..+++++|+++|+.|| .|.+++++.+     .+|||||+|.+.++|..|+. ++|..++ |++|.|.
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  192 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  192 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEE
Confidence            4578999999999999999999999999 9999999653     26899999999999999998 8999999 9999999


Q ss_pred             ecCCC
Q 008442          466 RSNPK  470 (565)
Q Consensus       466 ~a~~~  470 (565)
                      +++|+
T Consensus       193 ~a~~~  197 (198)
T 1qm9_A          193 FSKST  197 (198)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            99875

>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=99.23  E-value=2.4e-11  Score=114.17  Aligned_cols=77  Identities=23%  Similarity=0.300  Sum_probs=70.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccC-CeEEEEe
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVG-GVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFL-GKKLSIA  465 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~-g~~l~v~  465 (565)
                      ...++|||+|||.++++++|+++|+.|| .|..++++.+     ++|||||+|.+.++|.+|+. +++..+. |++|.|.
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~  223 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  223 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEE
Confidence            3468999999999999999999999999 9999999653     36899999999999999998 8999999 9999999


Q ss_pred             ecCCC
Q 008442          466 RSNPK  470 (565)
Q Consensus       466 ~a~~~  470 (565)
                      +++|+
T Consensus       224 ~a~~~  228 (229)
T 2adc_A          224 FSKST  228 (229)
T ss_dssp             ECSSC
T ss_pred             EecCC
Confidence            99875

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.23  E-value=4.8e-09  Score=96.92  Aligned_cols=202  Identities=12%  Similarity=0.048  Sum_probs=148.3

Q ss_pred             hHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHH
Q 008442           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSL   99 (565)
Q Consensus        20 ~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi   99 (565)
                      +.+...|...+......|+++.+..+|++++...|.+..+|..++..... .++.+.+..+|++++...|....+|....
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~A~~~~~~a~~~~~~~~~~~~~l~   83 (225)
T 2vq2_A            5 NQVSNIKTQLAMEYMRGQDYRQATASIEDALKSDPKNELAWLVRAEIYQY-LKVNDKAQESFRQALSIKPDSAEINNNYG   83 (225)
T ss_dssp             CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCccchHHHHHHHHHHHH-cCChHHHHHHHHHHHHhCCCChHHHHHHH
Confidence            45778899999999999999999999999999999999999988875554 44778899999999999999999988877


Q ss_pred             HHHHHhc-CCHHHHHHHHHHHHhc--ccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhc
Q 008442          100 LSLERSR-ASEEEISTVFEKSLLC--AFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMK  176 (565)
Q Consensus       100 ~~le~~~-~~~~~~~~if~ral~~--~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~  176 (565)
                      . +.... +..+++...|++++..  .+.....+..+-..+..        .      .++..+...|.+++..      
T Consensus        84 ~-~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--------~------~~~~~A~~~~~~~~~~------  142 (225)
T 2vq2_A           84 W-FLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAK--------Q------GQFGLAEAYLKRSLAA------  142 (225)
T ss_dssp             H-HHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHH--------T------TCHHHHHHHHHHHHHH------
T ss_pred             H-HHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHH--------c------CCHHHHHHHHHHHHHh------
Confidence            6 44457 8899999999999982  22222222222111110        0      1333344444444332      


Q ss_pred             CCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHcc-chHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          177 NTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG-AMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       177 ~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~-~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                       .+.....+...+.+....+ +++.|..+|++++...| .....|...+.++...|+.+.+..+++.++.
T Consensus       143 -~~~~~~~~~~la~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  210 (225)
T 2vq2_A          143 -QPQFPPAFKELARTKMLAG-QLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQA  210 (225)
T ss_dssp             -STTCHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -CCCCchHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence             2333456666777777777 88888888888888887 7777787777788888888888888888765

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.22  E-value=2.9e-11  Score=99.78  Aligned_cols=80  Identities=16%  Similarity=0.196  Sum_probs=69.3

Q ss_pred             CCCeEEEcCCCC--CC---CHHHHHHHhccCCCeeEEEEeecCC----CCCcceEEEEEecCHHHHHHHHH-cCCcccCC
Q 008442          390 DECTAFLSNINL--KA---TYEDLRRFFSDVGGVSSIRILHDKF----TGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLG  459 (565)
Q Consensus       390 ~~~~l~V~nl~~--~~---~~~~l~~~f~~~G~i~~~~~~~~~~----~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g  459 (565)
                      ..++|++.|+-.  ++   -+++|++.|++||.|.+|.|+.++.    ++.++||+||+|.++++|.+|+. |||..++|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            357899999832  22   3689999999999999999998863    45788999999999999999998 89999999


Q ss_pred             eEEEEeecCC
Q 008442          460 KKLSIARSNP  469 (565)
Q Consensus       460 ~~l~v~~a~~  469 (565)
                      |+|.|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999865

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.21  E-value=3.6e-09  Score=111.99  Aligned_cols=270  Identities=9%  Similarity=-0.036  Sum_probs=161.1

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...|+.+|...|.    +...|...+......|+++.+...|++++...|.+...|..++......+ ..+.+...|+
T Consensus        43 ~A~~~~~~al~~~p~----~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g-~~~~A~~~~~  117 (537)
T 3fp2_A           43 EAIKYYQYAIELDPN----EPVFYSNISACYISTGDLEKVIEFTTKALEIKPDHSKALLRRASANESLG-NFTDAMFDLS  117 (537)
T ss_dssp             -CHHHHHHHHHHCTT----CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHT-CHHHHHHHHH
T ss_pred             HHHHHHHHHHhhCCC----CcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHcC-CHHHHHHHHH
Confidence            467788999988876    77889888888888899999999999999999999999988887655433 5566666664


Q ss_pred             HHHHcCCCCHHHHH------------------------------------------------------------------
Q 008442           83 RATKNCPWVGELWV------------------------------------------------------------------   96 (565)
Q Consensus        83 rAl~~~p~~~~lW~------------------------------------------------------------------   96 (565)
                       ++...|.....|.                                                                  
T Consensus       118 -~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  196 (537)
T 3fp2_A          118 -VLSLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSSVNTSSNYDTAYALL  196 (537)
T ss_dssp             -HHC-----------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHHHTSCCCCSSCSSHHHH
T ss_pred             -HHhcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHHHHHhhccccccHHHHH
Confidence             5544443222111                                                                  


Q ss_pred             --HHHHH-------HHHhcCCHHHHHHHHHHHHhcccccHHHHH---HHHHHHHHH-------------HHHHhhccccc
Q 008442           97 --RSLLS-------LERSRASEEEISTVFEKSLLCAFSTFEEYL---DLFLTRIDG-------------LRRRILFSGEV  151 (565)
Q Consensus        97 --~yi~~-------le~~~~~~~~~~~if~ral~~~~~~~~~~~---~~~~~~~~~-------------~~r~~~~~~~~  151 (565)
                        .....       +....+.++++..+|++++...+.....+.   ..+......             +.+........
T Consensus       197 ~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~~~~  276 (537)
T 3fp2_A          197 SDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSANTVDDPLRENAALALCYTGIFHFLKNNLLDAQVLLQESINLHPTP  276 (537)
T ss_dssp             HHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCH
T ss_pred             HHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHCCCcchhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCCc
Confidence              00000       000012456778888888875544322111   111111100             00000000000


Q ss_pred             hhhhhHHHH---HHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHH
Q 008442          152 EGVLDYSLI---RETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEI  228 (565)
Q Consensus       152 e~~~~~~~~---~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~  228 (565)
                      ..+.....+   ...+..|+.++...+...+....++...+.+....+ +++.|...|++++...|....+|...+....
T Consensus       277 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~  355 (537)
T 3fp2_A          277 NSYIFLALTLADKENSQEFFKFFQKAVDLNPEYPPTYYHRGQMYFILQ-DYKNAKEDFQKAQSLNPENVYPYIQLACLLY  355 (537)
T ss_dssp             HHHHHHHHHTCCSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCSHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhcCHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            000000000   011234444444444434445566777777887777 8888999999998888888888888888888


Q ss_pred             HcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhh
Q 008442          229 ELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTP  282 (565)
Q Consensus       229 ~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~  282 (565)
                      ..|+++.|..+|++++.. .  +....+|..+.......|+.+.+...+.+++.
T Consensus       356 ~~g~~~~A~~~~~~~~~~-~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~  406 (537)
T 3fp2_A          356 KQGKFTESEAFFNETKLK-F--PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKR  406 (537)
T ss_dssp             HTTCHHHHHHHHHHHHHH-C--TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHh-C--CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            889999999999988873 1  22335666666777777888877777776643

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.21  E-value=3.1e-11  Score=110.63  Aligned_cols=76  Identities=25%  Similarity=0.425  Sum_probs=66.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccC----C-------CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDV----G-------GVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFL  458 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~----G-------~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~  458 (565)
                      ..++|||+|||+++++++|+++|+.|    |       .|.++.+      +.++|||||+|.++++|..|+.+++..|.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al~l~g~~~~   76 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAMAFDGIIFQ   76 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHGGGTTEEET
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHHHhcCCEEc
Confidence            46899999999999999999999999    5       5555554      45679999999999999999988999999


Q ss_pred             CeEEEEeecCCCC
Q 008442          459 GKKLSIARSNPKQ  471 (565)
Q Consensus       459 g~~l~v~~a~~~~  471 (565)
                      |++|.|.++.+..
T Consensus        77 g~~i~v~~~~~~~   89 (198)
T 2yh0_A           77 GQSLKIRRPHDYQ   89 (198)
T ss_dssp             TEEEEEECCCCCC
T ss_pred             CceEEEeCCCCCC
Confidence            9999999887653

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=99.19  E-value=3.5e-09  Score=107.22  Aligned_cols=203  Identities=9%  Similarity=0.007  Sum_probs=155.8

Q ss_pred             ChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHH
Q 008442           19 DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRS   98 (565)
Q Consensus        19 ~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~y   98 (565)
                      ++....+|..........|+.+++..+|+++|..+|.+..+|......+...+++.+.+...|++||...|.+..+|...
T Consensus        93 ~p~~~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P~~~~a~~~~  172 (382)
T 2h6f_A           93 SDKFRDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHR  172 (382)
T ss_dssp             CHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             ChhhHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCCCHHHHHHH
Confidence            56678899999998888999999999999999999999999999888666555448889999999999999999999887


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCC
Q 008442           99 LLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNT  178 (565)
Q Consensus        99 i~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~  178 (565)
                      ...+.. .+..+++...|++||...+..+..|..+-..+..                     ...+++|+.++...+...
T Consensus       173 g~~~~~-~g~~~eAl~~~~kal~ldP~~~~a~~~lg~~~~~---------------------~g~~~eAl~~~~~al~l~  230 (382)
T 2h6f_A          173 RVLVEW-LRDPSQELEFIADILNQDAKNYHAWQHRQWVIQE---------------------FKLWDNELQYVDQLLKED  230 (382)
T ss_dssp             HHHHHH-HTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHH---------------------HTCCTTHHHHHHHHHHHC
T ss_pred             HHHHHH-ccCHHHHHHHHHHHHHhCccCHHHHHHHHHHHHH---------------------cCChHHHHHHHHHHHHhC
Confidence            764444 6788899999999998776655444333322211                     011233444444444434


Q ss_pred             chhHHHHHHHHHHHHHcCCChHHH-----HHHHHHHHHHccchHHHHHHHHHHHHHcC--ChHHHHHHHHHH
Q 008442          179 DGLLRLYAYWAHLEQSMGKDMVSA-----RGVWERLLKISGAMLEAWQSYISMEIELD--HINEARSIYKRC  243 (565)
Q Consensus       179 ~~~~~l~~~~a~~e~~~~~~~~~a-----r~i~e~~l~~~~~~~~lw~~yi~~e~~~~--~~~~aR~i~~~a  243 (565)
                      +.....|...+.+....++..+.|     ...|+++|...|++...|.....+....|  +++.|.+.+.++
T Consensus       231 P~~~~a~~~lg~~l~~l~~~~~eA~~~~el~~~~~Al~l~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~  302 (382)
T 2h6f_A          231 VRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQDRGLSKYPNLLNQLLDL  302 (382)
T ss_dssp             TTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHccCccchHHHHHHHHHh
Confidence            555677887787777745354667     48899999999999999999998887777  688998888877

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.17  E-value=6.7e-09  Score=93.30  Aligned_cols=167  Identities=14%  Similarity=0.086  Sum_probs=132.8

Q ss_pred             HhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHH
Q 008442           21 EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (565)
Q Consensus        21 ~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~  100 (565)
                      ++..+|..........|+.+.+...|+++|..+|.+...|...+..... .+..+.+...+++++...|....+|.....
T Consensus         3 e~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~   81 (184)
T 3vtx_A            3 ETTTIYMDIGDKKRTKGDFDGAIRAYKKVLKADPNNVETLLKLGKTYMD-IGLPNDAIESLKKFVVLDTTSAEAYYILGS   81 (184)
T ss_dssp             -CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-CCCHHHHHHHHHHHHhcCchhHHHHHHHHH
Confidence            3567888888888889999999999999999999999999998875544 447778999999999999998888877665


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCch
Q 008442          101 SLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG  180 (565)
Q Consensus       101 ~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~  180 (565)
                      .. ...+..+.+...+.+++...+.                                                       
T Consensus        82 ~~-~~~~~~~~a~~~~~~a~~~~~~-------------------------------------------------------  105 (184)
T 3vtx_A           82 AN-FMIDEKQAAIDALQRAIALNTV-------------------------------------------------------  105 (184)
T ss_dssp             HH-HHTTCHHHHHHHHHHHHHHCTT-------------------------------------------------------
T ss_pred             HH-HHcCCHHHHHHHHHHHHHhCcc-------------------------------------------------------
Confidence            33 3345566666666665542221                                                       


Q ss_pred             hHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       181 ~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ....+...+.+....+ ++++|...|+++++..|.+..+|...+......|+++.|...|++||.
T Consensus       106 ~~~~~~~lg~~~~~~g-~~~~A~~~~~~~l~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  169 (184)
T 3vtx_A          106 YADAYYKLGLVYDSMG-EHDKAIEAYEKTISIKPGFIRAYQSIGLAYEGKGLRDEAVKYFKKALE  169 (184)
T ss_dssp             CHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHhC-CchhHHHHHHHHHHhcchhhhHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            1223444555666777 999999999999999999999999999999999999999999999987

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.13  E-value=7.7e-09  Score=98.95  Aligned_cols=234  Identities=7%  Similarity=0.003  Sum_probs=167.0

Q ss_pred             HHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCC----HHHHHHH
Q 008442           23 FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV----GELWVRS   98 (565)
Q Consensus        23 ~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~----~~lW~~y   98 (565)
                      .+.+..++......|+++.+..+|++++...|.+..+|...+.... ..++.+.+...|++++. .|..    ...|...
T Consensus         3 ~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~-~~~~~~~A~~~~~~a~~-~~~~~~~~~~~~~~l   80 (272)
T 3u4t_A            3 DDVEFRYADFLFKNNNYAEAIEVFNKLEAKKYNSPYIYNRRAVCYY-ELAKYDLAQKDIETYFS-KVNATKAKSADFEYY   80 (272)
T ss_dssp             --CHHHHHHHHHTTTCHHHHHHHHHHHHHTTCCCSTTHHHHHHHHH-HTTCHHHHHHHHHHHHT-TSCTTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH-HHhhHHHHHHHHHHHHh-ccCchhHHHHHHHHH
Confidence            4567888888889999999999999999999999999998887544 45578889999999999 4433    3446665


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCC
Q 008442           99 LLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNT  178 (565)
Q Consensus        99 i~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~  178 (565)
                      .. +....+..+++...|++++...+.....+..+-..+.                     ...-+++|+.++...+...
T Consensus        81 g~-~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~---------------------~~~~~~~A~~~~~~al~~~  138 (272)
T 3u4t_A           81 GK-ILMKKGQDSLAIQQYQAAVDRDTTRLDMYGQIGSYFY---------------------NKGNFPLAIQYMEKQIRPT  138 (272)
T ss_dssp             HH-HHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHH---------------------HTTCHHHHHHHHGGGCCSS
T ss_pred             HH-HHHHcccHHHHHHHHHHHHhcCcccHHHHHHHHHHHH---------------------HccCHHHHHHHHHHHhhcC
Confidence            55 3344688999999999999865543333332222221                     1234666777777777665


Q ss_pred             chhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCC---hHHHHHHHHHHHhcccCCCC--c
Q 008442          179 DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDH---INEARSIYKRCYSKRFTGTG--S  253 (565)
Q Consensus       179 ~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~---~~~aR~i~~~al~~~~~~~~--~  253 (565)
                      +.....|...+......+ ++++|..+|+++++..|+....|...+......++   .+.|...|++++......+.  .
T Consensus       139 ~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~  217 (272)
T 3u4t_A          139 TTDPKVFYELGQAYYYNK-EYVKADSSFVKVLELKPNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYK  217 (272)
T ss_dssp             CCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGH
T ss_pred             CCcHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccch
Confidence            556667777773333445 89999999999999999998888888888877787   88899999999874211111  1


Q ss_pred             H---HHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          254 E---DICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       254 ~---~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      .   .++.....+-...|+.+.+...+++++
T Consensus       218 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al  248 (272)
T 3u4t_A          218 DELIEANEYIAYYYTINRDKVKADAAWKNIL  248 (272)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            1   233444445556788887777776654

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.13  E-value=2e-08  Score=96.09  Aligned_cols=217  Identities=11%  Similarity=0.008  Sum_probs=156.3

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (565)
                      +...|+.++...+..++.....|...+......|+.+.+...|++++...|.+..+|...+..... .+..+.+...|++
T Consensus        24 A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~-~~~~~~A~~~~~~  102 (275)
T 1xnf_A           24 ILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQ-AGNFDAAYEAFDS  102 (275)
T ss_dssp             HHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHH-ccCHHHHHHHHHH
Confidence            456677777765443456788899999999999999999999999999999999999998876554 4578889999999


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHH
Q 008442           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRET  163 (565)
Q Consensus        84 Al~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~  163 (565)
                      |+...|....+|......+ ...+..+++...|++++...+......+  +....  .. .          .++......
T Consensus       103 al~~~~~~~~~~~~la~~~-~~~g~~~~A~~~~~~a~~~~~~~~~~~~--~~~~~--~~-~----------~~~~~A~~~  166 (275)
T 1xnf_A          103 VLELDPTYNYAHLNRGIAL-YYGGRDKLAQDDLLAFYQDDPNDPFRSL--WLYLA--EQ-K----------LDEKQAKEV  166 (275)
T ss_dssp             HHHHCTTCTHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCHHHHH--HHHHH--HH-H----------HCHHHHHHH
T ss_pred             HHhcCccccHHHHHHHHHH-HHhccHHHHHHHHHHHHHhCCCChHHHH--HHHHH--HH-h----------cCHHHHHHH
Confidence            9999999888888877644 4478899999999999986554332111  11111  00 0          133334444


Q ss_pred             HHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHcc----chHHHHHHHHHHHHHcCChHHHHHH
Q 008442          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG----AMLEAWQSYISMEIELDHINEARSI  239 (565)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~----~~~~lw~~yi~~e~~~~~~~~aR~i  239 (565)
                      |.+++...       +.....+. .+.+....+ +.+.|...+++++...+    ....+|...+.+....|+++.|...
T Consensus       167 ~~~~~~~~-------~~~~~~~~-~~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  237 (275)
T 1xnf_A          167 LKQHFEKS-------DKEQWGWN-IVEFYLGNI-SEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATAL  237 (275)
T ss_dssp             HHHHHHHS-------CCCSTHHH-HHHHHTTSS-CHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHhcC-------CcchHHHH-HHHHHHHhc-CHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHH
Confidence            44443321       11112222 334444455 67889999999887654    3368999999999999999999999


Q ss_pred             HHHHHhc
Q 008442          240 YKRCYSK  246 (565)
Q Consensus       240 ~~~al~~  246 (565)
                      |++++..
T Consensus       238 ~~~al~~  244 (275)
T 1xnf_A          238 FKLAVAN  244 (275)
T ss_dssp             HHHHHTT
T ss_pred             HHHHHhC
Confidence            9999973

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.12  E-value=5.6e-09  Score=97.90  Aligned_cols=200  Identities=9%  Similarity=0.036  Sum_probs=148.7

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (565)
                      +...|+.++...|.    +...|...+......|+++.+..+|++++...|.+..+|..++..... .++.+.+..+|++
T Consensus        42 A~~~~~~~l~~~~~----~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~-~~~~~~A~~~~~~  116 (243)
T 2q7f_A           42 AAEAFTKAIEENKE----DAIPYINFANLLSSVNELERALAFYDKALELDSSAATAYYGAGNVYVV-KEMYKEAKDMFEK  116 (243)
T ss_dssp             CCTTHHHHHTTCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCcc----cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcchHHHHHHHHHHHH-hccHHHHHHHHHH
Confidence            55678888887776    678899999988899999999999999999999999999998876554 4477889999999


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHH
Q 008442           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRET  163 (565)
Q Consensus        84 Al~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~  163 (565)
                      ++...|....+|......+ ...+..+++...|++++...+.....+..+-..+...              .++..+...
T Consensus       117 ~~~~~~~~~~~~~~~a~~~-~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~--------------~~~~~A~~~  181 (243)
T 2q7f_A          117 ALRAGMENGDLFYMLGTVL-VKLEQPKLALPYLQRAVELNENDTEARFQFGMCLANE--------------GMLDEALSQ  181 (243)
T ss_dssp             HHHHTCCSHHHHHHHHHHH-HHTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH--------------TCCHHHHHH
T ss_pred             HHHhCCCCHHHHHHHHHHH-HHhccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHc--------------CCHHHHHHH
Confidence            9999999999998877644 4478899999999999986554333332222222100              133344455


Q ss_pred             HHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcC
Q 008442          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELD  231 (565)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~  231 (565)
                      |.+++..       .+.....+..++.++...+ +++.|..+|++++...|++..+|..+..+....+
T Consensus       182 ~~~~~~~-------~~~~~~~~~~la~~~~~~~-~~~~A~~~~~~~~~~~p~~~~~~~~~~~l~~~~~  241 (243)
T 2q7f_A          182 FAAVTEQ-------DPGHADAFYNAGVTYAYKE-NREKALEMLDKAIDIQPDHMLALHAKKLLGHHHH  241 (243)
T ss_dssp             HHHHHHH-------CTTCHHHHHHHHHHHHHTT-CTTHHHHHHHHHHHHCTTCHHHHHHHTC------
T ss_pred             HHHHHHh-------CcccHHHHHHHHHHHHHcc-CHHHHHHHHHHHHccCcchHHHHHHHHHHHhhcc
Confidence            5544443       3334557778888888888 9999999999999999999999888777665443

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.12  E-value=1.3e-08  Score=94.40  Aligned_cols=210  Identities=11%  Similarity=0.010  Sum_probs=142.4

Q ss_pred             CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHH
Q 008442           53 FPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLD  132 (565)
Q Consensus        53 ~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~  132 (565)
                      .|.+...|......+...+ ..+.+...|++|+...|.+...|......+ ...+..+++...|++++...+.....+..
T Consensus         1 ~p~~~~~~~~lg~~~~~~g-~~~~A~~~~~~al~~~p~~~~a~~~lg~~~-~~~g~~~~A~~~~~~al~~~P~~~~a~~~   78 (217)
T 2pl2_A            1 MQTAEQNPLRLGVQLYALG-RYDAALTLFERALKENPQDPEALYWLARTQ-LKLGLVNPALENGKTLVARTPRYLGGYMV   78 (217)
T ss_dssp             ---CCHHHHHHHHHHHHTT-CHHHHHHHHHHHHTTSSSCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHhCCCcHHHHHH
Confidence            3778889998887665444 678899999999999999999998877644 44788999999999999877665544444


Q ss_pred             HHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH
Q 008442          133 LFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI  212 (565)
Q Consensus       133 ~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~  212 (565)
                      +-..+....    ....      +......-+++|+..+...+...+.....|...+.+....+ ++++|...|++++..
T Consensus        79 lg~~~~~~~----~~~~------~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~lg~~~~~~g-~~~~A~~~~~~al~~  147 (217)
T 2pl2_A           79 LSEAYVALY----RQAE------DRERGKGYLEQALSVLKDAERVNPRYAPLHLQRGLVYALLG-ERDKAEASLKQALAL  147 (217)
T ss_dssp             HHHHHHHHH----HTCS------SHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhh----hhhh------hhcccccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcC-ChHHHHHHHHHHHhc
Confidence            333332110    0000      01112245666666666666555566678888888998888 999999999999999


Q ss_pred             ccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHH
Q 008442          213 SGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQK  279 (565)
Q Consensus       213 ~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k  279 (565)
                      . ++..+|...+......|+++.|...|++++..  . +....++......-...|+.+.....+.+
T Consensus       148 ~-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~  210 (217)
T 2pl2_A          148 E-DTPEIRSALAELYLSMGRLDEALAQYAKALEQ--A-PKDLDLRVRYASALLLKGKAEEAARAAAL  210 (217)
T ss_dssp             C-CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--S-TTCHHHHHHHHHHHTC-------------
T ss_pred             c-cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--C-CCChHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            9 88999999999999999999999999999973  2 22335555455554555665555444433

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.11  E-value=6.8e-09  Score=109.04  Aligned_cols=250  Identities=9%  Similarity=0.043  Sum_probs=183.1

Q ss_pred             hhHHHHHHHh-----c--CCCC---ChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcch
Q 008442            4 ARAHLEEQIS-----R--QDLS---DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKV   73 (565)
Q Consensus         4 ~R~~~E~~l~-----~--~~~~---~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~   73 (565)
                      +...|+.++.     .  .|..   ++.....|...+......|+++.+..+|++++...|. ..+|...+.... ..+.
T Consensus       208 A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~~~-~~~~~~l~~~~~-~~~~  285 (514)
T 2gw1_A          208 ADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLKNDPLGAHEDIKKAIELFPR-VNSYIYMALIMA-DRND  285 (514)
T ss_dssp             HHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHCCC-HHHHHHHHHHHH-TSSC
T ss_pred             HHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcc-HHHHHHHHHHHH-HCCC
Confidence            4556666666     2  3322   1456778998999888999999999999999999999 889888887554 4447


Q ss_pred             hhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchh
Q 008442           74 GNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEG  153 (565)
Q Consensus        74 ~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~  153 (565)
                      .+.+...|++++...|....+|......+ ...+..+++...|++++...+.....+..+-..+.         .     
T Consensus       286 ~~~A~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~---------~-----  350 (514)
T 2gw1_A          286 STEYYNYFDKALKLDSNNSSVYYHRGQMN-FILQNYDQAGKDFDKAKELDPENIFPYIQLACLAY---------R-----  350 (514)
T ss_dssp             CTTGGGHHHHHHTTCTTCTHHHHHHHHHH-HHTTCTTHHHHHHHHHHHTCSSCSHHHHHHHHHTT---------T-----
T ss_pred             HHHHHHHHHHHhhcCcCCHHHHHHHHHHH-HHhCCHHHHHHHHHHHHHhChhhHHHHHHHHHHHH---------H-----
Confidence            77899999999999998888888877633 44678899999999999865543332222222111         0     


Q ss_pred             hhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchH------HHHHHHHHHH
Q 008442          154 VLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAML------EAWQSYISME  227 (565)
Q Consensus       154 ~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~------~lw~~yi~~e  227 (565)
                      ..++..+...|.+++..       .+.....+..++.+....+ +++.|..+|++++...|...      .+|...+...
T Consensus       351 ~~~~~~A~~~~~~~~~~-------~~~~~~~~~~la~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~  422 (514)
T 2gw1_A          351 ENKFDDCETLFSEAKRK-------FPEAPEVPNFFAEILTDKN-DFDKALKQYDLAIELENKLDGIYVGIAPLVGKATLL  422 (514)
T ss_dssp             TTCHHHHHHHHHHHHHH-------STTCSHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHTSSSCSSCSHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHH-------cccCHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHH
Confidence            01344445555555443       2333456777788888888 99999999999999876653      3889999998


Q ss_pred             HH---cCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          228 IE---LDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       228 ~~---~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      ..   .|+++.|..+|++++..   .+.....+..........|+.+.+...+.+++
T Consensus       423 ~~~~~~~~~~~A~~~~~~a~~~---~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~  476 (514)
T 2gw1_A          423 TRNPTVENFIEATNLLEKASKL---DPRSEQAKIGLAQMKLQQEDIDEAITLFEESA  476 (514)
T ss_dssp             HTSCCTTHHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             hhhhhcCCHHHHHHHHHHHHHh---CcccHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            88   99999999999999873   22344666666777778899888887777765

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=99.10  E-value=1.1e-08  Score=103.46  Aligned_cols=221  Identities=10%  Similarity=0.032  Sum_probs=161.0

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCC-chhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGD-PGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVY   81 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~-~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~   81 (565)
                      ++-..|+.+|..+|.    +..+|..........|. .+.+...|++||..+|.+..+|......+.. .+..+.+...|
T Consensus       115 ~Al~~~~~al~l~P~----~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P~~~~a~~~~g~~~~~-~g~~~eAl~~~  189 (382)
T 2h6f_A          115 RAFKLTRDAIELNAA----NYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVEW-LRDPSQELEFI  189 (382)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-HTCCTTHHHHH
T ss_pred             HHHHHHHHHHHhCcc----CHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-ccCHHHHHHHH
Confidence            356778888888887    88999999999888996 9999999999999999999999998875554 45778899999


Q ss_pred             HHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHH
Q 008442           82 SRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIR  161 (565)
Q Consensus        82 erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~  161 (565)
                      ++||...|.+...|......+ ...+..+++...|+++|...+.....+..+...+...       .+..+      .  
T Consensus       190 ~kal~ldP~~~~a~~~lg~~~-~~~g~~~eAl~~~~~al~l~P~~~~a~~~lg~~l~~l-------~~~~~------e--  253 (382)
T 2h6f_A          190 ADILNQDAKNYHAWQHRQWVI-QEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNT-------TGYND------R--  253 (382)
T ss_dssp             HHHHHHCTTCHHHHHHHHHHH-HHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHT-------TCSCS------H--
T ss_pred             HHHHHhCccCHHHHHHHHHHH-HHcCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHh-------cCcch------H--
Confidence            999999999999998866544 3467788999999999987766444443333332210       01100      0  


Q ss_pred             HHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCC-ChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcC--------C
Q 008442          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGK-DMVSARGVWERLLKISGAMLEAWQSYISMEIELD--------H  232 (565)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~-~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~--------~  232 (565)
                      .++..++.++...+...+.....|...+.+....+. +.++|...++++ ...|++..++...++++...+        +
T Consensus       254 A~~~~el~~~~~Al~l~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~~p~~~~al~~La~~~~~~~~~~~~~~~~  332 (382)
T 2h6f_A          254 AVLEREVQYTLEMIKLVPHNESAWNYLKGILQDRGLSKYPNLLNQLLDL-QPSHSSPYLIAFLVDIYEDMLENQCDNKED  332 (382)
T ss_dssp             HHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TTTCCCHHHHHHHHHHHHHHHHTTCSSHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHccCccchHHHHHHHHHh-ccCCCCHHHHHHHHHHHHHHhcccccchHH
Confidence            112222333333333344455677777776666542 578888888887 668888888888888876653        2


Q ss_pred             -hHHHHHHHHHH-Hh
Q 008442          233 -INEARSIYKRC-YS  245 (565)
Q Consensus       233 -~~~aR~i~~~a-l~  245 (565)
                       ++.|.++|+++ +.
T Consensus       333 ~~~~A~~~~~~l~~~  347 (382)
T 2h6f_A          333 ILNKALELCEILAKE  347 (382)
T ss_dssp             HHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHH
Confidence             58999999999 75

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.09  E-value=9.4e-09  Score=98.33  Aligned_cols=229  Identities=10%  Similarity=0.013  Sum_probs=163.2

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHH----HHHHHHHHHHhcchhhHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDL----WLDYTQYLDKTLKVGNVVR   78 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~l----W~~Y~~~l~~~~~~~~~~~   78 (565)
                      ++...|+.++...|.    +...|..........|+++.+...|++++. .|.+..+    |...+.... ..+..+.+.
T Consensus        21 ~A~~~~~~~l~~~p~----~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~-~~~~~~~~~~~~~~lg~~~~-~~~~~~~A~   94 (272)
T 3u4t_A           21 EAIEVFNKLEAKKYN----SPYIYNRRAVCYYELAKYDLAQKDIETYFS-KVNATKAKSADFEYYGKILM-KKGQDSLAI   94 (272)
T ss_dssp             HHHHHHHHHHHTTCC----CSTTHHHHHHHHHHTTCHHHHHHHHHHHHT-TSCTTTCCHHHHHHHHHHHH-HTTCHHHHH
T ss_pred             HHHHHHHHHHHhCCC----cHHHHHHHHHHHHHHhhHHHHHHHHHHHHh-ccCchhHHHHHHHHHHHHHH-HcccHHHHH
Confidence            467788888888876    566888888888889999999999999999 5555444    777776554 445788899


Q ss_pred             HHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHH-HHHHHHHHHHhhccccchhhhhH
Q 008442           79 DVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLF-LTRIDGLRRRILFSGEVEGVLDY  157 (565)
Q Consensus        79 ~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~-~~~~~~~~r~~~~~~~~e~~~~~  157 (565)
                      ..|++|+...|....+|......+ ...+..+++...|++++...+.....+..+- ..+..               .++
T Consensus        95 ~~~~~a~~~~~~~~~~~~~l~~~~-~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~---------------~~~  158 (272)
T 3u4t_A           95 QQYQAAVDRDTTRLDMYGQIGSYF-YNKGNFPLAIQYMEKQIRPTTTDPKVFYELGQAYYYN---------------KEY  158 (272)
T ss_dssp             HHHHHHHHHSTTCTHHHHHHHHHH-HHTTCHHHHHHHHGGGCCSSCCCHHHHHHHHHHHHHT---------------TCH
T ss_pred             HHHHHHHhcCcccHHHHHHHHHHH-HHccCHHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHH---------------HHH
Confidence            999999999999989998877634 4478999999999999987665444443333 22210               134


Q ss_pred             HHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCC---hHHHHHHHHHHHHHc---cc-----hHHHHHHHHHH
Q 008442          158 SLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKD---MVSARGVWERLLKIS---GA-----MLEAWQSYISM  226 (565)
Q Consensus       158 ~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~---~~~ar~i~e~~l~~~---~~-----~~~lw~~yi~~  226 (565)
                      ..+...|++++..       .+.....+...+.+....+ +   .+.|...|++++...   ++     ...+|.....+
T Consensus       159 ~~A~~~~~~a~~~-------~p~~~~~~~~~~~~~~~~~-~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  230 (272)
T 3u4t_A          159 VKADSSFVKVLEL-------KPNIYIGYLWRARANAAQD-PDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYY  230 (272)
T ss_dssp             HHHHHHHHHHHHH-------STTCHHHHHHHHHHHHHHS-TTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh-------CccchHHHHHHHHHHHHcC-cchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHH
Confidence            4455555555543       2333455556666666666 5   778999999999874   44     23688888888


Q ss_pred             HHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHH
Q 008442          227 EIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFE  264 (565)
Q Consensus       227 e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE  264 (565)
                      ....|+++.|...|++++..  . +.....++....+.
T Consensus       231 ~~~~~~~~~A~~~~~~al~~--~-p~~~~a~~~l~~~~  265 (272)
T 3u4t_A          231 YTINRDKVKADAAWKNILAL--D-PTNKKAIDGLKMKL  265 (272)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH--C-TTCHHHHHHHC---
T ss_pred             HHHcCCHHHHHHHHHHHHhc--C-ccHHHHHHHhhhhh
Confidence            89999999999999999973  2 23445555444333

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.09  E-value=4e-08  Score=103.92  Aligned_cols=252  Identities=9%  Similarity=-0.036  Sum_probs=171.1

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~  101 (565)
                      ....|..........|+++.+..+|++++...|.++.+|...+..... .++.+.+...|++++...|.....|......
T Consensus        24 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~-~g~~~~A~~~~~~al~~~p~~~~~~~~la~~  102 (537)
T 3fp2_A           24 YAVQLKNRGNHFFTAKNFNEAIKYYQYAIELDPNEPVFYSNISACYIS-TGDLEKVIEFTTKALEIKPDHSKALLRRASA  102 (537)
T ss_dssp             HHHHHHHHHHHHHHTTCCC-CHHHHHHHHHHCTTCHHHHHHHHHHHHH-HTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHH-cCCHHHHHHHHHHHHhcCCchHHHHHHHHHH
Confidence            456788888888899999999999999999999999999999876554 4478889999999999999999999887764


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcccccHHHHH-------------H------------------------------------
Q 008442          102 LERSRASEEEISTVFEKSLLCAFSTFEEYL-------------D------------------------------------  132 (565)
Q Consensus       102 le~~~~~~~~~~~if~ral~~~~~~~~~~~-------------~------------------------------------  132 (565)
                      + ...+..+++...|+ ++...+.....++             .                                    
T Consensus       103 ~-~~~g~~~~A~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  180 (537)
T 3fp2_A          103 N-ESLGNFTDAMFDLS-VLSLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEV  180 (537)
T ss_dssp             H-HHHTCHHHHHHHHH-HHC-----------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHH
T ss_pred             H-HHcCCHHHHHHHHH-HHhcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHH
Confidence            4 44677888888875 5532111000000             0                                    


Q ss_pred             ---------------HHHHHH---------------HHHHH-----Hhhc--cccchh-------hh---hHHHHHHHHH
Q 008442          133 ---------------LFLTRI---------------DGLRR-----RILF--SGEVEG-------VL---DYSLIRETFQ  165 (565)
Q Consensus       133 ---------------~~~~~~---------------~~~~r-----~~~~--~~~~e~-------~~---~~~~~~~~~~  165 (565)
                                     +.....               ++...     ..+.  ....+.       +.   ........++
T Consensus       181 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~  260 (537)
T 3fp2_A          181 SSVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSANTVDDPLRENAALALCYTGIFHFLKNNLL  260 (537)
T ss_dssp             HTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHCCCcchhhHHHHHHHHHHHHHHHhcccHH
Confidence                           000000               00000     0000  000000       00   0000112235


Q ss_pred             HHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          166 RASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       166 ~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      +|+.++...+...+. ...+...+.+....+ +++.|..+|++++...|+...+|...+.+....|+++.|..+|++++.
T Consensus       261 ~A~~~~~~~~~~~~~-~~~~~~l~~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~  338 (537)
T 3fp2_A          261 DAQVLLQESINLHPT-PNSYIFLALTLADKE-NSQEFFKFFQKAVDLNPEYPPTYYHRGQMYFILQDYKNAKEDFQKAQS  338 (537)
T ss_dssp             HHHHHHHHHHHHCCC-HHHHHHHHHHTCCSS-CCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCC-chHHHHHHHHHHHhc-CHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            666666665554444 566777777777777 999999999999999999999999999999999999999999999987


Q ss_pred             cccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          246 KRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       246 ~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      .  ..+ ...+|......-...|+.+.+...+.+++
T Consensus       339 ~--~~~-~~~~~~~la~~~~~~g~~~~A~~~~~~~~  371 (537)
T 3fp2_A          339 L--NPE-NVYPYIQLACLLYKQGKFTESEAFFNETK  371 (537)
T ss_dssp             H--CTT-CSHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             h--CCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3  222 23566666666667899888887777665

>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=99.07  E-value=2.2e-10  Score=112.24  Aligned_cols=74  Identities=14%  Similarity=0.184  Sum_probs=62.9

Q ss_pred             CCCCeEEEcC--CCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCccc---CCe--
Q 008442          389 TDECTAFLSN--INLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMF---LGK--  460 (565)
Q Consensus       389 ~~~~~l~V~n--l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~---~g~--  460 (565)
                      ....+|||+|  |++.+++++|+++|++||.|.+|.++.      +||||||+|.+.++|++|+. |||..+   .|+  
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~   89 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   89 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCce
Confidence            3457999999  578999999999999999999987743      46999999999999999998 899886   355  


Q ss_pred             EEEEeecC
Q 008442          461 KLSIARSN  468 (565)
Q Consensus       461 ~l~v~~a~  468 (565)
                      +|.|.++.
T Consensus        90 ~ly~~~~~   97 (345)
T 3tht_A           90 TLYLNFVE   97 (345)
T ss_dssp             ECEEEECS
T ss_pred             EEEEEEee
Confidence            57777763

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.07  E-value=1.4e-08  Score=106.17  Aligned_cols=199  Identities=11%  Similarity=-0.003  Sum_probs=120.8

Q ss_pred             hHHHHHHHHHHHHhcCCc-hhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDP-GRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~-~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~  100 (565)
                      +...|..........+++ +.+...|+++|...|.+...|...+...... ++.+.+...|++|+...|. ...|.....
T Consensus       101 ~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~-g~~~~A~~~~~~al~~~p~-~~~~~~lg~  178 (474)
T 4abn_A          101 EAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEPELVEAWNQLGEVYWKK-GDVTSAHTCFSGALTHCKN-KVSLQNLSM  178 (474)
T ss_dssp             CHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-TCHHHHHHHHHHHHTTCCC-HHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHHhhCCC-HHHHHHHHH
Confidence            567777777777777788 8888888888888888888888777655443 3667788888888887777 566666554


Q ss_pred             HHHHhc---------CCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHH
Q 008442          101 SLERSR---------ASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYL  171 (565)
Q Consensus       101 ~le~~~---------~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l  171 (565)
                       +....         +..+++...|++|+...+.....+..+-..+...                             ++
T Consensus       179 -~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~-----------------------------~~  228 (474)
T 4abn_A          179 -VLRQLQTDSGDEHSRHVMDSVRQAKLAVQMDVLDGRSWYILGNAYLSL-----------------------------YF  228 (474)
T ss_dssp             -HHTTCCCSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-----------------------------HH
T ss_pred             -HHHHhccCChhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHH-----------------------------HH
Confidence             33334         5567777777777765444332222221111100                             00


Q ss_pred             HhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHcc---chHHHHHHHHHHHHHcCChHHHHHHHHHHHhccc
Q 008442          172 SEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG---AMLEAWQSYISMEIELDHINEARSIYKRCYSKRF  248 (565)
Q Consensus       172 ~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~---~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~  248 (565)
                      .                  .-...+ ++++|...|++++...|   ....+|..++..+...|+++.|...|++++..  
T Consensus       229 ~------------------~~~~~g-~~~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--  287 (474)
T 4abn_A          229 N------------------TGQNPK-ISQQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAAL--  287 (474)
T ss_dssp             H------------------TTCCHH-HHHHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--
T ss_pred             h------------------hccccc-hHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--
Confidence            0                  000012 56677777777777776   67777777777777777777777777777752  


Q ss_pred             CCCCcHHHHHHHHHHHHHhCCHHHHH
Q 008442          249 TGTGSEDICHAWLRFEREYGTLEDFD  274 (565)
Q Consensus       249 ~~~~~~~i~~~~~~fE~~~G~~~~~~  274 (565)
                      ..+ ....|..........|..+.+.
T Consensus       288 ~p~-~~~a~~~l~~~~~~lg~~~eAi  312 (474)
T 4abn_A          288 DPA-WPEPQQREQQLLEFLSRLTSLL  312 (474)
T ss_dssp             CTT-CHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCC-CHHHHHHHHHHHHHHHHHHHHH
Confidence            222 2234444444444444444333

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.03  E-value=7.1e-10  Score=84.50  Aligned_cols=73  Identities=23%  Similarity=0.366  Sum_probs=63.2

Q ss_pred             CCCeEEEcCCCC----CCCH----HHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeE
Q 008442          390 DECTAFLSNINL----KATY----EDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKK  461 (565)
Q Consensus       390 ~~~~l~V~nl~~----~~~~----~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~  461 (565)
                      ...||+|..+|.    +.-.    .+|.+.|.+||.|..++++.++        +||+|.+.++|.+|+.|||..++|+.
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            357999988772    3333    6799999999999999998764        89999999999999999999999999


Q ss_pred             EEEeecCCC
Q 008442          462 LSIARSNPK  470 (565)
Q Consensus       462 l~v~~a~~~  470 (565)
                      |+|..+.|.
T Consensus        78 LkV~lkt~d   86 (91)
T 2dnr_A           78 ITIALKSPS   86 (91)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEeCCCC
Confidence            999998875

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.03  E-value=1.1e-07  Score=99.63  Aligned_cols=253  Identities=9%  Similarity=0.027  Sum_probs=167.5

Q ss_pred             HhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHH
Q 008442           21 EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (565)
Q Consensus        21 ~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~  100 (565)
                      +....|..........|+++.+..+|++++...| +..+|...+..... .+..+.+...|++++...|.....|.....
T Consensus         4 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~la~~~~~-~g~~~~A~~~~~~al~~~p~~~~~~~~l~~   81 (514)
T 2gw1_A            4 KYALALKDKGNQFFRNKKYDDAIKYYNWALELKE-DPVFYSNLSACYVS-VGDLKKVVEMSTKALELKPDYSKVLLRRAS   81 (514)
T ss_dssp             HHHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHH-HTCHHHHHHHHHHHHHHCSCCHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCc-cHHHHHhHHHHHHH-HhhHHHHHHHHHHHhccChHHHHHHHHHHH
Confidence            3567788888888889999999999999999998 68888887765544 447788999999999999999988888776


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhccccc---HHHHHHHHHHHHHHHHH-Hhh------------------------------
Q 008442          101 SLERSRASEEEISTVFEKSLLCAFST---FEEYLDLFLTRIDGLRR-RIL------------------------------  146 (565)
Q Consensus       101 ~le~~~~~~~~~~~if~ral~~~~~~---~~~~~~~~~~~~~~~~r-~~~------------------------------  146 (565)
                      .+ ...+..+++...|++++...+..   ....+...........- ..+                              
T Consensus        82 ~~-~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (514)
T 2gw1_A           82 AN-EGLGKFADAMFDLSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPS  160 (514)
T ss_dssp             HH-HHTTCHHHHHHHHHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCC
T ss_pred             HH-HHHhhHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCch
Confidence            44 44688999999999998754321   11111111110000000 000                              


Q ss_pred             ----------ccc-----------cchh-------------hhhHHHHHHHHHHHHHHHHhhhc-C------CchhHHHH
Q 008442          147 ----------FSG-----------EVEG-------------VLDYSLIRETFQRASDYLSEQMK-N------TDGLLRLY  185 (565)
Q Consensus       147 ----------~~~-----------~~e~-------------~~~~~~~~~~~~~a~~~l~~~~~-~------~~~~~~l~  185 (565)
                                ...           ....             ..++..+...|.+++..+...+. .      .+.....+
T Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  240 (514)
T 2gw1_A          161 VTSMASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISL  240 (514)
T ss_dssp             HHHHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHH
T ss_pred             hHHHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHH
Confidence                      000           0000             01233333444444442211110 0      13345566


Q ss_pred             HHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHH
Q 008442          186 AYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFER  265 (565)
Q Consensus       186 ~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~  265 (565)
                      ...+.+....+ +++.|..+|++++...|. ..+|...+......|+++.|..+|++++..  . +....+|........
T Consensus       241 ~~~~~~~~~~~-~~~~A~~~~~~~l~~~~~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~-~~~~~~~~~l~~~~~  315 (514)
T 2gw1_A          241 EHTGIFKFLKN-DPLGAHEDIKKAIELFPR-VNSYIYMALIMADRNDSTEYYNYFDKALKL--D-SNNSSVYYHRGQMNF  315 (514)
T ss_dssp             HHHHHHHHHSS-CHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHTSSCCTTGGGHHHHHHTT--C-TTCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHCC-CHHHHHHHHHHHHhhCcc-HHHHHHHHHHHHHCCCHHHHHHHHHHHhhc--C-cCCHHHHHHHHHHHH
Confidence            67777888888 999999999999999888 888999999888899999999999999873  1 223356666666666


Q ss_pred             HhCCHHHHHHHHHHHh
Q 008442          266 EYGTLEDFDHSVQKVT  281 (565)
Q Consensus       266 ~~G~~~~~~~~~~k~~  281 (565)
                      ..|+.+.+...+.+++
T Consensus       316 ~~~~~~~A~~~~~~~~  331 (514)
T 2gw1_A          316 ILQNYDQAGKDFDKAK  331 (514)
T ss_dssp             HTTCTTHHHHHHHHHH
T ss_pred             HhCCHHHHHHHHHHHH
Confidence            7787777776666654

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.02  E-value=2.8e-08  Score=93.80  Aligned_cols=206  Identities=10%  Similarity=-0.007  Sum_probs=153.3

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCC-------HHHHHHHHHHHHHhcchhh
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVS-------SDLWLDYTQYLDKTLKVGN   75 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~-------~~lW~~Y~~~l~~~~~~~~   75 (565)
                      ++...|+.++... .    +...|..........|+.+.+...|++++...|.+       ..+|...+.... ..++.+
T Consensus        23 ~A~~~~~~a~~~~-~----~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~   96 (258)
T 3uq3_A           23 EAIEHYNKAWELH-K----DITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFARIGNAYH-KLGDLK   96 (258)
T ss_dssp             HHHHHHHHHHHHS-C----CTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHH-HTTCHH
T ss_pred             HHHHHHHHHHHhh-c----cHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHHHHH-HcccHH
Confidence            3567788888777 4    56788888888889999999999999999988876       678877776554 445778


Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhh
Q 008442           76 VVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVL  155 (565)
Q Consensus        76 ~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~  155 (565)
                      .+...|++++...|. ..++..        .+..+++...|++++...+.....+..+-..+..        .      .
T Consensus        97 ~A~~~~~~a~~~~~~-~~~~~~--------~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~------~  153 (258)
T 3uq3_A           97 KTIEYYQKSLTEHRT-ADILTK--------LRNAEKELKKAEAEAYVNPEKAEEARLEGKEYFT--------K------S  153 (258)
T ss_dssp             HHHHHHHHHHHHCCC-HHHHHH--------HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH--------T------T
T ss_pred             HHHHHHHHHHhcCch-hHHHHH--------HhHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHH--------h------c
Confidence            899999999998876 232211        2446788889999887654433322222221110        0      1


Q ss_pred             hHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHH
Q 008442          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINE  235 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~  235 (565)
                      ++..+...|.+++..       .+....++...+.+....+ +++.|..+|++++...|+...+|...+......|+++.
T Consensus       154 ~~~~A~~~~~~a~~~-------~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~  225 (258)
T 3uq3_A          154 DWPNAVKAYTEMIKR-------APEDARGYSNRAAALAKLM-SFPEAIADCNKAIEKDPNFVRAYIRKATAQIAVKEYAS  225 (258)
T ss_dssp             CHHHHHHHHHHHHHH-------CTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             CHHHHHHHHHHHHhc-------CcccHHHHHHHHHHHHHhC-CHHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHhhHHH
Confidence            334444455544443       3344567777888888888 99999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHh
Q 008442          236 ARSIYKRCYS  245 (565)
Q Consensus       236 aR~i~~~al~  245 (565)
                      |...|++++.
T Consensus       226 A~~~~~~a~~  235 (258)
T 3uq3_A          226 ALETLDAART  235 (258)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999999986

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.00  E-value=1.2e-07  Score=87.25  Aligned_cols=206  Identities=10%  Similarity=-0.022  Sum_probs=147.0

Q ss_pred             cCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHH
Q 008442           52 DFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYL  131 (565)
Q Consensus        52 ~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~  131 (565)
                      ..|.+..+|...+...... ++.+.+..+|++++...|....+|......+ ...+..+++...|++++...+.....+.
T Consensus         3 ~~~~~~~~~~~~~~~~~~~-~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~A~~~~~~a~~~~~~~~~~~~   80 (225)
T 2vq2_A            3 KANQVSNIKTQLAMEYMRG-QDYRQATASIEDALKSDPKNELAWLVRAEIY-QYLKVNDKAQESFRQALSIKPDSAEINN   80 (225)
T ss_dssp             -CCHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             CCcccHHHHHHHHHHHHHH-hhHHHHHHHHHHHHHhCccchHHHHHHHHHH-HHcCChHHHHHHHHHHHHhCCCChHHHH
Confidence            3566778888887765544 4778899999999999999988888877634 4478899999999999986554433332


Q ss_pred             HHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHH
Q 008442          132 DLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLK  211 (565)
Q Consensus       132 ~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~  211 (565)
                      .+-..+.        ..     ..++..+...|++++.     ....+....++...+.+....+ +++.|..+|++++.
T Consensus        81 ~l~~~~~--------~~-----~~~~~~A~~~~~~~~~-----~~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~~~~  141 (225)
T 2vq2_A           81 NYGWFLC--------GR-----LNRPAESMAYFDKALA-----DPTYPTPYIANLNKGICSAKQG-QFGLAEAYLKRSLA  141 (225)
T ss_dssp             HHHHHHH--------TT-----TCCHHHHHHHHHHHHT-----STTCSCHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHH
T ss_pred             HHHHHHH--------Hh-----cCcHHHHHHHHHHHHc-----CcCCcchHHHHHHHHHHHHHcC-CHHHHHHHHHHHHH
Confidence            2222211        00     0133444455554443     1123334567777888888888 99999999999999


Q ss_pred             HccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHH
Q 008442          212 ISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (565)
Q Consensus       212 ~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~  280 (565)
                      ..|.+..+|...+......|+++.|..+|++++.. .+ ......+.....+....|+.+.+...+..+
T Consensus       142 ~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~  208 (225)
T 2vq2_A          142 AQPQFPPAFKELARTKMLAGQLGDADYYFKKYQSR-VE-VLQADDLLLGWKIAKALGNAQAAYEYEAQL  208 (225)
T ss_dssp             HSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH-HC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             hCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CC-CCCHHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence            99999999999999999999999999999999873 22 134455666677778889888776554443

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=99.00  E-value=2.5e-07  Score=87.24  Aligned_cols=202  Identities=9%  Similarity=0.011  Sum_probs=147.3

Q ss_pred             CCCC-HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHH
Q 008442           53 FPVS-SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYL  131 (565)
Q Consensus        53 ~p~~-~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~  131 (565)
                      .|.. ..+|...+..... .++.+.+..+|++++...|....+|......+ ...+..+++...|++++...+.....+.
T Consensus        32 ~~~~~~~~~~~~a~~~~~-~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~-~~~~~~~~A~~~~~~a~~~~~~~~~~~~  109 (252)
T 2ho1_A           32 GRDEARDAYIQLGLGYLQ-RGNTEQAKVPLRKALEIDPSSADAHAALAVVF-QTEMEPKLADEEYRKALASDSRNARVLN  109 (252)
T ss_dssp             CHHHHHHHHHHHHHHHHH-TTCTGGGHHHHHHHHHHCTTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             chHHHHHHHHHHHHHHHH-cCChHHHHHHHHHHHhcCCChHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHHCcCcHHHHH
Confidence            3443 5677777765554 34678899999999999999888888877634 4478899999999999986554333332


Q ss_pred             HHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhc--CCchhHHHHHHHHHHHHHcCCChHHHHHHHHHH
Q 008442          132 DLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMK--NTDGLLRLYAYWAHLEQSMGKDMVSARGVWERL  209 (565)
Q Consensus       132 ~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~--~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~  209 (565)
                      .+-..+.                     ....+++|+.++...+.  ..+....++..++.+....+ +++.|..+|+++
T Consensus       110 ~la~~~~---------------------~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~~  167 (252)
T 2ho1_A          110 NYGGFLY---------------------EQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMK-KPAQAKEYFEKS  167 (252)
T ss_dssp             HHHHHHH---------------------HTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTT-CHHHHHHHHHHH
T ss_pred             HHHHHHH---------------------HHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcC-CHHHHHHHHHHH
Confidence            2222221                     01223344444444443  34445667777888888888 999999999999


Q ss_pred             HHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          210 LKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       210 l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      +...|....+|..++.+....|+++.|..+|++++..   .+.....+.....+....|+.+.+...+.++.
T Consensus       168 ~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~  236 (252)
T 2ho1_A          168 LRLNRNQPSVALEMADLLYKEREYVPARQYYDLFAQG---GGQNARSLLLGIRLAKVFEDRDTAASYGLQLK  236 (252)
T ss_dssp             HHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT---SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HhcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CcCcHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999873   22345666667777778899888877766653

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=98.99  E-value=1.5e-07  Score=97.86  Aligned_cols=236  Identities=11%  Similarity=0.019  Sum_probs=158.6

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHH---hcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHH---hcchhhH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQ---SSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDK---TLKVGNV   76 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~---~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~---~~~~~~~   76 (565)
                      +|...|+.+|...|.    +...|..+.....   ..+..+.+...|++||..+|.+..+|..+...+..   ..+..+.
T Consensus       156 ~A~~~~~kal~~~p~----~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~p~~~~~~~~l~~~~~~~~~~~~~~~~  231 (472)
T 4g1t_A          156 RAKVCFEKALEKKPK----NPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLNPDNQYLKVLLALKLHKMREEGEEEGE  231 (472)
T ss_dssp             HHHHHHHHHHHHSTT----CHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHCSSCHHHHHHHHHHHHHCC------CH
T ss_pred             HHHHHHHHHHHhCCC----CHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHhhhhHHHH
Confidence            366778888887776    6677766665532   34666778889999999999999888776543322   2234567


Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhh
Q 008442           77 VRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLD  156 (565)
Q Consensus        77 ~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~  156 (565)
                      +..+|++|+...|....+|..... +-...+..+++...|++|+...+.....+..+-.++............  .....
T Consensus       232 a~~~~~~al~~~~~~~~~~~~lg~-~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~y~~~~~~~~~~~~--~~~~~  308 (472)
T 4g1t_A          232 GEKLVEEALEKAPGVTDVLRSAAK-FYRRKDEPDKAIELLKKALEYIPNNAYLHCQIGCCYRAKVFQVMNLRE--NGMYG  308 (472)
T ss_dssp             HHHHHHHHHHHCSSCHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHC--------C
T ss_pred             HHHHHHHHHHhCccHHHHHHHHHH-HHHHcCchHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHhhhHHH--HHHHH
Confidence            889999999999998888877665 344478889999999999987666555444443333221111000000  00012


Q ss_pred             HHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchH---HHHHHHHHHH-HHcCC
Q 008442          157 YSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAML---EAWQSYISME-IELDH  232 (565)
Q Consensus       157 ~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~---~lw~~yi~~e-~~~~~  232 (565)
                      .......++.|+..+.......+.....+...+.+....+ ++++|..+|++++...++..   .++..|..+. ...|+
T Consensus       309 ~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~lg~~~~~~~-~~~~A~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~  387 (472)
T 4g1t_A          309 KRKLLELIGHAVAHLKKADEANDNLFRVCSILASLHALAD-QYEEAEYYFQKEFSKELTPVAKQLLHLRYGNFQLYQMKC  387 (472)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCTTTCCCHHHHHHHHHHTT-CHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTSSC
T ss_pred             HHHHHhhHHHHHHHHHHHhhcCCchhhhhhhHHHHHHHhc-cHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHCCC
Confidence            2334455667777776665544455556677788888888 99999999999999865543   3566777664 46789


Q ss_pred             hHHHHHHHHHHHhc
Q 008442          233 INEARSIYKRCYSK  246 (565)
Q Consensus       233 ~~~aR~i~~~al~~  246 (565)
                      .+.|...|.+++..
T Consensus       388 ~~~Ai~~y~kal~i  401 (472)
T 4g1t_A          388 EDKAIHHFIEGVKI  401 (472)
T ss_dssp             HHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999999973

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=98.98  E-value=2.4e-07  Score=90.07  Aligned_cols=211  Identities=12%  Similarity=0.014  Sum_probs=114.5

Q ss_pred             HHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhc--CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHH
Q 008442            8 LEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITD--FPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRAT   85 (565)
Q Consensus         8 ~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~--~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl   85 (565)
                      |+.++......++........++.+....++.+.+...|++.+..  .|.+..+|...+..+.. .+..+.+..+|++  
T Consensus        50 ~~~al~~~~~~~~~~~~a~~~la~~~~~~~~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~-~g~~~~Al~~l~~--  126 (291)
T 3mkr_A           50 YGVVLDEIKPSSAPELQAVRMFAEYLASHSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFY-DQNPDAALRTLHQ--  126 (291)
T ss_dssp             HHHHHHHSCTTSCHHHHHHHHHHHHHHCSTTHHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHH-TTCHHHHHHHHTT--
T ss_pred             HHHHHHHhcccCChhHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHH-CCCHHHHHHHHhC--
Confidence            344444332234445556666666666666666777777776654  46677666666554433 3355556666666  


Q ss_pred             HcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHH
Q 008442           86 KNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQ  165 (565)
Q Consensus        86 ~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~  165 (565)
                         |.+..+|...+..+. ..+..+++...|++++...+....  ..+...++....     ..     .++..+...|+
T Consensus       127 ---~~~~~~~~~l~~~~~-~~g~~~~A~~~l~~~~~~~p~~~~--~~l~~a~~~l~~-----~~-----~~~~eA~~~~~  190 (291)
T 3mkr_A          127 ---GDSLECMAMTVQILL-KLDRLDLARKELKKMQDQDEDATL--TQLATAWVSLAA-----GG-----EKLQDAYYIFQ  190 (291)
T ss_dssp             ---CCSHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCHH--HHHHHHHHHHHH-----CT-----THHHHHHHHHH
T ss_pred             ---CCCHHHHHHHHHHHH-HCCCHHHHHHHHHHHHhhCcCcHH--HHHHHHHHHHHh-----Cc-----hHHHHHHHHHH
Confidence               556666665554332 356667777777777654433221  111111211110     00     02222333333


Q ss_pred             HHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHH-HHHHHHHHH
Q 008442          166 RASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINE-ARSIYKRCY  244 (565)
Q Consensus       166 ~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~-aR~i~~~al  244 (565)
                      +++.       ..+....+|...+......+ ++++|...|++++...|++...|..++.+....|+.+. +..++++++
T Consensus       191 ~~l~-------~~p~~~~~~~~la~~~~~~g-~~~eA~~~l~~al~~~p~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~  262 (291)
T 3mkr_A          191 EMAD-------KCSPTLLLLNGQAACHMAQG-RWEAAEGVLQEALDKDSGHPETLINLVVLSQHLGKPPEVTNRYLSQLK  262 (291)
T ss_dssp             HHHH-------HSCCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHH-------hCCCcHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            3332       22334445555666666666 77777777777777777777777777766666666543 566667666


Q ss_pred             h
Q 008442          245 S  245 (565)
Q Consensus       245 ~  245 (565)
                      .
T Consensus       263 ~  263 (291)
T 3mkr_A          263 D  263 (291)
T ss_dssp             H
T ss_pred             H
Confidence            5

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=98.97  E-value=3.8e-08  Score=107.61  Aligned_cols=170  Identities=12%  Similarity=0.108  Sum_probs=141.8

Q ss_pred             CChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHH
Q 008442           18 SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVR   97 (565)
Q Consensus        18 ~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~   97 (565)
                      +.|++.++|..........|+.+.+...|++||...|.+...|..+...+.. .+..+.+...|++||+..|.....|..
T Consensus         4 s~P~~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~P~~~~a~~nLg~~l~~-~g~~~eA~~~~~~Al~l~P~~~~a~~n   82 (723)
T 4gyw_A            4 SCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQ-QGKLQEALMHYKEAIRISPTFADAYSN   82 (723)
T ss_dssp             --CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHhCCCCHHHHHH
Confidence            4567899999999999999999999999999999999999999999886654 447788999999999999999999988


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcC
Q 008442           98 SLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKN  177 (565)
Q Consensus        98 yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~  177 (565)
                      ....+ ...+..+++...|++|+...+.                                                    
T Consensus        83 Lg~~l-~~~g~~~~A~~~~~kAl~l~P~----------------------------------------------------  109 (723)
T 4gyw_A           83 MGNTL-KEMQDVQGALQCYTRAIQINPA----------------------------------------------------  109 (723)
T ss_dssp             HHHHH-HHTTCHHHHHHHHHHHHHHCTT----------------------------------------------------
T ss_pred             HHHHH-HHcCCHHHHHHHHHHHHHhCCC----------------------------------------------------
Confidence            77644 3467788888888887754332                                                    


Q ss_pred             CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          178 TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       178 ~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                         ....|..++.++...+ ++++|...|+++++..|++...|..++......|+++.|.+.|++++.
T Consensus       110 ---~~~a~~~Lg~~~~~~g-~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~~~g~~~~A~~~~~kal~  173 (723)
T 4gyw_A          110 ---FADAHSNLASIHKDSG-NIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVS  173 (723)
T ss_dssp             ---CHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCCTTHHHHHHHHHH
T ss_pred             ---CHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCChHHHhhhhhHHHhcccHHHHHHHHHHHHH
Confidence               1223334555666777 999999999999999999999999999999999999999999999976

>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=98.94  E-value=1.1e-09  Score=89.50  Aligned_cols=76  Identities=24%  Similarity=0.195  Sum_probs=62.6

Q ss_pred             CCeEEEcCCCCCC----------CHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCC
Q 008442          391 ECTAFLSNINLKA----------TYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLG  459 (565)
Q Consensus       391 ~~~l~V~nl~~~~----------~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g  459 (565)
                      .+.|.+.|+=..-          -+++|++.|++||.|.+|.|..+.    ++|||||+|.+.++|.+|+. |||..++|
T Consensus         7 s~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~G   82 (114)
T 3s6e_A            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFAG   82 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            4567777773221          135889999999999999986542    58999999999999999998 89999999


Q ss_pred             eEEEEeecCCC
Q 008442          460 KKLSIARSNPK  470 (565)
Q Consensus       460 ~~l~v~~a~~~  470 (565)
                      |.|.|.++...
T Consensus        83 R~i~v~~~~~~   93 (114)
T 3s6e_A           83 KMITAAYVPLP   93 (114)
T ss_dssp             EECEEEEECHH
T ss_pred             EEEEEEEEcHH
Confidence            99999998643

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.89  E-value=1.3e-07  Score=98.94  Aligned_cols=191  Identities=10%  Similarity=0.033  Sum_probs=140.2

Q ss_pred             hhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchh-hHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 008442           40 GRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVG-NVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEK  118 (565)
Q Consensus        40 ~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~-~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~r  118 (565)
                      +.+...++.++...|.+..+|......+.. .++. +.+...|++|+...|.....|......+ ...++.+++...|++
T Consensus        85 ~~al~~l~~~~~~~~~~a~~~~~lg~~~~~-~g~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~-~~~g~~~~A~~~~~~  162 (474)
T 4abn_A           85 EKTLQQMEEVLGSAQVEAQALMLKGKALNV-TPDYSPEAEVLLSKAVKLEPELVEAWNQLGEVY-WKKGDVTSAHTCFSG  162 (474)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHHHHTS-SSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHH-HHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCchhHHHHHHHHHHHHh-ccccHHHHHHHHHHHHhhCCCCHHHHHHHHHHH-HHcCCHHHHHHHHHH
Confidence            445667788888889999999999886554 4477 8899999999999999999998877634 446889999999999


Q ss_pred             HHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCC
Q 008442          119 SLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKD  198 (565)
Q Consensus       119 al~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~  198 (565)
                      |+...+. ...+..+-..+.                                 .  ....           ..+...+ +
T Consensus       163 al~~~p~-~~~~~~lg~~~~---------------------------------~--~~~~-----------~~~~~~g-~  194 (474)
T 4abn_A          163 ALTHCKN-KVSLQNLSMVLR---------------------------------Q--LQTD-----------SGDEHSR-H  194 (474)
T ss_dssp             HHTTCCC-HHHHHHHHHHHT---------------------------------T--CCCS-----------CHHHHHH-H
T ss_pred             HHhhCCC-HHHHHHHHHHHH---------------------------------H--hccC-----------Chhhhhh-h
Confidence            9986654 221111111100                                 0  0000           0112334 7


Q ss_pred             hHHHHHHHHHHHHHccchHHHHHHHHHHHHHc--------CChHHHHHHHHHHHhcccCC-CCcHHHHHHHHHHHHHhCC
Q 008442          199 MVSARGVWERLLKISGAMLEAWQSYISMEIEL--------DHINEARSIYKRCYSKRFTG-TGSEDICHAWLRFEREYGT  269 (565)
Q Consensus       199 ~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~--------~~~~~aR~i~~~al~~~~~~-~~~~~i~~~~~~fE~~~G~  269 (565)
                      +++|...|++++...|++..+|..++......        |+++.|...|++++... +. .....+|..........|+
T Consensus       195 ~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~lg~~~~~~g~  273 (474)
T 4abn_A          195 VMDSVRQAKLAVQMDVLDGRSWYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVD-RKASSNPDLHLNRATLHKYEES  273 (474)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHC-GGGGGCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhC-CCcccCHHHHHHHHHHHHHcCC
Confidence            88999999999999999999999999999888        99999999999999731 10 0234666666677777899


Q ss_pred             HHHHHHHHHHHh
Q 008442          270 LEDFDHSVQKVT  281 (565)
Q Consensus       270 ~~~~~~~~~k~~  281 (565)
                      .+.+...+.+++
T Consensus       274 ~~~A~~~~~~al  285 (474)
T 4abn_A          274 YGEALEGFSQAA  285 (474)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            998888888775

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=98.88  E-value=9.8e-07  Score=89.75  Aligned_cols=261  Identities=11%  Similarity=-0.054  Sum_probs=161.6

Q ss_pred             HhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHH----HHHHHHHHHHHhcchhhHHHHHHHHHHHcC------CC
Q 008442           21 EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSD----LWLDYTQYLDKTLKVGNVVRDVYSRATKNC------PW   90 (565)
Q Consensus        21 ~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~----lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~------p~   90 (565)
                      .....+..........|+++.+..+|++++...|.+..    +|...+.... ..++.+.+...|++|+..+      |.
T Consensus        46 ~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~lg~~~~-~~g~~~~A~~~~~~al~~~~~~~~~~~  124 (411)
T 4a1s_A           46 SMCLELALEGERLCNAGDCRAGVAFFQAAIQAGTEDLRTLSAIYSQLGNAYF-YLGDYNKAMQYHKHDLTLAKSMNDRLG  124 (411)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHH-HHTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHH-HCCCHHHHHHHHHHHHHHHHHccCchH
Confidence            34455666666667789999999999999999999874    5666655444 3447788999999999863      33


Q ss_pred             CHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccc------ccHHHHHHHHHHHHHHHH--HHhhccc-cchhhhhHHHHH
Q 008442           91 VGELWVRSLLSLERSRASEEEISTVFEKSLLCAF------STFEEYLDLFLTRIDGLR--RRILFSG-EVEGVLDYSLIR  161 (565)
Q Consensus        91 ~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~------~~~~~~~~~~~~~~~~~~--r~~~~~~-~~e~~~~~~~~~  161 (565)
                      ...+|..... +....+..+++...|++++....      .....+..+-..+...-.  +...... ..+....+..+.
T Consensus       125 ~~~~~~~l~~-~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~  203 (411)
T 4a1s_A          125 EAKSSGNLGN-TLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAV  203 (411)
T ss_dssp             HHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHH-HHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHH
Confidence            3345555444 33446889999999999986421      111111111111111100  0000000 000011234444


Q ss_pred             HHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccch------HHHHHHHHHHHHHcCChHH
Q 008442          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM------LEAWQSYISMEIELDHINE  235 (565)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~------~~lw~~yi~~e~~~~~~~~  235 (565)
                      ..|.+++.+.... ...+.....+...+.+....+ +++.|...|++++...+..      ..+|...+.+....|+++.
T Consensus       204 ~~~~~al~~~~~~-~~~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~  281 (411)
T 4a1s_A          204 EFYQENLKLMRDL-GDRGAQGRACGNLGNTYYLLG-DFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFED  281 (411)
T ss_dssp             HHHHHHHHHHHHH-TCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHH
T ss_pred             HHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHHcC-ChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHH
Confidence            5555555544322 112223456667788888888 9999999999999875432      2377888888889999999


Q ss_pred             HHHHHHHHHhcccCCCCcH---HHHHHHHHHHHHhCCHHHHHHHHHHHhhHHH
Q 008442          236 ARSIYKRCYSKRFTGTGSE---DICHAWLRFEREYGTLEDFDHSVQKVTPRLE  285 (565)
Q Consensus       236 aR~i~~~al~~~~~~~~~~---~i~~~~~~fE~~~G~~~~~~~~~~k~~~~~~  285 (565)
                      |..+|++++...-....+.   .++..........|+.+.+...+++++....
T Consensus       282 A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~  334 (411)
T 4a1s_A          282 AAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQ  334 (411)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence            9999999987421122222   3444445566677999888888887765543

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=98.86  E-value=3.3e-07  Score=93.33  Aligned_cols=270  Identities=11%  Similarity=-0.052  Sum_probs=172.3

Q ss_pred             hhhHHHHHHHhcCCCCChH-hHHHHHHHHHHHHhcCCchhHHHHHHHHHhc------CCCCHHHHHHHHHHHHHhcchhh
Q 008442            3 NARAHLEEQISRQDLSDSE-KFQQYMIYLKYEQSSGDPGRVQLLYERAITD------FPVSSDLWLDYTQYLDKTLKVGN   75 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~-~~~~W~~yi~~e~~~~~~~~~~~lyERal~~------~p~~~~lW~~Y~~~l~~~~~~~~   75 (565)
                      ++...|+.++...+. ++. ...+|..........|+++.+...|++++..      .|....+|...+.... ..++.+
T Consensus        66 ~A~~~~~~al~~~~~-~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~-~~g~~~  143 (411)
T 4a1s_A           66 AGVAFFQAAIQAGTE-DLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNLGNTLK-VMGRFD  143 (411)
T ss_dssp             HHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH-HTTCHH
T ss_pred             HHHHHHHHHHHhccc-ChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHH-HCCCHH
Confidence            467788999988765 222 2357888888888889999999999999987      3555567777666544 444778


Q ss_pred             HHHHHHHHHHHcCC------CCHHHHHHHHHHHHHhcCC-----------------HHHHHHHHHHHHhccc--ccHHHH
Q 008442           76 VVRDVYSRATKNCP------WVGELWVRSLLSLERSRAS-----------------EEEISTVFEKSLLCAF--STFEEY  130 (565)
Q Consensus        76 ~~~~v~erAl~~~p------~~~~lW~~yi~~le~~~~~-----------------~~~~~~if~ral~~~~--~~~~~~  130 (565)
                      .+...|++|+...+      ....+|..... +....+.                 .+.+...|++++....  ......
T Consensus       144 ~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~-~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~  222 (411)
T 4a1s_A          144 EAAICCERHLTLARQLGDRLSEGRALYNLGN-VYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLMRDLGDRGAQ  222 (411)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-HHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHHHHhhchHHHHHHHHHHHH-HHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHcCCHHHH
Confidence            89999999998642      22334444333 2222345                 6677777777765321  111111


Q ss_pred             HHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHH
Q 008442          131 LDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLL  210 (565)
Q Consensus       131 ~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l  210 (565)
                      ...+........   .       ..++......|.+++....... ........+...+.++...+ ++++|...|++++
T Consensus       223 ~~~~~~la~~~~---~-------~g~~~~A~~~~~~al~~~~~~~-~~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~al  290 (411)
T 4a1s_A          223 GRACGNLGNTYY---L-------LGDFQAAIEHHQERLRIAREFG-DRAAERRANSNLGNSHIFLG-QFEDAAEHYKRTL  290 (411)
T ss_dssp             HHHHHHHHHHHH---H-------TTCHHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHHTTT-CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH---H-------cCChHHHHHHHHHHHHHHHhcC-CcHHHHHHHHHHHHHHHHCc-CHHHHHHHHHHHH
Confidence            111111111110   0       0145556667777776654321 11222345666778888888 9999999999999


Q ss_pred             HHccc------hHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcH---HHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          211 KISGA------MLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSE---DICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       211 ~~~~~------~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~---~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      ...+.      ...+|...+.+....|+++.|..+|++++...-....+.   .++..+...-...|+.+.+...+.+++
T Consensus       291 ~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  370 (411)
T 4a1s_A          291 ALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKYAEQHL  370 (411)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            87543      256888888899999999999999999986321112222   244445556667799998888888877


Q ss_pred             hHHHHH
Q 008442          282 PRLEEL  287 (565)
Q Consensus       282 ~~~~~~  287 (565)
                      ....++
T Consensus       371 ~~~~~~  376 (411)
T 4a1s_A          371 QLAXXX  376 (411)
T ss_dssp             HHCCHH
T ss_pred             HHHhhc
Confidence            655544

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=98.85  E-value=3.4e-07  Score=81.22  Aligned_cols=167  Identities=10%  Similarity=-0.024  Sum_probs=129.7

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~  101 (565)
                      ....|...+......|+++.+..+|++++...|.+..+|...+..... .++.+.+...|++++...|....+|......
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~   85 (186)
T 3as5_A            7 RQVYYRDKGISHAKAGRYSQAVMLLEQVYDADAFDVDVALHLGIAYVK-TGAVDRGTELLERSLADAPDNVKVATVLGLT   85 (186)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHTTTCCTTSCCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCccChHHHHHHHHHHHH-cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            455677777777788999999999999999999999988888775544 4477789999999999989888888776653


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchh
Q 008442          102 LERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGL  181 (565)
Q Consensus       102 le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~  181 (565)
                      + ...+..+++...|++++...+.                                                       .
T Consensus        86 ~-~~~~~~~~A~~~~~~~~~~~~~-------------------------------------------------------~  109 (186)
T 3as5_A           86 Y-VQVQKYDLAVPLLIKVAEANPI-------------------------------------------------------N  109 (186)
T ss_dssp             H-HHHTCHHHHHHHHHHHHHHCTT-------------------------------------------------------C
T ss_pred             H-HHhcCHHHHHHHHHHHHhcCcH-------------------------------------------------------h
Confidence            3 3356677777777766642211                                                       1


Q ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhc
Q 008442          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~  246 (565)
                      ..++..++.+....+ +++.|..+|++++...|....+|...+......|+++.|..+|++++..
T Consensus       110 ~~~~~~~a~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  173 (186)
T 3as5_A          110 FNVRFRLGVALDNLG-RFDEAIDSFKIALGLRPNEGKVHRAIAFSYEQMGRHEEALPHFKKANEL  173 (186)
T ss_dssp             HHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcC-cHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            223344555566667 8999999999999999888999999999999999999999999999863

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=98.85  E-value=3.2e-07  Score=89.78  Aligned_cols=125  Identities=10%  Similarity=0.026  Sum_probs=77.4

Q ss_pred             HHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccch------HHHHHHHHHHHHHc
Q 008442          157 YSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM------LEAWQSYISMEIEL  230 (565)
Q Consensus       157 ~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~------~~lw~~yi~~e~~~  230 (565)
                      +......|.+++...... .........+...+.+....+ +++.|..+|++++...+..      ..++...+......
T Consensus       199 ~~~A~~~~~~a~~~~~~~-~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~  276 (338)
T 3ro2_A          199 FRDAVIAHEQRLLIAKEF-GDKAAERRAYSNLGNAYIFLG-EFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLL  276 (338)
T ss_dssp             HHHHHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHhc-CChHHHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHh
Confidence            344445555555544321 111122335566677777777 8999999999988764332      55777778888888


Q ss_pred             CChHHHHHHHHHHHhcccCCCCcHH---HHHHHHHHHHHhCCHHHHHHHHHHHhhH
Q 008442          231 DHINEARSIYKRCYSKRFTGTGSED---ICHAWLRFEREYGTLEDFDHSVQKVTPR  283 (565)
Q Consensus       231 ~~~~~aR~i~~~al~~~~~~~~~~~---i~~~~~~fE~~~G~~~~~~~~~~k~~~~  283 (565)
                      |+++.|...|++++...-....+..   ++..........|+.+.+...+.+++..
T Consensus       277 g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  332 (338)
T 3ro2_A          277 QDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEI  332 (338)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHC
T ss_pred             cCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence            9999999999998763211112222   3344445556678887777777666543

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.84  E-value=1.5e-08  Score=82.83  Aligned_cols=75  Identities=15%  Similarity=0.111  Sum_probs=65.5

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecC-HHHHHHHHH-c--CCcccCCeEE
Q 008442          388 FTDECTAFLSNINLK-ATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFID-DEHLAAAVA-K--NKQMFLGKKL  462 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~-~~~a~~a~~-~--~~~~~~g~~l  462 (565)
                      ...++-|||+||+.+ ++.++|+.+|+.||.|..|.++.+..      .|||.|.+ +.+|..|+. +  ++..|+|..+
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            456899999999999 99999999999999999999987652      69999999 788998987 6  4678999988


Q ss_pred             EEeecC
Q 008442          463 SIARSN  468 (565)
Q Consensus       463 ~v~~a~  468 (565)
                      .+....
T Consensus        89 ~~evL~   94 (121)
T 1owx_A           89 TWEVLE   94 (121)
T ss_dssp             EEEECC
T ss_pred             EEEECC
Confidence            887654

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=98.83  E-value=5.5e-07  Score=91.08  Aligned_cols=129  Identities=11%  Similarity=0.029  Sum_probs=85.7

Q ss_pred             hHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccch------HHHHHHHHHHHHH
Q 008442          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM------LEAWQSYISMEIE  229 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~------~~lw~~yi~~e~~  229 (565)
                      ++......|.+++....... ........+...+.++...+ +++.|..+|++++...+..      ..+|...+.....
T Consensus       202 ~~~~A~~~~~~al~~~~~~~-~~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~  279 (406)
T 3sf4_A          202 NFRDAVIAHEQRLLIAKEFG-DKAAERRAYSNLGNAYIFLG-EFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTL  279 (406)
T ss_dssp             BHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhcC-CcHHHHHHHHHHHHHHHHcC-ChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHH
Confidence            34445555555555543311 11122345666778888888 9999999999999875433      5678888888899


Q ss_pred             cCChHHHHHHHHHHHhcccCCCCcH---HHHHHHHHHHHHhCCHHHHHHHHHHHhhHHHH
Q 008442          230 LDHINEARSIYKRCYSKRFTGTGSE---DICHAWLRFEREYGTLEDFDHSVQKVTPRLEE  286 (565)
Q Consensus       230 ~~~~~~aR~i~~~al~~~~~~~~~~---~i~~~~~~fE~~~G~~~~~~~~~~k~~~~~~~  286 (565)
                      .|+++.|...|++++...-....+.   .++......-...|+.+.+...+.+++.....
T Consensus       280 ~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~  339 (406)
T 3sf4_A          280 LQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEISRE  339 (406)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHH
T ss_pred             hCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence            9999999999999986422222222   23444445556678988888888887655443

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=98.79  E-value=5.9e-07  Score=87.20  Aligned_cols=248  Identities=12%  Similarity=0.063  Sum_probs=145.4

Q ss_pred             CChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHh--------cCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcC-
Q 008442           18 SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAIT--------DFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNC-   88 (565)
Q Consensus        18 ~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~--------~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~-   88 (565)
                      .++.....|..........|+++.+..+|++++.        ..|....+|...+.... ..+..+.+...|++|+... 
T Consensus        22 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~-~~g~~~~A~~~~~~al~~~~  100 (311)
T 3nf1_A           22 EIPARLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYR-DQNKYKDAANLLNDALAIRE  100 (311)
T ss_dssp             TSCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHH-HCCCHHHHHHHHHHHHHHHH
Confidence            3566788899999998999999999999999999        45666677777776544 3457788999999999864 


Q ss_pred             -------CCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcc-----cccHHHHHHHHHHHHHHHHHHhhccccchhhhh
Q 008442           89 -------PWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA-----FSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLD  156 (565)
Q Consensus        89 -------p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~-----~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~  156 (565)
                             |....+|..... +....+..+++...|++++...     ... ......+........    .      ..+
T Consensus       101 ~~~~~~~~~~~~~~~~l~~-~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~-~~~~~~~~~la~~~~----~------~~~  168 (311)
T 3nf1_A          101 KTLGKDHPAVAATLNNLAV-LYGKRGKYKEAEPLCKRALEIREKVLGKDH-PDVAKQLNNLALLCQ----N------QGK  168 (311)
T ss_dssp             HHHCTTCHHHHHHHHHHHH-HHHTTTCHHHHHHHHHHHHHHHHHHHCTTC-HHHHHHHHHHHHHHH----T------TTC
T ss_pred             HHhCCCChHHHHHHHHHHH-HHHHcCcHHHHHHHHHHHHHHHHHhcCCCC-hHHHHHHHHHHHHHH----H------cCC
Confidence                   333345555444 4445688999999999998642     111 111111111111110    0      125


Q ss_pred             HHHHHHHHHHHHHHHHhhhcC-CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccc---------hHHHHHHHHHH
Q 008442          157 YSLIRETFQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA---------MLEAWQSYISM  226 (565)
Q Consensus       157 ~~~~~~~~~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~---------~~~lw~~yi~~  226 (565)
                      +..+...|.+++..+...... .+.....+...+.++...+ ++++|..+|++++...+.         ...+|.....+
T Consensus       169 ~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~  247 (311)
T 3nf1_A          169 YEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQG-KFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEER  247 (311)
T ss_dssp             HHHHHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHH
Confidence            566777788887776554332 3334566777888888888 999999999999975321         11123222222


Q ss_pred             H------HHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhh
Q 008442          227 E------IELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTP  282 (565)
Q Consensus       227 e------~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~  282 (565)
                      .      ...+.+..+...+..++..   .+....+|......-...|+.+.+...+++++.
T Consensus       248 ~~~~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          248 EECKGKQKDGTSFGEYGGWYKACKVD---SPTVTTTLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             HHC-------CCSCCCC------------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHhcCchhhHHHHHHHHHHHhhcCCC---CchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            2      2223444444455555431   111223344444445555666666666655543

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=98.77  E-value=1.3e-06  Score=81.13  Aligned_cols=200  Identities=8%  Similarity=-0.062  Sum_probs=129.6

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCC-CCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFP-VSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p-~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~  100 (565)
                      +...|..........|+.+.+...|++++...| .+..+|...+. +....++.+.+...|++|+...|....+|.....
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~-~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~   84 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGV-CADNIKKYKEAADYFDIAIKKNYNLANAYIGKSA   84 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHTTCSHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHH-HHHHhhcHHHHHHHHHHHHHhCcchHHHHHHHHH
Confidence            347788888888889999999999999999998 88888887554 4445567888999999999999998899988776


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCch
Q 008442          101 SLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG  180 (565)
Q Consensus       101 ~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~  180 (565)
                      .+ ...+..+++...|++++...+........+...+...-              .......-+++|+.++...+...+.
T Consensus        85 ~~-~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g--------------~~~~~~~~~~~A~~~~~~al~~~p~  149 (228)
T 4i17_A           85 AY-RDMKNNQEYIATLTEGIKAVPGNATIEKLYAIYYLKEG--------------QKFQQAGNIEKAEENYKHATDVTSK  149 (228)
T ss_dssp             HH-HHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHH--------------HHHHHTTCHHHHHHHHHHHTTSSCH
T ss_pred             HH-HHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHh--------------HHHHHhccHHHHHHHHHHHHhcCCC
Confidence            44 44788999999999999865543322111111111100              0001113355555666555555555


Q ss_pred             --hHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          181 --LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       181 --~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                        ....|...+.+....      +..+++++....+.....+.  .......+.++.|...|++++.
T Consensus       150 ~~~~~~~~~l~~~~~~~------~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~~~~A~~~~~~a~~  208 (228)
T 4i17_A          150 KWKTDALYSLGVLFYNN------GADVLRKATPLASSNKEKYA--SEKAKADAAFKKAVDYLGEAVT  208 (228)
T ss_dssp             HHHHHHHHHHHHHHHHH------HHHHHHHHGGGTTTCHHHHH--HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHH------HHHHHHHHHhcccCCHHHHH--HHHHHHHHHHHHHHHHHHHHhh
Confidence              455555555555332      33445555554333322221  1123344567889999999987

>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=98.77  E-value=1.1e-08  Score=78.35  Aligned_cols=72  Identities=14%  Similarity=0.200  Sum_probs=61.8

Q ss_pred             CCCeEEEcCCCCC------CCH---HHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCe
Q 008442          390 DECTAFLSNINLK------ATY---EDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGK  460 (565)
Q Consensus       390 ~~~~l~V~nl~~~------~~~---~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~  460 (565)
                      ...||+|..++..      .++   .+|.+.|.+||.|..++++.++        +||+|.+.++|.+||.|+|..++||
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            3579999988743      232   5688999999999999998874        9999999999999999999999999


Q ss_pred             EEEEeecCC
Q 008442          461 KLSIARSNP  469 (565)
Q Consensus       461 ~l~v~~a~~  469 (565)
                      .|+|....|
T Consensus        86 ~L~V~~k~~   94 (95)
T 1ufw_A           86 AVKISGPSS   94 (95)
T ss_dssp             EEEEECCCC
T ss_pred             EEEEeccCC
Confidence            999987543

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=98.73  E-value=7.8e-07  Score=79.51  Aligned_cols=156  Identities=11%  Similarity=0.016  Sum_probs=122.3

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...|+.+|..+|.    +...|..........|+.+.+...|++++...|.+...|..+....... ++.+.+...++
T Consensus        23 ~A~~~~~~al~~~p~----~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~a~~~~~   97 (184)
T 3vtx_A           23 GAIRAYKKVLKADPN----NVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTTSAEAYYILGSANFMI-DEKQAAIDALQ   97 (184)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHT-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC----CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHc-CCHHHHHHHHH
Confidence            467889999998887    8899999999999999999999999999999999999999988765544 46778999999


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHH
Q 008442           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRE  162 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~  162 (565)
                      +|+...|....+|......+ ...+..+++...|++++...+.                                     
T Consensus        98 ~a~~~~~~~~~~~~~lg~~~-~~~g~~~~A~~~~~~~l~~~p~-------------------------------------  139 (184)
T 3vtx_A           98 RAIALNTVYADAYYKLGLVY-DSMGEHDKAIEAYEKTISIKPG-------------------------------------  139 (184)
T ss_dssp             HHHHHCTTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTT-------------------------------------
T ss_pred             HHHHhCccchHHHHHHHHHH-HHhCCchhHHHHHHHHHHhcch-------------------------------------
Confidence            99999999998888776533 3367777787777777753322                                     


Q ss_pred             HHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHH
Q 008442          163 TFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAW  220 (565)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw  220 (565)
                                        ....|...+.++...+ ++++|...|+++|+..|++...+
T Consensus       140 ------------------~~~~~~~lg~~~~~~g-~~~~A~~~~~~al~~~p~~a~~~  178 (184)
T 3vtx_A          140 ------------------FIRAYQSIGLAYEGKG-LRDEAVKYFKKALEKEEKKAKYE  178 (184)
T ss_dssp             ------------------CHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHTTHHHHHHC
T ss_pred             ------------------hhhHHHHHHHHHHHCC-CHHHHHHHHHHHHhCCccCHHHH
Confidence                              1223444455556667 88888888888888877765443

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=98.72  E-value=5.1e-07  Score=86.06  Aligned_cols=209  Identities=11%  Similarity=0.013  Sum_probs=137.8

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...|+.++...|.    +...|...+......|+.+.+...|++++...|.+..+|...+..+.. .++.+.+..+|+
T Consensus        61 ~A~~~~~~al~~~~~----~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~-~g~~~~A~~~~~  135 (275)
T 1xnf_A           61 LARNDFSQALAIRPD----MPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYY-GGRDKLAQDDLL  135 (275)
T ss_dssp             HHHHHHHHHHHHCCC----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHH-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCC----cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCccccHHHHHHHHHHHH-hccHHHHHHHHH
Confidence            366788888888876    788999999999999999999999999999999999999999886554 457888999999


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHH
Q 008442           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRE  162 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~  162 (565)
                      +++...|.....+..... . ...+..+++...|.+++...+.....+. +...+        . ...     +......
T Consensus       136 ~a~~~~~~~~~~~~~~~~-~-~~~~~~~~A~~~~~~~~~~~~~~~~~~~-~~~~~--------~-~~~-----~~~~a~~  198 (275)
T 1xnf_A          136 AFYQDDPNDPFRSLWLYL-A-EQKLDEKQAKEVLKQHFEKSDKEQWGWN-IVEFY--------L-GNI-----SEQTLME  198 (275)
T ss_dssp             HHHHHCTTCHHHHHHHHH-H-HHHHCHHHHHHHHHHHHHHSCCCSTHHH-HHHHH--------T-TSS-----CHHHHHH
T ss_pred             HHHHhCCCChHHHHHHHH-H-HHhcCHHHHHHHHHHHHhcCCcchHHHH-HHHHH--------H-Hhc-----CHHHHHH
Confidence            999999987644333222 2 2347789999999998875433211111 00000        0 000     1112222


Q ss_pred             HHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHH
Q 008442          163 TFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIY  240 (565)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~  240 (565)
                      .+.+++...   ....+....++...+.++...+ +++.|...|++++...|++..   .+.......|+++.|.+.|
T Consensus       199 ~~~~~~~~~---~~~~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~al~~~p~~~~---~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          199 RLKADATDN---TSLAEHLSETNFYLGKYYLSLG-DLDSATALFKLAVANNVHNFV---EHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             HHHHHCCSH---HHHHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHTTCCTTCH---HHHHHHHHHHHHHHC----
T ss_pred             HHHHHhccc---ccccccccHHHHHHHHHHHHcC-CHHHHHHHHHHHHhCCchhHH---HHHHHHHHHHHHHhhHHHH
Confidence            233222211   1001122467777888888888 999999999999999886533   2333344455666655544

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=98.69  E-value=8.2e-06  Score=79.57  Aligned_cols=259  Identities=9%  Similarity=-0.076  Sum_probs=157.3

Q ss_pred             HHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCH----HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCC------CCH
Q 008442           23 FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS----DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCP------WVG   92 (565)
Q Consensus        23 ~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~----~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p------~~~   92 (565)
                      ...|..........|+++.+..+|++++...|.+.    .+|...+.... ..++.+.+...|++|+...+      ...
T Consensus         5 ~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~-~~g~~~~A~~~~~~al~~~~~~~~~~~~~   83 (338)
T 3ro2_A            5 CLELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYF-YLHDYAKALEYHHHDLTLARTIGDQLGEA   83 (338)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHHHHHhhcccccHHHH
Confidence            34566666667788999999999999999999985    45555555443 34577889999999987532      223


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc--cHHHHHHHHHHHHHHHHHHhhc---cc-------cchhhhhHHHH
Q 008442           93 ELWVRSLLSLERSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRILF---SG-------EVEGVLDYSLI  160 (565)
Q Consensus        93 ~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~--~~~~~~~~~~~~~~~~~r~~~~---~~-------~~e~~~~~~~~  160 (565)
                      .+|..... +....+..+++...|++++.....  ........+..........-..   ..       ..+....+...
T Consensus        84 ~~~~~l~~-~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A  162 (338)
T 3ro2_A           84 KASGNLGN-TLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAA  162 (338)
T ss_dssp             HHHHHHHH-HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHH
T ss_pred             HHHHHHHH-HHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHH
Confidence            34444443 334468899999999999864221  1111111121111111111000   00       00000113334


Q ss_pred             HHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccc------hHHHHHHHHHHHHHcCChH
Q 008442          161 RETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA------MLEAWQSYISMEIELDHIN  234 (565)
Q Consensus       161 ~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~------~~~lw~~yi~~e~~~~~~~  234 (565)
                      ...|.+++...... ...+.....+...+.+....+ +++.|...|++++...+.      ...+|...+......|+++
T Consensus       163 ~~~~~~a~~~~~~~-~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  240 (338)
T 3ro2_A          163 VDLYEENLSLVTAL-GDRAAQGRAFGNLGNTHYLLG-NFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFE  240 (338)
T ss_dssp             HHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHHHHHHHHhc-CCHHHHHHHHHHHHHHHHHhC-CHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHH
Confidence            44455444443321 112223445666777888888 999999999999987432      1347888888888999999


Q ss_pred             HHHHHHHHHHhcccCCCCcHH---HHHHHHHHHHHhCCHHHHHHHHHHHhhHHH
Q 008442          235 EARSIYKRCYSKRFTGTGSED---ICHAWLRFEREYGTLEDFDHSVQKVTPRLE  285 (565)
Q Consensus       235 ~aR~i~~~al~~~~~~~~~~~---i~~~~~~fE~~~G~~~~~~~~~~k~~~~~~  285 (565)
                      .|..+|++++........+..   ++..........|+.+.+...+.+++....
T Consensus       241 ~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~  294 (338)
T 3ro2_A          241 TASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQ  294 (338)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHH
Confidence            999999999864222222322   334444556677998888888877765443

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=98.68  E-value=1.5e-05  Score=76.06  Aligned_cols=228  Identities=11%  Similarity=0.008  Sum_probs=149.3

Q ss_pred             hHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh---cchhhHHHHHHHHHHHcCCCCHHHHH
Q 008442           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKT---LKVGNVVRDVYSRATKNCPWVGELWV   96 (565)
Q Consensus        20 ~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~---~~~~~~~~~v~erAl~~~p~~~~lW~   96 (565)
                      +.+...|..........++++.+...|++++.  |.+...|..........   .++.+.+...|++|+...  ....|.
T Consensus         3 ~~~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~--~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~--~~~a~~   78 (273)
T 1ouv_A            3 EQDPKELVGLGAKSYKEKDFTQAKKYFEKACD--LKENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN--YSNGCH   78 (273)
T ss_dssp             --CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--TTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT--CHHHHH
T ss_pred             CCChHHHHHHHHHHHhCCCHHHHHHHHHHHHH--CCCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC--CHHHHH
Confidence            34677888888888888999999999999999  67888888877655430   457788999999999864  556665


Q ss_pred             HHHHHHHH---hcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHh
Q 008442           97 RSLLSLER---SRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSE  173 (565)
Q Consensus        97 ~yi~~le~---~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~  173 (565)
                      .....+..   ..++.+++...|++|+.....  ..+..+-..+..        ...+  ..++......|+++++.   
T Consensus        79 ~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~--~a~~~lg~~~~~--------~~~~--~~~~~~A~~~~~~a~~~---  143 (273)
T 1ouv_A           79 LLGNLYYSGQGVSQNTNKALQYYSKACDLKYA--EGCASLGGIYHD--------GKVV--TRDFKKAVEYFTKACDL---  143 (273)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCH--HHHHHHHHHHHH--------CSSS--CCCHHHHHHHHHHHHHT---
T ss_pred             HHHHHHhCCCCcccCHHHHHHHHHHHHHcCCc--cHHHHHHHHHHc--------CCCc--ccCHHHHHHHHHHHHhc---
Confidence            55443322   167889999999999976422  222222222210        0000  01444455555555442   


Q ss_pred             hhcCCchhHHHHHHHHHHHHH----cCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHH----cCChHHHHHHHHHHHh
Q 008442          174 QMKNTDGLLRLYAYWAHLEQS----MGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE----LDHINEARSIYKRCYS  245 (565)
Q Consensus       174 ~~~~~~~~~~l~~~~a~~e~~----~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~----~~~~~~aR~i~~~al~  245 (565)
                          .+  ...+..++.+...    .+ ++++|...|++++...  ....+.....+...    .++++.|...|++++.
T Consensus       144 ----~~--~~a~~~lg~~~~~~~~~~~-~~~~A~~~~~~a~~~~--~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~  214 (273)
T 1ouv_A          144 ----ND--GDGCTILGSLYDAGRGTPK-DLKKALASYDKACDLK--DSPGCFNAGNMYHHGEGATKNFKEALARYSKACE  214 (273)
T ss_dssp             ----TC--HHHHHHHHHHHHHTSSSCC-CHHHHHHHHHHHHHTT--CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHH
T ss_pred             ----Cc--HHHHHHHHHHHHcCCCCCC-CHHHHHHHHHHHHHCC--CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHh
Confidence                22  2344555666666    56 9999999999999873  46777788888888    8999999999999987


Q ss_pred             cccCCCCcHHHHHHHHHHHHH----hCCHHHHHHHHHHH
Q 008442          246 KRFTGTGSEDICHAWLRFERE----YGTLEDFDHSVQKV  280 (565)
Q Consensus       246 ~~~~~~~~~~i~~~~~~fE~~----~G~~~~~~~~~~k~  280 (565)
                      .     .+...+.....+-..    .|+.+.+...++++
T Consensus       215 ~-----~~~~a~~~l~~~~~~g~~~~~~~~~A~~~~~~a  248 (273)
T 1ouv_A          215 L-----ENGGGCFNLGAMQYNGEGVTRNEKQAIENFKKG  248 (273)
T ss_dssp             T-----TCHHHHHHHHHHHHTTSSSSCCSTTHHHHHHHH
T ss_pred             C-----CCHHHHHHHHHHHHcCCCcccCHHHHHHHHHHH
Confidence            3     123333333333333    45666555555554

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=98.67  E-value=4.4e-06  Score=86.68  Aligned_cols=126  Identities=11%  Similarity=-0.001  Sum_probs=81.6

Q ss_pred             hhHHHHHHHhcC-----CCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCC--------CCHHHHHHHHH-HHHH
Q 008442            4 ARAHLEEQISRQ-----DLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFP--------VSSDLWLDYTQ-YLDK   69 (565)
Q Consensus         4 ~R~~~E~~l~~~-----~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p--------~~~~lW~~Y~~-~l~~   69 (565)
                      |...|+.++.-.     ...++.....|..+.......|+.+.+...|++++..++        ....++..... ++..
T Consensus        70 Al~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~~~~~~~~~~~~~~g~~~~~~  149 (472)
T 4g1t_A           70 ALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSSPYRIESPELDCEEGWTRLKC  149 (472)
T ss_dssp             HHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCSSCCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcccccchhhHHHHHHHHHHHHHH
Confidence            455666665321     111233566788888777788999999999999987532        33445544322 2222


Q ss_pred             hcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHH--hcCCHHHHHHHHHHHHhcccccHHH
Q 008442           70 TLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER--SRASEEEISTVFEKSLLCAFSTFEE  129 (565)
Q Consensus        70 ~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~--~~~~~~~~~~if~ral~~~~~~~~~  129 (565)
                      ..+..+.+...|++|+...|..+.+|..+......  ..+..+++...|++|+...+.....
T Consensus       150 ~~~~y~~A~~~~~kal~~~p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~p~~~~~  211 (472)
T 4g1t_A          150 GGNQNERAKVCFEKALEKKPKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLNPDNQYL  211 (472)
T ss_dssp             CTTHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHCSSCHHH
T ss_pred             ccccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcCCcchHH
Confidence            33467789999999999999999888777643222  2344556778889998766554333

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=98.64  E-value=1.3e-05  Score=80.79  Aligned_cols=258  Identities=9%  Similarity=-0.086  Sum_probs=157.6

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCH----HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCC------CC
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS----DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCP------WV   91 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~----~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p------~~   91 (565)
                      ....|..........|+++.+..+|++++...|.+.    .+|...+.... ..++.+.+...|++|+...+      ..
T Consensus         8 ~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~-~~g~~~~A~~~~~~al~~~~~~~~~~~~   86 (406)
T 3sf4_A            8 SCLELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYF-YLHDYAKALEYHHHDLTLARTIGDQLGE   86 (406)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHH-HhcCHHHHHHHHHHHHHHHHhccccHHH
Confidence            345677777777888999999999999999999885    45666555443 44577889999999987532      12


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc--cHHHHHHHHHHHHHHHHHHhh-----ccc-----cchhhhhHHH
Q 008442           92 GELWVRSLLSLERSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRIL-----FSG-----EVEGVLDYSL  159 (565)
Q Consensus        92 ~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~--~~~~~~~~~~~~~~~~~r~~~-----~~~-----~~e~~~~~~~  159 (565)
                      ..+|..... +....+..+++...|++++.....  ........+..........-.     ...     ..+....+..
T Consensus        87 ~~~~~~la~-~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~  165 (406)
T 3sf4_A           87 AKASGNLGN-TLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQA  165 (406)
T ss_dssp             HHHHHHHHH-HHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHH
T ss_pred             HHHHHHHHH-HHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHH
Confidence            334444443 334468899999999999864221  111111111111111110000     000     0000011334


Q ss_pred             HHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccch------HHHHHHHHHHHHHcCCh
Q 008442          160 IRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM------LEAWQSYISMEIELDHI  233 (565)
Q Consensus       160 ~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~------~~lw~~yi~~e~~~~~~  233 (565)
                      +...|.+++.+.... ...+.....+...+.+....+ +++.|...|++++...+..      ..+|...+......|++
T Consensus       166 A~~~~~~al~~~~~~-~~~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~  243 (406)
T 3sf4_A          166 AVDFYEENLSLVTAL-GDRAAQGRAFGNLGNTHYLLG-NFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEF  243 (406)
T ss_dssp             HHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHHT-BHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHhc-cCcHHHHHHHHHHHHHHHHcc-CHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCh
Confidence            444455554444322 112223456667788888888 9999999999999874322      33777888888899999


Q ss_pred             HHHHHHHHHHHhcccCCCCcHH---HHHHHHHHHHHhCCHHHHHHHHHHHhhH
Q 008442          234 NEARSIYKRCYSKRFTGTGSED---ICHAWLRFEREYGTLEDFDHSVQKVTPR  283 (565)
Q Consensus       234 ~~aR~i~~~al~~~~~~~~~~~---i~~~~~~fE~~~G~~~~~~~~~~k~~~~  283 (565)
                      +.|..+|++++...-....+..   ++..........|+.+.+...+.+++..
T Consensus       244 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  296 (406)
T 3sf4_A          244 ETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAI  296 (406)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHH
Confidence            9999999999863222222222   3334444556678888888777776644

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.62  E-value=3.8e-06  Score=81.70  Aligned_cols=104  Identities=13%  Similarity=0.074  Sum_probs=58.5

Q ss_pred             hHHHHHHHHHHHHhcCCc-hhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc-chhhHHHHHHHHHHHcCCCCHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDP-GRVQLLYERAITDFPVSSDLWLDYTQYLDKTL-KVGNVVRDVYSRATKNCPWVGELWVRSL   99 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~-~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~-~~~~~~~~v~erAl~~~p~~~~lW~~yi   99 (565)
                      .+..-+.|+.-....+.. +++..+++++|..+|.+..+|..-...+.... ...+..+..++.+|...|.+..+|....
T Consensus        31 ~y~~~~~~~~a~~~~~e~s~~aL~~t~~~L~~nP~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk~y~aW~~R~  110 (306)
T 3dra_A           31 DYKQIMGLLLALMKAEEYSERALHITELGINELASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNEKNYQIWNYRQ  110 (306)
T ss_dssp             HHHHHHHHHHHHHHTTCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCcHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCcccHHHHHHHH
Confidence            334444444444444433 46666777777777777777766555444333 2555666677777776676666666654


Q ss_pred             HHH----HHhc--CCHHHHHHHHHHHHhcccc
Q 008442          100 LSL----ERSR--ASEEEISTVFEKSLLCAFS  125 (565)
Q Consensus       100 ~~l----e~~~--~~~~~~~~if~ral~~~~~  125 (565)
                      ..+    ....  ...++...++++++...+.
T Consensus       111 ~iL~~~~~~l~~~~~~~~EL~~~~~~l~~~pk  142 (306)
T 3dra_A          111 LIIGQIMELNNNDFDPYREFDILEAMLSSDPK  142 (306)
T ss_dssp             HHHHHHHHHTTTCCCTHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHhccccCCHHHHHHHHHHHHHhCCC
Confidence            444    2211  3455555666666654443

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=98.60  E-value=2.5e-05  Score=75.66  Aligned_cols=230  Identities=9%  Similarity=0.059  Sum_probs=148.7

Q ss_pred             CChHh-HHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHc--CCCCHHH
Q 008442           18 SDSEK-FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKN--CPWVGEL   94 (565)
Q Consensus        18 ~~~~~-~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~--~p~~~~l   94 (565)
                      .+|++ .+...-++......|.++.+...++.   ..|.+......++.++.. .+..+.+.++|++.+..  .|.+..+
T Consensus        28 ~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~---~~~~~~~a~~~la~~~~~-~~~~~~A~~~l~~ll~~~~~P~~~~~  103 (291)
T 3mkr_A           28 SSPERDVERDVFLYRAYLAQRKYGVVLDEIKP---SSAPELQAVRMFAEYLAS-HSRRDAIVAELDREMSRSVDVTNTTF  103 (291)
T ss_dssp             CSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT---TSCHHHHHHHHHHHHHHC-STTHHHHHHHHHHHHHSCCCCSCHHH
T ss_pred             CCchhhHHHHHHHHHHHHHCCCHHHHHHHhcc---cCChhHHHHHHHHHHHcC-CCcHHHHHHHHHHHHhcccCCCCHHH
Confidence            34444 34545555666677888777776654   234344455555665543 34677899999999975  4888888


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhh
Q 008442           95 WVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQ  174 (565)
Q Consensus        95 W~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~  174 (565)
                      |......+ ...+..+++..+|++     +.....+..+...+..        .      .+++.+...|++++..-   
T Consensus       104 ~~~la~~~-~~~g~~~~Al~~l~~-----~~~~~~~~~l~~~~~~--------~------g~~~~A~~~l~~~~~~~---  160 (291)
T 3mkr_A          104 LLMAASIY-FYDQNPDAALRTLHQ-----GDSLECMAMTVQILLK--------L------DRLDLARKELKKMQDQD---  160 (291)
T ss_dssp             HHHHHHHH-HHTTCHHHHHHHHTT-----CCSHHHHHHHHHHHHH--------T------TCHHHHHHHHHHHHHHC---
T ss_pred             HHHHHHHH-HHCCCHHHHHHHHhC-----CCCHHHHHHHHHHHHH--------C------CCHHHHHHHHHHHHhhC---
Confidence            87765534 346889999999887     2223323222222110        0      13344455555554431   


Q ss_pred             hcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcH
Q 008442          175 MKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSE  254 (565)
Q Consensus       175 ~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~  254 (565)
                        ..+....+...|+.+....+ ++++|..+|++++..+|++..+|...+......|+++.|...|++++..  ..+ ..
T Consensus       161 --p~~~~~~l~~a~~~l~~~~~-~~~eA~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~--~p~-~~  234 (291)
T 3mkr_A          161 --EDATLTQLATAWVSLAAGGE-KLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDK--DSG-HP  234 (291)
T ss_dssp             --TTCHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT-CH
T ss_pred             --cCcHHHHHHHHHHHHHhCch-HHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCC-CH
Confidence              11222344445666655445 8999999999999999999999999999999999999999999999973  333 34


Q ss_pred             HHHHHHHHHHHHhCCHH-HHHHHHHHH
Q 008442          255 DICHAWLRFEREYGTLE-DFDHSVQKV  280 (565)
Q Consensus       255 ~i~~~~~~fE~~~G~~~-~~~~~~~k~  280 (565)
                      ..|.....+-...|..+ .+...++++
T Consensus       235 ~~l~~l~~~~~~~g~~~eaa~~~~~~~  261 (291)
T 3mkr_A          235 ETLINLVVLSQHLGKPPEVTNRYLSQL  261 (291)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            56666666666678654 344455444

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=98.60  E-value=2.4e-06  Score=81.35  Aligned_cols=229  Identities=14%  Similarity=0.069  Sum_probs=132.8

Q ss_pred             hcCCchhHHHHHHHHHhc--------CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcC--------CCCHHHHHHH
Q 008442           35 SSGDPGRVQLLYERAITD--------FPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNC--------PWVGELWVRS   98 (565)
Q Consensus        35 ~~~~~~~~~~lyERal~~--------~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~--------p~~~~lW~~y   98 (565)
                      ..|+++.+..+|++|+..        .|....+|...+.... ..+..+.+...|++|+...        |....+|...
T Consensus        13 ~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~-~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l   91 (283)
T 3edt_B           13 GLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYR-DQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNL   91 (283)
T ss_dssp             CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH-HcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHH
Confidence            457888899999999884        3555667777666544 4457788999999999864        3334455555


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcc-----cccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHh
Q 008442           99 LLSLERSRASEEEISTVFEKSLLCA-----FSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSE  173 (565)
Q Consensus        99 i~~le~~~~~~~~~~~if~ral~~~-----~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~  173 (565)
                      .. +....+..+++...|++++...     ... ......+........          ...++..+...|++++..+..
T Consensus        92 ~~-~~~~~g~~~~A~~~~~~al~~~~~~~~~~~-~~~~~~~~~la~~~~----------~~g~~~~A~~~~~~al~~~~~  159 (283)
T 3edt_B           92 AV-LYGKRGKYKEAEPLCKRALEIREKVLGKFH-PDVAKQLNNLALLCQ----------NQGKAEEVEYYYRRALEIYAT  159 (283)
T ss_dssp             HH-HHHTTTCHHHHHHHHHHHHHHHHHHHCTTC-HHHHHHHHHHHHHHH----------TTTCHHHHHHHHHHHHHHHHH
T ss_pred             HH-HHHHhccHHHHHHHHHHHHHHHHHHcCCCC-hHHHHHHHHHHHHHH----------HcCCHHHHHHHHHHHHHHHHH
Confidence            54 3445788999999999998641     100 111111111111110          012556677788888877655


Q ss_pred             hhcC-CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHc---------cchHHHHHHHHHHHHHcCChH------HHH
Q 008442          174 QMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS---------GAMLEAWQSYISMEIELDHIN------EAR  237 (565)
Q Consensus       174 ~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~---------~~~~~lw~~yi~~e~~~~~~~------~aR  237 (565)
                      .... .+.....+..++.++...+ +++.|..+|++++...         +....+|.....++...+...      .+.
T Consensus       160 ~~~~~~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (283)
T 3edt_B          160 RLGPDDPNVAKTKNNLASCYLKQG-KYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYG  238 (283)
T ss_dssp             HSCTTCHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC--------
T ss_pred             hcCCCCHHHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHH
Confidence            4433 3334567777888888888 9999999999999862         222345555555554333222      222


Q ss_pred             HHHHHHHhcccCCCCcH--HHHHHHHHHHHHhCCHHHHHHHHHHHhh
Q 008442          238 SIYKRCYSKRFTGTGSE--DICHAWLRFEREYGTLEDFDHSVQKVTP  282 (565)
Q Consensus       238 ~i~~~al~~~~~~~~~~--~i~~~~~~fE~~~G~~~~~~~~~~k~~~  282 (565)
                      .+++...     ...+.  ..+......-...|+.+.+...+++++.
T Consensus       239 ~~~~~~~-----~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          239 SWYKACK-----VDSPTVNTTLRSLGALYRRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             ----CCC-----CCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHhcC-----CCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            2222111     11121  2333344455556776666666666543

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=98.56  E-value=3.6e-07  Score=81.44  Aligned_cols=164  Identities=13%  Similarity=0.057  Sum_probs=106.4

Q ss_pred             HHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Q 008442           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLE  103 (565)
Q Consensus        24 ~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le  103 (565)
                      +.+..........|+++.+...|++++...|.+...|..++..+.. .+..+.+...|++++...| ...++..... +.
T Consensus         7 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~-~g~~~~A~~~~~~a~~~~p-~~~~~~~~~~-~~   83 (176)
T 2r5s_A            7 EQLLKQVSELLQQGEHAQALNVIQTLSDELQSRGDVKLAKADCLLE-TKQFELAQELLATIPLEYQ-DNSYKSLIAK-LE   83 (176)
T ss_dssp             TTHHHHHHHHHHTTCHHHHHHHHHTSCHHHHTSHHHHHHHHHHHHH-TTCHHHHHHHHTTCCGGGC-CHHHHHHHHH-HH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHH-CCCHHHHHHHHHHhhhccC-ChHHHHHHHH-HH
Confidence            3455555555667777777788888888778888887777765543 3356667777777777767 5443322111 10


Q ss_pred             HhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHH
Q 008442          104 RSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLR  183 (565)
Q Consensus       104 ~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~  183 (565)
                      ..           .+                          .          +.......|++++..       .+....
T Consensus        84 ~~-----------~~--------------------------~----------~~~~a~~~~~~al~~-------~P~~~~  109 (176)
T 2r5s_A           84 LH-----------QQ--------------------------A----------AESPELKRLEQELAA-------NPDNFE  109 (176)
T ss_dssp             HH-----------HH--------------------------H----------TSCHHHHHHHHHHHH-------STTCHH
T ss_pred             HH-----------hh--------------------------c----------ccchHHHHHHHHHHh-------CCCCHH
Confidence            00           00                          0          000011223333221       233445


Q ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHHHHHccch--HHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          184 LYAYWAHLEQSMGKDMVSARGVWERLLKISGAM--LEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~--~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      .+..++.+....+ ++++|...|++++...|+.  ...|...+......|+.+.|...|.++|.
T Consensus       110 ~~~~la~~~~~~g-~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~~al~  172 (176)
T 2r5s_A          110 LACELAVQYNQVG-RDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYRRQLY  172 (176)
T ss_dssp             HHHHHHHHHHHTT-CHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcc-cHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHHHHHH
Confidence            6667777887888 9999999999999988765  56898999999899999999999999886

>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=98.53  E-value=1.9e-07  Score=86.90  Aligned_cols=67  Identities=16%  Similarity=0.198  Sum_probs=59.7

Q ss_pred             CCHHHHHHHhccCCCeeEEEEeecC----CCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          403 ATYEDLRRFFSDVGGVSSIRILHDK----FTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       403 ~~~~~l~~~f~~~G~i~~~~~~~~~----~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      -.+++|+..|++||.|.++.|+.+.    .+|.++|++||+|.+.++|.+|+. |||..++||+|.|.++..
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            3568999999999999999998554    345899999999999999999998 899999999999999764

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.52  E-value=2.3e-05  Score=74.34  Aligned_cols=185  Identities=11%  Similarity=-0.033  Sum_probs=126.6

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCC---HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCH---HHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVS---SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVG---ELW   95 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~---~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~---~lW   95 (565)
                      +...+..........|+++.+..+|++++..+|.+   ...|...+.... ..++.+.+...|++++...|.+.   ..|
T Consensus        14 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~-~~~~~~~A~~~~~~~l~~~p~~~~~~~a~   92 (261)
T 3qky_A           14 SPQEAFERAMEFYNQGKYDRAIEYFKAVFTYGRTHEWAADAQFYLARAYY-QNKEYLLAASEYERFIQIYQIDPRVPQAE   92 (261)
T ss_dssp             SHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGCSCSTTHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCTTHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHH-HhCcHHHHHHHHHHHHHHCCCCchhHHHH
Confidence            56777777777788999999999999999999998   777777765444 44578889999999999988543   333


Q ss_pred             HHHHHHHHH-------hcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHH
Q 008442           96 VRSLLSLER-------SRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRAS  168 (565)
Q Consensus        96 ~~yi~~le~-------~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~  168 (565)
                      ......+..       ..+..+++...|++++...+......  ....++.                   .+...+    
T Consensus        93 ~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~--~a~~~~~-------------------~~~~~~----  147 (261)
T 3qky_A           93 YERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRYPNHELVD--DATQKIR-------------------ELRAKL----  147 (261)
T ss_dssp             HHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCTTCTTHH--HHHHHHH-------------------HHHHHH----
T ss_pred             HHHHHHHHHhcccccccchhHHHHHHHHHHHHHHCcCchhHH--HHHHHHH-------------------HHHHHH----
Confidence            333322221       14667889999999887544321100  0000000                   000100    


Q ss_pred             HHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccc---hHHHHHHHHHHHHHc----------CChHH
Q 008442          169 DYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA---MLEAWQSYISMEIEL----------DHINE  235 (565)
Q Consensus       169 ~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~---~~~lw~~yi~~e~~~----------~~~~~  235 (565)
                                   ...+...+.++...+ +++.|...|++++..+|+   ....|...+......          |+++.
T Consensus       148 -------------~~~~~~la~~~~~~g-~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~  213 (261)
T 3qky_A          148 -------------ARKQYEAARLYERRE-LYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRR  213 (261)
T ss_dssp             -------------HHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHH
T ss_pred             -------------HHHHHHHHHHHHHcc-CHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHH
Confidence                         111334566677778 999999999999999877   456777776666544          88899


Q ss_pred             HHHHHHHHHhc
Q 008442          236 ARSIYKRCYSK  246 (565)
Q Consensus       236 aR~i~~~al~~  246 (565)
                      |...|++++..
T Consensus       214 A~~~~~~~~~~  224 (261)
T 3qky_A          214 AVELYERLLQI  224 (261)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999999973

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.51  E-value=1.4e-05  Score=77.65  Aligned_cols=220  Identities=9%  Similarity=0.057  Sum_probs=161.5

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcC--CchhHHHHHHHHHhcCCCCHHHHHHHHHHHH---Hhc---chhh
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSG--DPGRVQLLYERAITDFPVSSDLWLDYTQYLD---KTL---KVGN   75 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~--~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~---~~~---~~~~   75 (565)
                      +-..++.+|.-+|.    ++.+|..-.......+  ..+....+++.+|..+|.++.+|..-...+.   ...   ...+
T Consensus        52 aL~~t~~~L~~nP~----~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk~y~aW~~R~~iL~~~~~~l~~~~~~~  127 (306)
T 3dra_A           52 ALHITELGINELAS----HYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNEKNYQIWNYRQLIIGQIMELNNNDFDPY  127 (306)
T ss_dssp             HHHHHHHHHHHCTT----CHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHHHTTTCCCTH
T ss_pred             HHHHHHHHHHHCcH----HHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCcccHHHHHHHHHHHHHHHHhccccCCHH
Confidence            44667788888887    8999998888887777  8899999999999999999999998776552   222   4566


Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHH--HHHHHHHHHHhcccccHH--HHHHHHHHHHHHHHHHhhccccc
Q 008442           76 VVRDVYSRATKNCPWVGELWVRSLLSLERSRASEE--EISTVFEKSLLCAFSTFE--EYLDLFLTRIDGLRRRILFSGEV  151 (565)
Q Consensus        76 ~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~--~~~~if~ral~~~~~~~~--~~~~~~~~~~~~~~r~~~~~~~~  151 (565)
                      ....++++++...|.+...|....-.+.. .+..+  +....+++++...+..+.  .+....+..            . 
T Consensus       128 ~EL~~~~~~l~~~pkny~aW~~R~~vl~~-l~~~~~~~EL~~~~~~i~~d~~N~sAW~~R~~ll~~------------l-  193 (306)
T 3dra_A          128 REFDILEAMLSSDPKNHHVWSYRKWLVDT-FDLHNDAKELSFVDKVIDTDLKNNSAWSHRFFLLFS------------K-  193 (306)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCTTCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHS------------S-
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHH-hcccChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHh------------c-
Confidence            78899999999999999999887655554 34444  677888999876655332  222211100            0 


Q ss_pred             hhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHc---cchHHHHHHHHHHHH
Q 008442          152 EGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS---GAMLEAWQSYISMEI  228 (565)
Q Consensus       152 e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~---~~~~~lw~~yi~~e~  228 (565)
                          ........++++++++...+...+.....|.+..-+....+...+.+..+.++++...   +.+...|...++...
T Consensus       194 ----~~~~~~~~~~eEl~~~~~aI~~~p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~  269 (306)
T 3dra_A          194 ----KHLATDNTIDEELNYVKDKIVKCPQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYT  269 (306)
T ss_dssp             ----GGGCCHHHHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHH
T ss_pred             ----cccchhhhHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHH
Confidence                0001234588888888887776666777888877777777766776777777777643   566777777777777


Q ss_pred             HcCChHHHHHHHHHHHh
Q 008442          229 ELDHINEARSIYKRCYS  245 (565)
Q Consensus       229 ~~~~~~~aR~i~~~al~  245 (565)
                      ..|+.+.|.++|+.++.
T Consensus       270 ~~~~~~~A~~~~~~l~~  286 (306)
T 3dra_A          270 QQKKYNESRTVYDLLKS  286 (306)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHh
Confidence            88899999999999875

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=98.51  E-value=1e-05  Score=74.90  Aligned_cols=170  Identities=9%  Similarity=-0.017  Sum_probs=112.7

Q ss_pred             CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHH
Q 008442           54 PVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCP-WVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLD  132 (565)
Q Consensus        54 p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p-~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~  132 (565)
                      +.+++.|......... .++.+.+...|++|+...| ....+|..... .....+..+++...|++++...+.....+..
T Consensus         4 ~~~~~~~~~~g~~~~~-~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~-~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~   81 (228)
T 4i17_A            4 TTDPNQLKNEGNDALN-AKNYAVAFEKYSEYLKLTNNQDSVTAYNCGV-CADNIKKYKEAADYFDIAIKKNYNLANAYIG   81 (228)
T ss_dssp             CCCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHTTTCCHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHTTCSHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHH-ccCHHHHHHHHHHHHhccCCCCcHHHHHHHH-HHHHhhcHHHHHHHHHHHHHhCcchHHHHHH
Confidence            4566777777765554 4477889999999999998 77777766444 4445788999999999999876654443333


Q ss_pred             HHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH
Q 008442          133 LFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI  212 (565)
Q Consensus       133 ~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~  212 (565)
                      +-..+...              .++......|++++...............+|...+.+....+ ++++|...|++++..
T Consensus        82 l~~~~~~~--------------~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~~~~-~~~~A~~~~~~al~~  146 (228)
T 4i17_A           82 KSAAYRDM--------------KNNQEYIATLTEGIKAVPGNATIEKLYAIYYLKEGQKFQQAG-NIEKAEENYKHATDV  146 (228)
T ss_dssp             HHHHHHHT--------------TCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHTTS
T ss_pred             HHHHHHHc--------------ccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhHHHHHhc-cHHHHHHHHHHHHhc
Confidence            33322210              144455555665555321100000011144666677777888 999999999999999


Q ss_pred             ccc--hHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          213 SGA--MLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       213 ~~~--~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      .|+  ....|..........     ++.+++++..
T Consensus       147 ~p~~~~~~~~~~l~~~~~~~-----~~~~~~~a~~  176 (228)
T 4i17_A          147 TSKKWKTDALYSLGVLFYNN-----GADVLRKATP  176 (228)
T ss_dssp             SCHHHHHHHHHHHHHHHHHH-----HHHHHHHHGG
T ss_pred             CCCcccHHHHHHHHHHHHHH-----HHHHHHHHHh
Confidence            999  888888888877443     4455666654

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=98.50  E-value=6.8e-06  Score=89.85  Aligned_cols=171  Identities=14%  Similarity=0.155  Sum_probs=126.7

Q ss_pred             cCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHH
Q 008442           52 DFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYL  131 (565)
Q Consensus        52 ~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~  131 (565)
                      .+|.+.+.|......+.. .+..+.+...|++||...|.....|......+ ...+..+++...|++|+...+.      
T Consensus         4 s~P~~a~al~nLG~~~~~-~G~~~eAi~~~~kAl~l~P~~~~a~~nLg~~l-~~~g~~~eA~~~~~~Al~l~P~------   75 (723)
T 4gyw_A            4 SCPTHADSLNNLANIKRE-QGNIEEAVRLYRKALEVFPEFAAAHSNLASVL-QQQGKLQEALMHYKEAIRISPT------   75 (723)
T ss_dssp             --CHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTT------
T ss_pred             CCCCcHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHhCCC------
Confidence            467777888877765443 44677788888888888888888887766533 3357777777777777753332      


Q ss_pred             HHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHH
Q 008442          132 DLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLK  211 (565)
Q Consensus       132 ~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~  211 (565)
                                                                       ....|..++.++...+ ++++|...|+++++
T Consensus        76 -------------------------------------------------~~~a~~nLg~~l~~~g-~~~~A~~~~~kAl~  105 (723)
T 4gyw_A           76 -------------------------------------------------FADAYSNMGNTLKEMQ-DVQGALQCYTRAIQ  105 (723)
T ss_dssp             -------------------------------------------------CHHHHHHHHHHHHHTT-CHHHHHHHHHHHHH
T ss_pred             -------------------------------------------------CHHHHHHHHHHHHHcC-CHHHHHHHHHHHHH
Confidence                                                             2223444555566777 99999999999999


Q ss_pred             HccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhhH
Q 008442          212 ISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPR  283 (565)
Q Consensus       212 ~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~~  283 (565)
                      ..|++...|..........|+++.|...|++|+..  . +.....+..+...-...|+.+.+.+.+++++..
T Consensus       106 l~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l--~-P~~~~a~~~L~~~l~~~g~~~~A~~~~~kal~l  174 (723)
T 4gyw_A          106 INPAFADAHSNLASIHKDSGNIPEAIASYRTALKL--K-PDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSI  174 (723)
T ss_dssp             HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--C-SCCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHH
T ss_pred             hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--C-CCChHHHhhhhhHHHhcccHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999973  2 234456666666667778888777777766543

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=98.46  E-value=5.7e-05  Score=71.98  Aligned_cols=208  Identities=10%  Similarity=-0.052  Sum_probs=142.0

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHh----cCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh---cchhhH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQS----SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKT---LKVGNV   76 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~----~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~---~~~~~~   76 (565)
                      +...|+.++..  .    +...|.........    .++++.+...|++++...  +...|..........   .++.+.
T Consensus        25 A~~~~~~a~~~--~----~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~--~~~a~~~lg~~~~~g~~~~~~~~~   96 (273)
T 1ouv_A           25 AKKYFEKACDL--K----ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN--YSNGCHLLGNLYYSGQGVSQNTNK   96 (273)
T ss_dssp             HHHHHHHHHHT--T----CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT--CHHHHHHHHHHHHHTSSSCCCHHH
T ss_pred             HHHHHHHHHHC--C----CHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC--CHHHHHHHHHHHhCCCCcccCHHH
Confidence            45667777772  2    45677777777777    889999999999999885  788888777655431   457788


Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHh---cCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchh
Q 008442           77 VRDVYSRATKNCPWVGELWVRSLLSLERS---RASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEG  153 (565)
Q Consensus        77 ~~~v~erAl~~~p~~~~lW~~yi~~le~~---~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~  153 (565)
                      +...|++|+..-  ....|......+...   .++.+++...|++|+.....  ..+..+-..+..        ....  
T Consensus        97 A~~~~~~a~~~~--~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~~~--~a~~~lg~~~~~--------~~~~--  162 (273)
T 1ouv_A           97 ALQYYSKACDLK--YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLNDG--DGCTILGSLYDA--------GRGT--  162 (273)
T ss_dssp             HHHHHHHHHHTT--CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTTCH--HHHHHHHHHHHH--------TSSS--
T ss_pred             HHHHHHHHHHcC--CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcCcH--HHHHHHHHHHHc--------CCCC--
Confidence            999999999863  556666555433331   57899999999999986532  222222221110        0000  


Q ss_pred             hhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHH----cCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHH
Q 008442          154 VLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQS----MGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE  229 (565)
Q Consensus       154 ~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~----~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~  229 (565)
                      ..++......|+++++.       .+  ...+..++.++..    .+ ++++|...|++++...+  ...+.....+...
T Consensus       163 ~~~~~~A~~~~~~a~~~-------~~--~~a~~~lg~~~~~g~~~~~-~~~~A~~~~~~a~~~~~--~~a~~~l~~~~~~  230 (273)
T 1ouv_A          163 PKDLKKALASYDKACDL-------KD--SPGCFNAGNMYHHGEGATK-NFKEALARYSKACELEN--GGGCFNLGAMQYN  230 (273)
T ss_dssp             CCCHHHHHHHHHHHHHT-------TC--HHHHHHHHHHHHHTCSSCC-CHHHHHHHHHHHHHTTC--HHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHC-------CC--HHHHHHHHHHHHcCCCCCc-cHHHHHHHHHHHHhCCC--HHHHHHHHHHHHc
Confidence            01444445555555432       22  2345556677766    66 99999999999998854  6677777777777


Q ss_pred             ----cCChHHHHHHHHHHHh
Q 008442          230 ----LDHINEARSIYKRCYS  245 (565)
Q Consensus       230 ----~~~~~~aR~i~~~al~  245 (565)
                          .++++.|...|++++.
T Consensus       231 g~~~~~~~~~A~~~~~~a~~  250 (273)
T 1ouv_A          231 GEGVTRNEKQAIENFKKGCK  250 (273)
T ss_dssp             TSSSSCCSTTHHHHHHHHHH
T ss_pred             CCCcccCHHHHHHHHHHHHH
Confidence                8999999999999987

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=98.44  E-value=9.3e-05  Score=72.80  Aligned_cols=194  Identities=12%  Similarity=0.084  Sum_probs=133.8

Q ss_pred             HHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Q 008442           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLE  103 (565)
Q Consensus        24 ~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le  103 (565)
                      .+|..+..........+++..+++++|..+|.+..+|..-...+.......+.....++.+|...|.+..+|......++
T Consensus        55 ~~~~~~r~~~~~~e~se~AL~lt~~~L~~nP~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPKny~aW~hR~wlL~  134 (349)
T 3q7a_A           55 DAMDYFRAIAAKEEKSERALELTEIIVRMNPAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLKSYQVWHHRLLLLD  134 (349)
T ss_dssp             HHHHHHHHHHHTTCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHhCchhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH
Confidence            34444333333444557899999999999999999999887766654445778999999999999999999998877666


Q ss_pred             HhcC-CHHHHHHHHHHHHhcccccHH--HHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCch
Q 008442          104 RSRA-SEEEISTVFEKSLLCAFSTFE--EYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG  180 (565)
Q Consensus       104 ~~~~-~~~~~~~if~ral~~~~~~~~--~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~  180 (565)
                      ...+ ..++....+.+++...+..+.  .+.......+.      .....         ....+.++++++...+..++.
T Consensus       135 ~l~~~~~~~EL~~~~k~L~~dpkNy~AW~~R~wvl~~l~------~~~~~---------~~~~~~eELe~~~k~I~~dp~  199 (349)
T 3q7a_A          135 RISPQDPVSEIEYIHGSLLPDPKNYHTWAYLHWLYSHFS------TLGRI---------SEAQWGSELDWCNEMLRVDGR  199 (349)
T ss_dssp             HHCCSCCHHHHHHHHHHTSSCTTCHHHHHHHHHHHHHHH------HTTCC---------CHHHHHHHHHHHHHHHHHCTT
T ss_pred             HhcCCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhc------ccccc---------chhhHHHHHHHHHHHHHhCCC
Confidence            6524 566777899999986655333  23222222111      11100         123455666666666665555


Q ss_pred             hHHHHHHHHHHHHHcCCC------hHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCC
Q 008442          181 LLRLYAYWAHLEQSMGKD------MVSARGVWERLLKISGAMLEAWQSYISMEIELDH  232 (565)
Q Consensus       181 ~~~l~~~~a~~e~~~~~~------~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~  232 (565)
                      ....|.+-..+....+..      ++++.+.+.++|...|.+...|...--+....|.
T Consensus       200 N~SAW~~R~~lL~~l~~~~~~~~~~~eELe~~~~aI~~~P~n~SaW~Ylr~Ll~~~~~  257 (349)
T 3q7a_A          200 NNSAWGWRWYLRVSRPGAETSSRSLQDELIYILKSIHLIPHNVSAWNYLRGFLKHFSL  257 (349)
T ss_dssp             CHHHHHHHHHHHTTSTTCCCCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCC
Confidence            666777766666665521      5788889999999999999999877766666554

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=98.43  E-value=2.4e-05  Score=75.63  Aligned_cols=179  Identities=12%  Similarity=0.089  Sum_probs=120.5

Q ss_pred             CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHc--------CCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcc-
Q 008442           53 FPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKN--------CPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA-  123 (565)
Q Consensus        53 ~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~--------~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~-  123 (565)
                      .|....+|...+..... .++.+.+..+|++++..        .|....+|..... +....+..+++...|++++... 
T Consensus        23 ~~~~~~~~~~l~~~~~~-~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~-~~~~~g~~~~A~~~~~~al~~~~  100 (311)
T 3nf1_A           23 IPARLRTLHNLVIQYAS-QGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILAL-VYRDQNKYKDAANLLNDALAIRE  100 (311)
T ss_dssp             SCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH-HHHHCCCHHHHHHHHHHHHHHHH
Confidence            45555677776665544 34778899999999984        3444455555544 3344688999999999998642 


Q ss_pred             ----cccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcC-CchhHHHHHHHHHHHHHcCCC
Q 008442          124 ----FSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKD  198 (565)
Q Consensus       124 ----~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~  198 (565)
                          ... ......+........   .       ..++..+...|.+++......... .+.....+...+.+....+ +
T Consensus       101 ~~~~~~~-~~~~~~~~~l~~~~~---~-------~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~-~  168 (311)
T 3nf1_A          101 KTLGKDH-PAVAATLNNLAVLYG---K-------RGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQG-K  168 (311)
T ss_dssp             HHHCTTC-HHHHHHHHHHHHHHH---T-------TTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTT-C
T ss_pred             HHhCCCC-hHHHHHHHHHHHHHH---H-------cCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcC-C
Confidence                110 111111111111110   0       125566777788777776544322 2334566777788888888 9


Q ss_pred             hHHHHHHHHHHHHH--------ccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          199 MVSARGVWERLLKI--------SGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       199 ~~~ar~i~e~~l~~--------~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ++.|..+|++++..        .+....+|...+.+....|+++.|..+|++++.
T Consensus       169 ~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  223 (311)
T 3nf1_A          169 YEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILT  223 (311)
T ss_dssp             HHHHHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            99999999999987        555677899999999999999999999999986

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=98.43  E-value=2.1e-06  Score=93.86  Aligned_cols=171  Identities=15%  Similarity=0.016  Sum_probs=109.7

Q ss_pred             HhcCCchhHHHHHHHHH--------hcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHh
Q 008442           34 QSSGDPGRVQLLYERAI--------TDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERS  105 (565)
Q Consensus        34 ~~~~~~~~~~~lyERal--------~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~  105 (565)
                      ...++++.+...|++++        ...|.+..+|...+..+... ++.+.+...|++|+...|.+..+|......+ ..
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~-g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~-~~  479 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDL-GDVAKATRKLDDLAERVGWRWRLVWYRAVAE-LL  479 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHHCCCHHHHHHHHHHH-HH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhc-CCHHHHHHHHHHHhccCcchHHHHHHHHHHH-HH
Confidence            45688889999999999        88899999999887755443 4677899999999999999888888776533 34


Q ss_pred             cCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHH
Q 008442          106 RASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLY  185 (565)
Q Consensus       106 ~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~  185 (565)
                      .+..+++...|++|+...+.....+..+-..+..    .          .+++. ...|++++..       .+.....|
T Consensus       480 ~g~~~~A~~~~~~al~l~P~~~~~~~~lg~~~~~----~----------g~~~~-~~~~~~al~~-------~P~~~~a~  537 (681)
T 2pzi_A          480 TGDYDSATKHFTEVLDTFPGELAPKLALAATAEL----A----------GNTDE-HKFYQTVWST-------NDGVISAA  537 (681)
T ss_dssp             HTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHH----H----------TCCCT-TCHHHHHHHH-------CTTCHHHH
T ss_pred             cCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHH----c----------CChHH-HHHHHHHHHh-------CCchHHHH
Confidence            6888999999999987655433333222222110    0          01112 2334433332       22233455


Q ss_pred             HHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHH
Q 008442          186 AYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE  229 (565)
Q Consensus       186 ~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~  229 (565)
                      ...+.++...+ ++++|...|++++...|++...|...+.....
T Consensus       538 ~~lg~~~~~~g-~~~~A~~~~~~al~l~P~~~~a~~~~~~~~~~  580 (681)
T 2pzi_A          538 FGLARARSAEG-DRVGAVRTLDEVPPTSRHFTTARLTSAVTLLS  580 (681)
T ss_dssp             HHHHHHHHHTT-CHHHHHHHHHTSCTTSTTHHHHHHHHHHHTC-
T ss_pred             HHHHHHHHHcC-CHHHHHHHHHhhcccCcccHHHHHHHHHHHHc
Confidence            55566666666 66666667766666666666666666555433

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.43  E-value=9.7e-06  Score=78.42  Aligned_cols=169  Identities=14%  Similarity=-0.008  Sum_probs=111.0

Q ss_pred             CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHH
Q 008442           53 FPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLD  132 (565)
Q Consensus        53 ~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~  132 (565)
                      .|.+.+.+...+..+.. .++.+.+..+|++|+...|.+...|..... +....+..+++..+|++++...+......+.
T Consensus       113 lp~~~~~~~~~a~~~~~-~g~~~~A~~~~~~al~~~P~~~~a~~~la~-~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~~  190 (287)
T 3qou_A          113 LPREEELXAQQAMQLMQ-ESNYTDALPLLXDAWQLSNQNGEIGLLLAE-TLIALNRSEDAEAVLXTIPLQDQDTRYQGLV  190 (287)
T ss_dssp             SCCHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHTTSCHHHHHHHHH-HHHHTTCHHHHHHHHTTSCGGGCSHHHHHHH
T ss_pred             cCCchhhHHHHHHHHHh-CCCHHHHHHHHHHHHHhCCcchhHHHHHHH-HHHHCCCHHHHHHHHHhCchhhcchHHHHHH
Confidence            47777777777665443 346777889999999988988888888776 3344688888888888887654432111111


Q ss_pred             HHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH
Q 008442          133 LFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI  212 (565)
Q Consensus       133 ~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~  212 (565)
                      ....+   .. .                 ..+..++..+...+...+.....+..++.++...+ +++.|...|++++..
T Consensus       191 ~~~~l---~~-~-----------------~~~~~a~~~l~~al~~~P~~~~~~~~la~~l~~~g-~~~~A~~~l~~~l~~  248 (287)
T 3qou_A          191 AQIEL---LX-Q-----------------AADTPEIQQLQQQVAENPEDAALATQLALQLHQVG-RNEEALELLFGHLRX  248 (287)
T ss_dssp             HHHHH---HH-H-----------------HTSCHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHH
T ss_pred             HHHHH---Hh-h-----------------cccCccHHHHHHHHhcCCccHHHHHHHHHHHHHcc-cHHHHHHHHHHHHhc
Confidence            11111   00 0                 00111222222333323445567777777777777 888888888888888


Q ss_pred             ccch--HHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          213 SGAM--LEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       213 ~~~~--~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      .|+.  ...|...+.+....|+.+.|...|.+++.
T Consensus       249 ~p~~~~~~a~~~l~~~~~~~g~~~~a~~~~r~al~  283 (287)
T 3qou_A          249 DLTAADGQTRXTFQEILAALGTGDALASXYRRQLY  283 (287)
T ss_dssp             CTTGGGGHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             ccccccchHHHHHHHHHHHcCCCCcHHHHHHHHHH
Confidence            7776  77888888888888888888888888875

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.41  E-value=2.3e-05  Score=71.63  Aligned_cols=110  Identities=11%  Similarity=0.064  Sum_probs=87.0

Q ss_pred             HHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHH----------------HHHHHHHhcchhhHHHHHHHHHHH
Q 008442           23 FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLD----------------YTQYLDKTLKVGNVVRDVYSRATK   86 (565)
Q Consensus        23 ~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~----------------Y~~~l~~~~~~~~~~~~v~erAl~   86 (565)
                      .+.+..-.......|+++.+...|++++...|.+...|..                .+..+ ...+..+.+...|++|+.
T Consensus         4 ~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~-~~~g~~~~A~~~~~~al~   82 (208)
T 3urz_A            4 VDEMLQKVSAAIEAGQNGQAVSYFRQTIALNIDRTEMYYWTNVDKNSEISSKLATELALAY-KKNRNYDKAYLFYKELLQ   82 (208)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCHHHHHHHHHHHSCTTSHHHHHHHHHHHHHH-HHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHhhhcchhhhhHHHHHHHHHHH-HHCCCHHHHHHHHHHHHH
Confidence            4556666666677899999999999999999999998887                55533 345578889999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHH
Q 008442           87 NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLF  134 (565)
Q Consensus        87 ~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~  134 (565)
                      ..|.+...|......+ ...+..+++...|++++...+.....+..+-
T Consensus        83 ~~p~~~~~~~~lg~~~-~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg  129 (208)
T 3urz_A           83 KAPNNVDCLEACAEMQ-VCRGQEKDALRMYEKILQLEADNLAANIFLG  129 (208)
T ss_dssp             HCTTCHHHHHHHHHHH-HHHTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             HCCCCHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            9999999998877644 4468899999999999987766555444433

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=98.40  E-value=1.5e-05  Score=70.39  Aligned_cols=112  Identities=13%  Similarity=0.046  Sum_probs=88.5

Q ss_pred             hHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHH
Q 008442            5 RAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRA   84 (565)
Q Consensus         5 R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erA   84 (565)
                      ...|+.++...|.    +...|...+......|+.+.+..+|++++...|.+..+|..++...... ++.+.+..+|+++
T Consensus        28 ~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~-~~~~~A~~~~~~~  102 (186)
T 3as5_A           28 VMLLEQVYDADAF----DVDVALHLGIAYVKTGAVDRGTELLERSLADAPDNVKVATVLGLTYVQV-QKYDLAVPLLIKV  102 (186)
T ss_dssp             HHHHTTTCCTTSC----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-TCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCcc----ChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHh-cCHHHHHHHHHHH
Confidence            3344444444443    6778888888888899999999999999999999999999988765544 4778899999999


Q ss_pred             HHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 008442           85 TKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLC  122 (565)
Q Consensus        85 l~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~  122 (565)
                      +...|....+|......+ ...+..+++...|++++..
T Consensus       103 ~~~~~~~~~~~~~~a~~~-~~~~~~~~A~~~~~~~~~~  139 (186)
T 3as5_A          103 AEANPINFNVRFRLGVAL-DNLGRFDEAIDSFKIALGL  139 (186)
T ss_dssp             HHHCTTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHH
T ss_pred             HhcCcHhHHHHHHHHHHH-HHcCcHHHHHHHHHHHHhc
Confidence            999999988888777644 3467788888888877753

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.40  E-value=8.2e-06  Score=87.19  Aligned_cols=87  Identities=15%  Similarity=0.006  Sum_probs=48.7

Q ss_pred             CCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHH
Q 008442           37 GDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVF  116 (565)
Q Consensus        37 ~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if  116 (565)
                      |+.+.+...|++++...|.+...|..++..+... ++.+.+...|++|+...|.....|..+...+ ...+..+++...|
T Consensus         3 g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~-g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~-~~~g~~~~A~~~~   80 (568)
T 2vsy_A            3 ADGPRELLQLRAAVRHRPQDFVAWLMLADAELGM-GDTTAGEMAVQRGLALHPGHPEAVARLGRVR-WTQQRHAEAAVLL   80 (568)
T ss_dssp             ------------------CCHHHHHHHHHHHHHH-TCHHHHHHHHHHHHTTSTTCHHHHHHHHHHH-HHTTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH-HHCCCHHHHHHHH
Confidence            4566777888888888888888888877655433 3667788888888888888777777766533 3357777777778


Q ss_pred             HHHHhcccc
Q 008442          117 EKSLLCAFS  125 (565)
Q Consensus       117 ~ral~~~~~  125 (565)
                      ++|+...+.
T Consensus        81 ~~al~~~p~   89 (568)
T 2vsy_A           81 QQASDAAPE   89 (568)
T ss_dssp             HHHHHHCTT
T ss_pred             HHHHhcCCC
Confidence            777765443

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=98.38  E-value=7.3e-06  Score=70.80  Aligned_cols=125  Identities=10%  Similarity=-0.001  Sum_probs=97.4

Q ss_pred             chhhHHHHHHHhc---CCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHH
Q 008442            2 CNARAHLEEQISR---QDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVR   78 (565)
Q Consensus         2 ~~~R~~~E~~l~~---~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~   78 (565)
                      +..+..+|.+|..   ....++++...|..+.......|+++.+...|+++|..+|.++..|..+...... .++.+.+.
T Consensus         7 ~~~~~~~e~ai~~~~~a~~~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~-~~~~~~A~   85 (150)
T 4ga2_A            7 RRSKADVERYIASVQGSTPSPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQERDPKAHRFLGLLYEL-EENTDKAV   85 (150)
T ss_dssp             CCCHHHHHHHHHHHHHHSCSHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHH
T ss_pred             HHHcChHHHHHHHHHHhcccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-cCchHHHH
Confidence            4566677777633   2334566777888888888899999999999999999999999999999876554 45788899


Q ss_pred             HHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccH
Q 008442           79 DVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTF  127 (565)
Q Consensus        79 ~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~  127 (565)
                      ..|++|+...|....+|......+.......+.+...+++|+...+...
T Consensus        86 ~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P~~~  134 (150)
T 4ga2_A           86 ECYRRSVELNPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFPGSP  134 (150)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHSTTCH
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCcCCH
Confidence            9999999999999999998876555543333456666799998665543

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.36  E-value=1.9e-05  Score=65.96  Aligned_cols=109  Identities=16%  Similarity=0.024  Sum_probs=93.7

Q ss_pred             CChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHH
Q 008442           18 SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVR   97 (565)
Q Consensus        18 ~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~   97 (565)
                      .+|+..+.|..-.....+.|+++.+...|++||...|.+..+|...+..+. ..+..+.+...|++||...|.....|..
T Consensus         8 inP~~a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~-~~~~~~~A~~~~~~al~~~p~~~~a~~~   86 (126)
T 4gco_A            8 INPELAQEEKNKGNEYFKKGDYPTAMRHYNEAVKRDPENAILYSNRAACLT-KLMEFQRALDDCDTCIRLDSKFIKGYIR   86 (126)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             HCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHhhHHH-hhccHHHHHHHHHHHHHhhhhhhHHHHH
Confidence            477788899999998889999999999999999999999999999887555 4457888999999999999999999988


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcccccHH
Q 008442           98 SLLSLERSRASEEEISTVFEKSLLCAFSTFE  128 (565)
Q Consensus        98 yi~~le~~~~~~~~~~~if~ral~~~~~~~~  128 (565)
                      ....+ ...+..+++...|++++...+....
T Consensus        87 lg~~~-~~~~~~~~A~~~~~~al~l~P~~~~  116 (126)
T 4gco_A           87 KAACL-VAMREWSKAQRAYEDALQVDPSNEE  116 (126)
T ss_dssp             HHHHH-HHTTCHHHHHHHHHHHHHHCTTCHH
T ss_pred             HHHHH-HHCCCHHHHHHHHHHHHHHCcCCHH
Confidence            77644 4478899999999999987665433

>3esl_A Checkpoint serine/threonine-protein kinase BUB1; mitotic spindle checkpoint, TPR motif, all-alpha domain, MAD3-like domain; HET: NHE; 1.74A {Saccharomyces cerevisiae}

Probab=98.33  E-value=1.3e-05  Score=71.04  Aligned_cols=119  Identities=11%  Similarity=0.092  Sum_probs=87.5

Q ss_pred             chhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhc---CCc---hhHH-HHHHHHHhcCCCCH---------HHHHHHHH
Q 008442            2 CNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS---GDP---GRVQ-LLYERAITDFPVSS---------DLWLDYTQ   65 (565)
Q Consensus         2 ~~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~---~~~---~~~~-~lyERal~~~p~~~---------~lW~~Y~~   65 (565)
                      ...|..||..|.......++-++.|..||+|...+   |..   .... .++|||+..+-.+.         .+|+.|++
T Consensus         9 ~~~r~~fE~~l~~~l~~~dDPL~~w~~YIkW~ee~yP~g~~~~~s~L~~~lLErc~~~F~~~~rYkND~RYLklWl~Ya~   88 (202)
T 3esl_A            9 NQTKIAYEQRLLNDLEDMDDPLDLFLDYMIWISTSYIEVDSESGQEVLRSTMERCLIYIQDMETYRNDPRFLKIWIWYIN   88 (202)
T ss_dssp             HHHHHHHHHHHHHTGGGCSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHTTCGGGTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccccCCCchHHHHHHHHHHHHhCCCCCCcchhchHHHHHHHHHHHhcccccccCCHHHHHHHHHHHH
Confidence            45799999999882122223578999999997653   222   2345 89999999765443         49999999


Q ss_pred             HHHHhcchhhHHHHHHHHHHHc-C-CCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcc
Q 008442           66 YLDKTLKVGNVVRDVYSRATKN-C-PWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA  123 (565)
Q Consensus        66 ~l~~~~~~~~~~~~v~erAl~~-~-p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~  123 (565)
                      +..  ..+.....++|.....+ + -....+|..|+.++|. .+.+.++..||+.+++..
T Consensus        89 ~~~--~~~~~~p~~if~~L~~~~IG~~~AlfYe~wA~~lE~-~g~~~~A~~Vy~~GI~~~  145 (202)
T 3esl_A           89 LFL--SNNFHESENTFKYMFNKGIGTKLSLFYEEFSKLLEN-AQFFLEAKVLLELGAENN  145 (202)
T ss_dssp             HHS--TTCHHHHHHHHHHHHHHTSSTTBHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHTT
T ss_pred             hhc--ccccCCHHHHHHHHHHCCCcHHHHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHcC
Confidence            751  11133467888888874 3 3567899999998888 588999999999999754

>2wvi_A Mitotic checkpoint serine/threonine-protein kinase BUB1 beta; tumor suppressor, TPR, apoptosis, cell division, cell cycle, kinetochore, transferase; 1.80A {Homo sapiens} PDB: 3si5_A

Probab=98.31  E-value=2.7e-05  Score=66.90  Aligned_cols=110  Identities=16%  Similarity=0.316  Sum_probs=83.1

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhc---CCc-hhHHHHHHHHHhcCCCCH---------HHHHHHHHHHHHh
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS---GDP-GRVQLLYERAITDFPVSS---------DLWLDYTQYLDKT   70 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~---~~~-~~~~~lyERal~~~p~~~---------~lW~~Y~~~l~~~   70 (565)
                      .|..||..|...  ....-++.|..||+|...+   |.. .....++|||+..+..+.         .||+.|+++.   
T Consensus         2 ~r~~fE~~i~~~--~gdDPL~~w~~yIkW~e~~~p~~~~~s~L~~lLErc~~~f~~~~~YknD~RyLklWl~ya~~~---   76 (164)
T 2wvi_A            2 QKRAFEYEIRFY--TGNDPLDVWDRYISWTEQNYPQGGKESNMSTLLERAVEALQGEKRYYSDPRFLNLWLKLGRLC---   76 (164)
T ss_dssp             CTHHHHHHCCCC--CSSCTHHHHHHHHHHHHHHCCC----CCHHHHHHHHHHHTTTCGGGTTCHHHHHHHHHHHHHC---
T ss_pred             hHHHHHHHHhhc--CCCCChHHHHHHHHHHHHHCcCCCccchHHHHHHHHHHHhhhhhhhccCHHHHHHHHHHHHhc---
Confidence            578899999633  2233588999999998763   222 346789999999876654         4999999863   


Q ss_pred             cchhhHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcc
Q 008442           71 LKVGNVVRDVYSRATKNC--PWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA  123 (565)
Q Consensus        71 ~~~~~~~~~v~erAl~~~--p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~  123 (565)
                          +...++|.....+-  -....+|..|+.++|. .+.+..+..||..++...
T Consensus        77 ----~~p~~if~~L~~~~IG~~~AlfY~~wA~~lE~-~~~~~~A~~Iy~~Gi~~~  126 (164)
T 2wvi_A           77 ----NEPLDMYSYLHNQGIGVSLAQFYISWAEEYEA-RENFRKADAIFQEGIQQK  126 (164)
T ss_dssp             ----SCHHHHHHHHHHTTSSTTBHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHTT
T ss_pred             ----CCHHHHHHHHHHCCcchhhHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHcC
Confidence                12467888877742  3567899999998888 588999999999999854

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=98.27  E-value=1e-05  Score=69.68  Aligned_cols=113  Identities=8%  Similarity=-0.065  Sum_probs=94.7

Q ss_pred             hHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHH
Q 008442            5 RAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRA   84 (565)
Q Consensus         5 R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erA   84 (565)
                      ...|+.+|...|.    +...|..........|+++.+...|++++...|.+..+|..+...+. ..+..+.+...|++|
T Consensus         7 ~~~~~~al~~~p~----~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~-~~g~~~~A~~~~~~a   81 (148)
T 2vgx_A            7 GGTIAMLNEISSD----TLEQLYSLAFNQYQSGXYEDAHXVFQALCVLDHYDSRFFLGLGACRQ-AMGQYDLAIHSYSYG   81 (148)
T ss_dssp             CCSHHHHTTCCHH----HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHH
T ss_pred             hhhHHHHHcCCHh----hHHHHHHHHHHHHHcCChHHHHHHHHHHHHcCcccHHHHHHHHHHHH-HHhhHHHHHHHHHHH
Confidence            3456677766654    88899999999999999999999999999999999999998877544 445788899999999


Q ss_pred             HHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcc
Q 008442           85 TKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA  123 (565)
Q Consensus        85 l~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~  123 (565)
                      +...|.....|......+ ...+..+++...|++++...
T Consensus        82 l~l~p~~~~~~~~lg~~~-~~~g~~~~A~~~~~~al~~~  119 (148)
T 2vgx_A           82 AVMDIXEPRFPFHAAECL-LQXGELAEAESGLFLAQELI  119 (148)
T ss_dssp             HHHSTTCTHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHH
T ss_pred             HhcCCCCchHHHHHHHHH-HHcCCHHHHHHHHHHHHHHC
Confidence            999999988888776533 44788999999999999743

>4a1g_A Mitotic checkpoint serine/threonine-protein kinas; cell cycle, transferase, spindle assembly checkpoint, mitosi repeat, KNL1, KMN network; 2.60A {Homo sapiens} PDB: 2lah_A

Probab=98.27  E-value=2.9e-05  Score=65.80  Aligned_cols=109  Identities=13%  Similarity=0.228  Sum_probs=85.5

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhc---CCchhHHHHHHHHHhcCCCCH---------HHHHHHHHHHHHhc
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS---GDPGRVQLLYERAITDFPVSS---------DLWLDYTQYLDKTL   71 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~---~~~~~~~~lyERal~~~p~~~---------~lW~~Y~~~l~~~~   71 (565)
                      .|..||..|......|  -++.|..||+|...+   |. .....++|||+..+..+.         .+|+.|+++.    
T Consensus         9 ~~~~fE~~i~~y~gdD--PL~~w~~YI~W~e~~~P~g~-~~l~~lLErc~~~f~~~~~YknD~RyLklWl~ya~~~----   81 (152)
T 4a1g_A            9 VLQMLEAHMQSYKGND--PLGEWERYIQWVEENFPENK-EYLITLLEHLMKEFLDKKKYHNDPRFISYCLKFAEYN----   81 (152)
T ss_dssp             HHHHHHHHTTSCCSSC--HHHHHHHHHHHHHTTCSSCT-HHHHHHHHHHHHHHTTCGGGTTCHHHHHHHHHHHTTB----
T ss_pred             HHHHHHHHHHhCCCCC--CHHHHHHHHHHHHHHcCCCc-hhHHHHHHHHHHHhcccccccCCHHHHHHHHHHHHhc----
Confidence            6888999998864323  588999999998774   33 347789999999865543         4999999863    


Q ss_pred             chhhHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcc
Q 008442           72 KVGNVVRDVYSRATKNC--PWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA  123 (565)
Q Consensus        72 ~~~~~~~~v~erAl~~~--p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~  123 (565)
                         +...++|....++-  -....+|..|...+|. .+.+.++..||+.+++..
T Consensus        82 ---~dp~~if~~L~~~~IG~~~AlfYe~wA~~lE~-~g~~~~A~~Vy~~Gi~~~  131 (152)
T 4a1g_A           82 ---SDLHQFFEFLYNHGIGTLSSPLYIAWAGHLEA-QGELQHASAVLQRGIQNQ  131 (152)
T ss_dssp             ---SCHHHHHHHHHTTTTTTTBHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHTT
T ss_pred             ---CCHHHHHHHHHHCCCcHHHHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHcC
Confidence               12578888888743  3567899999998888 588999999999999754

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.25  E-value=2e-05  Score=68.16  Aligned_cols=106  Identities=8%  Similarity=-0.075  Sum_probs=92.2

Q ss_pred             CChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHH
Q 008442           18 SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVR   97 (565)
Q Consensus        18 ~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~   97 (565)
                      .+|++...|..........|+++.+...|++++...|.++..|......+. ..+..+.+...|++|+...|.++..|..
T Consensus        31 l~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~-~~g~~~~Ai~~~~~al~l~P~~~~~~~~  109 (151)
T 3gyz_A           31 IPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQ-IKEQFQQAADLYAVAFALGKNDYTPVFH  109 (151)
T ss_dssp             SCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHSSSCCHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH-HHccHHHHHHHHHHHHhhCCCCcHHHHH
Confidence            467799999999998999999999999999999999999999999887554 4457888999999999999999999988


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcccc
Q 008442           98 SLLSLERSRASEEEISTVFEKSLLCAFS  125 (565)
Q Consensus        98 yi~~le~~~~~~~~~~~if~ral~~~~~  125 (565)
                      ....+. ..+..+++...|++|+...++
T Consensus       110 lg~~~~-~lg~~~eA~~~~~~al~l~~~  136 (151)
T 3gyz_A          110 TGQCQL-RLKAPLKAKECFELVIQHSND  136 (151)
T ss_dssp             HHHHHH-HTTCHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHH-HcCCHHHHHHHHHHHHHhCCC
Confidence            776444 478899999999999985544

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.24  E-value=0.00022  Score=65.82  Aligned_cols=181  Identities=10%  Similarity=-0.010  Sum_probs=119.2

Q ss_pred             HHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCH---HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHH---H--
Q 008442           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS---DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGEL---W--   95 (565)
Q Consensus        24 ~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~---~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~l---W--   95 (565)
                      ..|...+......|+.+.+...|++++...|.++   ..|...+.... ..++.+.+...|+++++..|.+..+   |  
T Consensus         5 ~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~-~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~   83 (225)
T 2yhc_A            5 NEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYY-KNADLPLAQAAIDRFIRLNPTHPNIDYVMYM   83 (225)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCTTHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHH-hcCCHHHHHHHHHHHHHHCcCCCcHHHHHHH
Confidence            4455555556677999999999999999988874   56666554333 3457888999999999999976542   2  


Q ss_pred             HHHHHHHHH----------------hcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHH
Q 008442           96 VRSLLSLER----------------SRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSL  159 (565)
Q Consensus        96 ~~yi~~le~----------------~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~  159 (565)
                      ...+. ...                ..+..+++...|++++...+........  ...+.                   .
T Consensus        84 ~g~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P~~~~a~~a--~~~l~-------------------~  141 (225)
T 2yhc_A           84 RGLTN-MALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYPNSQYTTDA--TKRLV-------------------F  141 (225)
T ss_dssp             HHHHH-HHHHC--------------CCHHHHHHHHHHHHHHTTCTTCTTHHHH--HHHHH-------------------H
T ss_pred             HHHHH-HhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHCcCChhHHHH--HHHHH-------------------H
Confidence            22221 111                1234667777788777644332110000  00000                   0


Q ss_pred             HHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchH---HHHHHHHHHHHHcCChHHH
Q 008442          160 IRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAML---EAWQSYISMEIELDHINEA  236 (565)
Q Consensus       160 ~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~---~lw~~yi~~e~~~~~~~~a  236 (565)
                      +....                 .......+.++...+ +++.|...|+++++.+|++.   ..|...+......|+.+.|
T Consensus       142 ~~~~~-----------------~~~~~~~a~~~~~~~-~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A  203 (225)
T 2yhc_A          142 LKDRL-----------------AKYEYSVAEYYTERG-AWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQA  203 (225)
T ss_dssp             HHHHH-----------------HHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHH-----------------HHHHHHHHHHHHHcC-cHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHH
Confidence            00000                 011123456666777 99999999999999988764   6788889999999999999


Q ss_pred             HHHHHHHHh
Q 008442          237 RSIYKRCYS  245 (565)
Q Consensus       237 R~i~~~al~  245 (565)
                      .+.|++++.
T Consensus       204 ~~~~~~l~~  212 (225)
T 2yhc_A          204 EKVAKIIAA  212 (225)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            999999876

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=98.23  E-value=0.00068  Score=66.28  Aligned_cols=190  Identities=10%  Similarity=0.038  Sum_probs=126.5

Q ss_pred             HhcCCc-hhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcch---------hhHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Q 008442           34 QSSGDP-GRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKV---------GNVVRDVYSRATKNCPWVGELWVRSLLSLE  103 (565)
Q Consensus        34 ~~~~~~-~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~---------~~~~~~v~erAl~~~p~~~~lW~~yi~~le  103 (565)
                      ...|.. +++..+++.+|..+|.++.+|.---..+......         .+.....++.++...|.+..+|....-.+.
T Consensus        40 ~~~~e~s~eaL~~t~~~L~~nP~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~PKny~aW~hR~wlL~  119 (331)
T 3dss_A           40 RQAGELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLS  119 (331)
T ss_dssp             HHTTCCSHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHcCCCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHh
Confidence            345555 4799999999999999999999876665543321         356788999999999999999998876565


Q ss_pred             HhcC-CHHHHHHHHHHHHhcccccHH--HHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCch
Q 008442          104 RSRA-SEEEISTVFEKSLLCAFSTFE--EYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG  180 (565)
Q Consensus       104 ~~~~-~~~~~~~if~ral~~~~~~~~--~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~  180 (565)
                      .... ..++....+.+++...+..+.  .+..+....+         .       .      .++.+++++...+..++.
T Consensus       120 ~l~~~~~~~EL~~~~k~l~~dprNy~AW~~R~~vl~~l---------~-------~------~~~eel~~~~~~I~~~p~  177 (331)
T 3dss_A          120 RLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQA---------A-------V------APAEELAFTDSLITRNFS  177 (331)
T ss_dssp             HCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT---------T-------C------CHHHHHHHHHHHHHHCSC
T ss_pred             ccCcccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHh---------C-------c------CHHHHHHHHHHHHHHCCC
Confidence            5443 477888899999986654333  2222222111         0       0      123444555555544445


Q ss_pred             hHHHHHHHHHHHHHcC-------------CChHHHHHHHHHHHHHccchHHHHHHHHHHHHHc-----------CChHHH
Q 008442          181 LLRLYAYWAHLEQSMG-------------KDMVSARGVWERLLKISGAMLEAWQSYISMEIEL-----------DHINEA  236 (565)
Q Consensus       181 ~~~l~~~~a~~e~~~~-------------~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~-----------~~~~~a  236 (565)
                      ....|.+...+...+.             ..++++.+.+.++|...|++...|...--+....           +-++.+
T Consensus       178 N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~e  257 (331)
T 3dss_A          178 NYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSE  257 (331)
T ss_dssp             CHHHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhccCccccchHHHHHHHHH
Confidence            5566666555544441             1356788899999999999999997554444333           235677


Q ss_pred             HHHHHHHHh
Q 008442          237 RSIYKRCYS  245 (565)
Q Consensus       237 R~i~~~al~  245 (565)
                      .+.+..++.
T Consensus       258 l~~~~elle  266 (331)
T 3dss_A          258 LESCKELQE  266 (331)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            788888876

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=98.23  E-value=2.3e-05  Score=69.38  Aligned_cols=118  Identities=12%  Similarity=0.030  Sum_probs=99.9

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchh--hHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVG--NVVRDV   80 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~--~~~~~v   80 (565)
                      .+...|+.++...|.    +...|..+.......|+.+.+...|++++...|.+..+|..++..+....+..  +.+...
T Consensus        28 ~A~~~~~~al~~~p~----~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~l~~~~~~~~~~~A~~~  103 (177)
T 2e2e_A           28 AQLQALQDKIRANPQ----NSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGENAELYAALATVLYYQASQHMTAQTRAM  103 (177)
T ss_dssp             CCCHHHHHHHHHCCS----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHTTTCCCHHHHHH
T ss_pred             HHHHHHHHHHHhCCC----cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCcchHHHHHH
Confidence            356788999988887    77899999999999999999999999999999999999999988634344455  889999


Q ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc
Q 008442           81 YSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (565)
Q Consensus        81 ~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~  125 (565)
                      |++++...|....+|......+ ...+..+.+...|++++...+.
T Consensus       104 ~~~al~~~p~~~~~~~~la~~~-~~~g~~~~A~~~~~~al~~~p~  147 (177)
T 2e2e_A          104 IDKALALDSNEITALMLLASDA-FMQANYAQAIELWQKVMDLNSP  147 (177)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHTCCT
T ss_pred             HHHHHHhCCCcHHHHHHHHHHH-HHcccHHHHHHHHHHHHhhCCC
Confidence            9999999999999988877633 4468899999999999986544

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.21  E-value=6.4e-05  Score=63.89  Aligned_cols=105  Identities=9%  Similarity=-0.054  Sum_probs=89.6

Q ss_pred             CChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHH
Q 008442           18 SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVR   97 (565)
Q Consensus        18 ~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~   97 (565)
                      .+|.+...|..........|+++.+..+|++++...|.+..+|..+...+. ..+..+.+...|++|+...|.+..+|..
T Consensus        13 ~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~-~~g~~~~A~~~~~~al~~~p~~~~~~~~   91 (142)
T 2xcb_A           13 LSEDTLEQLYALGFNQYQAGKWDDAQKIFQALCMLDHYDARYFLGLGACRQ-SLGLYEQALQSYSYGALMDINEPRFPFH   91 (142)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCTHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHhCCccHHHHHHHHHHHH-HHhhHHHHHHHHHHHHhcCCCCcHHHHH
Confidence            355688899999998899999999999999999999999999998887554 4457888999999999999999998887


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhccc
Q 008442           98 SLLSLERSRASEEEISTVFEKSLLCAF  124 (565)
Q Consensus        98 yi~~le~~~~~~~~~~~if~ral~~~~  124 (565)
                      ....+ ...+..+++...|++++...+
T Consensus        92 lg~~~-~~~g~~~~A~~~~~~al~~~p  117 (142)
T 2xcb_A           92 AAECH-LQLGDLDGAESGFYSARALAA  117 (142)
T ss_dssp             HHHHH-HHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHH-HHcCCHHHHHHHHHHHHHhCC
Confidence            76644 447889999999999997543

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=98.20  E-value=0.0001  Score=69.89  Aligned_cols=162  Identities=13%  Similarity=0.091  Sum_probs=110.6

Q ss_pred             chhhHHHHHHHHHHHcC--------CCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcc-----cccHHHHHHHHHHHH
Q 008442           72 KVGNVVRDVYSRATKNC--------PWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA-----FSTFEEYLDLFLTRI  138 (565)
Q Consensus        72 ~~~~~~~~v~erAl~~~--------p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~-----~~~~~~~~~~~~~~~  138 (565)
                      ++.+.+...|++|+..+        |....+|..... +....+..+++...|++++...     ... ......+....
T Consensus        15 ~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~-~~~~~g~~~~A~~~~~~al~~~~~~~~~~~-~~~~~~~~~l~   92 (283)
T 3edt_B           15 VPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILAL-VYRDQNKYKEAAHLLNDALAIREKTLGKDH-PAVAATLNNLA   92 (283)
T ss_dssp             SCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHHHHHHTCTTC-HHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHH-HHHHcccHHHHHHHHHHHHHHHHHHcCCcc-hHHHHHHHHHH
Confidence            45666888888888743        333445555444 3344788999999999998642     111 11111221111


Q ss_pred             HHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCC-chhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH-----
Q 008442          139 DGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNT-DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI-----  212 (565)
Q Consensus       139 ~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~-~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~-----  212 (565)
                      ....   .       ..++..+...|.+++.......... +.....+...+.++...+ ++++|..+|++++..     
T Consensus        93 ~~~~---~-------~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~al~~~~~~~  161 (283)
T 3edt_B           93 VLYG---K-------RGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQG-KAEEVEYYYRRALEIYATRL  161 (283)
T ss_dssp             HHHH---T-------TTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTT-CHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHH---H-------hccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHHHHHhc
Confidence            1110   0       1256667788888888776554432 445667777888888888 999999999999988     


Q ss_pred             ---ccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhc
Q 008442          213 ---SGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       213 ---~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~  246 (565)
                         .+....+|...+......|+++.|..+|++++..
T Consensus       162 ~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~  198 (283)
T 3edt_B          162 GPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILTR  198 (283)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence               5556778999999999999999999999999863

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.19  E-value=4.9e-05  Score=81.07  Aligned_cols=116  Identities=9%  Similarity=0.075  Sum_probs=86.5

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...|+.++...|.    +...|..+.......|+.+.+...|++++...|.+...|..++..+.. .++.+.+...|+
T Consensus         7 ~A~~~~~~al~~~p~----~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~-~g~~~~A~~~~~   81 (568)
T 2vsy_A            7 RELLQLRAAVRHRPQ----DFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWT-QQRHAEAAVLLQ   81 (568)
T ss_dssp             --------------C----CHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTSTTCHHHHHHHHHHHHH-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC----CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-CCCHHHHHHHHH
Confidence            355677778777776    788999999988899999999999999999999999999999886554 447888999999


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccc
Q 008442           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAF  124 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~  124 (565)
                      +|+...|.+...|......+ ...+..+++...|++++...+
T Consensus        82 ~al~~~p~~~~~~~~la~~~-~~~g~~~~A~~~~~~al~~~p  122 (568)
T 2vsy_A           82 QASDAAPEHPGIALWLGHAL-EDAGQAEAAAAAYTRAHQLLP  122 (568)
T ss_dssp             HHHHHCTTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHhcCCCCHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHhCC
Confidence            99999999999988877633 446778888888888876443

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=98.18  E-value=2.9e-05  Score=84.81  Aligned_cols=152  Identities=11%  Similarity=-0.028  Sum_probs=114.9

Q ss_pred             hcchhhHHHHHHHHHH--------HcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHH
Q 008442           70 TLKVGNVVRDVYSRAT--------KNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGL  141 (565)
Q Consensus        70 ~~~~~~~~~~v~erAl--------~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~  141 (565)
                      ..++.+.+.+.|++|+        ...|.+..+|......+ ...+..+++...|++++...+..+..+..+-..+... 
T Consensus       403 ~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~-~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~-  480 (681)
T 2pzi_A          403 VLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRAL-LDLGDVAKATRKLDDLAERVGWRWRLVWYRAVAELLT-  480 (681)
T ss_dssp             TTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHH-HHHTCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH-
T ss_pred             cccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHH-HhcCCHHHHHHHHHHHhccCcchHHHHHHHHHHHHHc-
Confidence            3456788999999999        77798888888876633 3468899999999999987666554444333322210 


Q ss_pred             HHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHH
Q 008442          142 RRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQ  221 (565)
Q Consensus       142 ~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~  221 (565)
                                   .+++.+...|++++..       .+.....|..++.+....+ ++++ ...|++++...|++...|.
T Consensus       481 -------------g~~~~A~~~~~~al~l-------~P~~~~~~~~lg~~~~~~g-~~~~-~~~~~~al~~~P~~~~a~~  538 (681)
T 2pzi_A          481 -------------GDYDSATKHFTEVLDT-------FPGELAPKLALAATAELAG-NTDE-HKFYQTVWSTNDGVISAAF  538 (681)
T ss_dssp             -------------TCHHHHHHHHHHHHHH-------STTCSHHHHHHHHHHHHHT-CCCT-TCHHHHHHHHCTTCHHHHH
T ss_pred             -------------CCHHHHHHHHHHHHHh-------CCCChHHHHHHHHHHHHcC-ChHH-HHHHHHHHHhCCchHHHHH
Confidence                         1344444555555543       3444567777888888888 8888 9999999999999999999


Q ss_pred             HHHHHHHHcCChHHHHHHHHHHHh
Q 008442          222 SYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       222 ~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ..+......|+++.|...|++++.
T Consensus       539 ~lg~~~~~~g~~~~A~~~~~~al~  562 (681)
T 2pzi_A          539 GLARARSAEGDRVGAVRTLDEVPP  562 (681)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHTSCT
T ss_pred             HHHHHHHHcCCHHHHHHHHHhhcc
Confidence            999999999999999999999986

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=98.18  E-value=0.0012  Score=64.46  Aligned_cols=228  Identities=9%  Similarity=-0.024  Sum_probs=145.7

Q ss_pred             hHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCC----------chhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcc-h
Q 008442            5 RAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGD----------PGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLK-V   73 (565)
Q Consensus         5 R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~----------~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~-~   73 (565)
                      -..++.+|..+|.    ++.+|..--......+.          ......+++.+|..+|.++.+|..-.-.+..... .
T Consensus        50 L~~t~~~L~~nP~----~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~PKny~aW~hR~wlL~~l~~~~  125 (331)
T 3dss_A           50 LELTSQILGANPD----FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPN  125 (331)
T ss_dssp             HHHHHHHHTTCTT----CHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHCSSCC
T ss_pred             HHHHHHHHHHCch----hHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHhccCccc
Confidence            3556677777776    88999766555443322          3567789999999999999999977654443332 3


Q ss_pred             hhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccccc--HHHHHHHHHHHHHHHHHHhhccccc
Q 008442           74 GNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFST--FEEYLDLFLTRIDGLRRRILFSGEV  151 (565)
Q Consensus        74 ~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~--~~~~~~~~~~~~~~~~r~~~~~~~~  151 (565)
                      .+....++++++...|.+...|......+.......++....+.+++...+..  .|.+....+...       ......
T Consensus       126 ~~~EL~~~~k~l~~dprNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p~N~SAW~~R~~ll~~l-------~~~~~~  198 (331)
T 3dss_A          126 WARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQL-------HPQPDS  198 (331)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHH-------SCCC--
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHh-------hhcccc
Confidence            56788999999999999999998766545544333677888889999866553  333333322211       000000


Q ss_pred             hhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcC----------CChHHHHHHHHHHHHHccchHHHHH
Q 008442          152 EGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMG----------KDMVSARGVWERLLKISGAMLEAWQ  221 (565)
Q Consensus       152 e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~----------~~~~~ar~i~e~~l~~~~~~~~lw~  221 (565)
                      ..  ........++++++++..++...+.....|.+..-+.....          +-++++.+.++.++...|++.-..+
T Consensus       199 ~~--~~~~~~~~~~eEle~~~~ai~~~P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~~~~elle~~pd~~w~l~  276 (331)
T 3dss_A          199 GP--QGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELESCKELQELEPENKWCLL  276 (331)
T ss_dssp             ------CCCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             cc--ccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhccCccccchHHHHHHHHHHHHHHHHHhhCcccchHHH
Confidence            00  00001245667777777766655566677765544444332          1356888889999998898754445


Q ss_pred             HHHHHHHH---cCChHHHHHHHHHHHh
Q 008442          222 SYISMEIE---LDHINEARSIYKRCYS  245 (565)
Q Consensus       222 ~yi~~e~~---~~~~~~aR~i~~~al~  245 (565)
                      ..+.+...   .+..+.++..+.+.+.
T Consensus       277 ~~~~~~~~~~~~~~~~~~~~~l~~l~~  303 (331)
T 3dss_A          277 TIILLMRALDPLLYEKETLQYFSTLKA  303 (331)
T ss_dssp             HHHHHHHHHCTTTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcccccHHHHHHHHHHHHH
Confidence            55544432   4667789999999875

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=98.17  E-value=0.00016  Score=59.59  Aligned_cols=71  Identities=18%  Similarity=0.229  Sum_probs=34.3

Q ss_pred             HHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHH
Q 008442           26 YMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVR   97 (565)
Q Consensus        26 W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~   97 (565)
                      |...+......|+.+.+..+|++++...|.+...|..++...... ++.+.+..+|++++...|....+|..
T Consensus         4 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~-~~~~~A~~~~~~~~~~~~~~~~~~~~   74 (136)
T 2fo7_A            4 WYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQ-GDYDEAIEYYQKALELDPRSAEAWYN   74 (136)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             HHHHHHHHHHcCcHHHHHHHHHHHHHcCCcchhHHHHHHHHHHHh-cCHHHHHHHHHHHHHHCCCchHHHHH
Confidence            444444444455555555555555555555555555544432222 23444555555555544444444433

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.16  E-value=1.5e-05  Score=76.75  Aligned_cols=192  Identities=10%  Similarity=-0.022  Sum_probs=133.3

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~  101 (565)
                      ....|..........|+.+.+...|+++|...|.+..+|..++.... ..+..+.+...|++|+...|.+..+|......
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~-~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~   81 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYL-KMQQPEQALADCRRALELDGQSVKAHFFLGQC   81 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHH-HTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHH-HhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            45678888888888999999999999999999999999999887555 44578889999999999999999998887764


Q ss_pred             HHHhcCCHHHHHHHHHHHHhccccc---HHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCC
Q 008442          102 LERSRASEEEISTVFEKSLLCAFST---FEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNT  178 (565)
Q Consensus       102 le~~~~~~~~~~~if~ral~~~~~~---~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~  178 (565)
                      +. ..+..+++...|++++...+..   +...+........                    . ..+..    .....  .
T Consensus        82 ~~-~~g~~~~A~~~~~~al~l~p~~~~~~~~~~~~~~~~~~--------------------~-~~~~~----~~~~~--~  133 (281)
T 2c2l_A           82 QL-EMESYDEAIANLQRAYSLAKEQRLNFGDDIPSALRIAK--------------------K-KRWNS----IEERR--I  133 (281)
T ss_dssp             HH-HTTCHHHHHHHHHHHHHHHHHTTCCCCSHHHHHHHHHH--------------------H-HHHHH----HHHTC--C
T ss_pred             HH-HcCCHHHHHHHHHHHHHhCccchhhHHHHHHHHHHHHH--------------------H-HHHHH----HHHHH--H
Confidence            44 4688999999999999743321   0000110000000                    0 01111    11111  1


Q ss_pred             chhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHc-CChHHHHHHHHHHHh
Q 008442          179 DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIEL-DHINEARSIYKRCYS  245 (565)
Q Consensus       179 ~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~-~~~~~aR~i~~~al~  245 (565)
                      .....+...+..+.  .+ +.+.|.+.|++++...|.+..+......+.... +.++.|..+|.++..
T Consensus       134 ~~~~~i~~~l~~l~--~~-~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~  198 (281)
T 2c2l_A          134 HQESELHSYLTRLI--AA-ERERELEECQRNHEGHEDDGHIRAQQACIEAKHDKYMADMDELFSQVDE  198 (281)
T ss_dssp             CCCCHHHHHHHHHH--HH-HHHHHHTTTSGGGTTTSCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             hhhHHHHHHHHHHH--HH-HHHHHHHHHHhhhccccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            11122333444443  24 788899999999988888887777777776555 678899999999875

>4a1g_A Mitotic checkpoint serine/threonine-protein kinas; cell cycle, transferase, spindle assembly checkpoint, mitosi repeat, KNL1, KMN network; 2.60A {Homo sapiens} PDB: 2lah_A

Probab=98.15  E-value=3e-05  Score=65.65  Aligned_cols=83  Identities=11%  Similarity=0.144  Sum_probs=61.9

Q ss_pred             hcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH--ccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCC
Q 008442          175 MKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI--SGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTG  252 (565)
Q Consensus       175 ~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~--~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~  252 (565)
                      +.+.+.++++|+.|+++-   . +   ++.+|..+...  ......+|..|+.+....|++..|.+||+.+|..  ....
T Consensus        64 YknD~RyLklWl~ya~~~---~-d---p~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~~Vy~~Gi~~--~A~P  134 (152)
T 4a1g_A           64 YHNDPRFISYCLKFAEYN---S-D---LHQFFEFLYNHGIGTLSSPLYIAWAGHLEAQGELQHASAVLQRGIQN--QAEP  134 (152)
T ss_dssp             GTTCHHHHHHHHHHHTTB---S-C---HHHHHHHHHTTTTTTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TCBS
T ss_pred             ccCCHHHHHHHHHHHHhc---C-C---HHHHHHHHHHCCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCcc
Confidence            334556778888888552   2 3   78899888876  3455889999999999999999999999999984  2223


Q ss_pred             cHHHHHHHHHHHHH
Q 008442          253 SEDICHAWLRFERE  266 (565)
Q Consensus       253 ~~~i~~~~~~fE~~  266 (565)
                      -+.|-..+-+|+.+
T Consensus       135 ~~rL~~~~~~F~~R  148 (152)
T 4a1g_A          135 REFLQQQYRLFQTR  148 (152)
T ss_dssp             HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHH
Confidence            45677778788764

>3esl_A Checkpoint serine/threonine-protein kinase BUB1; mitotic spindle checkpoint, TPR motif, all-alpha domain, MAD3-like domain; HET: NHE; 1.74A {Saccharomyces cerevisiae}

Probab=98.14  E-value=0.00015  Score=64.21  Aligned_cols=101  Identities=9%  Similarity=0.239  Sum_probs=77.7

Q ss_pred             HHHHHHHHHHHh--hhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH--ccchHHHHHHHHHHHHHcCChHHHH
Q 008442          162 ETFQRASDYLSE--QMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI--SGAMLEAWQSYISMEIELDHINEAR  237 (565)
Q Consensus       162 ~~~~~a~~~l~~--~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~--~~~~~~lw~~yi~~e~~~~~~~~aR  237 (565)
                      .++++|+..+..  .+.+.+.++++|+.|+++-  ..++...++.+|..+...  ......+|..|+.+....|++..|.
T Consensus        58 ~lLErc~~~F~~~~rYkND~RYLklWl~Ya~~~--~~~~~~~p~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~  135 (202)
T 3esl_A           58 STMERCLIYIQDMETYRNDPRFLKIWIWYINLF--LSNNFHESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAK  135 (202)
T ss_dssp             HHHHHHHHHHTTCGGGTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHTSSTTBHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHhcccccccCCHHHHHHHHHHHHhh--cccccCCHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            566777776533  3445667889999999875  122477899999999987  3456889999999999999999999


Q ss_pred             HHHHHHHhcccCCCCcHHHHHHHHHHHHH
Q 008442          238 SIYKRCYSKRFTGTGSEDICHAWLRFERE  266 (565)
Q Consensus       238 ~i~~~al~~~~~~~~~~~i~~~~~~fE~~  266 (565)
                      +||+.+|...  ....+.|-..+-+|+.+
T Consensus       136 ~Vy~~GI~~~--A~P~~rL~~~~~~F~~R  162 (202)
T 3esl_A          136 VLLELGAENN--CRPYNRLLRSLSNYEDR  162 (202)
T ss_dssp             HHHHHHHHTT--CBSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcC--CccHHHHHHHHHHHHHH
Confidence            9999999852  23345677888888876

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=98.13  E-value=3e-05  Score=66.86  Aligned_cols=98  Identities=16%  Similarity=0.070  Sum_probs=82.7

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...|+.+|..+|.    +..+|..+.......|+++.+...|+++|...|.++++|..++..+....+..+.+...++
T Consensus        49 ~A~~~~~~al~~~p~----~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~aa~~~~~  124 (150)
T 4ga2_A           49 LAKKYICTYINVQER----DPKAHRFLGLLYELEENTDKAVECYRRSVELNPTQKDLVLKIAELLCKNDVTDGRAKYWVE  124 (150)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCSSSSHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC----CHHHHHHHHHHHHHcCchHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHH
Confidence            467788899988887    8899999999999999999999999999999999999999999876665544444555679


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHH
Q 008442           83 RATKNCPWVGELWVRSLLSLER  104 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~  104 (565)
                      +|++..|.++.+|......++.
T Consensus       125 ~al~l~P~~~~~~~l~~~ll~~  146 (150)
T 4ga2_A          125 RAAKLFPGSPAVYKLKEQLLDC  146 (150)
T ss_dssp             HHHHHSTTCHHHHHHHHHHHHT
T ss_pred             HHHHhCcCCHHHHHHHHHHHHH
Confidence            9999999999998877665544

>4aez_C MAD3, mitotic spindle checkpoint component MAD3; cell cycle, KEN-BOX, D-BOX, APC/C; 2.30A {Schizosaccharomyces pombe}

Probab=98.12  E-value=2.8e-05  Score=70.08  Aligned_cols=112  Identities=17%  Similarity=0.333  Sum_probs=85.8

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhc---CC--chhHHHHHHHHHhcCCCCH---------HHHHHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS---GD--PGRVQLLYERAITDFPVSS---------DLWLDYTQYLD   68 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~---~~--~~~~~~lyERal~~~p~~~---------~lW~~Y~~~l~   68 (565)
                      ..|..||..|...... ..-++.|..||+|...+   |.  ......++|||+..+..+.         .+|+.|+++. 
T Consensus        53 ~~r~~fE~~i~~~~~~-dDPL~~w~~YIkW~ee~yP~g~~~~s~L~~lLErc~~~F~~~~rYknD~RyLklWl~Ya~~~-  130 (223)
T 4aez_C           53 KERMGHERKIETSESL-DDPLQVWIDYIKWTLDNFPQGETKTSGLVTLLERCTREFVRNPLYKDDVRYLRIWMQYVNYI-  130 (223)
T ss_dssp             HHHHHHHHHHHHGGGS-SCTHHHHHHHHHHHHHHCTTCCCTTTCHHHHHHHHHHHTTTCGGGTTCHHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHhcccC-CCChHHHHHHHHHHHHhCcCCCcchhhHHHHHHHHHHHhcccccccCCHHHHHHHHHHHHcc-
Confidence            4789999999873111 12478999999998764   32  2347799999999876654         4999999863 


Q ss_pred             HhcchhhHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcc
Q 008442           69 KTLKVGNVVRDVYSRATKNC--PWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA  123 (565)
Q Consensus        69 ~~~~~~~~~~~v~erAl~~~--p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~  123 (565)
                            +...++|.....+-  -....+|..|..++|. .+.+.++..||+.+++..
T Consensus       131 ------~~p~~if~~L~~~~IG~~~AlfYe~wA~~lE~-~g~~~~A~~Vy~~Gi~~~  180 (223)
T 4aez_C          131 ------DEPVELFSFLAHHHIGQESSIFYEEYANYFES-RGLFQKADEVYQKGKRMK  180 (223)
T ss_dssp             ------SCHHHHHHHHHHTTCSTTBHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHT
T ss_pred             ------CCHHHHHHHHHHCCcchhHHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHcC
Confidence                  23567888888743  3567899999998888 588999999999999744

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=98.07  E-value=0.0018  Score=64.51  Aligned_cols=267  Identities=11%  Similarity=-0.053  Sum_probs=142.6

Q ss_pred             hhHHHHHHHhcCCCCChH-hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHH-----HHHHHHHHhcchhhHH
Q 008442            4 ARAHLEEQISRQDLSDSE-KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWL-----DYTQYLDKTLKVGNVV   77 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~-~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~-----~Y~~~l~~~~~~~~~~   77 (565)
                      ++..++.+|...+..++. ....+..........|+++.+...|++++...+...+.+.     ..+-.+....++.+.+
T Consensus        33 A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A  112 (373)
T 1hz4_A           33 AERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQGFLQTA  112 (373)
T ss_dssp             HHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHCCCHHHH
Confidence            556677777766542221 1223444445555678888888888888886554433221     1122223344567778


Q ss_pred             HHHHHHHHHcCC--------CCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc-cHHHHHHHHHHHHHHHHHHhhcc
Q 008442           78 RDVYSRATKNCP--------WVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS-TFEEYLDLFLTRIDGLRRRILFS  148 (565)
Q Consensus        78 ~~v~erAl~~~p--------~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~-~~~~~~~~~~~~~~~~~r~~~~~  148 (565)
                      ...|++++...+        .....+..... +....++.+++...|++++..... ........+........   .  
T Consensus       113 ~~~~~~al~~~~~~~~~~~~~~~~~~~~la~-~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~---~--  186 (373)
T 1hz4_A          113 WETQEKAFQLINEQHLEQLPMHEFLVRIRAQ-LLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSL---A--  186 (373)
T ss_dssp             HHHHHHHHHHHHHTTCTTSTHHHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHH---H--
T ss_pred             HHHHHHHHHHHHHhccccCcHHHHHHHHHHH-HHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHH---H--
Confidence            888888887542        11122222222 333467888888888888863221 00001111111110000   0  


Q ss_pred             ccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHH--HHHHHHHHHcCCChHHHHHHHHHHHHHccc----hHHHHHH
Q 008442          149 GEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLY--AYWAHLEQSMGKDMVSARGVWERLLKISGA----MLEAWQS  222 (565)
Q Consensus       149 ~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~--~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~----~~~lw~~  222 (565)
                           ..++......++++.......  ..+......  ...+.+....+ +++.|...+++++...+.    ....+..
T Consensus       187 -----~g~~~~A~~~l~~a~~~~~~~--~~~~~~~~~~~~~~~~~~~~~g-~~~~A~~~~~~a~~~~~~~~~~~~~~~~~  258 (373)
T 1hz4_A          187 -----RGDLDNARSQLNRLENLLGNG--KYHSDWISNANKVRVIYWQMTG-DKAAAANWLRHTAKPEFANNHFLQGQWRN  258 (373)
T ss_dssp             -----HTCHHHHHHHHHHHHHHHTTS--CCCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHSCCCCCTTCGGGHHHHHH
T ss_pred             -----cCCHHHHHHHHHHHHHHHhcc--CcchhHHHHHHHHHHHHHHHCC-CHHHHHHHHHhCCCCCCCcchhhHHHHHH
Confidence                 013444555566555543221  011111111  12233455667 999999999988875432    1335677


Q ss_pred             HHHHHHHcCChHHHHHHHHHHHhcccCCCCcHH---HHHHHHHHHHHhCCHHHHHHHHHHHhhHH
Q 008442          223 YISMEIELDHINEARSIYKRCYSKRFTGTGSED---ICHAWLRFEREYGTLEDFDHSVQKVTPRL  284 (565)
Q Consensus       223 yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~---i~~~~~~fE~~~G~~~~~~~~~~k~~~~~  284 (565)
                      ++......|+++.|..++++++...-....+..   ++......-...|+.+.....+.+++...
T Consensus       259 la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~~~  323 (373)
T 1hz4_A          259 IARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKLA  323 (373)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHh
Confidence            788888899999999999998763211111222   23333344556688887777777665443

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=98.05  E-value=0.00015  Score=59.95  Aligned_cols=100  Identities=11%  Similarity=-0.019  Sum_probs=86.4

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~  101 (565)
                      ....|..........|+.+.+...|+++|...|.+..+|...+.... ..+..+.+...|++|+...|.....|......
T Consensus         3 ~a~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~a~~~~-~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~   81 (126)
T 3upv_A            3 KAEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALA-KLMSFPEAIADCNKAIEKDPNFVRAYIRKATA   81 (126)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHH-HhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHH
Confidence            56778888888889999999999999999999999999999987555 44578889999999999999999999887764


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcc
Q 008442          102 LERSRASEEEISTVFEKSLLCA  123 (565)
Q Consensus       102 le~~~~~~~~~~~if~ral~~~  123 (565)
                      + ...+..+++...|++++...
T Consensus        82 ~-~~~~~~~~A~~~~~~al~~~  102 (126)
T 3upv_A           82 Q-IAVKEYASALETLDAARTKD  102 (126)
T ss_dssp             H-HHTTCHHHHHHHHHHHHHHH
T ss_pred             H-HHHhCHHHHHHHHHHHHHhC
Confidence            4 44788999999999999754

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=98.05  E-value=0.00013  Score=60.25  Aligned_cols=115  Identities=14%  Similarity=0.121  Sum_probs=94.8

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...|+.++...+.    +...|..++......++.+.+..+|++++...|.+..+|..++.... ..++.+.+..+|+
T Consensus        19 ~A~~~~~~~~~~~~~----~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~A~~~~~   93 (136)
T 2fo7_A           19 EAIEYYQKALELDPR----SAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYY-KQGDYDEAIEYYQ   93 (136)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-TTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCc----chhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCCCchHHHHHHHHHHH-HhcCHHHHHHHHH
Confidence            356678888877765    67788888888888899999999999999999999999998887554 4457788999999


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcc
Q 008442           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA  123 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~  123 (565)
                      +++...|....+|..... +....++.+.+...|++++...
T Consensus        94 ~~~~~~~~~~~~~~~la~-~~~~~~~~~~A~~~~~~~~~~~  133 (136)
T 2fo7_A           94 KALELDPRSAEAWYNLGN-AYYKQGDYDEAIEYYQKALELD  133 (136)
T ss_dssp             HHHHHCTTCHHHHHHHHH-HHHTTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHhCCCChHHHHHHHH-HHHHHccHHHHHHHHHHHHccC
Confidence            999999988888888776 3445788999999999988643

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=98.05  E-value=5.7e-05  Score=66.87  Aligned_cols=115  Identities=8%  Similarity=-0.083  Sum_probs=87.9

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (565)
                      +...|+.+|...|.    +...|..+.......|+++.+...|++++...| ++.++................+...|++
T Consensus        25 A~~~~~~al~~~P~----~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p-~~~~~~~~~~~~~~~~~~~~~a~~~~~~   99 (176)
T 2r5s_A           25 ALNVIQTLSDELQS----RGDVKLAKADCLLETKQFELAQELLATIPLEYQ-DNSYKSLIAKLELHQQAAESPELKRLEQ   99 (176)
T ss_dssp             HHHHHHTSCHHHHT----SHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGC-CHHHHHHHHHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHCCC----cHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccC-ChHHHHHHHHHHHHhhcccchHHHHHHH
Confidence            44556666666665    889999999999999999999999999999999 8876655433211111122236889999


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccc
Q 008442           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAF  124 (565)
Q Consensus        84 Al~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~  124 (565)
                      |+...|.+..+|..+...+. ..+..+++...|++++...+
T Consensus       100 al~~~P~~~~~~~~la~~~~-~~g~~~~A~~~~~~~l~~~p  139 (176)
T 2r5s_A          100 ELAANPDNFELACELAVQYN-QVGRDEEALELLWNILKVNL  139 (176)
T ss_dssp             HHHHSTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCT
T ss_pred             HHHhCCCCHHHHHHHHHHHH-HcccHHHHHHHHHHHHHhCc
Confidence            99999999999999887444 47889999999999987553

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.05  E-value=8.5e-05  Score=64.79  Aligned_cols=104  Identities=13%  Similarity=0.029  Sum_probs=89.5

Q ss_pred             hHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHH
Q 008442           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSL   99 (565)
Q Consensus        20 ~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi   99 (565)
                      +.+...|..........|+++.+..+|+++|..+|.+..+|..++..+.. .++.+.+...|++|+...|.....|....
T Consensus         8 ~~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~-~g~~~~A~~~~~~al~~~p~~~~~~~~lg   86 (164)
T 3sz7_A            8 TPESDKLKSEGNAAMARKEYSKAIDLYTQALSIAPANPIYLSNRAAAYSA-SGQHEKAAEDAELATVVDPKYSKAWSRLG   86 (164)
T ss_dssp             CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence            45677899999988999999999999999999999999999999875554 45788899999999999999999998887


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcccc
Q 008442          100 LSLERSRASEEEISTVFEKSLLCAFS  125 (565)
Q Consensus       100 ~~le~~~~~~~~~~~if~ral~~~~~  125 (565)
                      ..+ ...+..+++...|++++...+.
T Consensus        87 ~~~-~~~g~~~~A~~~~~~al~~~p~  111 (164)
T 3sz7_A           87 LAR-FDMADYKGAKEAYEKGIEAEGN  111 (164)
T ss_dssp             HHH-HHTTCHHHHHHHHHHHHHHHSS
T ss_pred             HHH-HHccCHHHHHHHHHHHHHhCCC
Confidence            644 4478899999999999975544

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=98.04  E-value=0.00023  Score=57.16  Aligned_cols=103  Identities=16%  Similarity=0.046  Sum_probs=87.3

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~  101 (565)
                      ....|...+......|+.+.+...|++++...|.+..+|..++..... .++.+.+...|++++...|....+|..+...
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~-~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~   81 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAK-KGDYQKAYEDGCKTVDLKPDWGKGYSRKAAA   81 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-HTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHh-hccHHHHHHHHHHHHHhCcccHHHHHHHHHH
Confidence            456788888888889999999999999999999999999998876554 4477889999999999999999999888764


Q ss_pred             HHHhcCCHHHHHHHHHHHHhccccc
Q 008442          102 LERSRASEEEISTVFEKSLLCAFST  126 (565)
Q Consensus       102 le~~~~~~~~~~~if~ral~~~~~~  126 (565)
                      + ...+..+++...|++++...+..
T Consensus        82 ~-~~~~~~~~A~~~~~~~~~~~~~~  105 (118)
T 1elw_A           82 L-EFLNRFEEAKRTYEEGLKHEANN  105 (118)
T ss_dssp             H-HHTTCHHHHHHHHHHHHTTCTTC
T ss_pred             H-HHHhhHHHHHHHHHHHHHcCCCC
Confidence            4 44788999999999999866543

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=98.03  E-value=7e-05  Score=66.14  Aligned_cols=85  Identities=15%  Similarity=0.106  Sum_probs=56.9

Q ss_pred             cCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCH--HHHH
Q 008442           36 SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASE--EEIS  113 (565)
Q Consensus        36 ~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~--~~~~  113 (565)
                      .|+++.+...|++++...|.+..+|..++..... .++.+.+...|++|+...|.+..+|..+...+....+..  +++.
T Consensus        23 ~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~-~~~~~~A~~~~~~al~~~p~~~~~~~~la~~l~~~~~~~~~~~A~  101 (177)
T 2e2e_A           23 QQNPEAQLQALQDKIRANPQNSEQWALLGEYYLW-QNDYSNSLLAYRQALQLRGENAELYAALATVLYYQASQHMTAQTR  101 (177)
T ss_dssp             ----CCCCHHHHHHHHHCCSCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHTTTCCCHHHH
T ss_pred             ccCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCcchHHHH
Confidence            3566777788888888888888888888775543 346777888888888888877777777665423333444  5565


Q ss_pred             HHHHHHHh
Q 008442          114 TVFEKSLL  121 (565)
Q Consensus       114 ~if~ral~  121 (565)
                      ..|++++.
T Consensus       102 ~~~~~al~  109 (177)
T 2e2e_A          102 AMIDKALA  109 (177)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            66665554

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.02  E-value=0.00015  Score=60.04  Aligned_cols=105  Identities=14%  Similarity=0.043  Sum_probs=89.5

Q ss_pred             ChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHH
Q 008442           19 DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRS   98 (565)
Q Consensus        19 ~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~y   98 (565)
                      .+.....|..........++.+.+..+|++++...|.+..+|..++.... ..++.+.+...|++++...|....+|...
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~-~~~~~~~A~~~~~~a~~~~~~~~~~~~~l   90 (133)
T 2lni_A           12 NPDLALMVKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYT-KLLEFQLALKDCEECIQLEPTFIKGYTRK   90 (133)
T ss_dssp             SSCHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTCTTCHHHHHHHHHHHT-TTTCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHH-HhccHHHHHHHHHHHHHhCCCchHHHHHH
Confidence            34578899999999999999999999999999999999999999887543 44577889999999999999999999887


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcccc
Q 008442           99 LLSLERSRASEEEISTVFEKSLLCAFS  125 (565)
Q Consensus        99 i~~le~~~~~~~~~~~if~ral~~~~~  125 (565)
                      ...+ ...+..+++...|++++...+.
T Consensus        91 a~~~-~~~~~~~~A~~~~~~~~~~~p~  116 (133)
T 2lni_A           91 AAAL-EAMKDYTKAMDVYQKALDLDSS  116 (133)
T ss_dssp             HHHH-HHTTCHHHHHHHHHHHHHHCGG
T ss_pred             HHHH-HHHhhHHHHHHHHHHHHHhCCC
Confidence            7644 4468899999999999976544

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.02  E-value=2e-05  Score=61.38  Aligned_cols=71  Identities=20%  Similarity=0.186  Sum_probs=63.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccC-----CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHH-HcCCcccCCeEEE
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDV-----GGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV-AKNKQMFLGKKLS  463 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~-----G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~~~~~~~~g~~l~  463 (565)
                      ..++|-+-|||..+++..|+.+..++     |.|..|.++.|-      |-|+|+|.|...|-+|. .++|..|.|++|+
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            35788999999999999999999999     999999998875      57999999999887776 6999999999999


Q ss_pred             Eee
Q 008442          464 IAR  466 (565)
Q Consensus       464 v~~  466 (565)
                      +.-
T Consensus        94 ~gT   96 (117)
T 2l9w_A           94 SGT   96 (117)
T ss_dssp             EEC
T ss_pred             ecC
Confidence            854

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.01  E-value=0.00026  Score=58.04  Aligned_cols=105  Identities=15%  Similarity=0.023  Sum_probs=88.6

Q ss_pred             hHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHH
Q 008442           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSL   99 (565)
Q Consensus        20 ~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi   99 (565)
                      +.....|...+......++.+.+...|++++...|.+..+|..++..... .++.+.+...|++++...|....+|....
T Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~-~~~~~~A~~~~~~~~~~~~~~~~~~~~~~   87 (131)
T 2vyi_A            9 SAEAERLKTEGNEQMKVENFEAAVHFYGKAIELNPANAVYFCNRAAAYSK-LGNYAGAVQDCERAICIDPAYSKAYGRMG   87 (131)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             hhhhHHHHHHHHHHHHccCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH-hhchHHHHHHHHHHHhcCccCHHHHHHHH
Confidence            44667888888888889999999999999999999999999998876554 45778899999999999999988888877


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhccccc
Q 008442          100 LSLERSRASEEEISTVFEKSLLCAFST  126 (565)
Q Consensus       100 ~~le~~~~~~~~~~~if~ral~~~~~~  126 (565)
                      .. ....+..+.+...|++++...+..
T Consensus        88 ~~-~~~~~~~~~A~~~~~~~~~~~p~~  113 (131)
T 2vyi_A           88 LA-LSSLNKHVEAVAYYKKALELDPDN  113 (131)
T ss_dssp             HH-HHHTTCHHHHHHHHHHHHHHSTTC
T ss_pred             HH-HHHhCCHHHHHHHHHHHHhcCccc
Confidence            63 444788999999999999865543

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.00  E-value=0.00026  Score=67.31  Aligned_cols=187  Identities=7%  Similarity=-0.049  Sum_probs=129.8

Q ss_pred             hcCCchhHHHHHHHHHhcCCCCHHHHHHHH-------HHHHHhcchhhHHHHHHHHHHHcCC-----------CC-----
Q 008442           35 SSGDPGRVQLLYERAITDFPVSSDLWLDYT-------QYLDKTLKVGNVVRDVYSRATKNCP-----------WV-----   91 (565)
Q Consensus        35 ~~~~~~~~~~lyERal~~~p~~~~lW~~Y~-------~~l~~~~~~~~~~~~v~erAl~~~p-----------~~-----   91 (565)
                      ..+++..+...|.+++...|...+.|+..+       .-+..-. ....+.-.+.|++..-|           ..     
T Consensus        18 ~~~d~~~A~~~F~~a~~~dP~~~Daw~g~~a~g~~~~~~L~~~~-r~~~a~~~~~~~l~l~p~~l~a~~~~~g~y~~~~~   96 (282)
T 4f3v_A           18 LPMSEARSLDLFTEITNYDESACDAWIGRIRCGDTDRVTLFRAW-YSRRNFGQLSGSVQISMSTLNARIAIGGLYGDITY   96 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHTTCCCHHHHHHHH-HTGGGTTHHHHTTTCCGGGGCCEEECCTTTCCCEE
T ss_pred             cCCCHHHHHHHHHHHHHhChhhhHHHHhHHHccCCcHHHHHHHH-HHHHHHHHHHHHhcCChhhhhhhhccCCccccccc
Confidence            367889999999999999999999999883       4333222 22335557777776333           11     


Q ss_pred             -----HHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHH
Q 008442           92 -----GELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQR  166 (565)
Q Consensus        92 -----~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~  166 (565)
                           ..|++.|...| ...+.++++..+|..++...+...    ..|..-+      .            .....-|..
T Consensus        97 ~v~~r~dl~LayA~~L-~~~g~y~eA~~~l~~~~~~~p~~~----~~~~~a~------l------------~~~~~r~~d  153 (282)
T 4f3v_A           97 PVTSPLAITMGFAACE-AAQGNYADAMEALEAAPVAGSEHL----VAWMKAV------V------------YGAAERWTD  153 (282)
T ss_dssp             ECSSHHHHHHHHHHHH-HHHTCHHHHHHHHTSSCCTTCHHH----HHHHHHH------H------------HHHTTCHHH
T ss_pred             ccCCHhHHHHHHHHHH-HHCCCHHHHHHHHHHHHhcCCchH----HHHHHHH------H------------HHHcCCHHH
Confidence                 47889998744 446889999999988776544322    1111100      0            011133555


Q ss_pred             HHHHHHhhhcCCchh--HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHc--cc-hHHHHHHHHHHHHHcCChHHHHHHHH
Q 008442          167 ASDYLSEQMKNTDGL--LRLYAYWAHLEQSMGKDMVSARGVWERLLKIS--GA-MLEAWQSYISMEIELDHINEARSIYK  241 (565)
Q Consensus       167 a~~~l~~~~~~~~~~--~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~--~~-~~~lw~~yi~~e~~~~~~~~aR~i~~  241 (565)
                      ++.++.......++.  ...+.........+| ++++|...|++++...  |. ..+.++.........|+.+.|+.+|+
T Consensus       154 A~~~l~~a~~~~d~~~~~~a~~~LG~al~~LG-~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~  232 (282)
T 4f3v_A          154 VIDQVKSAGKWPDKFLAGAAGVAHGVAAANLA-LFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLE  232 (282)
T ss_dssp             HHHHHTTGGGCSCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHhhccCCcccHHHHHHHHHHHHHHCC-CHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            566665544433443  235666778888889 9999999999999653  54 56799999999999999999999999


Q ss_pred             HHHhc
Q 008442          242 RCYSK  246 (565)
Q Consensus       242 ~al~~  246 (565)
                      +++..
T Consensus       233 ~a~a~  237 (282)
T 4f3v_A          233 WLQTT  237 (282)
T ss_dssp             HHHHH
T ss_pred             HHHhc
Confidence            99873

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=97.97  E-value=0.0009  Score=57.62  Aligned_cols=103  Identities=10%  Similarity=-0.088  Sum_probs=86.8

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~  101 (565)
                      ....|..........|+.+.+...|++++...|.+..+|..++.... ..+..+.+...|++++...|....+|......
T Consensus        12 ~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~-~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~   90 (166)
T 1a17_A           12 RAEELKTQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYL-RTECYGYALGDATRAIELDKKYIKGYYRRAAS   90 (166)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCChHHHHHHHHHHH-HcCCHHHHHHHHHHHHHhCcccHHHHHHHHHH
Confidence            45678888888888999999999999999999999999999887554 44577889999999999999999999887764


Q ss_pred             HHHhcCCHHHHHHHHHHHHhccccc
Q 008442          102 LERSRASEEEISTVFEKSLLCAFST  126 (565)
Q Consensus       102 le~~~~~~~~~~~if~ral~~~~~~  126 (565)
                      + ...+..+++...|++++...+..
T Consensus        91 ~-~~~~~~~~A~~~~~~a~~~~p~~  114 (166)
T 1a17_A           91 N-MALGKFRAALRDYETVVKVKPHD  114 (166)
T ss_dssp             H-HHTTCHHHHHHHHHHHHHHSTTC
T ss_pred             H-HHhccHHHHHHHHHHHHHhCCCC
Confidence            4 44788999999999999865543

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=97.97  E-value=0.00077  Score=63.54  Aligned_cols=146  Identities=5%  Similarity=-0.131  Sum_probs=86.8

Q ss_pred             hcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCC---HHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccccc-
Q 008442           51 TDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV---GELWVRSLLSLERSRASEEEISTVFEKSLLCAFST-  126 (565)
Q Consensus        51 ~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~---~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~-  126 (565)
                      ...|.+.+.+...+..... .+..+.+...|++++...|.+   ...|..... +....+..+++...|++++...+.. 
T Consensus         9 ~~~~~~~~~~~~~a~~~~~-~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~-~~~~~~~~~~A~~~~~~~l~~~p~~~   86 (261)
T 3qky_A            9 RLRHSSPQEAFERAMEFYN-QGKYDRAIEYFKAVFTYGRTHEWAADAQFYLAR-AYYQNKEYLLAASEYERFIQIYQIDP   86 (261)
T ss_dssp             --CCSSHHHHHHHHHHHHH-TTCHHHHHHHHHHHGGGCSCSTTHHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHHCTTCT
T ss_pred             CCCCCCHHHHHHHHHHHHH-hCCHHHHHHHHHHHHHhCCCCcchHHHHHHHHH-HHHHhCcHHHHHHHHHHHHHHCCCCc
Confidence            3456666666666654443 346788999999999988877   666655544 3334678888999999988753321 


Q ss_pred             --HHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHH
Q 008442          127 --FEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARG  204 (565)
Q Consensus       127 --~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~  204 (565)
                        ...+..+-.++..                                 ..    +          .+....+ +++.|..
T Consensus        87 ~~~~a~~~lg~~~~~---------------------------------~~----~----------~~~~~~~-~~~~A~~  118 (261)
T 3qky_A           87 RVPQAEYERAMCYYK---------------------------------LS----P----------PYELDQT-DTRKAIE  118 (261)
T ss_dssp             THHHHHHHHHHHHHH---------------------------------HC----C----------CTTSCCH-HHHHHHH
T ss_pred             hhHHHHHHHHHHHHH---------------------------------hc----c----------cccccch-hHHHHHH
Confidence              1111111111100                                 00    0          0000023 4555556


Q ss_pred             HHHHHHHHccchHHH-----------------HHHHHHHHHHcCChHHHHHHHHHHHhc
Q 008442          205 VWERLLKISGAMLEA-----------------WQSYISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       205 i~e~~l~~~~~~~~l-----------------w~~yi~~e~~~~~~~~aR~i~~~al~~  246 (565)
                      .|++++..+|++...                 |...+.+....|+++.|...|++++..
T Consensus       119 ~~~~~l~~~p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~  177 (261)
T 3qky_A          119 AFQLFIDRYPNHELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAAVTYEAVFDA  177 (261)
T ss_dssp             HHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            666666555544333                 366678888899999999999999973

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=97.96  E-value=0.0004  Score=68.29  Aligned_cols=222  Identities=10%  Similarity=-0.001  Sum_probs=140.6

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcC-CchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcc-hhhHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSG-DPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLK-VGNVVRDVY   81 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~-~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~-~~~~~~~v~   81 (565)
                      +-..++.+|..+|.    ++.+|..--......+ ..+....+++.+|..+|.++.+|..-.-.+....+ ..+...+.+
T Consensus        73 AL~lt~~~L~~nP~----~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPKny~aW~hR~wlL~~l~~~~~~~EL~~~  148 (349)
T 3q7a_A           73 ALELTEIIVRMNPA----HYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLKSYQVWHHRLLLLDRISPQDPVSEIEYI  148 (349)
T ss_dssp             HHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHCCSCCHHHHHHH
T ss_pred             HHHHHHHHHHhCch----hHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhcCCChHHHHHHH
Confidence            44567788888887    8999988777777777 58899999999999999999999987765555424 567788999


Q ss_pred             HHHHHcCCCCHHHHHHHHHHHHHhcCC-------HHHHHHHHHHHHhccccc--HHHHHHHHHHHHHHHHHHhhccccch
Q 008442           82 SRATKNCPWVGELWVRSLLSLERSRAS-------EEEISTVFEKSLLCAFST--FEEYLDLFLTRIDGLRRRILFSGEVE  152 (565)
Q Consensus        82 erAl~~~p~~~~lW~~yi~~le~~~~~-------~~~~~~if~ral~~~~~~--~~~~~~~~~~~~~~~~r~~~~~~~~e  152 (565)
                      ++++...|.+...|....-.+......       .++....+++++...+..  .|.+..+.+...         ... .
T Consensus       149 ~k~L~~dpkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp~N~SAW~~R~~lL~~l---------~~~-~  218 (349)
T 3q7a_A          149 HGSLLPDPKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDGRNNSAWGWRWYLRVSR---------PGA-E  218 (349)
T ss_dssp             HHHTSSCTTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHTTS---------TTC-C
T ss_pred             HHHHHhCCCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhc---------ccc-c
Confidence            999999999999997755433332111       125556777777655543  232222221110         000 0


Q ss_pred             hhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChH----------------HHHHHHHHHHHH---c
Q 008442          153 GVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMV----------------SARGVWERLLKI---S  213 (565)
Q Consensus       153 ~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~----------------~ar~i~e~~l~~---~  213 (565)
                            .....++++++++...+...+.....|.+..-+....+....                ..-.+.+.++..   .
T Consensus       219 ------~~~~~~~eELe~~~~aI~~~P~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  292 (349)
T 3q7a_A          219 ------TSSRSLQDELIYILKSIHLIPHNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDP  292 (349)
T ss_dssp             ------CCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCCC-C
T ss_pred             ------cchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHHhcc
Confidence                  012456667777766666556666788776666666553300                011222222222   1


Q ss_pred             ------cchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          214 ------GAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       214 ------~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                            ..+.-++-..++.+...|+.++|.++|+....
T Consensus       293 ~~~~~~~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~  330 (349)
T 3q7a_A          293 LPEDTPLPVPLALEYLADSFIEQNRVDDAAKVFEKLSS  330 (349)
T ss_dssp             CCSSCCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cccccCCCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Confidence                  24455666666777778888999999998765

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=97.96  E-value=0.00066  Score=68.14  Aligned_cols=223  Identities=10%  Similarity=-0.026  Sum_probs=131.0

Q ss_pred             hhHHHHHHHhcCCCC--ChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHH-------HHHHHHHHHHHhcchh
Q 008442            4 ARAHLEEQISRQDLS--DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSD-------LWLDYTQYLDKTLKVG   74 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~--~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~-------lW~~Y~~~l~~~~~~~   74 (565)
                      +...|+.++......  .+.....|..........|+++.+...|++|+...+...+       .+...+. +....+..
T Consensus       122 A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~-~~~~~g~~  200 (383)
T 3ulq_A          122 AIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLFAT-NFLDLKQY  200 (383)
T ss_dssp             HHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHHHH-HHHHTTCH
T ss_pred             HHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHH-HHHHhcCH
Confidence            455667776542111  2234567777777777788888999999999887554432       3333332 33344577


Q ss_pred             hHHHHHHHHHHHcCCCCH------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhc-----c-cccHHHHHHHHHHHHHHHH
Q 008442           75 NVVRDVYSRATKNCPWVG------ELWVRSLLSLERSRASEEEISTVFEKSLLC-----A-FSTFEEYLDLFLTRIDGLR  142 (565)
Q Consensus        75 ~~~~~v~erAl~~~p~~~------~lW~~yi~~le~~~~~~~~~~~if~ral~~-----~-~~~~~~~~~~~~~~~~~~~  142 (565)
                      +.+...|++|+...+...      .+|..... +-...+..+++...|++|+..     . +.....+..+-..+..   
T Consensus       201 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~-~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~---  276 (383)
T 3ulq_A          201 EDAISHFQKAYSMAEAEKQPQLMGRTLYNIGL-CKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHYK---  276 (383)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHH---
T ss_pred             HHHHHHHHHHHHHHHHcCChHHHHHHHHHHHH-HHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHH---
Confidence            888899999987654221      23333222 334467888899999998862     2 2212222222221110   


Q ss_pred             HHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCC---hHHHHHHHHHHHHHccchHHH
Q 008442          143 RRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKD---MVSARGVWERLLKISGAMLEA  219 (565)
Q Consensus       143 r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~---~~~ar~i~e~~l~~~~~~~~l  219 (565)
                                 ..++..+...|++++.......  .+.....+...+.+....+ +   +.+|..++++. ...+....+
T Consensus       277 -----------~g~~~~A~~~~~~al~~~~~~~--~~~~~~~~~~l~~~~~~~~-~~~~~~~al~~~~~~-~~~~~~~~~  341 (383)
T 3ulq_A          277 -----------LGKIDKAHEYHSKGMAYSQKAG--DVIYLSEFEFLKSLYLSGP-DEEAIQGFFDFLESK-MLYADLEDF  341 (383)
T ss_dssp             -----------TTCHHHHHHHHHHHHHHHHHHT--CHHHHHHHHHHHHHHTSSC-CHHHHHHHHHHHHHT-TCHHHHHHH
T ss_pred             -----------CCCHHHHHHHHHHHHHHHHHcC--CHHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHC-cCHHHHHHH
Confidence                       0145556666777766653321  1111222334555665555 6   55566666554 223444668


Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHhc
Q 008442          220 WQSYISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       220 w~~yi~~e~~~~~~~~aR~i~~~al~~  246 (565)
                      +...+.+....|+++.|...|++++..
T Consensus       342 ~~~la~~y~~~g~~~~A~~~~~~al~~  368 (383)
T 3ulq_A          342 AIDVAKYYHERKNFQKASAYFLKVEQV  368 (383)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            888889999999999999999999863

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=97.95  E-value=0.0006  Score=65.65  Aligned_cols=170  Identities=9%  Similarity=-0.037  Sum_probs=114.9

Q ss_pred             cCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHH
Q 008442           87 NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQR  166 (565)
Q Consensus        87 ~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~  166 (565)
                      ..|.....+......+ ...++.+++..+|++++...+.....+..+-..+.                     ...-+++
T Consensus       112 ~lp~~~~~~~~~a~~~-~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~---------------------~~g~~~~  169 (287)
T 3qou_A          112 VLPREEELXAQQAMQL-MQESNYTDALPLLXDAWQLSNQNGEIGLLLAETLI---------------------ALNRSED  169 (287)
T ss_dssp             HSCCHHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHTTSCHHHHHHHHHHHH---------------------HTTCHHH
T ss_pred             HcCCchhhHHHHHHHH-HhCCCHHHHHHHHHHHHHhCCcchhHHHHHHHHHH---------------------HCCCHHH
Confidence            4587777776655533 34688999999999999877665544443333222                     1133555


Q ss_pred             HHHHHHhhhcCCchhHHHHHHHHHH-HHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          167 ASDYLSEQMKNTDGLLRLYAYWAHL-EQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       167 a~~~l~~~~~~~~~~~~l~~~~a~~-e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      |+..+...+...+... .....+.+ ....+ ..+.|...|++++...|++..+|..++..+...|+++.|...|.+++.
T Consensus       170 A~~~l~~~~~~~p~~~-~~~~~~~~~l~~~~-~~~~a~~~l~~al~~~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~  247 (287)
T 3qou_A          170 AEAVLXTIPLQDQDTR-YQGLVAQIELLXQA-ADTPEIQQLQQQVAENPEDAALATQLALQLHQVGRNEEALELLFGHLR  247 (287)
T ss_dssp             HHHHHTTSCGGGCSHH-HHHHHHHHHHHHHH-TSCHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhCchhhcchH-HHHHHHHHHHHhhc-ccCccHHHHHHHHhcCCccHHHHHHHHHHHHHcccHHHHHHHHHHHHh
Confidence            6666655544333222 22222222 22334 566789999999999999999999999999999999999999999997


Q ss_pred             cccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          246 KRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       246 ~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      .. +.......+.....+-...|..+.+....++++
T Consensus       248 ~~-p~~~~~~a~~~l~~~~~~~g~~~~a~~~~r~al  282 (287)
T 3qou_A          248 XD-LTAADGQTRXTFQEILAALGTGDALASXYRRQL  282 (287)
T ss_dssp             HC-TTGGGGHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             cc-cccccchHHHHHHHHHHHcCCCCcHHHHHHHHH
Confidence            42 322235678888888888887766655555544

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=97.95  E-value=2.8e-05  Score=77.01  Aligned_cols=94  Identities=7%  Similarity=0.032  Sum_probs=54.6

Q ss_pred             HHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHh
Q 008442          188 WAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREY  267 (565)
Q Consensus       188 ~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~  267 (565)
                      ++.++...+ ++++|...|++++...|++...|...+......|+++.|...|++++..  . +....++..........
T Consensus       202 la~~~~~~g-~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~-P~~~~a~~~l~~~~~~~  277 (336)
T 1p5q_A          202 LAMCHLKLQ-AFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQL--Y-PNNKAAKTQLAVCQQRI  277 (336)
T ss_dssp             HHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--C-SSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcC-CHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--C-CCCHHHHHHHHHHHHHH
Confidence            334444555 6777777777777777777777777777777777777777777777652  1 12234444444444455


Q ss_pred             CCHHHH-HHHHHHHhhHHH
Q 008442          268 GTLEDF-DHSVQKVTPRLE  285 (565)
Q Consensus       268 G~~~~~-~~~~~k~~~~~~  285 (565)
                      |..+.. +..+.+...++.
T Consensus       278 ~~~~~a~~~~~~~~~~~~~  296 (336)
T 1p5q_A          278 RRQLAREKKLYANMFERLA  296 (336)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhh
Confidence            555444 234444444443

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=97.92  E-value=0.00049  Score=55.77  Aligned_cols=102  Identities=15%  Similarity=0.143  Sum_probs=86.2

Q ss_pred             HHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHH
Q 008442           23 FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSL  102 (565)
Q Consensus        23 ~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~l  102 (565)
                      ...|...+......++.+.+..+|++++...|.+..+|..++...... +..+.+..+|++++...|....+|......+
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~-~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~   87 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQ-GDYDEAIEYYQKALELDPNNAEAWYNLGNAY   87 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHhCCccHHHHHHHHHHH
Confidence            567888888888899999999999999999999999999988765544 4778899999999999999988888877644


Q ss_pred             HHhcCCHHHHHHHHHHHHhccccc
Q 008442          103 ERSRASEEEISTVFEKSLLCAFST  126 (565)
Q Consensus       103 e~~~~~~~~~~~if~ral~~~~~~  126 (565)
                       ...+..+.+...|++++...+..
T Consensus        88 -~~~~~~~~A~~~~~~~~~~~~~~  110 (125)
T 1na0_A           88 -YKQGDYDEAIEYYQKALELDPNN  110 (125)
T ss_dssp             -HHTTCHHHHHHHHHHHHHHCTTC
T ss_pred             -HHhcCHHHHHHHHHHHHHhCCCc
Confidence             44688999999999999865543

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=97.92  E-value=0.0014  Score=63.02  Aligned_cols=210  Identities=10%  Similarity=-0.022  Sum_probs=124.7

Q ss_pred             hHHHHHHHHHhcCCCCHHHHHHHHHHHHHh-cchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 008442           41 RVQLLYERAITDFPVSSDLWLDYTQYLDKT-LKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKS  119 (565)
Q Consensus        41 ~~~~lyERal~~~p~~~~lW~~Y~~~l~~~-~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ra  119 (565)
                      ++..++.+|-...+.+..+| .|..   .. ....+.+...|++|..               +-...+..+++...|++|
T Consensus         3 ~a~~~~~~a~k~~~~~~~~~-~~~~---~~~~~~~~~A~~~~~~a~~---------------~~~~~g~~~~A~~~~~~a   63 (292)
T 1qqe_A            3 DPVELLKRAEKKGVPSSGFM-KLFS---GSDSYKFEEAADLCVQAAT---------------IYRLRKELNLAGDSFLKA   63 (292)
T ss_dssp             CHHHHHHHHHHHSSCCCTHH-HHHS---CCSHHHHHHHHHHHHHHHH---------------HHHHTTCTHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhCcCCCcc-hhcC---CCCCccHHHHHHHHHHHHH---------------HHHHcCCHHHHHHHHHHH
Confidence            46677777777777666777 4431   11 1135667778887733               112256777888888888


Q ss_pred             Hhccc--ccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHc-C
Q 008442          120 LLCAF--STFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSM-G  196 (565)
Q Consensus       120 l~~~~--~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~-~  196 (565)
                      +....  .........+........          ...++..+...|++++.+.... .........+...+.++... +
T Consensus        64 l~~~~~~~~~~~~a~~~~~lg~~~~----------~~g~~~~A~~~~~~Al~l~~~~-g~~~~~a~~~~~lg~~~~~~lg  132 (292)
T 1qqe_A           64 ADYQKKAGNEDEAGNTYVEAYKCFK----------SGGNSVNAVDSLENAIQIFTHR-GQFRRGANFKFELGEILENDLH  132 (292)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHH----------HTTCHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHHHH----------HCCCHHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHHhhc
Confidence            76421  111111111111111110          0014455666677777655321 11111234555667777774 7


Q ss_pred             CChHHHHHHHHHHHHHccch------HHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcH--H---HHHHHHHHHH
Q 008442          197 KDMVSARGVWERLLKISGAM------LEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSE--D---ICHAWLRFER  265 (565)
Q Consensus       197 ~~~~~ar~i~e~~l~~~~~~------~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~--~---i~~~~~~fE~  265 (565)
                       ++++|...|++++...+..      ..+|...+.+....|+++.|..+|++++... +.....  .   .+......-.
T Consensus       133 -~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~lg~~~~  210 (292)
T 1qqe_A          133 -DYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSS-MGNRLSQWSLKDYFLKKGLCQL  210 (292)
T ss_dssp             -CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT-SSCTTTGGGHHHHHHHHHHHHH
T ss_pred             -CHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH-hcCCcccHHHHHHHHHHHHHHH
Confidence             9999999999999985532      4678888999999999999999999998742 211110  1   2333333445


Q ss_pred             HhCCHHHHHHHHHHHhh
Q 008442          266 EYGTLEDFDHSVQKVTP  282 (565)
Q Consensus       266 ~~G~~~~~~~~~~k~~~  282 (565)
                      ..|+.+.+..++++++.
T Consensus       211 ~~g~~~~A~~~~~~al~  227 (292)
T 1qqe_A          211 AATDAVAAARTLQEGQS  227 (292)
T ss_dssp             HTTCHHHHHHHHHGGGC
T ss_pred             HcCCHHHHHHHHHHHHh
Confidence            56888888888888764

>4aez_C MAD3, mitotic spindle checkpoint component MAD3; cell cycle, KEN-BOX, D-BOX, APC/C; 2.30A {Schizosaccharomyces pombe}

Probab=97.90  E-value=0.00012  Score=65.88  Aligned_cols=95  Identities=9%  Similarity=0.125  Sum_probs=69.8

Q ss_pred             HHHHHHHHHHHh--hhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH--ccchHHHHHHHHHHHHHcCChHHHH
Q 008442          162 ETFQRASDYLSE--QMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI--SGAMLEAWQSYISMEIELDHINEAR  237 (565)
Q Consensus       162 ~~~~~a~~~l~~--~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~--~~~~~~lw~~yi~~e~~~~~~~~aR  237 (565)
                      .++++|+..+..  .+.+.+.++++|+.|+++    .   +.++.+|..+...  ......+|..|+.+....|++..|.
T Consensus        98 ~lLErc~~~F~~~~rYknD~RyLklWl~Ya~~----~---~~p~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~  170 (223)
T 4aez_C           98 TLLERCTREFVRNPLYKDDVRYLRIWMQYVNY----I---DEPVELFSFLAHHHIGQESSIFYEEYANYFESRGLFQKAD  170 (223)
T ss_dssp             HHHHHHHHHTTTCGGGTTCHHHHHHHHHHHTT----C---SCHHHHHHHHHHTTCSTTBHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHhcccccccCCHHHHHHHHHHHHc----c---CCHHHHHHHHHHCCcchhHHHHHHHHHHHHHHcCCHHHHH
Confidence            566666666533  344566788999999874    2   2567899998887  3456889999999999999999999


Q ss_pred             HHHHHHHhcccCCCCcHHHHHHHHHHHH
Q 008442          238 SIYKRCYSKRFTGTGSEDICHAWLRFER  265 (565)
Q Consensus       238 ~i~~~al~~~~~~~~~~~i~~~~~~fE~  265 (565)
                      +||..+|...  ...-+.|-..+-.|+.
T Consensus       171 ~Vy~~Gi~~~--A~P~~rL~~~~~~F~~  196 (223)
T 4aez_C          171 EVYQKGKRMK--AKPFLRFQQKYQQFTH  196 (223)
T ss_dssp             HHHHHHHHHT--CBSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcC--CccHHHHHHHHHHHHH
Confidence            9999999842  2223455666666653

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.90  E-value=8.1e-05  Score=59.44  Aligned_cols=101  Identities=19%  Similarity=0.151  Sum_probs=85.7

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCC--CHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPW--VGELWVRSL   99 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~--~~~lW~~yi   99 (565)
                      +...|..........|+.+.+...|++++...|.+..+|..++..... .+..+.+...|++++...|.  ...+|....
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~-~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l~   83 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLDPEESKYWLMKGKALYN-LERYEEAVDCYNYVINVIEDEYNKDVWAAKA   83 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHTSCCTTCHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhCcccchHHHHHHHH
Confidence            556777788888889999999999999999999999999998876554 44778899999999999999  899998877


Q ss_pred             HHHHHhc-CCHHHHHHHHHHHHhccc
Q 008442          100 LSLERSR-ASEEEISTVFEKSLLCAF  124 (565)
Q Consensus       100 ~~le~~~-~~~~~~~~if~ral~~~~  124 (565)
                      . +.... +..+++...|++++...+
T Consensus        84 ~-~~~~~~~~~~~A~~~~~~~~~~~p  108 (112)
T 2kck_A           84 D-ALRYIEGKEVEAEIAEARAKLEHH  108 (112)
T ss_dssp             H-HHTTCSSCSHHHHHHHHHHGGGCC
T ss_pred             H-HHHHHhCCHHHHHHHHHHHhhccc
Confidence            6 44557 888999999999987544

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=97.89  E-value=0.0013  Score=65.87  Aligned_cols=234  Identities=12%  Similarity=0.013  Sum_probs=135.5

Q ss_pred             HHHHHhcCCchhHHHHHHHHHhc---CCCC---HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCH-------HHHH
Q 008442           30 LKYEQSSGDPGRVQLLYERAITD---FPVS---SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVG-------ELWV   96 (565)
Q Consensus        30 i~~e~~~~~~~~~~~lyERal~~---~p~~---~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~-------~lW~   96 (565)
                      ..+....|+++.+...|++|+..   .+..   ..+|...+.. ....++.+.+...|++|+..++...       ..+.
T Consensus       110 g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~-~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  188 (383)
T 3ulq_A          110 GMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSES-YYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHS  188 (383)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHH-HHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHH-HHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHH
Confidence            34455679999999999999986   2322   2455544443 3345577889999999998654321       1222


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcccc--cHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhh
Q 008442           97 RSLLSLERSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQ  174 (565)
Q Consensus        97 ~yi~~le~~~~~~~~~~~if~ral~~~~~--~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~  174 (565)
                      .... +-...+..+++...|++|+.....  ........+........          ...++..+...|.+++.+....
T Consensus       189 ~lg~-~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~----------~~g~~~~A~~~~~~al~~~~~~  257 (383)
T 3ulq_A          189 LFAT-NFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKN----------SQSQYEDAIPYFKRAIAVFEES  257 (383)
T ss_dssp             HHHH-HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH----------HTTCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHH-HHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHH----------HCCCHHHHHHHHHHHHHHHHhh
Confidence            2222 333468899999999999964221  11111111111111010          0024556666777777665332


Q ss_pred             hcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHcc-----chHHHHHHHHHHHHHcCC---hHHHHHHHHHHHhc
Q 008442          175 MKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG-----AMLEAWQSYISMEIELDH---INEARSIYKRCYSK  246 (565)
Q Consensus       175 ~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~-----~~~~lw~~yi~~e~~~~~---~~~aR~i~~~al~~  246 (565)
                      . ..+.....+...+.+....+ +++.|...|++++...+     .....+.....+....|+   ++.|..++++.-. 
T Consensus       258 ~-~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~~~-  334 (383)
T 3ulq_A          258 N-ILPSLPQAYFLITQIHYKLG-KIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKML-  334 (383)
T ss_dssp             T-CGGGHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHTTC-
T ss_pred             c-cchhHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCcC-
Confidence            2 11334566777788888888 99999999999998732     222233344455556677   6666666666511 


Q ss_pred             ccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          247 RFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       247 ~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                         .+....++.....+-...|+.+.+...+++++
T Consensus       335 ---~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al  366 (383)
T 3ulq_A          335 ---YADLEDFAIDVAKYYHERKNFQKASAYFLKVE  366 (383)
T ss_dssp             ---HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence               01112344444455666788777776666654

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=97.87  E-value=0.00016  Score=60.18  Aligned_cols=92  Identities=13%  Similarity=-0.030  Sum_probs=80.5

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...|+.+|...|.    +...|..........|+.+.+...|++||...|.+...|...+..+. ..+..+.+...|+
T Consensus        31 ~A~~~~~~al~~~p~----~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~-~~~~~~~A~~~~~  105 (126)
T 4gco_A           31 TAMRHYNEAVKRDPE----NAILYSNRAACLTKLMEFQRALDDCDTCIRLDSKFIKGYIRKAACLV-AMREWSKAQRAYE  105 (126)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC----CHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhhhhHHHHHHHHHHH-HCCCHHHHHHHHH
Confidence            366788999988887    78899999999999999999999999999999999999999987555 4557888999999


Q ss_pred             HHHHcCCCCHHHHHHHH
Q 008442           83 RATKNCPWVGELWVRSL   99 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi   99 (565)
                      +|++..|.+..++....
T Consensus       106 ~al~l~P~~~~a~~~l~  122 (126)
T 4gco_A          106 DALQVDPSNEEAREGVR  122 (126)
T ss_dssp             HHHHHCTTCHHHHHHHH
T ss_pred             HHHHHCcCCHHHHHHHH
Confidence            99999999988876643

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=97.87  E-value=0.00014  Score=60.02  Aligned_cols=99  Identities=10%  Similarity=-0.026  Sum_probs=80.4

Q ss_pred             HHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Q 008442           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLE  103 (565)
Q Consensus        24 ~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le  103 (565)
                      ..|..........|+.+.+...|+++|...|.+...|......+. ..+..+.+...|++|+...|.....|......+ 
T Consensus        18 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~-~~g~~~~A~~~~~~al~l~P~~~~~~~~la~~~-   95 (121)
T 1hxi_A           18 ENPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQA-ENEKDGLAIIALNHARMLDPKDIAVHAALAVSH-   95 (121)
T ss_dssp             SCHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH-
T ss_pred             hhHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH-HcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH-
Confidence            356667777778899999999999999999999999998887555 445778899999999999999999988776534 


Q ss_pred             HhcCCHHHHHHHHHHHHhccc
Q 008442          104 RSRASEEEISTVFEKSLLCAF  124 (565)
Q Consensus       104 ~~~~~~~~~~~if~ral~~~~  124 (565)
                      ...+..+++...|++++...+
T Consensus        96 ~~~g~~~~A~~~~~~al~~~P  116 (121)
T 1hxi_A           96 TNEHNANAALASLRAWLLSQP  116 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHC---
T ss_pred             HHcCCHHHHHHHHHHHHHhCc
Confidence            335778899999999987543

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=97.87  E-value=0.00024  Score=59.40  Aligned_cols=100  Identities=13%  Similarity=-0.065  Sum_probs=86.8

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~  101 (565)
                      +...|..........|+++.+...|++++...|.+..+|..++..... .++.+.+...|++|+...|.....|......
T Consensus         8 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~-~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~   86 (137)
T 3q49_B            8 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLK-MQQPEQALADCRRALELDGQSVKAHFFLGQC   86 (137)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHH-hcCHHHHHHHHHHHHHhCchhHHHHHHHHHH
Confidence            677899999999999999999999999999999999999999876554 4577889999999999999999999887764


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcc
Q 008442          102 LERSRASEEEISTVFEKSLLCA  123 (565)
Q Consensus       102 le~~~~~~~~~~~if~ral~~~  123 (565)
                      + ...+..+.+...|++++...
T Consensus        87 ~-~~~~~~~~A~~~~~~a~~~~  107 (137)
T 3q49_B           87 Q-LEMESYDEAIANLQRAYSLA  107 (137)
T ss_dssp             H-HHTTCHHHHHHHHHHHHHHH
T ss_pred             H-HHHhhHHHHHHHHHHHHHHC
Confidence            4 44688999999999999643

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=97.83  E-value=0.0041  Score=59.70  Aligned_cols=163  Identities=11%  Similarity=-0.041  Sum_probs=100.3

Q ss_pred             chhhHHHHHHHHHHHcCCCCHHH-----HHHHHHHHHHhcCCHHHHHHHHHHHHhccc--ccHHHHHHHHHHHHHHHHHH
Q 008442           72 KVGNVVRDVYSRATKNCPWVGEL-----WVRSLLSLERSRASEEEISTVFEKSLLCAF--STFEEYLDLFLTRIDGLRRR  144 (565)
Q Consensus        72 ~~~~~~~~v~erAl~~~p~~~~l-----W~~yi~~le~~~~~~~~~~~if~ral~~~~--~~~~~~~~~~~~~~~~~~r~  144 (565)
                      ++.+.+..+|+.++...+..+..     |...+..+....+..+++...|++|+....  ..+...+.++........  
T Consensus        89 ~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~--  166 (293)
T 3u3w_A           89 KRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYA--  166 (293)
T ss_dssp             TCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHHHHHHH--
T ss_pred             hhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHH--
Confidence            35666778888888766554431     333333333444577888888888886321  111111111111110000  


Q ss_pred             hhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccc------hHH
Q 008442          145 ILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA------MLE  218 (565)
Q Consensus       145 ~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~------~~~  218 (565)
                              ...+++.+...|++++..+.......+....++...+.+....+ ++++|...+++++...+.      ...
T Consensus       167 --------~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~-~y~~A~~~~~~al~~~~~~~~~~~~~~  237 (293)
T 3u3w_A          167 --------ENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDS-RYEESLYQVNKAIEISCRINSMALIGQ  237 (293)
T ss_dssp             --------HTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHTTBCTTHHH
T ss_pred             --------HcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHh-HHHHHHHHHHHHHHHHHHcCcHHHHHH
Confidence                    00145556667777776654432333334456667788888888 999999999999986422      256


Q ss_pred             HHHHHHHHHHHcC-ChHHHHHHHHHHHh
Q 008442          219 AWQSYISMEIELD-HINEARSIYKRCYS  245 (565)
Q Consensus       219 lw~~yi~~e~~~~-~~~~aR~i~~~al~  245 (565)
                      +|..........| +++.|...|++|+.
T Consensus       238 ~~~~lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          238 LYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            8888888888899 46999999999985

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=97.81  E-value=0.0085  Score=59.50  Aligned_cols=237  Identities=12%  Similarity=0.067  Sum_probs=140.4

Q ss_pred             HHHHHhcCCchhHHHHHHHHHhcCCCCHHH-H----HHHHHHHHHhcchhhHHHHHHHHHHHcCCCCH----HHHHHH-H
Q 008442           30 LKYEQSSGDPGRVQLLYERAITDFPVSSDL-W----LDYTQYLDKTLKVGNVVRDVYSRATKNCPWVG----ELWVRS-L   99 (565)
Q Consensus        30 i~~e~~~~~~~~~~~lyERal~~~p~~~~l-W----~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~----~lW~~y-i   99 (565)
                      .......|+++.+..++++++...|..... |    ..... +....++.+.+...|++|+...|..+    ..|..+ +
T Consensus        21 a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~-~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l   99 (373)
T 1hz4_A           21 AQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGE-VLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQ   99 (373)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHH-HHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHH-HHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence            334456799999999999999988765432 1    11122 22234577889999999998654322    122221 2


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcccc------cHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHh
Q 008442          100 LSLERSRASEEEISTVFEKSLLCAFS------TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSE  173 (565)
Q Consensus       100 ~~le~~~~~~~~~~~if~ral~~~~~------~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~  173 (565)
                      -.+....+.++++...|++++.....      .........+..+-+.            ..+++.....+.+++.....
T Consensus       100 a~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~------------~g~~~~A~~~~~~al~~~~~  167 (373)
T 1hz4_A          100 SEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWA------------WARLDEAEASARSGIEVLSS  167 (373)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHH------------TTCHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHH------------hcCHHHHHHHHHHHHHHhhc
Confidence            22344578999999999999863210      1111111111111000            01455666677776665432


Q ss_pred             hhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHcc--chHHHHHHH-----HHHHHHcCChHHHHHHHHHHHhc
Q 008442          174 QMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG--AMLEAWQSY-----ISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       174 ~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~--~~~~lw~~y-----i~~e~~~~~~~~aR~i~~~al~~  246 (565)
                      ..  .+.....+...+.+....+ +++.|...+++++...+  .....|...     +.+....|+++.|+.++.+++..
T Consensus       168 ~~--~~~~~~~~~~la~~~~~~g-~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~  244 (373)
T 1hz4_A          168 YQ--PQQQLQCLAMLIQCSLARG-DLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKP  244 (373)
T ss_dssp             SC--GGGGHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCC
T ss_pred             cC--cHHHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCC
Confidence            11  1112345566778888888 99999999999997632  121234332     33456789999999999999763


Q ss_pred             ccCCCC--cHHHHHHHHHHHHHhCCHHHHHHHHHHHhhH
Q 008442          247 RFTGTG--SEDICHAWLRFEREYGTLEDFDHSVQKVTPR  283 (565)
Q Consensus       247 ~~~~~~--~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~~  283 (565)
                      . +.+.  ....+..........|+.+.+...+.++...
T Consensus       245 ~-~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~  282 (373)
T 1hz4_A          245 E-FANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNEN  282 (373)
T ss_dssp             C-CTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             C-CCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            2 2111  1223444555666778888887777776544

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=97.81  E-value=0.00039  Score=59.89  Aligned_cols=107  Identities=8%  Similarity=-0.026  Sum_probs=83.9

Q ss_pred             HHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCC
Q 008442          171 LSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTG  250 (565)
Q Consensus       171 l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~  250 (565)
                      +...+...+.....+...+......+ +++.|..+|++++...|++..+|..........|+++.|...|++++..  ..
T Consensus        25 l~~al~l~p~~~~~~~~lg~~~~~~g-~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l--~P  101 (151)
T 3gyz_A           25 LKDINAIPDDMMDDIYSYAYDFYNKG-RIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFAL--GK  101 (151)
T ss_dssp             TGGGCCSCHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SS
T ss_pred             HHHHhCCCHHHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhh--CC
Confidence            34444445556667777777777888 9999999999999999999999999999999999999999999999973  33


Q ss_pred             CCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          251 TGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       251 ~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      +.+ ..|...-..-...|+.+.+..++++++
T Consensus       102 ~~~-~~~~~lg~~~~~lg~~~eA~~~~~~al  131 (151)
T 3gyz_A          102 NDY-TPVFHTGQCQLRLKAPLKAKECFELVI  131 (151)
T ss_dssp             SCC-HHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CCc-HHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            334 445445555557788888888887775

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=97.80  E-value=0.0014  Score=63.23  Aligned_cols=209  Identities=13%  Similarity=0.075  Sum_probs=127.5

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHh-cCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQS-SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVY   81 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~-~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~   81 (565)
                      ++...+.++-+..+.    ....| .|+.+  + .++++.+...|+++...               ....+..+.+...|
T Consensus         3 ~a~~~~~~a~k~~~~----~~~~~-~~~~~--~~~~~~~~A~~~~~~a~~~---------------~~~~g~~~~A~~~~   60 (292)
T 1qqe_A            3 DPVELLKRAEKKGVP----SSGFM-KLFSG--SDSYKFEEAADLCVQAATI---------------YRLRKELNLAGDSF   60 (292)
T ss_dssp             CHHHHHHHHHHHSSC----CCTHH-HHHSC--CSHHHHHHHHHHHHHHHHH---------------HHHTTCTHHHHHHH
T ss_pred             cHHHHHHHHHHHhCc----CCCcc-hhcCC--CCCccHHHHHHHHHHHHHH---------------HHHcCCHHHHHHHH
Confidence            345555555555543    11234 44321  1 11367788889888431               22345678899999


Q ss_pred             HHHHHcCCC------CHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc--cHHHHHHHHHHHHHHHHHHhhccccchh
Q 008442           82 SRATKNCPW------VGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRILFSGEVEG  153 (565)
Q Consensus        82 erAl~~~p~------~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~--~~~~~~~~~~~~~~~~~r~~~~~~~~e~  153 (565)
                      ++|+...+.      ....|..... +-...++.+++...|++|+.....  ........+........ .   .     
T Consensus        61 ~~al~~~~~~~~~~~~a~~~~~lg~-~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~-~---~-----  130 (292)
T 1qqe_A           61 LKAADYQKKAGNEDEAGNTYVEAYK-CFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILE-N---D-----  130 (292)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH-H---T-----
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHH-HHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH-H---h-----
Confidence            999985421      1345555444 334468899999999999974321  11111112211111110 0   0     


Q ss_pred             hhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchH-------HHHHHHHHH
Q 008442          154 VLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAML-------EAWQSYISM  226 (565)
Q Consensus       154 ~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~-------~lw~~yi~~  226 (565)
                      ..+++.+...|++|+.+..... ........+...+.+....+ ++++|..+|++++...+...       .+|......
T Consensus       131 lg~~~~A~~~~~~Al~~~~~~~-~~~~~~~~~~~lg~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~  208 (292)
T 1qqe_A          131 LHDYAKAIDCYELAGEWYAQDQ-SVALSNKCFIKCADLKALDG-QYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLC  208 (292)
T ss_dssp             TCCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHHHHHhCC-ChHHHHHHHHHHHHHHHHhC-CHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHH
Confidence            0145566677787777654211 01112345667788888888 99999999999999865432       267777778


Q ss_pred             HHHcCChHHHHHHHHHHHh
Q 008442          227 EIELDHINEARSIYKRCYS  245 (565)
Q Consensus       227 e~~~~~~~~aR~i~~~al~  245 (565)
                      ....|+++.|...|++++.
T Consensus       209 ~~~~g~~~~A~~~~~~al~  227 (292)
T 1qqe_A          209 QLAATDAVAAARTLQEGQS  227 (292)
T ss_dssp             HHHTTCHHHHHHHHHGGGC
T ss_pred             HHHcCCHHHHHHHHHHHHh
Confidence            8889999999999999986

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=97.79  E-value=0.00066  Score=61.76  Aligned_cols=114  Identities=9%  Similarity=-0.025  Sum_probs=85.2

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHH----------------HHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMI----------------YLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQY   66 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~----------------yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~   66 (565)
                      ++...|+.+|...|.    +...|..                ........|+++.+...|+++|...|.+...|..+...
T Consensus        22 ~A~~~~~~al~~~p~----~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~   97 (208)
T 3urz_A           22 QAVSYFRQTIALNID----RTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQKAPNNVDCLEACAEM   97 (208)
T ss_dssp             HHHHHHHHHHHHCHH----HHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC----ChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence            356677888877765    7777777                77777889999999999999999999999999999886


Q ss_pred             HHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHH-hcCCHHHHHHHHHHHHh
Q 008442           67 LDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER-SRASEEEISTVFEKSLL  121 (565)
Q Consensus        67 l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~-~~~~~~~~~~if~ral~  121 (565)
                      +... +..+.+...|++++...|.....|......+-. .......+...|.+++.
T Consensus        98 ~~~~-g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~~  152 (208)
T 3urz_A           98 QVCR-GQEKDALRMYEKILQLEADNLAANIFLGNYYYLTAEQEKKKLETDYKKLSS  152 (208)
T ss_dssp             HHHH-TCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHC---C
T ss_pred             HHHc-CCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhC
Confidence            6544 477889999999999999999988776543321 11223445555666553

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=97.78  E-value=0.00041  Score=59.85  Aligned_cols=112  Identities=13%  Similarity=-0.153  Sum_probs=86.9

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      .+...|+.++...|.    +...|..++......|+.+.+...|++++...|.+..+|..++..... .++.+.+...|+
T Consensus        31 ~A~~~~~~al~~~~~----~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~-~~~~~~A~~~~~  105 (166)
T 1a17_A           31 NAIKFYSQAIELNPS----NAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMA-LGKFRAALRDYE  105 (166)
T ss_dssp             HHHHHHHHHHHHSTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC----ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHH-hccHHHHHHHHH
Confidence            356778888888876    788899999988999999999999999999999999999998876554 447788999999


Q ss_pred             HHHHcCCCCHHHHHHHHHHH-HHhcCCHHHHHHHHHHH
Q 008442           83 RATKNCPWVGELWVRSLLSL-ERSRASEEEISTVFEKS  119 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~l-e~~~~~~~~~~~if~ra  119 (565)
                      +++...|....+|..+.... ....+.++++...++++
T Consensus       106 ~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~  143 (166)
T 1a17_A          106 TVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEHK  143 (166)
T ss_dssp             HHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHcccch
Confidence            99999999888885544321 11234445555555543

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=97.77  E-value=0.0057  Score=58.72  Aligned_cols=162  Identities=10%  Similarity=-0.057  Sum_probs=98.8

Q ss_pred             hhhHHHHHHHHHHHcCCCCHH-----HHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc--cHHHHHHHHHHHHHHHHHHh
Q 008442           73 VGNVVRDVYSRATKNCPWVGE-----LWVRSLLSLERSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRI  145 (565)
Q Consensus        73 ~~~~~~~v~erAl~~~p~~~~-----lW~~yi~~le~~~~~~~~~~~if~ral~~~~~--~~~~~~~~~~~~~~~~~r~~  145 (565)
                      +.+.+...|+.++...+....     .|..++-.+....+..+++...|++|+.....  ........+........   
T Consensus        90 ~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~---  166 (293)
T 2qfc_A           90 RYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYA---  166 (293)
T ss_dssp             CHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHHHHHHHHHHH---
T ss_pred             hHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHH---
Confidence            566677788888876654332     33333333444456788888888888853211  11111111111110000   


Q ss_pred             hccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccc------hHHH
Q 008442          146 LFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA------MLEA  219 (565)
Q Consensus       146 ~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~------~~~l  219 (565)
                             ...+++.+...|++++...............++...+.++...+ ++++|...|++++...+.      ...+
T Consensus       167 -------~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~-~y~~Al~~~~kal~~~~~~~~~~~~~~~  238 (293)
T 2qfc_A          167 -------ENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDS-RYEESLYQVNKAIEISCRINSMALIGQL  238 (293)
T ss_dssp             -------HTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHTTBCSSHHHH
T ss_pred             -------HcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHh-hHHHHHHHHHHHHHHHHhcCcHHHHHHH
Confidence                   00145566677777776654332211112245666777888888 999999999999987422      2678


Q ss_pred             HHHHHHHHHHcCChHHH-HHHHHHHHh
Q 008442          220 WQSYISMEIELDHINEA-RSIYKRCYS  245 (565)
Q Consensus       220 w~~yi~~e~~~~~~~~a-R~i~~~al~  245 (565)
                      +..........|+++.| ...|++|+.
T Consensus       239 ~~~lg~~y~~~g~~~~Ai~~~~~~Al~  265 (293)
T 2qfc_A          239 YYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence            88888889999999999 888999975

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=97.73  E-value=0.0014  Score=69.47  Aligned_cols=172  Identities=10%  Similarity=0.029  Sum_probs=118.4

Q ss_pred             CchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcch---------hhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcC-
Q 008442           38 DPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKV---------GNVVRDVYSRATKNCPWVGELWVRSLLSLERSRA-  107 (565)
Q Consensus        38 ~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~---------~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~-  107 (565)
                      -.+++..+|+++|..+|.++.+|..-...+.....+         .+...+.|++|+...|.+..+|....-.++. .+ 
T Consensus        44 ~~eeal~~~~~~l~~nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK~y~aW~hR~w~l~~-l~~  122 (567)
T 1dce_A           44 LDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSR-LPE  122 (567)
T ss_dssp             CSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHT-CSS
T ss_pred             CCHHHHHHHHHHHHHCchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-ccc
Confidence            346789999999999999999999877666554432         5678899999999999999999987765554 44 


Q ss_pred             -CHHHHHHHHHHHHhcccccHH--HHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHH
Q 008442          108 -SEEEISTVFEKSLLCAFSTFE--EYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRL  184 (565)
Q Consensus       108 -~~~~~~~if~ral~~~~~~~~--~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l  184 (565)
                       ..++....+++++...+..+.  .+........                 .     ..++++++++...+..++.....
T Consensus       123 ~~~~~el~~~~k~l~~d~~N~~aW~~R~~~l~~l-----------------~-----~~~~~el~~~~~~I~~~p~n~sa  180 (567)
T 1dce_A          123 PNWARELELCARFLEADERNFHCWDYRRFVAAQA-----------------A-----VAPAEELAFTDSLITRNFSNYSS  180 (567)
T ss_dssp             CCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT-----------------C-----CCHHHHHHHHHTTTTTTCCCHHH
T ss_pred             ccHHHHHHHHHHHHhhccccccHHHHHHHHHHHc-----------------C-----CChHHHHHHHHHHHHHCCCCccH
Confidence             568888999999986554322  2222111110                 0     02455667777776666556667


Q ss_pred             HHHHHHHHHHcC-------------CChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCC
Q 008442          185 YAYWAHLEQSMG-------------KDMVSARGVWERLLKISGAMLEAWQSYISMEIELDH  232 (565)
Q Consensus       185 ~~~~a~~e~~~~-------------~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~  232 (565)
                      |.+...+.....             +.++++.+.+.+++...|++..+|..+--+....+.
T Consensus       181 W~~r~~ll~~l~~~~~~~~~~~~~~~~~~eel~~~~~ai~~~P~~~saW~y~~~ll~~~~~  241 (567)
T 1dce_A          181 WHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEP  241 (567)
T ss_dssp             HHHHHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCCCC
T ss_pred             HHHHHHHHHhhcccccccccccccHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHHhcCCC
Confidence            766555544431             135678888888888888888888876666554444

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.73  E-value=0.00077  Score=56.77  Aligned_cols=104  Identities=12%  Similarity=-0.045  Sum_probs=87.2

Q ss_pred             hHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCC---HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHH
Q 008442           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVS---SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWV   96 (565)
Q Consensus        20 ~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~---~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~   96 (565)
                      +.....|..........|+++.+..+|++++...|.+   ..+|..++.... ..++.+.+...|++++...|....+|.
T Consensus        25 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~a~~~~-~~~~~~~A~~~~~~~~~~~~~~~~~~~  103 (148)
T 2dba_A           25 ASSVEQLRKEGNELFKCGDYGGALAAYTQALGLDATPQDQAVLHRNRAACHL-KLEDYDKAETEASKAIEKDGGDVKALY  103 (148)
T ss_dssp             CCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHTSCCHHHHH
T ss_pred             hHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHH-HHccHHHHHHHHHHHHhhCccCHHHHH
Confidence            3467889999998899999999999999999999987   788888877544 445788899999999999999988888


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcccc
Q 008442           97 RSLLSLERSRASEEEISTVFEKSLLCAFS  125 (565)
Q Consensus        97 ~yi~~le~~~~~~~~~~~if~ral~~~~~  125 (565)
                      .....+ ...+..+++...|++++...+.
T Consensus       104 ~~a~~~-~~~~~~~~A~~~~~~al~~~p~  131 (148)
T 2dba_A          104 RRSQAL-EKLGRLDQAVLDLQRCVSLEPK  131 (148)
T ss_dssp             HHHHHH-HHHTCHHHHHHHHHHHHHHCSS
T ss_pred             HHHHHH-HHcCCHHHHHHHHHHHHHcCCC
Confidence            877644 3468899999999999986554

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=97.71  E-value=0.013  Score=60.87  Aligned_cols=259  Identities=8%  Similarity=-0.012  Sum_probs=132.5

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHh----cCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh---cchhhH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQS----SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKT---LKVGNV   76 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~----~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~---~~~~~~   76 (565)
                      +...|+.++...      +...+..+......    .++.+.+...|++++..  .+...|..........   .++.+.
T Consensus       134 A~~~~~~a~~~~------~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~--~~~~a~~~Lg~~y~~g~g~~~~~~~  205 (490)
T 2xm6_A          134 SVKWFRLAAEQG------RDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQ--GNVWSCNQLGYMYSRGLGVERNDAI  205 (490)
T ss_dssp             HHHHHHHHHHTT------CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT--TCHHHHHHHHHHHHHTSSSCCCHHH
T ss_pred             HHHHHHHHHHCC------CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHC--CCHHHHHHHHHHHhcCCCCCcCHHH
Confidence            556677776553      23455555555554    56777888888888775  4566666666544431   346667


Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHH---hcCCHHHHHHHHHHHHhcccccHHHHHHHHHHH-----------HHHHH
Q 008442           77 VRDVYSRATKNCPWVGELWVRSLLSLER---SRASEEEISTVFEKSLLCAFSTFEEYLDLFLTR-----------IDGLR  142 (565)
Q Consensus        77 ~~~v~erAl~~~p~~~~lW~~yi~~le~---~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~-----------~~~~~  142 (565)
                      +...|++|+..-+.....++..+  +..   ...+.+++...|++++..........+......           +.+++
T Consensus       206 A~~~~~~a~~~~~~~a~~~lg~~--y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~  283 (490)
T 2xm6_A          206 SAQWYRKSATSGDELGQLHLADM--YYFGIGVTQDYTQSRVLFSQSAEQGNSIAQFRLGYILEQGLAGAKEPLKALEWYR  283 (490)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHH--HHHTSSSCCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHTTTSSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHH--HHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHH
Confidence            78888888775332222222222  222   145677777778877764432211111111100           01111


Q ss_pred             HHhhccccchhhhhHHHHH--------HHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcC--CChHHHHHHHHHHHHH
Q 008442          143 RRILFSGEVEGVLDYSLIR--------ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMG--KDMVSARGVWERLLKI  212 (565)
Q Consensus       143 r~~~~~~~~e~~~~~~~~~--------~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~--~~~~~ar~i~e~~l~~  212 (565)
                      +-.. ....+.......+.        ..+++|+.++.......+.  ..+...+.++...+  .++++|...|++++..
T Consensus       284 ~a~~-~~~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~~~--~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~  360 (490)
T 2xm6_A          284 KSAE-QGNSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQGDA--TAQANLGAIYFRLGSEEEHKKAVEWFRKAAAK  360 (490)
T ss_dssp             HHHT-TTCHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTTCH--HHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHT
T ss_pred             HHHH-cCCHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcCCH--HHHHHHHHHHHhCCCcccHHHHHHHHHHHHHC
Confidence            1110 00000000000000        1233344444443333222  22333444444422  1567888888888876


Q ss_pred             ccchHHHHHHHHHHHHH----cCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHH----hCCHHHHHHHHHHHhh
Q 008442          213 SGAMLEAWQSYISMEIE----LDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFERE----YGTLEDFDHSVQKVTP  282 (565)
Q Consensus       213 ~~~~~~lw~~yi~~e~~----~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~----~G~~~~~~~~~~k~~~  282 (565)
                        .+...|..+..+...    .++++.|...|++++..    ..+ ..+...-.+-..    .|+.+.+...+.++..
T Consensus       361 --~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~----~~~-~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~  431 (490)
T 2xm6_A          361 --GEKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQ----GLS-AAQVQLGEIYYYGLGVERDYVQAWAWFDTAST  431 (490)
T ss_dssp             --TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT----TCH-HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH
T ss_pred             --CCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhC----CCH-HHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHH
Confidence              346777788887776    68889999999998863    223 333222222222    4666666666666543

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=97.69  E-value=0.0071  Score=57.05  Aligned_cols=186  Identities=16%  Similarity=0.131  Sum_probs=111.0

Q ss_pred             HHHHHHHHhcCCCCHH-------HHHHHHH-HHHHhc------------chhhHHHHHHHHHHHcCCCCHHHHHHHHHHH
Q 008442           43 QLLYERAITDFPVSSD-------LWLDYTQ-YLDKTL------------KVGNVVRDVYSRATKNCPWVGELWVRSLLSL  102 (565)
Q Consensus        43 ~~lyERal~~~p~~~~-------lW~~Y~~-~l~~~~------------~~~~~~~~v~erAl~~~p~~~~lW~~yi~~l  102 (565)
                      ..+||-.+..+|.+..       +...|+. |++...            ....+++.+|.||....          ++.|
T Consensus        52 Lk~~e~Ll~~~P~~~~Ll~~~a~ly~~Ya~afV~~~a~~~~~~~~~~~~~~~~RA~~Ly~ra~~y~----------~raL  121 (301)
T 3u64_A           52 LKVYEALHLQNPAHRGLSLAVGRLYIMYANAFVQTPAQYLPEDEFEAQNEAYSRARKLYLRGARYA----------LSSL  121 (301)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHTHHHHHTSCGGGHHHHHHHHHHHHHHHHHHHHHH----------HHHH
T ss_pred             HHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHHhcCchhhcchhhHhhhhhhHHHHHHHHHHHHHHH----------HHHH
Confidence            4788999999999975       6777765 554311            12345677777777632          1233


Q ss_pred             HHhcCCHH-HHH----HHHHHHHh-cccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhc
Q 008442          103 ERSRASEE-EIS----TVFEKSLL-CAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMK  176 (565)
Q Consensus       103 e~~~~~~~-~~~----~if~ral~-~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~  176 (565)
                      +.....+. .++    .-|..++. +....+..  .+|....-... ................++..+++++++=..+. 
T Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~dve~--L~W~ai~~ss~-a~~~~gg~~Al~~l~~A~a~lerAleLDP~~~-  197 (301)
T 3u64_A          122 ETAYPGFTREVFSGDEQRLHKVLSRCTRVDVGT--LYWVGTGYVAA-FALTPLGSALPDTVHAAVMMLERACDLWPSYQ-  197 (301)
T ss_dssp             HHHSTTHHHHHTSSCHHHHHHHHTTCCGGGHHH--HHHHHHHHHHH-HTTSCTTSCCHHHHHHHHHHHHHHHHHCTTHH-
T ss_pred             HHhCccHHHHHHhcchhhHHHHHHHcCccccHH--HHHHHHHHHHH-HhcCCCChHHHHhHHHHHHHHHHHHHhCCCcc-
Confidence            33322222 111    23444553 33332221  22222110000 00111112222344555666666666422111 


Q ss_pred             CCchhHHHHHHHHHHHHHc----CCChHHHHHHHHHHHHHccch-HHHHHHHHHHHHH-cCChHHHHHHHHHHHhc
Q 008442          177 NTDGLLRLYAYWAHLEQSM----GKDMVSARGVWERLLKISGAM-LEAWQSYISMEIE-LDHINEARSIYKRCYSK  246 (565)
Q Consensus       177 ~~~~~~~l~~~~a~~e~~~----~~~~~~ar~i~e~~l~~~~~~-~~lw~~yi~~e~~-~~~~~~aR~i~~~al~~  246 (565)
                          .-..|..++.++...    +++.++|+..|+++|..+|+. ...+..|++|... .++.+.++..+++++.-
T Consensus       198 ----~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a  269 (301)
T 3u64_A          198 ----EGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAI  269 (301)
T ss_dssp             ----HHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHC
T ss_pred             ----cCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHHcC
Confidence                234677778888774    449999999999999999975 9999999999977 59999999999999973

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=97.66  E-value=0.0009  Score=53.59  Aligned_cols=66  Identities=14%  Similarity=0.066  Sum_probs=57.7

Q ss_pred             chhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          179 DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       179 ~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      +....++...+.+....+ +++.|...|++++...|+...+|..++......|+++.|..+|++++.
T Consensus        35 ~~~~~~~~~~a~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~  100 (118)
T 1elw_A           35 PHNHVLYSNRSAAYAKKG-DYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRFEEAKRTYEEGLK  100 (118)
T ss_dssp             TTCHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             CCcHHHHHHHHHHHHhhc-cHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            334567777788888888 999999999999999998899999999999999999999999999987

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=97.66  E-value=0.057  Score=55.89  Aligned_cols=228  Identities=11%  Similarity=-0.029  Sum_probs=131.2

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHh----cCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh---cchhh
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQS----SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKT---LKVGN   75 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~----~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~---~~~~~   75 (565)
                      ++...|+.++...      +...+.........    .++.+.+...|++++..  .++..+..+.......   .++.+
T Consensus        97 ~A~~~~~~a~~~~------~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~--~~~~a~~~Lg~~y~~g~g~~~d~~  168 (490)
T 2xm6_A           97 QAVIWYKKAALKG------LPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQ--GRDSGQQSMGDAYFEGDGVTRDYV  168 (490)
T ss_dssp             HHHHHHHHHHHTT------CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT--TCHHHHHHHHHHHHHTSSSCCCHH
T ss_pred             HHHHHHHHHHHCC------CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHC--CCHHHHHHHHHHHHcCCCCCCCHH
Confidence            4667788887654      34556666666666    67899999999999886  5677777776654431   35678


Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHH---hcCCHHHHHHHHHHHHhcccccHHHHHHHHHHH-----------HHHH
Q 008442           76 VVRDVYSRATKNCPWVGELWVRSLLSLER---SRASEEEISTVFEKSLLCAFSTFEEYLDLFLTR-----------IDGL  141 (565)
Q Consensus        76 ~~~~v~erAl~~~p~~~~lW~~yi~~le~---~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~-----------~~~~  141 (565)
                      .+...|++|+..  .....|......+..   ...+.+++...|++++..........+......           +.++
T Consensus       169 ~A~~~~~~a~~~--~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~y~~g~g~~~~~~~A~~~~  246 (490)
T 2xm6_A          169 MAREWYSKAAEQ--GNVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSGDELGQLHLADMYYFGIGVTQDYTQSRVLF  246 (490)
T ss_dssp             HHHHHHHHHHHT--TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHC--CCHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Confidence            899999999985  344555444433333   157889999999999976533221111111110           1111


Q ss_pred             HHHhhccccchhhhhHHHH-------HHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHc----CCChHHHHHHHHHHH
Q 008442          142 RRRILFSGEVEGVLDYSLI-------RETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSM----GKDMVSARGVWERLL  210 (565)
Q Consensus       142 ~r~~~~~~~~e~~~~~~~~-------~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~----~~~~~~ar~i~e~~l  210 (565)
                      ++-.. .........+..+       ...+.+|+.++.......++  ..+...+.++...    .+++++|...|++++
T Consensus       247 ~~a~~-~~~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~~~--~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~  323 (490)
T 2xm6_A          247 SQSAE-QGNSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQGNS--DGQYYLAHLYDKGAEGVAKNREQAISWYTKSA  323 (490)
T ss_dssp             HHHHT-TTCHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTTCH--HHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHH
T ss_pred             HHHHH-CCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcCCH--HHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHH
Confidence            11111 1111100011110       11234555555555443322  2333445555443    138888888888888


Q ss_pred             HHccchHHHHHHHHHHHHHcC---ChHHHHHHHHHHHh
Q 008442          211 KISGAMLEAWQSYISMEIELD---HINEARSIYKRCYS  245 (565)
Q Consensus       211 ~~~~~~~~lw~~yi~~e~~~~---~~~~aR~i~~~al~  245 (565)
                      +..+  ...|.....+....|   +++.|..+|++++.
T Consensus       324 ~~~~--~~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~  359 (490)
T 2xm6_A          324 EQGD--ATAQANLGAIYFRLGSEEEHKKAVEWFRKAAA  359 (490)
T ss_dssp             HTTC--HHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHH
T ss_pred             hcCC--HHHHHHHHHHHHhCCCcccHHHHHHHHHHHHH
Confidence            7632  345555555554445   77888888888876

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=97.66  E-value=0.00025  Score=58.37  Aligned_cols=85  Identities=8%  Similarity=-0.053  Sum_probs=69.7

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...|+.+|...|.    +...|..........|+.+.+...|+++|...|.+...|...+..+.. .+..+.+...|+
T Consensus        35 ~A~~~~~~al~~~P~----~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~la~~~~~-~g~~~~A~~~~~  109 (121)
T 1hxi_A           35 EAALAFEAVCQKEPE----REEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTN-EHNANAALASLR  109 (121)
T ss_dssp             HHHHHHHHHHHHSTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCC----CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-cCCHHHHHHHHH
Confidence            467789999999887    889999999999999999999999999999999999999988875554 447788999999


Q ss_pred             HHHHcCCCCH
Q 008442           83 RATKNCPWVG   92 (565)
Q Consensus        83 rAl~~~p~~~   92 (565)
                      +++...|...
T Consensus       110 ~al~~~P~~~  119 (121)
T 1hxi_A          110 AWLLSQPQYE  119 (121)
T ss_dssp             HHHC------
T ss_pred             HHHHhCcCCC
Confidence            9999877543

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=97.65  E-value=0.003  Score=58.02  Aligned_cols=176  Identities=11%  Similarity=-0.031  Sum_probs=107.2

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHH---HHHHHHHHHH----------
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDL---WLDYTQYLDK----------   69 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~l---W~~Y~~~l~~----------   69 (565)
                      ++...|+.++...|. ++.....|...+......|+.+.+...|++++..+|.+..+   |.........          
T Consensus        22 ~A~~~~~~~~~~~p~-~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~~g~~~~~~~~~~~~~~~  100 (225)
T 2yhc_A           22 QAITQLEALDNRYPF-GPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFF  100 (225)
T ss_dssp             HHHHHHHHHHHHCTT-STTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHC-------
T ss_pred             HHHHHHHHHHHhCCC-ChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHHHHHHHHHhhhhhhhhhhh
Confidence            367788888888774 22234577777777788899999999999999999998753   2221111111          


Q ss_pred             -------hcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHH
Q 008442           70 -------TLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLR  142 (565)
Q Consensus        70 -------~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~  142 (565)
                             ..+..+.+...|++++...|.+...|..+.. +..       +...+..        ..  +.+-..+.  . 
T Consensus       101 ~~~~~~~~~~~~~~A~~~~~~~l~~~P~~~~a~~a~~~-l~~-------~~~~~~~--------~~--~~~a~~~~--~-  159 (225)
T 2yhc_A          101 GVDRSDRDPQQARAAFSDFSKLVRGYPNSQYTTDATKR-LVF-------LKDRLAK--------YE--YSVAEYYT--E-  159 (225)
T ss_dssp             -------CCHHHHHHHHHHHHHHTTCTTCTTHHHHHHH-HHH-------HHHHHHH--------HH--HHHHHHHH--H-
T ss_pred             ccchhhcCcHHHHHHHHHHHHHHHHCcCChhHHHHHHH-HHH-------HHHHHHH--------HH--HHHHHHHH--H-
Confidence                   1346678999999999999998877765433 111       1100000        00  00000000  0 


Q ss_pred             HHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccch
Q 008442          143 RRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM  216 (565)
Q Consensus       143 r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~  216 (565)
                                 ..++..+...|+++++...    ..+.....+...+......+ +.+.|...++.++...|++
T Consensus       160 -----------~~~~~~A~~~~~~~l~~~p----~~~~~~~a~~~l~~~~~~~g-~~~~A~~~~~~l~~~~~~~  217 (225)
T 2yhc_A          160 -----------RGAWVAVVNRVEGMLRDYP----DTQATRDALPLMENAYRQMQ-MNAQAEKVAKIIAANSSNT  217 (225)
T ss_dssp             -----------HTCHHHHHHHHHHHHHHST----TSHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHCCSCC
T ss_pred             -----------cCcHHHHHHHHHHHHHHCc----CCCccHHHHHHHHHHHHHcC-CcHHHHHHHHHHHhhCCCc
Confidence                       0133344444554444321    12222356667788888888 9999999999988876654

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=97.64  E-value=0.00098  Score=54.53  Aligned_cols=101  Identities=12%  Similarity=-0.049  Sum_probs=82.9

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCC-------HHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV-------GEL   94 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~-------~~l   94 (565)
                      ....|..........|+.+.+...|++++...|.+..+|..++..... .++.+.+...|++++...|..       ..+
T Consensus         3 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~-~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~   81 (131)
T 1elr_A            3 QALKEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFE-KGDYNKCRELCEKAIEVGRENREDYRQIAKA   81 (131)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-HTCHHHHHHHHHHHHHHHHHSTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHH-hccHHHHHHHHHHHHhhccccchhHHHHHHH
Confidence            556788888888889999999999999999999999999988876554 447788999999999987755       667


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhccc
Q 008442           95 WVRSLLSLERSRASEEEISTVFEKSLLCAF  124 (565)
Q Consensus        95 W~~yi~~le~~~~~~~~~~~if~ral~~~~  124 (565)
                      |......+ ...++.+.+...|++++...+
T Consensus        82 ~~~la~~~-~~~~~~~~A~~~~~~~~~~~~  110 (131)
T 1elr_A           82 YARIGNSY-FKEEKYKDAIHFYNKSLAEHR  110 (131)
T ss_dssp             HHHHHHHH-HHTTCHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHH-HHhccHHHHHHHHHHHHHhCC
Confidence            77666533 346889999999999998554

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=97.63  E-value=0.0011  Score=55.92  Aligned_cols=100  Identities=9%  Similarity=0.016  Sum_probs=73.6

Q ss_pred             CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHH
Q 008442          178 TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDIC  257 (565)
Q Consensus       178 ~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~  257 (565)
                      .+.....+...+......+ +++.|..+|++++...|++..+|..........|+++.|...|++++..  ..+.+ .++
T Consensus        14 ~p~~~~~~~~~a~~~~~~g-~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~-~~~   89 (142)
T 2xcb_A           14 SEDTLEQLYALGFNQYQAG-KWDDAQKIFQALCMLDHYDARYFLGLGACRQSLGLYEQALQSYSYGALM--DINEP-RFP   89 (142)
T ss_dssp             CHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCT-HHH
T ss_pred             CHHHHHHHHHHHHHHHHHc-cHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc--CCCCc-HHH
Confidence            3444555556666666777 8999999999999988888899998888888899999999999999873  22333 444


Q ss_pred             HHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          258 HAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       258 ~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      ......-...|+.+.+...+++++
T Consensus        90 ~~lg~~~~~~g~~~~A~~~~~~al  113 (142)
T 2xcb_A           90 FHAAECHLQLGDLDGAESGFYSAR  113 (142)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHH
Confidence            444455556788887777777665

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=97.62  E-value=0.0033  Score=61.89  Aligned_cols=106  Identities=12%  Similarity=-0.071  Sum_probs=89.1

Q ss_pred             HhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCC---------------HHHHHHHHHHHHHhcchhhHHHHHHHHHH
Q 008442           21 EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVS---------------SDLWLDYTQYLDKTLKVGNVVRDVYSRAT   85 (565)
Q Consensus        21 ~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~---------------~~lW~~Y~~~l~~~~~~~~~~~~v~erAl   85 (565)
                      .....|..........|+++.+...|++||...|.+               ..+|..++..+.. .+..+.+...|++|+
T Consensus       145 ~~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~-~g~~~~A~~~~~~al  223 (336)
T 1p5q_A          145 EQSTIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLK-LQAFSAAIESCNKAL  223 (336)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHH-cCCHHHHHHHHHHHH
Confidence            366788888888889999999999999999999998               5888888875544 457888999999999


Q ss_pred             HcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHH
Q 008442           86 KNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFE  128 (565)
Q Consensus        86 ~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~  128 (565)
                      ...|.....|......+ ...+..+++...|++|+...+....
T Consensus       224 ~~~p~~~~a~~~lg~~~-~~~g~~~~A~~~~~~al~l~P~~~~  265 (336)
T 1p5q_A          224 ELDSNNEKGLSRRGEAH-LAVNDFELARADFQKVLQLYPNNKA  265 (336)
T ss_dssp             HHCTTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCSSCHH
T ss_pred             HhCCCcHHHHHHHHHHH-HHCCCHHHHHHHHHHHHHHCCCCHH
Confidence            99999999988877644 4478899999999999987665443

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=97.60  E-value=0.00073  Score=58.67  Aligned_cols=79  Identities=13%  Similarity=0.109  Sum_probs=59.9

Q ss_pred             HHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          166 RASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       166 ~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      +|+.++...+...+....+|...+.++...+ +++.|...|++++...|++..+|..+.......|+++.|...|++++.
T Consensus        29 ~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g-~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  107 (164)
T 3sz7_A           29 KAIDLYTQALSIAPANPIYLSNRAAAYSASG-QHEKAAEDAELATVVDPKYSKAWSRLGLARFDMADYKGAKEAYEKGIE  107 (164)
T ss_dssp             HHHHHHHHHHHHSTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCcCHHHHHHHHHHHHHcc-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            3333333333333444567777777787877 888899999999988888888888888888888999999999998886

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.60  E-value=0.002  Score=49.85  Aligned_cols=78  Identities=17%  Similarity=0.209  Sum_probs=64.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhcc---C--CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEE
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSD---V--GGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLS  463 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~---~--G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~  463 (565)
                      ..+.+|.|.|||+.++++.|.-+|+.   -  |.|.++....        +-|+|+|.+...|+..|+...+.|.|.+|.
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~H~L~~~~Ls   77 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQADHELHGAQLS   77 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSCCBSSSSBCE
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCcceecCeEEE
Confidence            45689999999999999999999976   2  5677776532        468999999999999999878999999999


Q ss_pred             EeecCCCCCCC
Q 008442          464 IARSNPKQRKD  474 (565)
Q Consensus       464 v~~a~~~~~~~  474 (565)
                      |....+.-..+
T Consensus        78 V~P~~~~~~~r   88 (104)
T 2dhx_A           78 LRPAPPRAPAR   88 (104)
T ss_dssp             EEECCCCCCCC
T ss_pred             EEcCCCCCcce
Confidence            98876665433

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=97.59  E-value=0.011  Score=59.00  Aligned_cols=240  Identities=14%  Similarity=-0.010  Sum_probs=136.0

Q ss_pred             HHHHHHhcCCchhHHHHHHHHHhcCCCC------HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCC----H---HHH
Q 008442           29 YLKYEQSSGDPGRVQLLYERAITDFPVS------SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV----G---ELW   95 (565)
Q Consensus        29 yi~~e~~~~~~~~~~~lyERal~~~p~~------~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~----~---~lW   95 (565)
                      ...+....|+.+.+...|++|+......      ..++...+. +....++.+.+...|++|+...+..    .   ..+
T Consensus       107 ~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~-~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  185 (378)
T 3q15_A          107 RGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAE-AYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSL  185 (378)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHH-HHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHH
Confidence            3444566799999999999999864321      123333333 3334557788999999999865421    1   122


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhccc--ccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHh
Q 008442           96 VRSLLSLERSRASEEEISTVFEKSLLCAF--STFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSE  173 (565)
Q Consensus        96 ~~yi~~le~~~~~~~~~~~if~ral~~~~--~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~  173 (565)
                      ..... +-...+..+.+...|++|+....  .........+........ .         ..+++.+...|.+++.+...
T Consensus       186 ~~lg~-~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~-~---------~~~~~~A~~~~~~al~~~~~  254 (378)
T 3q15_A          186 FVIAG-NYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYD-R---------SGDDQMAVEHFQKAAKVSRE  254 (378)
T ss_dssp             HHHHH-HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH-H---------HTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHH-HHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH-H---------CCCHHHHHHHHHHHHHHHHh
Confidence            22222 33446889999999999996321  111111111111110000 0         01445566666766665543


Q ss_pred             hhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHcc-----chHHHHHHHHHHHHHcCC---hHHHHHHHHHHHh
Q 008442          174 QMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG-----AMLEAWQSYISMEIELDH---INEARSIYKRCYS  245 (565)
Q Consensus       174 ~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~-----~~~~lw~~yi~~e~~~~~---~~~aR~i~~~al~  245 (565)
                      .  ..+.....+...+.+....+ +++.|...|++++...+     ...........+....++   +..|..++++.-.
T Consensus       255 ~--~~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~~~  331 (378)
T 3q15_A          255 K--VPDLLPKVLFGLSWTLCKAG-QTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKKNL  331 (378)
T ss_dssp             H--CGGGHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHTTC
T ss_pred             h--CChhHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhCCC
Confidence            2  22233556666788888888 99999999999998732     222333333333444566   5566666555311


Q ss_pred             cccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhhHHHHH
Q 008442          246 KRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEEL  287 (565)
Q Consensus       246 ~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~~~~~~~  287 (565)
                          .+....++.....+-...|+.+.+...+.+++...+++
T Consensus       332 ----~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~~~~~~  369 (378)
T 3q15_A          332 ----HAYIEACARSAAAVFESSCHFEQAAAFYRKVLKAQEDI  369 (378)
T ss_dssp             ----HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             ----hhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence                01122344445556667788888887777776555443

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=97.59  E-value=0.0012  Score=53.80  Aligned_cols=94  Identities=15%  Similarity=-0.033  Sum_probs=79.6

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (565)
                      +...|+.++...|.    +...|..++......++.+.+...|++++...|.+..+|..++..... .++.+.+...|++
T Consensus        31 A~~~~~~~~~~~~~----~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~A~~~~~~  105 (131)
T 2vyi_A           31 AVHFYGKAIELNPA----NAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPAYSKAYGRMGLALSS-LNKHVEAVAYYKK  105 (131)
T ss_dssp             HHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCC----CHHHHHHHHHHHHHhhchHHHHHHHHHHHhcCccCHHHHHHHHHHHHH-hCCHHHHHHHHHH
Confidence            55678888887776    678899999988899999999999999999999999999998876554 4477889999999


Q ss_pred             HHHcCCCCHHHHHHHHHHH
Q 008442           84 ATKNCPWVGELWVRSLLSL  102 (565)
Q Consensus        84 Al~~~p~~~~lW~~yi~~l  102 (565)
                      ++...|....+|..+...+
T Consensus       106 ~~~~~p~~~~~~~~l~~~~  124 (131)
T 2vyi_A          106 ALELDPDNETYKSNLKIAE  124 (131)
T ss_dssp             HHHHSTTCHHHHHHHHHHH
T ss_pred             HHhcCccchHHHHHHHHHH
Confidence            9999999888887766533

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=97.58  E-value=0.0018  Score=55.30  Aligned_cols=100  Identities=10%  Similarity=-0.018  Sum_probs=75.0

Q ss_pred             CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHH
Q 008442          178 TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDIC  257 (565)
Q Consensus       178 ~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~  257 (565)
                      .+.....+...+......+ +++.|...|++++...|.+..+|..........|+++.|...|++++..  ..+.+ ..|
T Consensus        17 ~p~~~~~~~~~g~~~~~~g-~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~-~~~   92 (148)
T 2vgx_A           17 SSDTLEQLYSLAFNQYQSG-XYEDAHXVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVM--DIXEP-RFP   92 (148)
T ss_dssp             CHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCT-HHH
T ss_pred             CHhhHHHHHHHHHHHHHcC-ChHHHHHHHHHHHHcCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc--CCCCc-hHH
Confidence            3444556666677777777 8999999999999999988999999888888999999999999999873  22333 444


Q ss_pred             HHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          258 HAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       258 ~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      ......-...|+.+.+...+.+++
T Consensus        93 ~~lg~~~~~~g~~~~A~~~~~~al  116 (148)
T 2vgx_A           93 FHAAECLLQXGELAEAESGLFLAQ  116 (148)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHH
Confidence            444445556788888777777765

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=97.58  E-value=0.00078  Score=55.41  Aligned_cols=93  Identities=13%  Similarity=-0.077  Sum_probs=79.5

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...|+.+|...|.    +...|..........|+.+.+...|+++|...|.+...|..++..+.. .++.+.+...|+
T Consensus        22 ~A~~~~~~al~~~p~----~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~-~~~~~~A~~~~~   96 (126)
T 3upv_A           22 NAVKAYTEMIKRAPE----DARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQIA-VKEYASALETLD   96 (126)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC----ChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHH-HhCHHHHHHHHH
Confidence            366788888988887    788999999999999999999999999999999999999999875554 457888999999


Q ss_pred             HHHHcC------CCCHHHHHHHHH
Q 008442           83 RATKNC------PWVGELWVRSLL  100 (565)
Q Consensus        83 rAl~~~------p~~~~lW~~yi~  100 (565)
                      +++...      |....+|.....
T Consensus        97 ~al~~~p~~~~~p~~~~~~~~l~~  120 (126)
T 3upv_A           97 AARTKDAEVNNGSSAREIDQLYYK  120 (126)
T ss_dssp             HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred             HHHHhCcccCCchhHHHHHHHHHH
Confidence            999988      877777766544

>2wvi_A Mitotic checkpoint serine/threonine-protein kinase BUB1 beta; tumor suppressor, TPR, apoptosis, cell division, cell cycle, kinetochore, transferase; 1.80A {Homo sapiens} PDB: 3si5_A

Probab=97.57  E-value=0.0016  Score=55.90  Aligned_cols=96  Identities=13%  Similarity=0.198  Sum_probs=71.9

Q ss_pred             HHHHHHHHHHHh--hhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH--ccchHHHHHHHHHHHHHcCChHHHH
Q 008442          162 ETFQRASDYLSE--QMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI--SGAMLEAWQSYISMEIELDHINEAR  237 (565)
Q Consensus       162 ~~~~~a~~~l~~--~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~--~~~~~~lw~~yi~~e~~~~~~~~aR  237 (565)
                      .++++|+..+..  .+.+.+.++++|+.|+++-   . +   ++.+|..+...  ......+|..|+.+....|++..|.
T Consensus        44 ~lLErc~~~f~~~~~YknD~RyLklWl~ya~~~---~-~---p~~if~~L~~~~IG~~~AlfY~~wA~~lE~~~~~~~A~  116 (164)
T 2wvi_A           44 TLLERAVEALQGEKRYYSDPRFLNLWLKLGRLC---N-E---PLDMYSYLHNQGIGVSLAQFYISWAEEYEARENFRKAD  116 (164)
T ss_dssp             HHHHHHHHHTTTCGGGTTCHHHHHHHHHHHHHC---S-C---HHHHHHHHHHTTSSTTBHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHhhhhhhhccCHHHHHHHHHHHHhc---C-C---HHHHHHHHHHCCcchhhHHHHHHHHHHHHHcCCHHHHH
Confidence            455666665532  3445666889999888763   3 3   67899988887  4456889999999999999999999


Q ss_pred             HHHHHHHhcccCCCCcHHHHHHHHHHHHH
Q 008442          238 SIYKRCYSKRFTGTGSEDICHAWLRFERE  266 (565)
Q Consensus       238 ~i~~~al~~~~~~~~~~~i~~~~~~fE~~  266 (565)
                      +||..+|...  ....+.|-..+-.|+.+
T Consensus       117 ~Iy~~Gi~~~--A~P~~~L~~~~~~F~~R  143 (164)
T 2wvi_A          117 AIFQEGIQQK--AEPLERLQSQHRQFQAR  143 (164)
T ss_dssp             HHHHHHHHTT--CBSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcC--CCcHHHHHHHHHHHHHH
Confidence            9999999852  23345677888888766

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=97.57  E-value=0.0034  Score=60.88  Aligned_cols=48  Identities=13%  Similarity=0.113  Sum_probs=21.3

Q ss_pred             ChHHHHHHHHHHHHHccch------HHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          198 DMVSARGVWERLLKISGAM------LEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       198 ~~~~ar~i~e~~l~~~~~~------~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ++++|...|++++...+..      ..++.....+....|+++.|...|++++.
T Consensus       130 ~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  183 (307)
T 2ifu_A          130 DLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKS  183 (307)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            4444444444444432211      23444444444444444444444444443

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=97.56  E-value=0.00076  Score=55.54  Aligned_cols=95  Identities=17%  Similarity=-0.010  Sum_probs=79.4

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      .+...|+.++...|.    +...|..+.......++.+.+...|++++...|.+..+|..++..... .++.+.+...|+
T Consensus        34 ~A~~~~~~al~~~~~----~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~-~~~~~~A~~~~~  108 (133)
T 2lni_A           34 QAMKHYTEAIKRNPK----DAKLYSNRAACYTKLLEFQLALKDCEECIQLEPTFIKGYTRKAAALEA-MKDYTKAMDVYQ  108 (133)
T ss_dssp             HHHHHHHHHHTTCTT----CHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCC----cHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCchHHHHHHHHHHHH-HhhHHHHHHHHH
Confidence            356778888887776    678899999888889999999999999999999999999999876554 447788999999


Q ss_pred             HHHHcCCCCHHHHHHHHHHH
Q 008442           83 RATKNCPWVGELWVRSLLSL  102 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~l  102 (565)
                      +++...|....+|......+
T Consensus       109 ~~~~~~p~~~~~~~~l~~~~  128 (133)
T 2lni_A          109 KALDLDSSCKEAADGYQRCM  128 (133)
T ss_dssp             HHHHHCGGGTHHHHHHHHHH
T ss_pred             HHHHhCCCchHHHHHHHHHH
Confidence            99999998877777665433

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.53  E-value=0.0011  Score=55.81  Aligned_cols=97  Identities=13%  Similarity=0.055  Sum_probs=70.4

Q ss_pred             HHHHHHHHHhhhcCCchh---HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHH
Q 008442          164 FQRASDYLSEQMKNTDGL---LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIY  240 (565)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~---~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~  240 (565)
                      |..|+.++...+...+..   ..+|..++..+...+ ++++|...|++++...|+...+|..++......|+++.|..+|
T Consensus        44 ~~~A~~~~~~a~~~~~~~~~~~~~~~~~a~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~  122 (148)
T 2dba_A           44 YGGALAAYTQALGLDATPQDQAVLHRNRAACHLKLE-DYDKAETEASKAIEKDGGDVKALYRRSQALEKLGRLDQAVLDL  122 (148)
T ss_dssp             HHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHc-cHHHHHHHHHHHHhhCccCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            344444444444333332   566777788888888 9999999999999999988999999999999999999999999


Q ss_pred             HHHHhcccCCCCcHHHHHHHHHHH
Q 008442          241 KRCYSKRFTGTGSEDICHAWLRFE  264 (565)
Q Consensus       241 ~~al~~~~~~~~~~~i~~~~~~fE  264 (565)
                      ++++..   .+....++..+..+.
T Consensus       123 ~~al~~---~p~~~~~~~~l~~~~  143 (148)
T 2dba_A          123 QRCVSL---EPKNKVFQEALRNIS  143 (148)
T ss_dssp             HHHHHH---CSSCHHHHHHHHHHH
T ss_pred             HHHHHc---CCCcHHHHHHHHHHH
Confidence            999873   223345555444443

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=97.52  E-value=0.0072  Score=60.34  Aligned_cols=222  Identities=9%  Similarity=-0.037  Sum_probs=130.6

Q ss_pred             hhHHHHHHHhcCCC--CChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCH-------HHHHHHHHHHHHhcchh
Q 008442            4 ARAHLEEQISRQDL--SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS-------DLWLDYTQYLDKTLKVG   74 (565)
Q Consensus         4 ~R~~~E~~l~~~~~--~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~-------~lW~~Y~~~l~~~~~~~   74 (565)
                      +...|+.++.....  ..+.....+..........|+++.+...|++|+...+...       ..+...+. +....+..
T Consensus       120 A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~-~y~~~~~~  198 (378)
T 3q15_A          120 AIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAG-NYDDFKHY  198 (378)
T ss_dssp             HHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHH-HHHHTTCH
T ss_pred             HHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHH-HHHHhCCH
Confidence            55667777754321  1233456677777777788999999999999998765432       13333333 33345578


Q ss_pred             hHHHHHHHHHHHcCC---CCH---HHHHHHHHHHHHhcCCHHHHHHHHHHHHh-----cccccHHHHHHHHHHHHHHHHH
Q 008442           75 NVVRDVYSRATKNCP---WVG---ELWVRSLLSLERSRASEEEISTVFEKSLL-----CAFSTFEEYLDLFLTRIDGLRR  143 (565)
Q Consensus        75 ~~~~~v~erAl~~~p---~~~---~lW~~yi~~le~~~~~~~~~~~if~ral~-----~~~~~~~~~~~~~~~~~~~~~r  143 (565)
                      +.+...|++|+..++   ...   .++..... +-...+..+++...|++|+.     ..+.....+..+-..+..    
T Consensus       199 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~-~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~----  273 (378)
T 3q15_A          199 DKALPHLEAALELAMDIQNDRFIAISLLNIAN-SYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCK----  273 (378)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHH----
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-HHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHHHH----
Confidence            889999999998543   221   22222222 33346889999999999997     222222222222221110    


Q ss_pred             HhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCC---hHHHHHHHHHHHHHccchHHHH
Q 008442          144 RILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKD---MVSARGVWERLLKISGAMLEAW  220 (565)
Q Consensus       144 ~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~---~~~ar~i~e~~l~~~~~~~~lw  220 (565)
                                ..++..+...|++++.......  .+.....+.....+....+ +   +.+|..++++. ...+....++
T Consensus       274 ----------~g~~~~A~~~~~~al~~~~~~~--~~~~~~~~~~l~~ly~~~~-~~~~~~~al~~~~~~-~~~~~~~~~~  339 (378)
T 3q15_A          274 ----------AGQTQKAFQFIEEGLDHITARS--HKFYKELFLFLQAVYKETV-DERKIHDLLSYFEKK-NLHAYIEACA  339 (378)
T ss_dssp             ----------TTCHHHHHHHHHHHHHHCCTTC--CSCHHHHHHHHHHHHSSSC-CHHHHHHHHHHHHHT-TCHHHHHHHH
T ss_pred             ----------CCCHHHHHHHHHHHHHHHHHcC--CHHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHhC-CChhHHHHHH
Confidence                      0144556666776666543211  1222222333344444444 5   44555555441 1134445688


Q ss_pred             HHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          221 QSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       221 ~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ...+.+....|+++.|...|++++.
T Consensus       340 ~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          340 RSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            8889999999999999999999986

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=97.48  E-value=0.024  Score=54.73  Aligned_cols=179  Identities=12%  Similarity=0.065  Sum_probs=107.4

Q ss_pred             CCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCC------HHHHHHHHHHHHHhcCCHH
Q 008442           37 GDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV------GELWVRSLLSLERSRASEE  110 (565)
Q Consensus        37 ~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~------~~lW~~yi~~le~~~~~~~  110 (565)
                      ++++.+..+|+++..               +....+..+.+...|++|+...+..      ...|..... +-...++.+
T Consensus        30 ~~~~~A~~~~~~a~~---------------~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~-~~~~~g~~~   93 (307)
T 2ifu_A           30 PDYDSAASEYAKAAV---------------AFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGM-MLKDLQRMP   93 (307)
T ss_dssp             CCHHHHHHHHHHHHH---------------HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HHHHTTCGG
T ss_pred             CCHHHHHHHHHHHHH---------------HHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-HHHhCCCHH
Confidence            455566666666532               1223346677888888888754321      123333222 233457788


Q ss_pred             HHHHHHHHHHhccc--ccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHH
Q 008442          111 EISTVFEKSLLCAF--STFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYW  188 (565)
Q Consensus       111 ~~~~if~ral~~~~--~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~  188 (565)
                      ++...|++|+....  .........+.......      .    . .++......|++++.+.... .........+...
T Consensus        94 ~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~------~----~-g~~~~A~~~~~~Al~~~~~~-~~~~~~~~~~~~l  161 (307)
T 2ifu_A           94 EAVQYIEKASVMYVENGTPDTAAMALDRAGKLM------E----P-LDLSKAVHLYQQAAAVFENE-ERLRQAAELIGKA  161 (307)
T ss_dssp             GGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHH------T----T-TCHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH------H----c-CCHHHHHHHHHHHHHHHHhC-CChhHHHHHHHHH
Confidence            88888988886321  11111111111111111      0    0 15566677788777766431 1111224566677


Q ss_pred             HHHHHHcCCChHHHHHHHHHHHHHccch------HHHHHHHHHHHHHcCChHHHHHHHHHHH
Q 008442          189 AHLEQSMGKDMVSARGVWERLLKISGAM------LEAWQSYISMEIELDHINEARSIYKRCY  244 (565)
Q Consensus       189 a~~e~~~~~~~~~ar~i~e~~l~~~~~~------~~lw~~yi~~e~~~~~~~~aR~i~~~al  244 (565)
                      +.+....+ ++++|..+|++++...+..      ...|+..+......|+++.|...|++++
T Consensus       162 g~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          162 SRLLVRQQ-KFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHHHHTT-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHcC-CHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            88888888 9999999999999874322      3466666777778899999999999998

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=97.45  E-value=0.0024  Score=51.50  Aligned_cols=93  Identities=13%  Similarity=0.052  Sum_probs=78.0

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      .+...|+.++...|.    +...|..++......|+.+.+..+|++++...|.+..+|...+..... .++.+.+...|+
T Consensus        27 ~A~~~~~~~~~~~~~----~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~-~~~~~~A~~~~~  101 (125)
T 1na0_A           27 EAIEYYQKALELDPN----NAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYK-QGDYDEAIEYYQ  101 (125)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCcC----cHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHH-hcCHHHHHHHHH
Confidence            356778888887765    677899999988899999999999999999999999999988876554 447788999999


Q ss_pred             HHHHcCCCCHHHHHHHHH
Q 008442           83 RATKNCPWVGELWVRSLL  100 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~  100 (565)
                      +++...|....+|.....
T Consensus       102 ~~~~~~~~~~~~~~~l~~  119 (125)
T 1na0_A          102 KALELDPNNAEAKQNLGN  119 (125)
T ss_dssp             HHHHHCTTCHHHHHHHHH
T ss_pred             HHHHhCCCcHHHHHHHHH
Confidence            999999988877766543

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=97.45  E-value=0.0058  Score=54.72  Aligned_cols=103  Identities=11%  Similarity=-0.139  Sum_probs=84.7

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCH----------------HHHHHHHHHHHHhcchhhHHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS----------------DLWLDYTQYLDKTLKVGNVVRDVYSRAT   85 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~----------------~lW~~Y~~~l~~~~~~~~~~~~v~erAl   85 (565)
                      ....|..........++++.+..+|++++...|.++                .+|..++.... ..+..+.+...|++|+
T Consensus        37 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~-~~~~~~~A~~~~~~al  115 (198)
T 2fbn_A           37 SAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYN-KNKDYPKAIDHASKVL  115 (198)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHH-HhcCHHHHHHHHHHHH
Confidence            455677888878889999999999999999999887                78888776554 4457788999999999


Q ss_pred             HcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccccc
Q 008442           86 KNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFST  126 (565)
Q Consensus        86 ~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~  126 (565)
                      ...|.....|......+ ...+..+.+...|++++...+..
T Consensus       116 ~~~p~~~~~~~~lg~~~-~~~~~~~~A~~~~~~al~~~p~~  155 (198)
T 2fbn_A          116 KIDKNNVKALYKLGVAN-MYFGFLEEAKENLYKAASLNPNN  155 (198)
T ss_dssp             HHSTTCHHHHHHHHHHH-HHHTCHHHHHHHHHHHHHHSTTC
T ss_pred             HhCcccHHHHHHHHHHH-HHcccHHHHHHHHHHHHHHCCCc
Confidence            99999998888877644 44688999999999999865543

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.45  E-value=0.00051  Score=55.91  Aligned_cols=89  Identities=12%  Similarity=0.085  Sum_probs=46.1

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (565)
                      +...|+.+|...+ .++.+...|..........|+++.+...|++++...|.+..+|..++..+.. .+..+.+...|++
T Consensus         9 A~~~~~~al~~~~-~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~-~g~~~~A~~~~~~   86 (117)
T 3k9i_A            9 AVPYYEKAIASGL-QGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPNHQALRVFYAMVLYN-LGRYEQGVELLLK   86 (117)
T ss_dssp             CHHHHHHHHSSCC-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-HTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCC-CCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHH-cCCHHHHHHHHHH
Confidence            3445555555421 1233455555555555555555556666666666666555555555543332 2244555555666


Q ss_pred             HHHcCCCCHHH
Q 008442           84 ATKNCPWVGEL   94 (565)
Q Consensus        84 Al~~~p~~~~l   94 (565)
                      ++...|.+..+
T Consensus        87 al~~~p~~~~~   97 (117)
T 3k9i_A           87 IIAETSDDETI   97 (117)
T ss_dssp             HHHHHCCCHHH
T ss_pred             HHHhCCCcHHH
Confidence            65555555443

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=97.43  E-value=0.00078  Score=57.84  Aligned_cols=88  Identities=9%  Similarity=-0.083  Sum_probs=61.2

Q ss_pred             CchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcc---------hhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhc--
Q 008442           38 DPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLK---------VGNVVRDVYSRATKNCPWVGELWVRSLLSLERSR--  106 (565)
Q Consensus        38 ~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~---------~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~--  106 (565)
                      .++.+...|++++..+|.+.+.|..+..-+.....         ..+.+...|++||...|.....|...-..+....  
T Consensus        17 ~feeA~~~~~~Ai~l~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~~~~A~~~LG~ay~~lg~l   96 (158)
T 1zu2_A           17 LFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYTSFAFL   96 (158)
T ss_dssp             HHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHhccc
Confidence            34567788888888888888888877764443221         2356888888888888888877766544332221  


Q ss_pred             --------CCHHHHHHHHHHHHhcccc
Q 008442          107 --------ASEEEISTVFEKSLLCAFS  125 (565)
Q Consensus       107 --------~~~~~~~~if~ral~~~~~  125 (565)
                              +.++++...|++|+...+.
T Consensus        97 ~P~~~~a~g~~~eA~~~~~kAl~l~P~  123 (158)
T 1zu2_A           97 TPDETEAKHNFDLATQFFQQAVDEQPD  123 (158)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHCTT
T ss_pred             CcchhhhhccHHHHHHHHHHHHHhCCC
Confidence                    3678888888888876655

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.42  E-value=0.00072  Score=54.68  Aligned_cols=80  Identities=10%  Similarity=0.013  Sum_probs=49.6

Q ss_pred             hHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 008442           41 RVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSL  120 (565)
Q Consensus        41 ~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral  120 (565)
                      .+...|++++...|.+..+|..++..... .+..+.+...|++|+...|.....|..+...+. ..+..+++...|++++
T Consensus         3 ~a~~~~~~al~~~p~~~~~~~~lg~~~~~-~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~-~~g~~~~A~~~~~~al   80 (115)
T 2kat_A            3 AITERLEAMLAQGTDNMLLRFTLGKTYAE-HEQFDAALPHLRAALDFDPTYSVAWKWLGKTLQ-GQGDRAGARQAWESGL   80 (115)
T ss_dssp             CHHHHHHHHHTTTCCCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCcHHHHHHHHHHHHH-ccCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHH-HcCCHHHHHHHHHHHH
Confidence            34556777777777777777666654433 335566677777777766766666665554332 3566667777777776


Q ss_pred             hc
Q 008442          121 LC  122 (565)
Q Consensus       121 ~~  122 (565)
                      ..
T Consensus        81 ~~   82 (115)
T 2kat_A           81 AA   82 (115)
T ss_dssp             HH
T ss_pred             Hh
Confidence            53

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=97.40  E-value=0.00061  Score=64.77  Aligned_cols=195  Identities=8%  Similarity=-0.086  Sum_probs=127.3

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHH-------HHHHhcCCchhHHHHHHHHHhcCCCC-------------------
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYL-------KYEQSSGDPGRVQLLYERAITDFPVS-------------------   56 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi-------~~e~~~~~~~~~~~lyERal~~~p~~-------------------   56 (565)
                      .++..|..++..+|.    ..+.|+..+       ......+....+...+.|++...|..                   
T Consensus        24 ~A~~~F~~a~~~dP~----~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~l~p~~l~a~~~~~g~y~~~~~~v~   99 (282)
T 4f3v_A           24 RSLDLFTEITNYDES----ACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQISMSTLNARIAIGGLYGDITYPVT   99 (282)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTTCCGGGGCCEEECCTTTCCCEEECS
T ss_pred             HHHHHHHHHHHhChh----hhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhccCCcccccccccC
Confidence            478899999999998    889999884       44433333345556778888854422                   


Q ss_pred             --HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHH-HHHhcCCHHHHHHHHHHHHhcccccHHHHHHH
Q 008442           57 --SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS-LERSRASEEEISTVFEKSLLCAFSTFEEYLDL  133 (565)
Q Consensus        57 --~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~-le~~~~~~~~~~~if~ral~~~~~~~~~~~~~  133 (565)
                        .++++.|+..+.... ..+.+.++|+.++...|...   ..|+.. +-...+..+.+...|+.++..+.+....-+.+
T Consensus       100 ~r~dl~LayA~~L~~~g-~y~eA~~~l~~~~~~~p~~~---~~~~~a~l~~~~~r~~dA~~~l~~a~~~~d~~~~~~a~~  175 (282)
T 4f3v_A          100 SPLAITMGFAACEAAQG-NYADAMEALEAAPVAGSEHL---VAWMKAVVYGAAERWTDVIDQVKSAGKWPDKFLAGAAGV  175 (282)
T ss_dssp             SHHHHHHHHHHHHHHHT-CHHHHHHHHTSSCCTTCHHH---HHHHHHHHHHHTTCHHHHHHHHTTGGGCSCHHHHHHHHH
T ss_pred             CHhHHHHHHHHHHHHCC-CHHHHHHHHHHHHhcCCchH---HHHHHHHHHHHcCCHHHHHHHHHHhhccCCcccHHHHHH
Confidence              468888998766544 77889999999888767443   334322 33346889999999998776542211111222


Q ss_pred             HHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCC--ch-hHHHHHHHHHHHHHcCCChHHHHHHHHHHH
Q 008442          134 FLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNT--DG-LLRLYAYWAHLEQSMGKDMVSARGVWERLL  210 (565)
Q Consensus       134 ~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~--~~-~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l  210 (565)
                      ++-..  +                 .....|.+|+.++.......  +. ....+...+.....+| +.++|+.+|++++
T Consensus       176 ~LG~a--l-----------------~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lG-r~deA~~~l~~a~  235 (282)
T 4f3v_A          176 AHGVA--A-----------------ANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQG-NESAAVALLEWLQ  235 (282)
T ss_dssp             HHHHH--H-----------------HHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHT-CHHHHHHHHHHHH
T ss_pred             HHHHH--H-----------------HHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcC-CHHHHHHHHHHHH
Confidence            22111  0                 11133555555555554322  22 3456677777888889 9999999999999


Q ss_pred             HHccchHHHHHHHHHH
Q 008442          211 KISGAMLEAWQSYISM  226 (565)
Q Consensus       211 ~~~~~~~~lw~~yi~~  226 (565)
                      ...|. ..+|....+.
T Consensus       236 a~~P~-~~~~~aL~~~  250 (282)
T 4f3v_A          236 TTHPE-PKVAAALKDP  250 (282)
T ss_dssp             HHSCC-HHHHHHHHCT
T ss_pred             hcCCc-HHHHHHHhCC
Confidence            99998 8877766543

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.33  E-value=0.00096  Score=54.23  Aligned_cols=81  Identities=12%  Similarity=0.123  Sum_probs=67.0

Q ss_pred             HHHHHHHHhhhcC---CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHH
Q 008442          165 QRASDYLSEQMKN---TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYK  241 (565)
Q Consensus       165 ~~a~~~l~~~~~~---~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~  241 (565)
                      ++|+.++...+..   .+.....+...+.++...+ ++++|...|++++...|++..+|..++......|+++.|...|+
T Consensus         7 ~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~-~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~   85 (117)
T 3k9i_A            7 AQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLG-EYRKAEAVLANGVKQFPNHQALRVFYAMVLYNLGRYEQGVELLL   85 (117)
T ss_dssp             CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            3344444444443   2445677888888888888 99999999999999999999999999999999999999999999


Q ss_pred             HHHhc
Q 008442          242 RCYSK  246 (565)
Q Consensus       242 ~al~~  246 (565)
                      +++..
T Consensus        86 ~al~~   90 (117)
T 3k9i_A           86 KIIAE   90 (117)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            99973

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.31  E-value=0.0016  Score=51.52  Aligned_cols=93  Identities=13%  Similarity=0.130  Sum_probs=58.3

Q ss_pred             HHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHH
Q 008442          186 AYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFER  265 (565)
Q Consensus       186 ~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~  265 (565)
                      ...+.+....+ +++.|..+|++++...|....+|..++......|+++.|..+|++++.. .+......+|........
T Consensus        10 ~~~~~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~-~~~~~~~~~~~~l~~~~~   87 (112)
T 2kck_A           10 YLEGVLQYDAG-NYTESIDLFEKAIQLDPEESKYWLMKGKALYNLERYEEAVDCYNYVINV-IEDEYNKDVWAAKADALR   87 (112)
T ss_dssp             GGHHHHHHSSC-CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT-SCCTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhh-hHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh-CcccchHHHHHHHHHHHH
Confidence            34444555555 7777777777777777777777777777777777777777777777762 111003345555555555


Q ss_pred             Hh-CCHHHHHHHHHHH
Q 008442          266 EY-GTLEDFDHSVQKV  280 (565)
Q Consensus       266 ~~-G~~~~~~~~~~k~  280 (565)
                      .. |+.+.+...+.++
T Consensus        88 ~~~~~~~~A~~~~~~~  103 (112)
T 2kck_A           88 YIEGKEVEAEIAEARA  103 (112)
T ss_dssp             TCSSCSHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHH
Confidence            56 6666655555544

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.30  E-value=0.0037  Score=51.20  Aligned_cols=62  Identities=6%  Similarity=-0.037  Sum_probs=53.3

Q ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHHHccch---HHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM---LEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~---~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ..+...+......+ +++.|...|++++...|++   ...|...+......|+++.|...|++++.
T Consensus        40 ~~~~~lg~~~~~~~-~~~~A~~~~~~~~~~~p~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~  104 (129)
T 2xev_A           40 NALYWLGESYYATR-NFQLAEAQFRDLVSRYPTHDKAAGGLLKLGLSQYGEGKNTEAQQTLQQVAT  104 (129)
T ss_dssp             HHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhc-cHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            45666777777778 9999999999999998887   77888888888899999999999999987

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=97.30  E-value=0.003  Score=52.29  Aligned_cols=101  Identities=11%  Similarity=-0.096  Sum_probs=77.0

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCH----H---H
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVG----E---L   94 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~----~---l   94 (565)
                      ....|........+.|+++.+...|++||..+|.+..+|...+.... ..+..+.+...|++||...|...    .   +
T Consensus         7 ~A~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~p~~~~~~~nlg~~~~-~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~   85 (127)
T 4gcn_A            7 AAIAEKDLGNAAYKQKDFEKAHVHYDKAIELDPSNITFYNNKAAVYF-EEKKFAECVQFCEKAVEVGRETRADYKLIAKA   85 (127)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHH-HhhhHHHHHHHHHHHHHhCcccchhhHHHHHH
Confidence            44567788888888999999999999999999999999998876444 45578889999999998765432    2   2


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhccc
Q 008442           95 WVRSLLSLERSRASEEEISTVFEKSLLCAF  124 (565)
Q Consensus        95 W~~yi~~le~~~~~~~~~~~if~ral~~~~  124 (565)
                      |..... .....+.++++...|++++...+
T Consensus        86 ~~~lg~-~~~~~~~~~~A~~~~~kal~~~~  114 (127)
T 4gcn_A           86 MSRAGN-AFQKQNDLSLAVQWFHRSLSEFR  114 (127)
T ss_dssp             HHHHHH-HHHHTTCHHHHHHHHHHHHHHSC
T ss_pred             HHHHHH-HHHHcCCHHHHHHHHHHHHhhCc
Confidence            322222 33346889999999999997543

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.28  E-value=0.002  Score=51.93  Aligned_cols=76  Identities=11%  Similarity=0.013  Sum_probs=63.4

Q ss_pred             HHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          169 DYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       169 ~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ..+...+...+.....|..++.++...+ +++.|...|++++...|.....|..++......|+++.|+..|++++.
T Consensus         6 ~~~~~al~~~p~~~~~~~~lg~~~~~~g-~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~   81 (115)
T 2kat_A            6 ERLEAMLAQGTDNMLLRFTLGKTYAEHE-QFDAALPHLRAALDFDPTYSVAWKWLGKTLQGQGDRAGARQAWESGLA   81 (115)
T ss_dssp             HHHHHHHTTTCCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCcHHHHHHHHHHHHHcc-CHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3333344434445567778888888888 999999999999999999999999999999999999999999999986

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=97.28  E-value=0.0032  Score=56.88  Aligned_cols=102  Identities=4%  Similarity=-0.129  Sum_probs=79.6

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCH---------
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVG---------   92 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~---------   92 (565)
                      +...|..........|+.+.+...|++++...|.+...|..++..... .+..+.+...|++|+...|...         
T Consensus        36 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~lg~~~~~-~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~  114 (213)
T 1hh8_A           36 HSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQ-TEKYDLAIKDLKEALIQLRGNQLIDYKILGL  114 (213)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHTTTTCSEEECGGGTB
T ss_pred             ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHH-cccHHHHHHHHHHHHHhCCCccHHHHHHhcc
Confidence            456888888888888999999999999999999999999888875544 4477788999999999777654         


Q ss_pred             -------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc
Q 008442           93 -------ELWVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (565)
Q Consensus        93 -------~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~  125 (565)
                             .+|......+ ...+..+.+...|++++...+.
T Consensus       115 ~~~~~~~~~~~~l~~~~-~~~g~~~~A~~~~~~al~~~p~  153 (213)
T 1hh8_A          115 QFKLFACEVLYNIAFMY-AKKEEWKKAEEQLALATSMKSE  153 (213)
T ss_dssp             CCEEEHHHHHHHHHHHH-HHTTCHHHHHHHHHHHHTTCCS
T ss_pred             ccCccchHHHHHHHHHH-HHccCHHHHHHHHHHHHHcCcc
Confidence                   6666655533 3467888999999999876543

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.27  E-value=0.008  Score=51.75  Aligned_cols=103  Identities=11%  Similarity=-0.088  Sum_probs=84.5

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhc------------------CCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITD------------------FPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~------------------~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (565)
                      ....|..-.......|+++.+...|++||..                  .|.+..+|...+.... ..+..+.+...|++
T Consensus        10 ~a~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~-~~~~~~~A~~~~~~   88 (162)
T 3rkv_A           10 SVEALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYL-NIGDLHEAEETSSE   88 (162)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHH-HHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHH-hcCcHHHHHHHHHH
Confidence            4567888888888899999999999999998                  6666678887776444 34477889999999


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccccc
Q 008442           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFST  126 (565)
Q Consensus        84 Al~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~  126 (565)
                      ||...|.....|......+ ...+.++++...|++|+...+..
T Consensus        89 al~~~p~~~~a~~~~g~~~-~~~g~~~~A~~~~~~al~l~p~~  130 (162)
T 3rkv_A           89 VLKREETNEKALFRRAKAR-IAAWKLDEAEEDLKLLLRNHPAA  130 (162)
T ss_dssp             HHHHSTTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCGGG
T ss_pred             HHhcCCcchHHHHHHHHHH-HHHhcHHHHHHHHHHHHhcCCCC
Confidence            9999999999888877644 44788999999999999876553

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=97.27  E-value=0.0064  Score=50.33  Aligned_cols=95  Identities=7%  Similarity=-0.029  Sum_probs=63.9

Q ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHH
Q 008442          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLR  262 (565)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~  262 (565)
                      ..|...+......+ +++.|..+|++++...|++..+|...+......|+++.|...|++++..  . +.....|.....
T Consensus        10 ~~~~~~g~~~~~~~-~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~-p~~~~~~~~l~~   85 (137)
T 3q49_B           10 QELKEQGNRLFVGR-KYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALEL--D-GQSVKAHFFLGQ   85 (137)
T ss_dssp             HHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--C-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-cHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--C-chhHHHHHHHHH
Confidence            44555566666666 7788888888888877777778887777777788888888888888762  1 223344544455


Q ss_pred             HHHHhCCHHHHHHHHHHHh
Q 008442          263 FEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       263 fE~~~G~~~~~~~~~~k~~  281 (565)
                      .-...|+.+.+...+.+++
T Consensus        86 ~~~~~~~~~~A~~~~~~a~  104 (137)
T 3q49_B           86 CQLEMESYDEAIANLQRAY  104 (137)
T ss_dssp             HHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHH
Confidence            5555677776666666554

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.22  E-value=0.011  Score=48.28  Aligned_cols=97  Identities=7%  Similarity=-0.034  Sum_probs=75.1

Q ss_pred             HHHHHHHHhcCCchhHHHHHHHHHhcCCCCH---HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCC---HHHHHHHHH
Q 008442           27 MIYLKYEQSSGDPGRVQLLYERAITDFPVSS---DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV---GELWVRSLL  100 (565)
Q Consensus        27 ~~yi~~e~~~~~~~~~~~lyERal~~~p~~~---~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~---~~lW~~yi~  100 (565)
                      ..........|+++.+...|++++...|.+.   ..|...+.... ..++.+.+...|++++...|.+   ...|.....
T Consensus         6 ~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~-~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~la~   84 (129)
T 2xev_A            6 YNVAFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYY-ATRNFQLAEAQFRDLVSRYPTHDKAAGGLLKLGL   84 (129)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHH-HhccHHHHHHHHHHHHHHCCCCcccHHHHHHHHH
Confidence            3344455668899999999999999999888   78877776444 3457788999999999999987   666666555


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcccc
Q 008442          101 SLERSRASEEEISTVFEKSLLCAFS  125 (565)
Q Consensus       101 ~le~~~~~~~~~~~if~ral~~~~~  125 (565)
                      .+ ...+..+++...|++++...+.
T Consensus        85 ~~-~~~g~~~~A~~~~~~~~~~~p~  108 (129)
T 2xev_A           85 SQ-YGEGKNTEAQQTLQQVATQYPG  108 (129)
T ss_dssp             HH-HHTTCHHHHHHHHHHHHHHSTT
T ss_pred             HH-HHcCCHHHHHHHHHHHHHHCCC
Confidence            33 3468899999999999975544

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=97.21  E-value=0.013  Score=55.81  Aligned_cols=163  Identities=12%  Similarity=-0.003  Sum_probs=98.3

Q ss_pred             CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHH
Q 008442           54 PVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDL  133 (565)
Q Consensus        54 p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~  133 (565)
                      |.+...|...+..+.. .+..+.+...|++|+...|....+|......+ ...+..+++...|++|+...+.....+..+
T Consensus         1 p~~a~~~~~~g~~~~~-~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~-~~~~~~~~A~~~~~~al~~~p~~~~~~~~l   78 (281)
T 2c2l_A            1 SPSAQELKEQGNRLFV-GRKYPEAAACYGRAITRNPLVAVYYTNRALCY-LKMQQPEQALADCRRALELDGQSVKAHFFL   78 (281)
T ss_dssp             CCCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHH-HHTTCHHHHHHHHHHHTTSCTTCHHHHHHH
T ss_pred             ChhHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHhCCccHHHHHHHHHHH-HHhcCHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence            4456667776665544 34778899999999999999999998877644 447889999999999998776655544433


Q ss_pred             HHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHc
Q 008442          134 FLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS  213 (565)
Q Consensus       134 ~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~  213 (565)
                      -..+..              ..++..+...|.+++............  .++....         ..++...........
T Consensus        79 g~~~~~--------------~g~~~~A~~~~~~al~l~p~~~~~~~~--~~~~~~~---------~~~~~~~~~~~~~~~  133 (281)
T 2c2l_A           79 GQCQLE--------------MESYDEAIANLQRAYSLAKEQRLNFGD--DIPSALR---------IAKKKRWNSIEERRI  133 (281)
T ss_dssp             HHHHHH--------------TTCHHHHHHHHHHHHHHHHHTTCCCCS--HHHHHHH---------HHHHHHHHHHHHTCC
T ss_pred             HHHHHH--------------cCCHHHHHHHHHHHHHhCccchhhHHH--HHHHHHH---------HHHHHHHHHHHHHHH
Confidence            333221              014555666677666654322111111  1222111         111112222222234


Q ss_pred             cchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          214 GAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       214 ~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      +....++..+..+.  .|+.+.|.+.|++++.
T Consensus       134 ~~~~~i~~~l~~l~--~~~~~~A~~~~~~al~  163 (281)
T 2c2l_A          134 HQESELHSYLTRLI--AAERERELEECQRNHE  163 (281)
T ss_dssp             CCCCHHHHHHHHHH--HHHHHHHHTTTSGGGT
T ss_pred             hhhHHHHHHHHHHH--HHHHHHHHHHHHhhhc
Confidence            55555655555554  5788889888988876

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=97.20  E-value=0.01  Score=53.36  Aligned_cols=114  Identities=11%  Similarity=0.057  Sum_probs=85.3

Q ss_pred             HHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHH
Q 008442          163 TFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKR  242 (565)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~  242 (565)
                      -|++|+..+...+.   +....|...+.+....+ +++.|...|++++...|....+|...+......|+++.|...|++
T Consensus        21 ~~~~A~~~~~~a~~---~~~~~~~~lg~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~   96 (213)
T 1hh8_A           21 DWKGALDAFSAVQD---PHSRICFNIGCMYTILK-NMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDLAIKDLKE   96 (213)
T ss_dssp             CHHHHHHHHHTSSS---CCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHcC---CChHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcccHHHHHHHHHH
Confidence            35556666655542   23457777888888888 999999999999999999999999999999999999999999999


Q ss_pred             HHhcccCCCC--------------cHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          243 CYSKRFTGTG--------------SEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       243 al~~~~~~~~--------------~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      ++.. .+.+.              ...+|......-...|+.+.+...+++++
T Consensus        97 al~~-~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al  148 (213)
T 1hh8_A           97 ALIQ-LRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALAT  148 (213)
T ss_dssp             HHHT-TTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHh-CCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            9973 22211              11444444445556788888777776664

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=97.17  E-value=0.0082  Score=61.87  Aligned_cols=103  Identities=12%  Similarity=-0.063  Sum_probs=85.2

Q ss_pred             HhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCC---------------HHHHHHHHHHHHHhcchhhHHHHHHHHHH
Q 008442           21 EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVS---------------SDLWLDYTQYLDKTLKVGNVVRDVYSRAT   85 (565)
Q Consensus        21 ~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~---------------~~lW~~Y~~~l~~~~~~~~~~~~v~erAl   85 (565)
                      .....|..........++++.+...|++||..+|.+               ..+|..++..+. ..+..+.+...|++||
T Consensus       266 ~~a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~-~~g~~~~A~~~~~~al  344 (457)
T 1kt0_A          266 EQAAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYL-KLREYTKAVECCDKAL  344 (457)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHH-HhcCHHHHHHHHHHHH
Confidence            356788888888889999999999999999999988               578888776544 4457888999999999


Q ss_pred             HcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccc
Q 008442           86 KNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (565)
Q Consensus        86 ~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~  125 (565)
                      ...|.....|......+ ...+.++++...|++|+...+.
T Consensus       345 ~~~p~~~~a~~~~g~a~-~~~g~~~~A~~~~~~al~l~P~  383 (457)
T 1kt0_A          345 GLDSANEKGLYRRGEAQ-LLMNEFESAKGDFEKVLEVNPQ  383 (457)
T ss_dssp             HHSTTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHTTC--
T ss_pred             hcCCccHHHHHHHHHHH-HHccCHHHHHHHHHHHHHhCCC
Confidence            99999988888877644 4468899999999999986654

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=97.14  E-value=0.036  Score=50.24  Aligned_cols=178  Identities=10%  Similarity=-0.081  Sum_probs=94.6

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHh--cCCHHHHHHHHHHH
Q 008442           42 VQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERS--RASEEEISTVFEKS  119 (565)
Q Consensus        42 ~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~--~~~~~~~~~if~ra  119 (565)
                      +...|+++...  .++..+......... .++.+.+...|++|+..-  ....+......+...  ..+.+++...|++|
T Consensus         5 A~~~~~~aa~~--g~~~a~~~lg~~~~~-~~~~~~A~~~~~~a~~~g--~~~a~~~lg~~y~~~g~~~~~~~A~~~~~~A   79 (212)
T 3rjv_A            5 PGSQYQQQAEA--GDRRAQYYLADTWVS-SGDYQKAEYWAQKAAAQG--DGDALALLAQLKIRNPQQADYPQARQLAEKA   79 (212)
T ss_dssp             TTHHHHHHHHT--TCHHHHHHHHHHHHH-HTCHHHHHHHHHHHHHTT--CHHHHHHHHHHTTSSTTSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHC--CCHHHHHHHHHHHhc-CCCHHHHHHHHHHHHHcC--CHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            44567777665  556666655544433 346666777777777642  233333322212211  01677777777777


Q ss_pred             HhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCc--hhHHHHHHHHHHHHH---
Q 008442          120 LLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTD--GLLRLYAYWAHLEQS---  194 (565)
Q Consensus       120 l~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~--~~~~l~~~~a~~e~~---  194 (565)
                      +.....  ..+..+-..+.        ....+         ...+.+|+.++.......+  .....+..++.++..   
T Consensus        80 ~~~g~~--~a~~~Lg~~y~--------~g~g~---------~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g  140 (212)
T 3rjv_A           80 VEAGSK--SGEIVLARVLV--------NRQAG---------ATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVH  140 (212)
T ss_dssp             HHTTCH--HHHHHHHHHHT--------CGGGS---------SCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSS
T ss_pred             HHCCCH--HHHHHHHHHHH--------cCCCC---------ccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCC
Confidence            654322  11111111111        00000         0123444444444444333  123344455555555   


Q ss_pred             -cCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHH-cC-----ChHHHHHHHHHHHh
Q 008442          195 -MGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE-LD-----HINEARSIYKRCYS  245 (565)
Q Consensus       195 -~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~-~~-----~~~~aR~i~~~al~  245 (565)
                       .. ++++|...|++++.. +.+...+.....+... .|     +++.|...|++++.
T Consensus       141 ~~~-d~~~A~~~~~~A~~~-~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~  196 (212)
T 3rjv_A          141 GPE-DDVKASEYFKGSSSL-SRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCL  196 (212)
T ss_dssp             SSC-CHHHHHHHHHHHHHT-SCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHH
T ss_pred             CCC-CHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHH
Confidence             44 899999999999988 3333444555555433 34     89999999999986

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.13  E-value=0.0067  Score=45.97  Aligned_cols=78  Identities=14%  Similarity=0.061  Sum_probs=66.1

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~  100 (565)
                      ....|..........++.+.+...|++++...|.+..+|..++..... .++.+.+...|++++...|.....|.....
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~-~~~~~~A~~~~~~a~~~~p~~~~~~~~l~~   85 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYK-QGDYDEAIEYYQKALELDPNNAEAKQNLGN   85 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHH-HhhHHHHHHHHHHHHhcCCCCHHHHHHHHH
Confidence            566788888888888999999999999999999999999988875554 447788999999999999988888876554

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=97.13  E-value=0.11  Score=59.65  Aligned_cols=206  Identities=11%  Similarity=0.063  Sum_probs=101.1

Q ss_pred             CCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHH
Q 008442           37 GDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVF  116 (565)
Q Consensus        37 ~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if  116 (565)
                      ++.+++..+++|+     .++.+|..|+...+..+ ..+.+.+.|++|     .+..-|..-+..++. .+.++++...|
T Consensus      1090 ~nldrAiE~Aerv-----n~p~vWsqLAKAql~~G-~~kEAIdsYiKA-----dD~say~eVa~~~~~-lGkyEEAIeyL 1157 (1630)
T 1xi4_A         1090 GNLDRAYEFAERC-----NEPAVWSQLAKAQLQKG-MVKEAIDSYIKA-----DDPSSYMEVVQAANT-SGNWEELVKYL 1157 (1630)
T ss_pred             hhHHHHHHHHHhc-----CCHHHHHHHHHHHHhCC-CHHHHHHHHHhc-----CChHHHHHHHHHHHH-cCCHHHHHHHH
Confidence            3445555555544     66788888887665444 556677777776     344566665555544 56777777777


Q ss_pred             HHHHhcccc-cHHHHHHHHHHHHHH---HHHHhhccccchhhhhH---HHHHHHHHHHHHHHHhhhcCCchhHHHHHHHH
Q 008442          117 EKSLLCAFS-TFEEYLDLFLTRIDG---LRRRILFSGEVEGVLDY---SLIRETFQRASDYLSEQMKNTDGLLRLYAYWA  189 (565)
Q Consensus       117 ~ral~~~~~-~~~~~~~~~~~~~~~---~~r~~~~~~~~e~~~~~---~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a  189 (565)
                      ..|...... .....+.+..+..+.   +...+. .....++..+   ..-...|+.|..++...        ..|...+
T Consensus      1158 ~mArk~~~e~~Idt~LafaYAKl~rleele~fI~-~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA--------~ny~rLA 1228 (1630)
T 1xi4_A         1158 QMARKKARESYVETELIFALAKTNRLAELEEFIN-GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV--------SNFGRLA 1228 (1630)
T ss_pred             HHHHhhcccccccHHHHHHHHhhcCHHHHHHHHh-CCCHHHHHHHHHHHHhcCCHHHHHHHHHhh--------hHHHHHH
Confidence            777754311 111111111111110   111110 0000111111   11112344455554332        2344555


Q ss_pred             HHHHHcCCChHHHHHHHHHHHHHcc-------------------------chHHHHHHHHHHHHHcCChHHHHHHHHHHH
Q 008442          190 HLEQSMGKDMVSARGVWERLLKISG-------------------------AMLEAWQSYISMEIELDHINEARSIYKRCY  244 (565)
Q Consensus       190 ~~e~~~~~~~~~ar~i~e~~l~~~~-------------------------~~~~lw~~yi~~e~~~~~~~~aR~i~~~al  244 (565)
                      ..+.+++ +++.|.+.+.++.....                         .+.+.....+.++...|.++.|..+|+.+|
T Consensus      1229 ~tLvkLg-e~q~AIEaarKA~n~~aWkev~~acve~~Ef~LA~~cgl~Iiv~~deLeeli~yYe~~G~feEAI~LlE~aL 1307 (1630)
T 1xi4_A         1229 STLVHLG-EYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAAL 1307 (1630)
T ss_pred             HHHHHhC-CHHHHHHHHHHhCCHHHHHHHHHHHhhhhHHHHHHHHHHhhhcCHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            5566666 77777777766632110                         011122244556667788888888888887


Q ss_pred             hcccCCCCcHHHHHHHHHHHHHh
Q 008442          245 SKRFTGTGSEDICHAWLRFEREY  267 (565)
Q Consensus       245 ~~~~~~~~~~~i~~~~~~fE~~~  267 (565)
                      ..  + +....+|.....+-.+|
T Consensus      1308 ~L--e-raH~gmftELaiLyaKy 1327 (1630)
T 1xi4_A         1308 GL--E-RAHMGMFTELAILYSKF 1327 (1630)
T ss_pred             cc--C-hhHhHHHHHHHHHHHhC
Confidence            52  2 22334554444444444

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=97.10  E-value=0.0049  Score=52.86  Aligned_cols=86  Identities=9%  Similarity=-0.008  Sum_probs=70.3

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCC----------chhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc-
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGD----------PGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL-   71 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~----------~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~-   71 (565)
                      +++..|+.++..+|.    +.+.|..+.......+.          ++.+...|++||..+|.+.+.|.....-+.... 
T Consensus        20 eA~~~~~~Ai~l~P~----~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~~~~A~~~LG~ay~~lg~   95 (158)
T 1zu2_A           20 QIRQDAENTYKSNPL----DADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYTSFAF   95 (158)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCC----CHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHhcc
Confidence            477888888988887    78888888887766554          458999999999999999999998876555432 


Q ss_pred             ---------chhhHHHHHHHHHHHcCCCCH
Q 008442           72 ---------KVGNVVRDVYSRATKNCPWVG   92 (565)
Q Consensus        72 ---------~~~~~~~~v~erAl~~~p~~~   92 (565)
                               +..+.+...|++||...|.+.
T Consensus        96 l~P~~~~a~g~~~eA~~~~~kAl~l~P~~~  125 (158)
T 1zu2_A           96 LTPDETEAKHNFDLATQFFQQAVDEQPDNT  125 (158)
T ss_dssp             HCCCHHHHHHHHHHHHHHHHHHHHHCTTCH
T ss_pred             cCcchhhhhccHHHHHHHHHHHHHhCCCCH
Confidence                     367889999999999999764

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.09  E-value=0.0011  Score=65.41  Aligned_cols=116  Identities=11%  Similarity=-0.011  Sum_probs=65.1

Q ss_pred             hhhHHHHHHHhcCCCCChHhH-----------------HHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKF-----------------QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQ   65 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~-----------------~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~   65 (565)
                      .+...|+.+|...+.    +.                 .+|..+.......++++.+...|+++|...|.+...|..++.
T Consensus       197 ~A~~~y~~Al~~~p~----~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~  272 (338)
T 2if4_A          197 EAMQQYEMAIAYMGD----DFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIVLTEEEKNPKALFRRGK  272 (338)
T ss_dssp             HHHHHHHHHHHHSCH----HHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcc----chhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            356678888877764    32                 378888888888999999999999999999999999999887


Q ss_pred             HHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcc
Q 008442           66 YLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA  123 (565)
Q Consensus        66 ~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~  123 (565)
                      .+. ..++.+.+...|++|+...|.+..+|..............+..+.+|.+++...
T Consensus       273 a~~-~~g~~~~A~~~l~~al~l~p~~~~a~~~L~~l~~~~~~~~~~a~~~~~~~l~~~  329 (338)
T 2if4_A          273 AKA-ELGQMDSARDDFRKAQKYAPDDKAIRRELRALAEQEKALYQKQKEMYKGIFKGK  329 (338)
T ss_dssp             HHH-TTTCHHHHHHHHHHTTC-------------------------------------
T ss_pred             HHH-HcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC
Confidence            554 455788899999999998898888777655433444455667777888877643

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=97.06  E-value=0.0091  Score=51.27  Aligned_cols=100  Identities=14%  Similarity=0.075  Sum_probs=80.6

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCC-------CHH-----HHHHHHHHHHHhcchhhHHHHHHHHHHHc--
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPV-------SSD-----LWLDYTQYLDKTLKVGNVVRDVYSRATKN--   87 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~-------~~~-----lW~~Y~~~l~~~~~~~~~~~~v~erAl~~--   87 (565)
                      ....|.....-..+.|+++.+...|++||...|.       +..     +|..-..-+. ..+..+.+...|++||..  
T Consensus        10 ~a~~~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~-~Lgr~~eAl~~~~kAL~l~n   88 (159)
T 2hr2_A           10 GAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALA-GLRSFDEALHSADKALHYFN   88 (159)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHH-HCCCHHHHHHHHHHHHHhhh
Confidence            3456777787778889999999999999999998       444     8888776444 445778899999999998  


Q ss_pred             -----CCCCHHHH----HHHHHHHHHhcCCHHHHHHHHHHHHhcc
Q 008442           88 -----CPWVGELW----VRSLLSLERSRASEEEISTVFEKSLLCA  123 (565)
Q Consensus        88 -----~p~~~~lW----~~yi~~le~~~~~~~~~~~if~ral~~~  123 (565)
                           .|.....|    ..-...+. ..+..+++...|++|+...
T Consensus        89 ~~~e~~pd~~~A~~~~~~~rG~aL~-~lgr~eEAl~~y~kAlel~  132 (159)
T 2hr2_A           89 RRGELNQDEGKLWISAVYSRALALD-GLGRGAEAMPEFKKVVEMI  132 (159)
T ss_dssp             HHCCTTSTHHHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHH
T ss_pred             ccccCCCchHHHHHHHHHhHHHHHH-HCCCHHHHHHHHHHHHhcC
Confidence                 99999999    66655444 4788999999999999754

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=97.03  E-value=0.0039  Score=55.84  Aligned_cols=96  Identities=6%  Similarity=-0.117  Sum_probs=76.4

Q ss_pred             hhHHHHHHHhcCCCCC-hH-----------hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc
Q 008442            4 ARAHLEEQISRQDLSD-SE-----------KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL   71 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~-~~-----------~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~   71 (565)
                      +...|+.+|...|... ..           ...+|..+.......|+.+.+...|++++...|.+...|...+..+.. .
T Consensus        57 A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~-~  135 (198)
T 2fbn_A           57 AIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMY-F  135 (198)
T ss_dssp             HHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHH-H
T ss_pred             HHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHH-c
Confidence            5567788887665411 00           026788888888889999999999999999999999999998876554 4


Q ss_pred             chhhHHHHHHHHHHHcCCCCHHHHHHHHH
Q 008442           72 KVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (565)
Q Consensus        72 ~~~~~~~~v~erAl~~~p~~~~lW~~yi~  100 (565)
                      ++.+.+...|++|+...|....+|.....
T Consensus       136 ~~~~~A~~~~~~al~~~p~~~~~~~~l~~  164 (198)
T 2fbn_A          136 GFLEEAKENLYKAASLNPNNLDIRNSYEL  164 (198)
T ss_dssp             TCHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHCCCcHHHHHHHHH
Confidence            47788999999999999999888877655

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=97.02  E-value=0.068  Score=47.22  Aligned_cols=89  Identities=16%  Similarity=0.178  Sum_probs=59.5

Q ss_pred             hHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHc---cch---HHHHHHHHHHHHH
Q 008442          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS---GAM---LEAWQSYISMEIE  229 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~---~~~---~~lw~~yi~~e~~  229 (565)
                      ++......|.+++..+.............+...+.+....+ +++.|...+++++...   ++.   ..++...+.....
T Consensus        81 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~  159 (203)
T 3gw4_A           81 NWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFG-DLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQ  159 (203)
T ss_dssp             CHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhC-CHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHH
Confidence            44455566666666554221111122344556677777788 9999999999999752   222   2345667777888


Q ss_pred             cCChHHHHHHHHHHHh
Q 008442          230 LDHINEARSIYKRCYS  245 (565)
Q Consensus       230 ~~~~~~aR~i~~~al~  245 (565)
                      .|+++.|...|++++.
T Consensus       160 ~g~~~~A~~~~~~al~  175 (203)
T 3gw4_A          160 EKNLLEAQQHWLRARD  175 (203)
T ss_dssp             TTCHHHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHH
Confidence            9999999999999986

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.01  E-value=0.0061  Score=52.50  Aligned_cols=89  Identities=19%  Similarity=0.164  Sum_probs=71.2

Q ss_pred             hHHHHHHHHHHHHHHHHhhhcC-----------CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHH
Q 008442          156 DYSLIRETFQRASDYLSEQMKN-----------TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYI  224 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~~~-----------~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi  224 (565)
                      ++..+...|.+++.++......           .+....+|...+......+ +++.|...++++|...|++...|...+
T Consensus        26 ~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~-~~~~A~~~~~~al~~~p~~~~a~~~~g  104 (162)
T 3rkv_A           26 DYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIG-DLHEAEETSSEVLKREETNEKALFRRA  104 (162)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHSTTCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcC-cHHHHHHHHHHHHhcCCcchHHHHHHH
Confidence            4556667777777765433211           1223456777788888888 999999999999999999999999999


Q ss_pred             HHHHHcCChHHHHHHHHHHHh
Q 008442          225 SMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       225 ~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ......|+++.|...|++++.
T Consensus       105 ~~~~~~g~~~~A~~~~~~al~  125 (162)
T 3rkv_A          105 KARIAAWKLDEAEEDLKLLLR  125 (162)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhcHHHHHHHHHHHHh
Confidence            999999999999999999987

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.01  E-value=0.0024  Score=62.99  Aligned_cols=36  Identities=11%  Similarity=-0.116  Sum_probs=28.0

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS   57 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~   57 (565)
                      ....|..........++++.+...|++||...|.+.
T Consensus       178 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~  213 (338)
T 2if4_A          178 AADRRKMDGNSLFKEEKLEEAMQQYEMAIAYMGDDF  213 (338)
T ss_dssp             HHHHHHHHHHHTCSSSCCHHHHHHHHHHHHHSCHHH
T ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhccch
Confidence            345566666666677899999999999999888655

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=97.00  E-value=0.024  Score=59.95  Aligned_cols=179  Identities=9%  Similarity=-0.028  Sum_probs=116.6

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCC----------chhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcc-
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGD----------PGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLK-   72 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~----------~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~-   72 (565)
                      +-..++.+|..+|.    ++.+|..-.......+.          .+.....|+++|..+|.++.+|..-.-. ....+ 
T Consensus        48 al~~~~~~l~~nP~----~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK~y~aW~hR~w~-l~~l~~  122 (567)
T 1dce_A           48 VLELTSQILGANPD----FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWL-LSRLPE  122 (567)
T ss_dssp             HHHHHHHHHHHCTT----CHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHH-HHTCSS
T ss_pred             HHHHHHHHHHHCch----hHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHH-HHHccc
Confidence            34667888888887    88999766665555554          6788999999999999999999987644 44555 


Q ss_pred             -hhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccccc--HHHHHHHHHHHHHHHHHHhhccc
Q 008442           73 -VGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFST--FEEYLDLFLTRIDGLRRRILFSG  149 (565)
Q Consensus        73 -~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~--~~~~~~~~~~~~~~~~r~~~~~~  149 (565)
                       ..+...+.|++|+..-|.+...|......+.......++..+.+++++...+..  .|.+....+...      .....
T Consensus       123 ~~~~~el~~~~k~l~~d~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~n~saW~~r~~ll~~l------~~~~~  196 (567)
T 1dce_A          123 PNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQL------HPQPD  196 (567)
T ss_dssp             CCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHHH------SCCCC
T ss_pred             ccHHHHHHHHHHHHhhccccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCCCccHHHHHHHHHHhh------ccccc
Confidence             347789999999999999999998766545543337788888899999876653  333332222110      00000


Q ss_pred             cchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcC
Q 008442          150 EVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMG  196 (565)
Q Consensus       150 ~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~  196 (565)
                      ....  . ......++++++++..++...+.....|.++.-+....+
T Consensus       197 ~~~~--~-~~~~~~~~eel~~~~~ai~~~P~~~saW~y~~~ll~~~~  240 (567)
T 1dce_A          197 SGPQ--G-RLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAE  240 (567)
T ss_dssp             SSSC--C-SSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCCC
T ss_pred             cccc--c-cccHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHHhcCC
Confidence            0000  0 000144566666666665544555667877666655444

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=96.99  E-value=0.0062  Score=50.28  Aligned_cols=64  Identities=11%  Similarity=0.065  Sum_probs=33.6

Q ss_pred             hHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccch-------HHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM-------LEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       181 ~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~-------~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ...+|...+.++...+ +++.|...|+++|...|+.       ..+|......+...|+++.|...|+++|.
T Consensus        41 ~~~~~~nlg~~~~~~~-~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~kal~  111 (127)
T 4gcn_A           41 NITFYNNKAAVYFEEK-KFAECVQFCEKAVEVGRETRADYKLIAKAMSRAGNAFQKQNDLSLAVQWFHRSLS  111 (127)
T ss_dssp             CHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHhHHHHHHHhh-hHHHHHHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            3444555555555555 6666666666666543322       12333444445555666666666666654

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=96.96  E-value=0.094  Score=50.35  Aligned_cols=181  Identities=12%  Similarity=-0.011  Sum_probs=90.0

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCC--CCHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 008442           42 VQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCP--WVGELWVRSLLSLERSRASEEEISTVFEKS  119 (565)
Q Consensus        42 ~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p--~~~~lW~~yi~~le~~~~~~~~~~~if~ra  119 (565)
                      +...|++.+...+.+...+. ++.-+....++.+.++.++.+++...|  .+.++....+. +....+..+.++.+++++
T Consensus        85 a~~~l~~l~~~~~~~~~~~~-~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vq-i~L~~~r~d~A~k~l~~~  162 (310)
T 3mv2_B           85 NIEELENLLKDKQNSPYELY-LLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIE-VALLNNNVSTASTIFDNY  162 (310)
T ss_dssp             CCHHHHHTTTTSCCCHHHHH-HHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHH-HHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCcHHHH-HHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHH-HHHHCCCHHHHHHHHHHH
Confidence            34556666655444444444 332333344566677777777776665  45566666555 333356677777777776


Q ss_pred             Hhcccc----cHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHc
Q 008442          120 LLCAFS----TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSM  195 (565)
Q Consensus       120 l~~~~~----~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~  195 (565)
                      ....++    .-...+.+...++....     +..     ++.....+|++       .....+.+......|. .+...
T Consensus       163 ~~~~~d~~~~~d~~l~~Laea~v~l~~-----g~~-----~~q~A~~~f~E-------l~~~~p~~~~~~lLln-~~~~~  224 (310)
T 3mv2_B          163 TNAIEDTVSGDNEMILNLAESYIKFAT-----NKE-----TATSNFYYYEE-------LSQTFPTWKTQLGLLN-LHLQQ  224 (310)
T ss_dssp             HHHSCHHHHHHHHHHHHHHHHHHHHHH-----TCS-----TTTHHHHHHHH-------HHTTSCSHHHHHHHHH-HHHHH
T ss_pred             HhcCccccccchHHHHHHHHHHHHHHh-----CCc-----cHHHHHHHHHH-------HHHhCCCcccHHHHHH-HHHHc
Confidence            654431    11112233333332221     000     11112233332       2222221111111122 45555


Q ss_pred             CCChHHHHHHHHHHHHHc----------cchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          196 GKDMVSARGVWERLLKIS----------GAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       196 ~~~~~~ar~i~e~~l~~~----------~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      + ++++|..+++.+++..          |++...-...|.+....|+  .|.+++.++..
T Consensus       225 g-~~~eAe~~L~~l~~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~  281 (310)
T 3mv2_B          225 R-NIAEAQGIVELLLSDYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVK  281 (310)
T ss_dssp             T-CHHHHHHHHHHHHSHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHH
T ss_pred             C-CHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHH
Confidence            6 7777777777655542          5566666666666666665  66677777665

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=96.93  E-value=0.35  Score=49.42  Aligned_cols=48  Identities=8%  Similarity=-0.029  Sum_probs=20.8

Q ss_pred             hhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHh---cCCHHHHHHHHHHHH
Q 008442           73 VGNVVRDVYSRATKNCPWVGELWVRSLLSLERS---RASEEEISTVFEKSL  120 (565)
Q Consensus        73 ~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~---~~~~~~~~~if~ral  120 (565)
                      +.+.+...|++|+..-|.....|......+...   ..+.+++...|+++.
T Consensus       194 ~~~~A~~~~~~aa~~g~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa  244 (452)
T 3e4b_A          194 QQAELLKQMEAGVSRGTVTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA  244 (452)
T ss_dssp             HHHHHHHHHHHHHHTTCSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc
Confidence            334455555555555554444332222212110   134455555555555

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=96.91  E-value=0.021  Score=46.20  Aligned_cols=95  Identities=8%  Similarity=-0.027  Sum_probs=57.8

Q ss_pred             HHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCC--CCc---HHHHHH
Q 008442          185 YAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTG--TGS---EDICHA  259 (565)
Q Consensus       185 ~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~--~~~---~~i~~~  259 (565)
                      +...+......+ +++.|..+|++++...|....+|...+......|+++.|..+|++++... +.  ...   ..++..
T Consensus         7 ~~~l~~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~   84 (131)
T 1elr_A            7 EKELGNDAYKKK-DFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVG-RENREDYRQIAKAYAR   84 (131)
T ss_dssp             HHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-HHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhc-CHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhc-cccchhHHHHHHHHHH
Confidence            344455555556 77777777777777777777777777777777777777777777776531 11  111   233333


Q ss_pred             HHHHHHHhCCHHHHHHHHHHHh
Q 008442          260 WLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       260 ~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      ....-...|+.+.+...+.+++
T Consensus        85 la~~~~~~~~~~~A~~~~~~~~  106 (131)
T 1elr_A           85 IGNSYFKEEKYKDAIHFYNKSL  106 (131)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhccHHHHHHHHHHHH
Confidence            3344445566666666555554

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=96.91  E-value=0.0033  Score=47.99  Aligned_cols=52  Identities=23%  Similarity=0.335  Sum_probs=45.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA  451 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~  451 (565)
                      .+-++| ++|......||.++|++||. ..|+++.|.       -|||.|.+++.|..|+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~   67 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEETT-------EEEEECSCHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHH
Confidence            355556 99999999999999999994 558888874       79999999999999987

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=96.89  E-value=0.0028  Score=63.38  Aligned_cols=79  Identities=11%  Similarity=-0.092  Sum_probs=64.5

Q ss_pred             HhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHH
Q 008442           21 EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (565)
Q Consensus        21 ~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~  100 (565)
                      .....|..+.......++++.+...|++||...|.+...|..++..+. ..++.+.+...|++|+...|....+|..+..
T Consensus       271 ~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~-~~g~~~eA~~~l~~Al~l~P~~~~~~~~l~~  349 (370)
T 1ihg_A          271 VALSCVLNIGACKLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQ-GLKEYDQALADLKKAQEIAPEDKAIQAELLK  349 (370)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhCchhHHHHHHHHHHHH-HccCHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            366788888888888899999999999999999999999888877554 3457778899999999998988888776554

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=96.86  E-value=0.0048  Score=48.45  Aligned_cols=64  Identities=13%  Similarity=0.071  Sum_probs=58.1

Q ss_pred             hHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       181 ~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ...+|..++.++...+ +++.|...|++++...|+...+|..........|+++.|...|++++.
T Consensus         6 ~~~~~~~lg~~~~~~g-~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   69 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHD-NASRALALFEELVETDPDYVGTYYHLGKLYERLDRTDDAIDTYAQGIE   69 (100)
T ss_dssp             CHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            3456777788888888 999999999999999999999999999999999999999999999986

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=96.84  E-value=0.012  Score=46.36  Aligned_cols=69  Identities=12%  Similarity=-0.015  Sum_probs=59.5

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCC
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV   91 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~   91 (565)
                      +...|..........|+.+.+...|++++...|.+..+|..++..+. ..+..+.+...|++|+...|..
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~-~~g~~~~A~~~~~~al~~~p~~   71 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLITAQPQNPVGYSNKAMALI-KLGEYTQAIQMCQQGLRYTSTA   71 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTSCSST
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHH-HhcCHHHHHHHHHHHHHhCCCc
Confidence            45678888888888999999999999999999999999998887554 4457788999999999998876

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=96.84  E-value=0.0046  Score=63.76  Aligned_cols=99  Identities=5%  Similarity=-0.065  Sum_probs=75.8

Q ss_pred             hhhHHHHHHHhcCCCCC-----------hHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc
Q 008442            3 NARAHLEEQISRQDLSD-----------SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL   71 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~-----------~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~   71 (565)
                      .+...|+.+|...|...           +....+|..+.....+.++++.+...|++||...|.+...|...+..+. ..
T Consensus       286 ~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~~g~a~~-~~  364 (457)
T 1kt0_A          286 QAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQL-LM  364 (457)
T ss_dssp             HHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH-HT
T ss_pred             HHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHH-Hc
Confidence            35677888887776520           1115788888888889999999999999999999999999998887554 44


Q ss_pred             chhhHHHHHHHHHHHcCCCCHHHHHHHHHHH
Q 008442           72 KVGNVVRDVYSRATKNCPWVGELWVRSLLSL  102 (565)
Q Consensus        72 ~~~~~~~~v~erAl~~~p~~~~lW~~yi~~l  102 (565)
                      ++.+.+...|++|+...|....+|......+
T Consensus       365 g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~  395 (457)
T 1kt0_A          365 NEFESAKGDFEKVLEVNPQNKAARLQISMCQ  395 (457)
T ss_dssp             TCHHHHHHHHHHHHTTC----CHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            5788899999999999998888877765533

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=96.81  E-value=0.025  Score=42.68  Aligned_cols=64  Identities=16%  Similarity=0.195  Sum_probs=56.5

Q ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhc
Q 008442          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~  246 (565)
                      ...+...+......+ +++.|...|++++...|....+|..++......|+++.|...|++++..
T Consensus         9 ~~~~~~la~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~   72 (91)
T 1na3_A            9 AEAWYNLGNAYYKQG-DYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL   72 (91)
T ss_dssp             HHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcc-CHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            345556677777777 9999999999999999999999999999999999999999999999873

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=96.80  E-value=0.44  Score=54.70  Aligned_cols=81  Identities=11%  Similarity=0.120  Sum_probs=53.3

Q ss_pred             HHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcC-CChHHHHHHHHHHHHHcc-----chHHHHHHHHHHHHHcC
Q 008442          158 SLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMG-KDMVSARGVWERLLKISG-----AMLEAWQSYISMEIELD  231 (565)
Q Consensus       158 ~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~-~~~~~ar~i~e~~l~~~~-----~~~~lw~~yi~~e~~~~  231 (565)
                      -..+..|++++.+++..+...+.+..+|..++.++.+.. ..+.++-+.|..-+...+     .+..+|..++-++...|
T Consensus      1290 Ye~~G~feEAI~LlE~aL~LeraH~gmftELaiLyaKy~peklmEhlk~f~~rini~k~~r~~e~~~lW~elv~LY~~~~ 1369 (1630)
T 1xi4_A         1290 YQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYE 1369 (1630)
T ss_pred             HHHcCCHHHHHHHHHHHhccChhHhHHHHHHHHHHHhCCHHHHHHHHHHHHHhcccchHhHHHHHHHHHHHHHHHHHhcc
Confidence            334456777888888777666666666655555554432 134455556666665544     56778999999998889


Q ss_pred             ChHHHHH
Q 008442          232 HINEARS  238 (565)
Q Consensus       232 ~~~~aR~  238 (565)
                      ++++|..
T Consensus      1370 e~dnA~~ 1376 (1630)
T 1xi4_A         1370 EYDNAII 1376 (1630)
T ss_pred             cHHHHHH
Confidence            9988873

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=96.78  E-value=0.0018  Score=50.99  Aligned_cols=69  Identities=12%  Similarity=0.133  Sum_probs=51.4

Q ss_pred             hHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCC
Q 008442           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCP   89 (565)
Q Consensus        20 ~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p   89 (565)
                      |.+...|..+.......|+++.+...|+++|...|.+...|..+..... ..+..+.+...|++|+...|
T Consensus         4 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~-~~g~~~~A~~~~~~al~l~~   72 (100)
T 3ma5_A            4 PEDPFTRYALAQEHLKHDNASRALALFEELVETDPDYVGTYYHLGKLYE-RLDRTDDAIDTYAQGIEVAR   72 (100)
T ss_dssp             -CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH-HcCCHHHHHHHHHHHHhhhh
Confidence            3466778888887778888888888888888888888888887776544 34466778888888887544

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=96.75  E-value=0.0025  Score=66.21  Aligned_cols=90  Identities=12%  Similarity=-0.149  Sum_probs=49.8

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (565)
                      +...|+.+|...|.    +...|..+.......|+.+.+...|++|+...|.+...|...+..+.. .+..+.+...|++
T Consensus        25 A~~~~~~Al~~~p~----~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~~~-~g~~~eA~~~~~~   99 (477)
T 1wao_1           25 AIKFYSQAIELNPS----NAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMA-LGKFRAALRDYET   99 (477)
T ss_dssp             HHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHH-HTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCc----cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-cCCHHHHHHHHHH
Confidence            44455555555554    455565555555556666666666666666666666666555543332 2345556666666


Q ss_pred             HHHcCCCCHHHHHHH
Q 008442           84 ATKNCPWVGELWVRS   98 (565)
Q Consensus        84 Al~~~p~~~~lW~~y   98 (565)
                      |+...|.....|..+
T Consensus       100 al~~~p~~~~~~~~l  114 (477)
T 1wao_1          100 VVKVKPHDKDAKMKY  114 (477)
T ss_dssp             HHHHSTTCTTHHHHH
T ss_pred             HHHhCCCCHHHHHHH
Confidence            666555554444443

>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=0.0032  Score=49.00  Aligned_cols=74  Identities=14%  Similarity=0.149  Sum_probs=59.9

Q ss_pred             CCeEEEcCCCCCC-C----HHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEE
Q 008442          391 ECTAFLSNINLKA-T----YEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSI  464 (565)
Q Consensus       391 ~~~l~V~nl~~~~-~----~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v  464 (565)
                      .++|+|.||+.++ .    ...++.+|..|+.+........      -+=..|.|.++++|.+|-. +++..+.|++|+|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS------FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc------ceEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            3689999998875 2    2577999999998877665542      1246899999999999976 8999999999999


Q ss_pred             eecCCC
Q 008442          465 ARSNPK  470 (565)
Q Consensus       465 ~~a~~~  470 (565)
                      -++.+.
T Consensus        79 YFgq~~   84 (104)
T 1wey_A           79 YFAQTL   84 (104)
T ss_dssp             ECCCCS
T ss_pred             EecCCC
Confidence            998854

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=96.73  E-value=0.16  Score=44.64  Aligned_cols=129  Identities=12%  Similarity=0.114  Sum_probs=81.6

Q ss_pred             HHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH---ccc----hHHHHHHHHHHHHH
Q 008442          157 YSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI---SGA----MLEAWQSYISMEIE  229 (565)
Q Consensus       157 ~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~---~~~----~~~lw~~yi~~e~~  229 (565)
                      +......|.+++...... ...+.....+...+.+....+ +++.|...|++++..   .++    ...++.........
T Consensus        42 ~~~A~~~~~~al~~~~~~-~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~  119 (203)
T 3gw4_A           42 FDEARASFQALQQQAQKS-GDHTAEHRALHQVGMVERMAG-NWDAARRCFLEERELLASLPEDPLAASANAYEVATVALH  119 (203)
T ss_dssp             HHHHHHHHHHHHHHHHTT-CCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHc-CCcHHHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHH
Confidence            344445555555544321 111222344555677777778 999999999999987   442    23466777777888


Q ss_pred             cCChHHHHHHHHHHHhcccCCCCcHHHH---HHHHHHHHHhCCHHHHHHHHHHHhhHHHHH
Q 008442          230 LDHINEARSIYKRCYSKRFTGTGSEDIC---HAWLRFEREYGTLEDFDHSVQKVTPRLEEL  287 (565)
Q Consensus       230 ~~~~~~aR~i~~~al~~~~~~~~~~~i~---~~~~~fE~~~G~~~~~~~~~~k~~~~~~~~  287 (565)
                      .|+++.|...|++++...-....+....   ..........|+.+.+...+.+++...++.
T Consensus       120 ~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~  180 (203)
T 3gw4_A          120 FGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRARDIFAEL  180 (203)
T ss_dssp             HTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             hCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHc
Confidence            9999999999999986321222333222   233344556789888888887776655443

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=96.72  E-value=0.011  Score=59.11  Aligned_cols=89  Identities=13%  Similarity=0.065  Sum_probs=71.3

Q ss_pred             hHHHHHHHHHHHHHHHHhhh---------cCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHH
Q 008442          156 DYSLIRETFQRASDYLSEQM---------KNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISM  226 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~---------~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~  226 (565)
                      ++..+...|.+++.++....         ...+....+|..++..+...+ ++++|...|++++...|++..+|...+..
T Consensus       238 ~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g-~~~~A~~~~~~al~~~p~~~~a~~~lg~~  316 (370)
T 1ihg_A          238 NWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMS-DWQGAVDSCLEALEIDPSNTKALYRRAQG  316 (370)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHTTCTTCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhcc-CHHHHHHHHHHHHHhCchhHHHHHHHHHH
Confidence            45566667777776543321         112334567777888888888 99999999999999999999999999999


Q ss_pred             HHHcCChHHHHHHHHHHHh
Q 008442          227 EIELDHINEARSIYKRCYS  245 (565)
Q Consensus       227 e~~~~~~~~aR~i~~~al~  245 (565)
                      ....|+++.|...|++|+.
T Consensus       317 ~~~~g~~~eA~~~l~~Al~  335 (370)
T 1ihg_A          317 WQGLKEYDQALADLKKAQE  335 (370)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHccCHHHHHHHHHHHHH
Confidence            9999999999999999997

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=96.72  E-value=0.22  Score=44.89  Aligned_cols=185  Identities=12%  Similarity=-0.048  Sum_probs=110.9

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc--chhhHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL--KVGNVVRDV   80 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~--~~~~~~~~v   80 (565)
                      ++...|+.+....      +...+..+.......++++.+...|++|+..  .++..+..+........  .+.+.+...
T Consensus         4 eA~~~~~~aa~~g------~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~--g~~~a~~~lg~~y~~~g~~~~~~~A~~~   75 (212)
T 3rjv_A            4 EPGSQYQQQAEAG------DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQ--GDGDALALLAQLKIRNPQQADYPQARQL   75 (212)
T ss_dssp             CTTHHHHHHHHTT------CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHT--TCHHHHHHHHHHTTSSTTSCCHHHHHHH
T ss_pred             hHHHHHHHHHHCC------CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHc--CCHHHHHHHHHHHHcCCCCCCHHHHHHH
Confidence            3556777777653      4566777777766789999999999999986  56777777665544311  167789999


Q ss_pred             HHHHHHcCCCCHHHHHHHHHHHHH---hcCCHHHHHHHHHHHHhcccc--cHHHHHHHHHHHHHHHHHHhhccccchhhh
Q 008442           81 YSRATKNCPWVGELWVRSLLSLER---SRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRILFSGEVEGVL  155 (565)
Q Consensus        81 ~erAl~~~p~~~~lW~~yi~~le~---~~~~~~~~~~if~ral~~~~~--~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~  155 (565)
                      |++|+..  .....+......+..   ...+.+++...|++|+.....  ....+..+-..+..        ...+.  .
T Consensus        76 ~~~A~~~--g~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~--------g~g~~--~  143 (212)
T 3rjv_A           76 AEKAVEA--GSKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYAS--------GVHGP--E  143 (212)
T ss_dssp             HHHHHHT--TCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHH--------TSSSS--C
T ss_pred             HHHHHHC--CCHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHc--------CCCCC--C
Confidence            9999874  344444443332221   146789999999999987652  12222222222221        00011  1


Q ss_pred             hHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHc-----CCChHHHHHHHHHHHHHccc
Q 008442          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSM-----GKDMVSARGVWERLLKISGA  215 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~-----~~~~~~ar~i~e~~l~~~~~  215 (565)
                      ++......|+++.+.      ..++.  .+..++.++...     ..++++|...|++++..-..
T Consensus       144 d~~~A~~~~~~A~~~------~~~~~--a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g~~  200 (212)
T 3rjv_A          144 DDVKASEYFKGSSSL------SRTGY--AEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEGFD  200 (212)
T ss_dssp             CHHHHHHHHHHHHHT------SCTTH--HHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHTCH
T ss_pred             CHHHHHHHHHHHHHc------CCCHH--HHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcCCH
Confidence            444455555555442      01111  233344455442     33899999999999987443

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=96.63  E-value=0.078  Score=54.33  Aligned_cols=110  Identities=9%  Similarity=0.035  Sum_probs=65.9

Q ss_pred             HHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHc---CCChHHHHHHHHHHHHHccchHHHHHHHHHH-H--HHcCChHHH
Q 008442          163 TFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSM---GKDMVSARGVWERLLKISGAMLEAWQSYISM-E--IELDHINEA  236 (565)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~---~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~-e--~~~~~~~~a  236 (565)
                      .+.+++.++.......+.....+..++.++...   .+++++|...|+++.   +.+...+.....+ +  ...++++.|
T Consensus       194 ~~~~A~~~~~~aa~~g~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa---~g~~~a~~~Lg~~~~~~~~~~d~~~A  270 (452)
T 3e4b_A          194 QQAELLKQMEAGVSRGTVTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA---PGYPASWVSLAQLLYDFPELGDVEQM  270 (452)
T ss_dssp             HHHHHHHHHHHHHHTTCSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG---GGSTHHHHHHHHHHHHSGGGCCHHHH
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc---CCCHHHHHHHHHHHHhCCCCCCHHHH
Confidence            456666666666555554444444445554332   148889999999988   5566666666665 3  457899999


Q ss_pred             HHHHHHHHhcccCCCCcHHHHHHHHHHHHHhC-----CHHHHHHHHHHHh
Q 008442          237 RSIYKRCYSKRFTGTGSEDICHAWLRFEREYG-----TLEDFDHSVQKVT  281 (565)
Q Consensus       237 R~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G-----~~~~~~~~~~k~~  281 (565)
                      ...|++++..    ..+...+..-.-++  .|     +.+.....+.++.
T Consensus       271 ~~~~~~Aa~~----g~~~A~~~Lg~~y~--~G~g~~~d~~~A~~~~~~Aa  314 (452)
T 3e4b_A          271 MKYLDNGRAA----DQPRAELLLGKLYY--EGKWVPADAKAAEAHFEKAV  314 (452)
T ss_dssp             HHHHHHHHHT----TCHHHHHHHHHHHH--HCSSSCCCHHHHHHHHHTTT
T ss_pred             HHHHHHHHHC----CCHHHHHHHHHHHH--cCCCCCCCHHHHHHHHHHHh
Confidence            9999999862    23332222222222  45     6666655555554

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=96.58  E-value=0.43  Score=45.22  Aligned_cols=165  Identities=12%  Similarity=-0.021  Sum_probs=95.3

Q ss_pred             cCCHHHHHHHHHHHHhcccccHHH--HHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCch--h
Q 008442          106 RASEEEISTVFEKSLLCAFSTFEE--YLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG--L  181 (565)
Q Consensus       106 ~~~~~~~~~if~ral~~~~~~~~~--~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~--~  181 (565)
                      .+..+++...|++++.........  .+........+    ....      .++..+...|.+++....   ...+.  .
T Consensus        88 ~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~----~~~~------~~~~~A~~~~~~al~~~~---~~~~~~~~  154 (293)
T 2qfc_A           88 QKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAY----VLKK------VDYEYCILELKKLLNQQL---TGIDVYQN  154 (293)
T ss_dssp             TTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHH----HHTS------SCHHHHHHHHHHHHTTCC---CSSCTTHH
T ss_pred             hhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHH----HhcC------CCHHHHHHHHHHHHHHHh---cCCchHHH
Confidence            578899999999998754332111  11111111000    0000      023333344444433221   11222  2


Q ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHH---ccch----HHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCc-
Q 008442          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKI---SGAM----LEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGS-  253 (565)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~---~~~~----~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~-  253 (565)
                      ...+...+.++...+ +++.|...|++++..   .++.    ..++...+......|+++.|...|++++......... 
T Consensus       155 ~~~~~~lg~~y~~~~-~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~  233 (293)
T 2qfc_A          155 LYIENAIANIYAENG-YLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMA  233 (293)
T ss_dssp             HHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCS
T ss_pred             HHHHHHHHHHHHHcC-CHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHH
Confidence            445666777888888 999999999999953   4442    2577888888899999999999999998642111111 


Q ss_pred             --HHHHHHHHHHHHHhCCHHHH-HHHHHHHhhHH
Q 008442          254 --EDICHAWLRFEREYGTLEDF-DHSVQKVTPRL  284 (565)
Q Consensus       254 --~~i~~~~~~fE~~~G~~~~~-~~~~~k~~~~~  284 (565)
                        ..++......-...|+.+.+ ...+++++.-.
T Consensus       234 ~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al~~~  267 (293)
T 2qfc_A          234 LIGQLYYQRGECLRKLEYEEAEIEDAYKKASFFF  267 (293)
T ss_dssp             SHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHH
Confidence              23333334445566877666 65566665443

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=96.54  E-value=0.02  Score=43.74  Aligned_cols=77  Identities=12%  Similarity=0.151  Sum_probs=58.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCC--cceEEEEEecCHHHHHHHHH-cCCcccCCe-----EEE
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGK--SRGLAYVDFIDDEHLAAAVA-KNKQMFLGK-----KLS  463 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~--~~g~afv~f~~~~~a~~a~~-~~~~~~~g~-----~l~  463 (565)
                      ++|.|++||+.+|++++.+.+...+.+.....+..+.+.+  .-+-|||.|.+.+++..-.. .+|+.+.+.     +..
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~   81 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeE
Confidence            4789999999999999999999998877777665543332  23678999999998888887 688876322     334


Q ss_pred             EeecC
Q 008442          464 IARSN  468 (565)
Q Consensus       464 v~~a~  468 (565)
                      |++|.
T Consensus        82 VE~AP   86 (91)
T 1uw4_A           82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            55553

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=96.52  E-value=0.017  Score=54.41  Aligned_cols=84  Identities=15%  Similarity=0.124  Sum_probs=47.8

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHh-----cCCchhHHHHHHHHHhcCCCC-HHHHHHHHHHHHHhcchhhHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQS-----SGDPGRVQLLYERAITDFPVS-SDLWLDYTQYLDKTLKVGNVV   77 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~-----~~~~~~~~~lyERal~~~p~~-~~lW~~Y~~~l~~~~~~~~~~   77 (565)
                      ++..+|.+|.-+|.  ..+-..|..+..+...     .|+++++...|+|||..+|.. .+.+..|++|+....++.+.+
T Consensus       182 A~a~lerAleLDP~--~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~a  259 (301)
T 3u64_A          182 AVMMLERACDLWPS--YQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGF  259 (301)
T ss_dssp             HHHHHHHHHHHCTT--HHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHHH
T ss_pred             HHHHHHHHHHhCCC--cccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHHH
Confidence            45556666666554  1122355555555554     356666666666666666643 666666666655444455556


Q ss_pred             HHHHHHHHHcCC
Q 008442           78 RDVYSRATKNCP   89 (565)
Q Consensus        78 ~~v~erAl~~~p   89 (565)
                      ...+++|+..-|
T Consensus       260 ~~~L~kAL~a~p  271 (301)
T 3u64_A          260 DEALDRALAIDP  271 (301)
T ss_dssp             HHHHHHHHHCCG
T ss_pred             HHHHHHHHcCCC
Confidence            666666666444

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=96.47  E-value=0.25  Score=51.30  Aligned_cols=60  Identities=10%  Similarity=0.021  Sum_probs=46.0

Q ss_pred             HHHHHHHHHHcCCChHHHHHHHHHHHHH-ccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          185 YAYWAHLEQSMGKDMVSARGVWERLLKI-SGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       185 ~~~~a~~e~~~~~~~~~ar~i~e~~l~~-~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      |...+....+.+ +++.|..+|+.+... ...+...|...++.....|+.+.|.++|++.-.
T Consensus       143 yn~lI~~~~~~g-~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~  203 (501)
T 4g26_A          143 YGPALFGFCRKG-DADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRD  203 (501)
T ss_dssp             HHHHHHHHHHTT-CHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ehHHHHHHHHCC-CHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHH
Confidence            344444455667 888999999988876 444577888888888889999999999988854

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=96.44  E-value=0.1  Score=43.57  Aligned_cols=125  Identities=10%  Similarity=-0.005  Sum_probs=80.2

Q ss_pred             hHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccc------hHHHHHHHHHHHHH
Q 008442          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA------MLEAWQSYISMEIE  229 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~------~~~lw~~yi~~e~~  229 (565)
                      ++......|.+++....... ........+...+.+....+ ++++|...|++++...+.      ...++...+.....
T Consensus        24 ~~~~A~~~~~~al~~~~~~~-~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~  101 (164)
T 3ro3_A           24 NFRDAVIAHEQRLLIAKEFG-DKAAERIAYSNLGNAYIFLG-EFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTL  101 (164)
T ss_dssp             CHHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHhC-CchHHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHH
Confidence            44556666777766654321 11112345556677777888 999999999999986332      24577777888889


Q ss_pred             cCChHHHHHHHHHHHhcccCCCCcHHH---HHHHHHHHHHhCCHHHHHHHHHHHhh
Q 008442          230 LDHINEARSIYKRCYSKRFTGTGSEDI---CHAWLRFEREYGTLEDFDHSVQKVTP  282 (565)
Q Consensus       230 ~~~~~~aR~i~~~al~~~~~~~~~~~i---~~~~~~fE~~~G~~~~~~~~~~k~~~  282 (565)
                      .|+++.|...|++++........+...   +..........|+.+.+...+.+++.
T Consensus       102 ~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  157 (164)
T 3ro3_A          102 LQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  157 (164)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            999999999999998642222223222   22233344556777777666666543

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=96.43  E-value=0.021  Score=48.99  Aligned_cols=89  Identities=15%  Similarity=0.006  Sum_probs=69.0

Q ss_pred             hHHHHHHHHHHHHHHHHhhhc----CCc-hhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH-------ccchHHHH---
Q 008442          156 DYSLIRETFQRASDYLSEQMK----NTD-GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI-------SGAMLEAW---  220 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~~----~~~-~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~-------~~~~~~lw---  220 (565)
                      +++.....|.+|+.+......    ... ....+|...+.....++ ++++|...|+++|..       .|+....|   
T Consensus        26 ~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lg-r~~eAl~~~~kAL~l~n~~~e~~pd~~~A~~~~  104 (159)
T 2hr2_A           26 EYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLR-SFDEALHSADKALHYFNRRGELNQDEGKLWISA  104 (159)
T ss_dssp             CHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhhhccccCCCchHHHHHHH
Confidence            455666777777776544211    000 01226777777788888 999999999999999       99999999   


Q ss_pred             -HHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          221 -QSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       221 -~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                       ..-.......|+++.|...|++++.
T Consensus       105 ~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A          105 VYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence             8888888999999999999999987

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=96.36  E-value=0.19  Score=49.29  Aligned_cols=62  Identities=10%  Similarity=-0.027  Sum_probs=48.8

Q ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ...+..++-.....+ +++.|...+++++..+++ +..|..........|+.+.|.+.|.+|+.
T Consensus       277 a~~~~alal~~l~~g-d~d~A~~~l~rAl~Ln~s-~~a~~llG~~~~~~G~~~eA~e~~~~Alr  338 (372)
T 3ly7_A          277 SIIYQIKAVSALVKG-KTDESYQAINTGIDLEMS-WLNYVLLGKVYEMKGMNREAADAYLTAFN  338 (372)
T ss_dssp             HHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCC-CHHHHHHHHHHHHhcCCC-HHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            344555544444456 999999999999999865 55666667777889999999999999987

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.35  E-value=0.014  Score=46.89  Aligned_cols=71  Identities=8%  Similarity=0.089  Sum_probs=58.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCC-eEEEEeec
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLG-KKLSIARS  467 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g-~~l~v~~a  467 (565)
                      ..+.|.|-++|+.. ...|-..|++||.|.+....    ++  ..+-.|.|.++.+|++||..||..|+| -.|-|...
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~----~~--~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS----NT--GNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC----SS--SSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC----CC--CCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEEEC
Confidence            46789999999885 57778889999999988762    22  248999999999999999999999985 56777775

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.30  E-value=0.18  Score=50.74  Aligned_cols=195  Identities=11%  Similarity=0.034  Sum_probs=118.2

Q ss_pred             HhcCCchhHHHHHHHHHhcCCCCHH-----------------HHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHH--
Q 008442           34 QSSGDPGRVQLLYERAITDFPVSSD-----------------LWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGEL--   94 (565)
Q Consensus        34 ~~~~~~~~~~~lyERal~~~p~~~~-----------------lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~l--   94 (565)
                      .+.|++..+..+|..++...+...+                 .....+.. ....++.+.+.+.|.+++...+....-  
T Consensus        15 ~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~-y~~~~~~~~a~~~~~~~~~~~~~~~~~~~   93 (434)
T 4b4t_Q           15 VNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQL-YVTMGAKDKLREFIPHSTEYMMQFAKSKT   93 (434)
T ss_dssp             HHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHH-HHHHTCHHHHHHHHHHTHHHHHTSCHHHH
T ss_pred             HHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHH-HHHCCCHHHHHHHHHHHHHHHHHccchHH
Confidence            3468899999999999998876543                 12333332 233457788999999998865443221  


Q ss_pred             ---HHHHHHHHHHhcCCHHHHHHHHHHHHhcccc------cHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHH
Q 008442           95 ---WVRSLLSLERSRASEEEISTVFEKSLLCAFS------TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQ  165 (565)
Q Consensus        95 ---W~~yi~~le~~~~~~~~~~~if~ral~~~~~------~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~  165 (565)
                         -...+..+....+..+.+..++++++.....      ....+..+-..+.+              ..++..+...+.
T Consensus        94 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~--------------~g~~~~A~~~l~  159 (434)
T 4b4t_Q           94 VKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQ--------------KKQYKDSLALIN  159 (434)
T ss_dssp             HHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHH--------------HTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHH--------------ccChHHHHHHHH
Confidence               1111222333446778888888888753211      01111111111110              013444555555


Q ss_pred             HHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHc---cch----HHHHHHHHHHHHHcCChHHHHH
Q 008442          166 RASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS---GAM----LEAWQSYISMEIELDHINEARS  238 (565)
Q Consensus       166 ~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~---~~~----~~lw~~yi~~e~~~~~~~~aR~  238 (565)
                      ++...+.. ..+.+....++...++++...+ ++++|+.+|++++...   ++.    ..++.....+....++++.|..
T Consensus       160 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~  237 (434)
T 4b4t_Q          160 DLLREFKK-LDDKPSLVDVHLLESKVYHKLR-NLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFS  237 (434)
T ss_dssp             HHHHHHTT-SSCSTHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHH
T ss_pred             HHHHHHHh-cccchhHHHHHHHHHHHHHHhC-cHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence            55444322 2223344567777788888888 9999999999999762   222    3466666666777899999999


Q ss_pred             HHHHHHh
Q 008442          239 IYKRCYS  245 (565)
Q Consensus       239 i~~~al~  245 (565)
                      .|..++.
T Consensus       238 ~~~~a~~  244 (434)
T 4b4t_Q          238 YFFESFE  244 (434)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999875

>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=96.26  E-value=0.0062  Score=46.68  Aligned_cols=50  Identities=24%  Similarity=0.311  Sum_probs=44.1

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH
Q 008442          394 AFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA  451 (565)
Q Consensus       394 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~  451 (565)
                      ||+-++|.+....||.++|++|| -..|+++.|.       -|||.|.+++.|..|+.
T Consensus         8 V~~l~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~   57 (101)
T 3ctr_A            8 VLHVTFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVN   57 (101)
T ss_dssp             EEEEECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHH
T ss_pred             EEEEeCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHH
Confidence            44449999999999999999999 5678888874       79999999999999997

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=96.25  E-value=0.018  Score=59.70  Aligned_cols=83  Identities=12%  Similarity=0.094  Sum_probs=68.0

Q ss_pred             hHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHH
Q 008442          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINE  235 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~  235 (565)
                      +++.+...|+++++.       .+.....|..++..+...+ ++++|...|++++...|+....|...+......|+++.
T Consensus        21 ~~~~A~~~~~~Al~~-------~p~~~~~~~~lg~~~~~~g-~~~~A~~~~~~al~l~p~~~~~~~~lg~~~~~~g~~~e   92 (477)
T 1wao_1           21 DYENAIKFYSQAIEL-------NPSNAIYYGNRSLAYLRTE-CYGYALGDATRAIELDKKYIKGYYRRAASNMALGKFRA   92 (477)
T ss_dssp             CHHHHHHHHHHHHHH-------CTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHTCHHH
T ss_pred             CHHHHHHHHHHHHHh-------CCccHHHHHHHHHHHHHhc-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHH
Confidence            344444555555443       4445667888888888888 99999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhc
Q 008442          236 ARSIYKRCYSK  246 (565)
Q Consensus       236 aR~i~~~al~~  246 (565)
                      |.+.|++++..
T Consensus        93 A~~~~~~al~~  103 (477)
T 1wao_1           93 ALRDYETVVKV  103 (477)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            99999999973

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.21  E-value=0.27  Score=49.41  Aligned_cols=198  Identities=8%  Similarity=-0.072  Sum_probs=117.0

Q ss_pred             chhhHHHHHHHHHHHcCCCCHH-----------------HHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHH-HHHH
Q 008442           72 KVGNVVRDVYSRATKNCPWVGE-----------------LWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEE-YLDL  133 (565)
Q Consensus        72 ~~~~~~~~v~erAl~~~p~~~~-----------------lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~-~~~~  133 (565)
                      ++.+.+.++|..++...|....                 ....... +-...+..+++...|.+++......-.. ....
T Consensus        18 ~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~-~y~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~   96 (434)
T 4b4t_Q           18 KQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQ-LYVTMGAKDKLREFIPHSTEYMMQFAKSKTVKV   96 (434)
T ss_dssp             TCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHH-HHHHHTCHHHHHHHHHHTHHHHHTSCHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHH-HHHHCCCHHHHHHHHHHHHHHHHHccchHHHHH
Confidence            3567788999999987764221                 1111112 3334678889999999887632110011 1111


Q ss_pred             HHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHc
Q 008442          134 FLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS  213 (565)
Q Consensus       134 ~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~  213 (565)
                      ....++.+    ....     .+.+.....+..++....... .......++...+.+....+ ++..|..+++.++...
T Consensus        97 ~~~~l~~~----~~~~-----~~~~~a~~~~~~~~~~~~~~~-~~~~~~~~~~~la~~~~~~g-~~~~A~~~l~~~~~~~  165 (434)
T 4b4t_Q           97 LKTLIEKF----EQVP-----DSLDDQIFVCEKSIEFAKREK-RVFLKHSLSIKLATLHYQKK-QYKDSLALINDLLREF  165 (434)
T ss_dssp             HHHHHHHH----CSCC-----SCHHHHHHHHHHHHHHHHHSS-CCSSHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHH----HhCC-----CCHHHHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHHHHcc-ChHHHHHHHHHHHHHH
Confidence            11111111    0000     134455566776666654322 22234567778899998999 9999999999998762


Q ss_pred             ------cchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHH----HHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          214 ------GAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDI----CHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       214 ------~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i----~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                            +..+++++.-+.+....|++++|+.+|++++........+..+    +.....+....|+.+.+...+..+.
T Consensus       166 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~  243 (434)
T 4b4t_Q          166 KKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESF  243 (434)
T ss_dssp             TTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHH
T ss_pred             HhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence                  2346788888999999999999999999998643333334332    2222233333466665555444443

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=96.14  E-value=0.82  Score=43.24  Aligned_cols=165  Identities=11%  Similarity=-0.001  Sum_probs=97.4

Q ss_pred             cCCHHHHHHHHHHHHhcccccHHH--HHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCch--h
Q 008442          106 RASEEEISTVFEKSLLCAFSTFEE--YLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG--L  181 (565)
Q Consensus       106 ~~~~~~~~~if~ral~~~~~~~~~--~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~--~  181 (565)
                      .++.+++..+|++++.........  ++..+.....+.    . ..     .++..+...|.+++...   ....+.  .
T Consensus        88 ~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~----~-~~-----~~~~~Ai~~~~~al~~~---~~~~~~~~~  154 (293)
T 3u3w_A           88 QKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYV----L-KK-----VDYEYCILELKKLLNQQ---LTGIDVYQN  154 (293)
T ss_dssp             TTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHH----T-TS-----SCHHHHHHHHHHHHHTC---CCCSCTTHH
T ss_pred             HhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHH----H-cc-----cCHHHHHHHHHHHHHHh---cccccHHHH
Confidence            578999999999999754332221  111111111110    0 00     13444555566555532   111222  2


Q ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHH---c----cchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCc-
Q 008442          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKI---S----GAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGS-  253 (565)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~---~----~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~-  253 (565)
                      ..++...+.++...+ ++++|..+|+++++.   .    +....++...+......|+++.|...|++|+......... 
T Consensus       155 ~~~~~~lg~~y~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~  233 (293)
T 3u3w_A          155 LYIENAIANIYAENG-YLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMA  233 (293)
T ss_dssp             HHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCT
T ss_pred             HHHHHHHHHHHHHcC-CHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHH
Confidence            335566777888888 999999999999964   2    2234578888888999999999999999998642122111 


Q ss_pred             --HHHHHHHHHHHHHhC-CHHHHHHHHHHHhhHH
Q 008442          254 --EDICHAWLRFEREYG-TLEDFDHSVQKVTPRL  284 (565)
Q Consensus       254 --~~i~~~~~~fE~~~G-~~~~~~~~~~k~~~~~  284 (565)
                        ..++...-..-...| ..+.+...+++++...
T Consensus       234 ~~~~~~~~lg~~~~~~g~~~~~A~~~~~~Al~i~  267 (293)
T 3u3w_A          234 LIGQLYYQRGECLRKLEYEEAEIEDAYKKASFFF  267 (293)
T ss_dssp             THHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHH
Confidence              233333334445567 4466666666665443

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=96.14  E-value=0.091  Score=41.08  Aligned_cols=62  Identities=10%  Similarity=0.001  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhc
Q 008442          184 LYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~  246 (565)
                      .|...+......+ ++++|...|++++...|.+..+|..........|+++.|...|++++..
T Consensus         6 ~~~~~g~~~~~~~-~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~   67 (111)
T 2l6j_A            6 KQKEQGNSLFKQG-LYREAVHCYDQLITAQPQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRY   67 (111)
T ss_dssp             HHHHHHHHHHTTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHcC-CHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            4555666666777 9999999999999999999999999999999999999999999999973

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.10  E-value=0.049  Score=41.97  Aligned_cols=63  Identities=19%  Similarity=0.088  Sum_probs=53.1

Q ss_pred             HHhcCCchhHHHHHHHHHhcCCCCHH-HHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHH
Q 008442           33 EQSSGDPGRVQLLYERAITDFPVSSD-LWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWV   96 (565)
Q Consensus        33 e~~~~~~~~~~~lyERal~~~p~~~~-lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~   96 (565)
                      ....|+.+.+...|++++...|.+.. +|..++..... .+..+.+...|++|+...|.....|.
T Consensus        10 ~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~-~~~~~~A~~~~~~al~~~p~~~~~~~   73 (99)
T 2kc7_A           10 LINQGDIENALQALEEFLQTEPVGKDEAYYLMGNAYRK-LGDWQKALNNYQSAIELNPDSPALQA   73 (99)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHH-HTCHHHHHHHHHHHHHHCTTSTHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHH-cCCHHHHHHHHHHHHhcCCCcHHHHH
Confidence            34568889999999999999999999 99988875554 44778899999999999998888773

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=96.09  E-value=0.48  Score=39.30  Aligned_cols=88  Identities=10%  Similarity=-0.009  Sum_probs=60.8

Q ss_pred             hHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHc---cc---hHHHHHHHHHHHHH
Q 008442          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS---GA---MLEAWQSYISMEIE  229 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~---~~---~~~lw~~yi~~e~~  229 (565)
                      ++......|.+++....... ........+...+.+....+ +++.|...+++++...   ++   ...++...+.....
T Consensus        64 ~~~~A~~~~~~a~~~~~~~~-~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~  141 (164)
T 3ro3_A           64 EFETASEYYKKTLLLARQLK-DRAVEAQSCYSLGNTYTLLQ-DYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTA  141 (164)
T ss_dssp             CHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHhC-CcHHHHHHHHHHHHHHHHHh-hHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHH
Confidence            44455566666666553321 11122345556677777888 9999999999999763   22   23466777777888


Q ss_pred             cCChHHHHHHHHHHHh
Q 008442          230 LDHINEARSIYKRCYS  245 (565)
Q Consensus       230 ~~~~~~aR~i~~~al~  245 (565)
                      .|+++.|...|++++.
T Consensus       142 ~g~~~~A~~~~~~a~~  157 (164)
T 3ro3_A          142 LGNHDQAMHFAEKHLE  157 (164)
T ss_dssp             HTCHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHH
Confidence            9999999999999986

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=95.79  E-value=0.098  Score=40.16  Aligned_cols=56  Identities=16%  Similarity=0.093  Sum_probs=50.0

Q ss_pred             HHHHHcCCChHHHHHHHHHHHHHccchHH-HHHHHHHHHHHcCChHHHHHHHHHHHhc
Q 008442          190 HLEQSMGKDMVSARGVWERLLKISGAMLE-AWQSYISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       190 ~~e~~~~~~~~~ar~i~e~~l~~~~~~~~-lw~~yi~~e~~~~~~~~aR~i~~~al~~  246 (565)
                      ......+ +++.|...|++++...|++.. +|...+......|+++.|...|++++..
T Consensus         8 ~~~~~~~-~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A            8 KELINQG-DIENALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHT-CHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHcC-CHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            3444566 999999999999999999998 9999999999999999999999999973

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=95.76  E-value=1.3  Score=45.87  Aligned_cols=162  Identities=10%  Similarity=0.014  Sum_probs=104.2

Q ss_pred             hcCCHHHHHHHHHHHHhcccc-cHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHH
Q 008442          105 SRASEEEISTVFEKSLLCAFS-TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLR  183 (565)
Q Consensus       105 ~~~~~~~~~~if~ral~~~~~-~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~  183 (565)
                      ..++++++..+|++....+.. ....|-.+...+.     +...........++..+..+|.+-   ....   ..+...
T Consensus        38 k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~-----~~~~~~~~~~~~~l~~A~~lf~~M---~~~G---~~Pd~~  106 (501)
T 4g26_A           38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCS-----LAEAATESSPNPGLSRGFDIFKQM---IVDK---VVPNEA  106 (501)
T ss_dssp             TSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHT-----TCCCCSSSSCCHHHHHHHHHHHHH---HHTT---CCCCHH
T ss_pred             hCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHH-----hCCchhhhhhcchHHHHHHHHHHH---HHhC---CCCCHH
Confidence            357889999999998875432 2222322222111     000000000001233333444422   1121   233344


Q ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHHHHH-ccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHH
Q 008442          184 LYAYWAHLEQSMGKDMVSARGVWERLLKI-SGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLR  262 (565)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~e~~l~~-~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~  262 (565)
                      .|...+....+.+ +++.|..+|+.+... ...+...|...|......|+++.|.++|+.....  ........|...+.
T Consensus       107 tyn~lI~~~~~~g-~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~--G~~Pd~~ty~~Li~  183 (501)
T 4g26_A          107 TFTNGARLAVAKD-DPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVES--EVVPEEPELAALLK  183 (501)
T ss_dssp             HHHHHHHHHHHHT-CHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHhcC-CHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhc--CCCCCHHHHHHHHH
Confidence            5666777778888 999999999999886 4456888999999999999999999999999874  33345567888888


Q ss_pred             HHHHhCCHHHHHHHHHHH
Q 008442          263 FEREYGTLEDFDHSVQKV  280 (565)
Q Consensus       263 fE~~~G~~~~~~~~~~k~  280 (565)
                      --...|+.+.+..++++-
T Consensus       184 ~~~~~g~~d~A~~ll~~M  201 (501)
T 4g26_A          184 VSMDTKNADKVYKTLQRL  201 (501)
T ss_dssp             HHHHTTCHHHHHHHHHHH
T ss_pred             HHhhCCCHHHHHHHHHHH
Confidence            888899998888777653

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=95.75  E-value=0.048  Score=42.12  Aligned_cols=68  Identities=12%  Similarity=-0.151  Sum_probs=33.3

Q ss_pred             hHHHHHHHHHHHHhcCC---chhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCC
Q 008442           22 KFQQYMIYLKYEQSSGD---PGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPW   90 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~---~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~   90 (565)
                      +.+.|..|.....-.++   ...+..+|++||...|.++..++........ .++...+...|++++...|.
T Consensus         5 ~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~-~g~y~~Ai~~w~~~l~~~p~   75 (93)
T 3bee_A            5 TATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFI-SFRFQEAIDTWVLLLDSNDP   75 (93)
T ss_dssp             CHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTCCCT
T ss_pred             CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHHHHHH-cCCHHHHHHHHHHHHhhCCC
Confidence            44555555555433222   3455555555555555555555554443332 22444555555555554443

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=95.57  E-value=0.08  Score=40.84  Aligned_cols=66  Identities=12%  Similarity=-0.105  Sum_probs=56.8

Q ss_pred             hHHHHHHHHHHHHHcCC--ChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhc
Q 008442          181 LLRLYAYWAHLEQSMGK--DMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       181 ~~~l~~~~a~~e~~~~~--~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~  246 (565)
                      ...++..|+......++  ..+.|+.+++++|...|+++..++.........|+++.|...|++++..
T Consensus         5 ~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A            5 TATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             CHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            35677788887765542  2689999999999999999999999999999999999999999999973

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.43  E-value=0.011  Score=48.02  Aligned_cols=79  Identities=11%  Similarity=0.194  Sum_probs=56.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeE-EEEeec------------CCCC-CcceEEEEEecCHHHHHHHHHcCCc
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSS-IRILHD------------KFTG-KSRGLAYVDFIDDEHLAAAVAKNKQ  455 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~-~~~~~~------------~~~g-~~~g~afv~f~~~~~a~~a~~~~~~  455 (565)
                      ....|.|-+.|++.+ ..+-..|++||.|.+ ..+..+            +..+ .....-.|.|.++.+|.+||..||.
T Consensus         6 ~e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~   84 (132)
T 3p3d_A            6 GELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGA   84 (132)
T ss_dssp             --CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTC
T ss_pred             CceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCe
Confidence            346788889987654 566678999999876 221110            0001 1235779999999999999999999


Q ss_pred             ccCCeEEEEeecCC
Q 008442          456 MFLGKKLSIARSNP  469 (565)
Q Consensus       456 ~~~g~~l~v~~a~~  469 (565)
                      .|+|..|-|....+
T Consensus        85 ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           85 VFNGVLLGVIPYTK   98 (132)
T ss_dssp             EETTEECEEEECCH
T ss_pred             EeCcEEEEEEECCH
Confidence            99999888888754

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=95.18  E-value=3  Score=41.96  Aligned_cols=98  Identities=10%  Similarity=0.043  Sum_probs=54.3

Q ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHH------------ccchHHHHHHHHHHHHHcC---------------ChH
Q 008442          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKI------------SGAMLEAWQSYISMEIELD---------------HIN  234 (565)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~------------~~~~~~lw~~yi~~e~~~~---------------~~~  234 (565)
                      ..+|..++-++...+ +++.|....-.....            ...+.++....+.|+....               +.+
T Consensus       282 ~~~w~e~~~ly~~~~-e~d~A~~tm~~h~~~a~~~~~f~~~~~kv~n~elyYkai~fyl~~~p~~l~~ll~~l~~~ld~~  360 (449)
T 1b89_A          282 AHLWAELVFLYDKYE-EYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYLEFKPLLLNDLLMVLSPRLDHT  360 (449)
T ss_dssp             TTCHHHHHHHHHHTT-CHHHHHHHHHHSTTTTCCHHHHHHHHHHCSSTHHHHHHHHHHHHHCGGGHHHHHHHHGGGCCHH
T ss_pred             HHHHHHHHHHHHhhc-hHHHHHHHHHhCChhhhhhHHHHHHHhchhHHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCcH
Confidence            357888888887777 888776543322211            3445778888888875332               344


Q ss_pred             HHHHHHHHHHhc--------ccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHH
Q 008442          235 EARSIYKRCYSK--------RFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (565)
Q Consensus       235 ~aR~i~~~al~~--------~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~  280 (565)
                      ++..+|++.=.-        .....+...|=+++.++--+.+|.+.++..++..
T Consensus       361 r~v~~~~~~~~l~l~~~yl~~v~~~n~~~vnealn~l~ieeed~~~lr~si~~~  414 (449)
T 1b89_A          361 RAVNYFSKVKQLPLVKPYLRSVQNHNNKSVNESLNNLFITEEDYQALRTSIDAY  414 (449)
T ss_dssp             HHHHHHHHTTCTTTTHHHHHHHHTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHC
T ss_pred             HHHHHHHHcCCcHHHHHHHHHHHHhhHHHHHHHHHHHHHhhhhHHHHHHHHHHh
Confidence            455555544110        0001122345566666666666777666666543

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=94.87  E-value=1.3  Score=45.69  Aligned_cols=90  Identities=11%  Similarity=0.042  Sum_probs=70.1

Q ss_pred             hHHHHHHHHHHHHHHHHhhhcC-CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH--------ccchHHHHHHHHHH
Q 008442          156 DYSLIRETFQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI--------SGAMLEAWQSYISM  226 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~--------~~~~~~lw~~yi~~  226 (565)
                      +++.+...++++++.....+.. ++.....+...+.++...| ++++|..+++++|..        +|+........+..
T Consensus       324 ~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g-~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~  402 (490)
T 3n71_A          324 LYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQ-AYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAGLT  402 (490)
T ss_dssp             CHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhc-CHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            4566777788888877776664 4445677777888998989 999999999999976        23334566677777


Q ss_pred             HHHcCChHHHHHHHHHHHhc
Q 008442          227 EIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       227 e~~~~~~~~aR~i~~~al~~  246 (565)
                      +..+|+++.|..+|++|+..
T Consensus       403 ~~~~G~~~eA~~~~~~Al~i  422 (490)
T 3n71_A          403 NWHAGHIEVGHGMICKAYAI  422 (490)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHH
Confidence            88999999999999999853

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=94.69  E-value=0.093  Score=52.94  Aligned_cols=82  Identities=10%  Similarity=0.108  Sum_probs=56.8

Q ss_pred             HHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCC-ChHHHHHHHHHHHHHcc-----chHHHHHHHHHHHHHcCChHH
Q 008442          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGK-DMVSARGVWERLLKISG-----AMLEAWQSYISMEIELDHINE  235 (565)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~-~~~~ar~i~e~~l~~~~-----~~~~lw~~yi~~e~~~~~~~~  235 (565)
                      .-|++++.+++..+...+....+|..++-++.+... .+.+..+.|...+...+     .+..+|..++-+....+++++
T Consensus       221 G~~eEai~lLe~aL~le~ah~~~ftel~il~~ky~p~k~~ehl~~~~~~ini~k~~~~~~~~~~w~e~~~ly~~~~e~d~  300 (449)
T 1b89_A          221 GYFEELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDN  300 (449)
T ss_dssp             TCHHHHHHHHHHHTTSTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHSTTSCHHHHHHHHHTTTCHHHHHHHHHHTTCHHH
T ss_pred             CCHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHHHhhchHHH
Confidence            457788888888887666667778777777765430 23334444544444445     567799999999999999999


Q ss_pred             HHHHHHHH
Q 008442          236 ARSIYKRC  243 (565)
Q Consensus       236 aR~i~~~a  243 (565)
                      |....-..
T Consensus       301 A~~tm~~h  308 (449)
T 1b89_A          301 AIITMMNH  308 (449)
T ss_dssp             HHHHHHHS
T ss_pred             HHHHHHhC
Confidence            87655444

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=94.62  E-value=0.091  Score=40.38  Aligned_cols=78  Identities=10%  Similarity=0.108  Sum_probs=52.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCC--cceEEEEEecCHHHHHHHHH-cCCcccCC---e--EE
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGK--SRGLAYVDFIDDEHLAAAVA-KNKQMFLG---K--KL  462 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~--~~g~afv~f~~~~~a~~a~~-~~~~~~~g---~--~l  462 (565)
                      .-+|.|+.||+.+|++++.+.+...-.+.....+..+.+.+  .-.-|||.|.+.+++..-.. .+|..+.+   .  +.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a   88 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPA   88 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeee
Confidence            46899999999999999988887765543333322221211  12568999999999888887 68887532   2  45


Q ss_pred             EEeecC
Q 008442          463 SIARSN  468 (565)
Q Consensus       463 ~v~~a~  468 (565)
                      .|++|.
T Consensus        89 ~VE~AP   94 (97)
T 2l08_A           89 VVEFAP   94 (97)
T ss_dssp             EEEECC
T ss_pred             EEEecC
Confidence            566653

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=94.43  E-value=0.021  Score=57.79  Aligned_cols=62  Identities=15%  Similarity=0.215  Sum_probs=45.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFL  458 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~  458 (565)
                      .++|||. .|..+++.+|.++|++||.|.++.+..++  |   -||.|+|.+.+++.+++...+..+.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~--g---~~~~vef~~~~~~~~~~~~~~~p~~  114 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF--G---LYAVVEFCQKESIGSLQNGTHTPXX  114 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS--S---EEEEEECC---CCHHHHSSCCCCCC
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC--C---eEEEEEeCCHHHHHHHHhccCCCcc
Confidence            4799997 79999999999999999999999887653  3   5999999999999987764444433

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=94.32  E-value=0.28  Score=49.75  Aligned_cols=89  Identities=13%  Similarity=0.110  Sum_probs=68.5

Q ss_pred             hHHHHHHHHHHHHHHHHhhhcC-CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH--------ccchHHHHHHHHHH
Q 008442          156 DYSLIRETFQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI--------SGAMLEAWQSYISM  226 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~--------~~~~~~lw~~yi~~  226 (565)
                      +++.+...++++++.....+.. ++.....+...+.++...| ++++|..+++++|..        +|+-...+...+..
T Consensus       313 ~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g-~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~  391 (433)
T 3qww_A          313 SPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQ-DWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRL  391 (433)
T ss_dssp             CHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhc-CHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHH
Confidence            4556667778887777666654 3444566777888888888 999999999999976        23334466677777


Q ss_pred             HHHcCChHHHHHHHHHHHh
Q 008442          227 EIELDHINEARSIYKRCYS  245 (565)
Q Consensus       227 e~~~~~~~~aR~i~~~al~  245 (565)
                      +..+|+++.|..+|++|+.
T Consensus       392 ~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          392 YMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHhccCHHHHHHHHHHHHH
Confidence            8899999999999999986

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=94.12  E-value=0.63  Score=47.95  Aligned_cols=126  Identities=12%  Similarity=0.041  Sum_probs=80.1

Q ss_pred             hcCCHHHHHHHHHHHHhcc---c--cc---HHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhc
Q 008442          105 SRASEEEISTVFEKSLLCA---F--ST---FEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMK  176 (565)
Q Consensus       105 ~~~~~~~~~~if~ral~~~---~--~~---~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~  176 (565)
                      .++..+++..+|+++|...   +  ..   ...+..+...|.+              ..+++.+...++++++.....+.
T Consensus       321 ~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~--------------~g~~~eA~~~~~~aL~i~~~~lG  386 (490)
T 3n71_A          321 SEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSY--------------LQAYEEASHYARRMVDGYMKLYH  386 (490)
T ss_dssp             TTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHH--------------TTCHHHHHHHHHHHHHHHHHHSC
T ss_pred             hCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHH--------------hcCHHHHHHHHHHHHHHHHHHcC
Confidence            4678889999999998521   1  11   1122222222211              12667788889999988887776


Q ss_pred             CC-chhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH----c-cch---HHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          177 NT-DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI----S-GAM---LEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       177 ~~-~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~----~-~~~---~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      .. +.....+...+.++...| ++++|..+|++++..    + +++   .++-....+.+...+.++.|-.+|.++..
T Consensus       387 ~~Hp~~a~~l~nLa~~~~~~G-~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          387 HNNAQLGMAVMRAGLTNWHAG-HIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             TTCHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            54 444566777889999999 999999999999976    2 222   23333333334455566667777766644

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=93.91  E-value=1.3  Score=42.38  Aligned_cols=114  Identities=10%  Similarity=0.134  Sum_probs=79.9

Q ss_pred             HHHHHHHHHHHhhhcCCc--hhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHcc------chHH--HHHHHHHHHHHcC
Q 008442          162 ETFQRASDYLSEQMKNTD--GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG------AMLE--AWQSYISMEIELD  231 (565)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~--~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~------~~~~--lw~~yi~~e~~~~  231 (565)
                      .-++.|+.++...+...+  ...+++...++++...+ +.+.|+++++++....|      +...  +...|+.+...-+
T Consensus       114 g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~-r~d~A~k~l~~~~~~~~d~~~~~d~~l~~Laea~v~l~~g~~  192 (310)
T 3mv2_B          114 GDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNN-NVSTASTIFDNYTNAIEDTVSGDNEMILNLAESYIKFATNKE  192 (310)
T ss_dssp             TCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHTCS
T ss_pred             CCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCC-CHHHHHHHHHHHHhcCccccccchHHHHHHHHHHHHHHhCCc
Confidence            446667777766665553  56788888899999988 99999999999988887      3332  3345556665555


Q ss_pred             ChHHHHHHHHHHHhcccCC-CCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          232 HINEARSIYKRCYSKRFTG-TGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       232 ~~~~aR~i~~~al~~~~~~-~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      .+..|..+|+.+... ++. ..+..+|.    ....-|+.+.++..++...
T Consensus       193 ~~q~A~~~f~El~~~-~p~~~~~~lLln----~~~~~g~~~eAe~~L~~l~  238 (310)
T 3mv2_B          193 TATSNFYYYEELSQT-FPTWKTQLGLLN----LHLQQRNIAEAQGIVELLL  238 (310)
T ss_dssp             TTTHHHHHHHHHHTT-SCSHHHHHHHHH----HHHHHTCHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHh-CCCcccHHHHHH----HHHHcCCHHHHHHHHHHHH
Confidence            899999999998763 221 01233444    4556699998888876543

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=92.55  E-value=6.7  Score=38.35  Aligned_cols=155  Identities=10%  Similarity=0.052  Sum_probs=82.4

Q ss_pred             HHHHHHhcCCCCHHHHHHHHHHHHHhc----chhhHHHHHHHHHHHcCCCCHHHHHH----HHHHHHHhcCC---HHHHH
Q 008442           45 LYERAITDFPVSSDLWLDYTQYLDKTL----KVGNVVRDVYSRATKNCPWVGELWVR----SLLSLERSRAS---EEEIS  113 (565)
Q Consensus        45 lyERal~~~p~~~~lW~~Y~~~l~~~~----~~~~~~~~v~erAl~~~p~~~~lW~~----yi~~le~~~~~---~~~~~  113 (565)
                      --+|+...-|.+.+.|-.|+.......    .....++.+|++|+..-|.....|..    |+...-.....   ...+.
T Consensus       182 e~~r~~~~~p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~lDP~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~  261 (372)
T 3ly7_A          182 MQETLQKILPHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQSSPEFTYARAEKALVDIVRHSQHPLDEKQLAALN  261 (372)
T ss_dssp             HHHHHHHHSCSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHH
T ss_pred             HHHHHhccCCCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhccCCCchhhHHHHH
Confidence            345666778888888888876543211    23466899999999999987765543    33111111011   12222


Q ss_pred             HHHHHHHhcc--cccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHH
Q 008442          114 TVFEKSLLCA--FSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHL  191 (565)
Q Consensus       114 ~if~ral~~~--~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~  191 (565)
                      ..+.++....  +.....+..+.....  .      .      .+++.....+++|+..       ++. .-.|...+.+
T Consensus       262 ~a~~a~~a~~~~~~~a~~~~alal~~l--~------~------gd~d~A~~~l~rAl~L-------n~s-~~a~~llG~~  319 (372)
T 3ly7_A          262 TEIDNIVTLPELNNLSIIYQIKAVSAL--V------K------GKTDESYQAINTGIDL-------EMS-WLNYVLLGKV  319 (372)
T ss_dssp             HHHHHHHTCGGGTTCHHHHHHHHHHHH--H------H------TCHHHHHHHHHHHHHH-------CCC-HHHHHHHHHH
T ss_pred             HHHHHHHhcccCCcCHHHHHHHHHHHH--h------C------CCHHHHHHHHHHHHhc-------CCC-HHHHHHHHHH
Confidence            3333222111  112222211111110  0      0      1333444445554443       222 2344566777


Q ss_pred             HHHcCCChHHHHHHHHHHHHHccchH-HHHHH
Q 008442          192 EQSMGKDMVSARGVWERLLKISGAML-EAWQS  222 (565)
Q Consensus       192 e~~~~~~~~~ar~i~e~~l~~~~~~~-~lw~~  222 (565)
                      ....| +.+.|.+.|++++...|... -+|..
T Consensus       320 ~~~~G-~~~eA~e~~~~AlrL~P~~~t~~~~~  350 (372)
T 3ly7_A          320 YEMKG-MNREAADAYLTAFNLRPGANTLYWIE  350 (372)
T ss_dssp             HHHTT-CHHHHHHHHHHHHHHSCSHHHHHHHH
T ss_pred             HHHCC-CHHHHHHHHHHHHhcCCCcChHHHHh
Confidence            77778 99999999999999988753 34443

>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=92.44  E-value=0.13  Score=44.13  Aligned_cols=34  Identities=6%  Similarity=0.141  Sum_probs=26.9

Q ss_pred             EEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCc
Q 008442          420 SIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQ  455 (565)
Q Consensus       420 ~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~  455 (565)
                      .+.|..+.  ++++|||||+|.++++|++|+. +++.
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhccc
Confidence            35566664  4789999999999999999997 5543

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=91.02  E-value=0.79  Score=46.40  Aligned_cols=87  Identities=10%  Similarity=-0.016  Sum_probs=61.1

Q ss_pred             HHHHHHHHHHHHHHHhhhcC-CchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH----c-cch---HHHHHHHHHHHH
Q 008442          158 SLIRETFQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI----S-GAM---LEAWQSYISMEI  228 (565)
Q Consensus       158 ~~~~~~~~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~----~-~~~---~~lw~~yi~~e~  228 (565)
                      +.+...++++++.....+.. ++.....+...+.++...| ++++|..+++++|..    + +++   ...+...+..+.
T Consensus       304 ~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g-~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~l~nLa~~~~  382 (429)
T 3qwp_A          304 EQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLG-LLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQL  382 (429)
T ss_dssp             HHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhc-cHHHHHHHHHHHHHhHHHHcCCCChHHHHHHHHHHHHHH
Confidence            33444455444443333333 3334566677788888888 999999999999975    2 333   446667777788


Q ss_pred             HcCChHHHHHHHHHHHh
Q 008442          229 ELDHINEARSIYKRCYS  245 (565)
Q Consensus       229 ~~~~~~~aR~i~~~al~  245 (565)
                      ..|+++.|..+|++|+.
T Consensus       383 ~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          383 HQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHH
Confidence            99999999999999985

>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=89.97  E-value=0.2  Score=42.37  Aligned_cols=41  Identities=10%  Similarity=0.089  Sum_probs=36.1

Q ss_pred             CCCcceEEEEEecCHHHHHHHHH-c-CCcccCCeEEEEeecCCC
Q 008442          429 TGKSRGLAYVDFIDDEHLAAAVA-K-NKQMFLGKKLSIARSNPK  470 (565)
Q Consensus       429 ~g~~~g~afv~f~~~~~a~~a~~-~-~~~~~~g~~l~v~~a~~~  470 (565)
                      ....+|+++|+|.+.++|++|+. + |+..++| ++.|..+.+.
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~   51 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKT   51 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTE
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCc
Confidence            45678999999999999999997 8 9999999 9999987653

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=87.36  E-value=2.7  Score=35.41  Aligned_cols=84  Identities=8%  Similarity=-0.105  Sum_probs=46.0

Q ss_pred             hHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcc--hhhHHHHHHHHHHHcC-C-CCHHHHHHHHHHHHHhcCCHHHHHHHH
Q 008442           41 RVQLLYERAITDFPVSSDLWLDYTQYLDKTLK--VGNVVRDVYSRATKNC-P-WVGELWVRSLLSLERSRASEEEISTVF  116 (565)
Q Consensus        41 ~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~--~~~~~~~v~erAl~~~-p-~~~~lW~~yi~~le~~~~~~~~~~~if  116 (565)
                      .++..|++.+...+.+.+....|+--+.++..  +..+...+++..++.- | ...+.+.. +-..-...++.++++..+
T Consensus        16 ~~~~~y~~e~~~~~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~-LAv~~~kl~~Y~~A~~y~   94 (152)
T 1pc2_A           16 KFEKKFQSEKAAGSVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFY-LAVGNYRLKEYEKALKYV   94 (152)
T ss_dssp             HHHHHHHHHHHTTCCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHH-HHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHccCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHH-HHHHHHHccCHHHHHHHH
Confidence            45566777776666777777777654443221  3335666677666655 4 11222211 111113356677777777


Q ss_pred             HHHHhcccc
Q 008442          117 EKSLLCAFS  125 (565)
Q Consensus       117 ~ral~~~~~  125 (565)
                      +++|+..|.
T Consensus        95 ~~lL~ieP~  103 (152)
T 1pc2_A           95 RGLLQTEPQ  103 (152)
T ss_dssp             HHHHHHCTT
T ss_pred             HHHHhcCCC
Confidence            777776554

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=87.13  E-value=5.6  Score=30.64  Aligned_cols=70  Identities=19%  Similarity=0.114  Sum_probs=44.9

Q ss_pred             hHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHH
Q 008442          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISM  226 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~  226 (565)
                      ++..+..-|+.|+...............++..++....+.+ +++.|...++++++..|++..+.....-|
T Consensus        20 ~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g-~~~~A~~~~~~al~l~P~~~~~~~n~~~~   89 (104)
T 2v5f_A           20 DYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQG-DLDKALLLTKKLLELDPEHQRANGNLKYF   89 (104)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHcc-CHHHHHHHHHHHHhcCCCCHHHHhhHHHH
Confidence            44445555565555443221112334567777788888888 89999999999998888876665444433

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=86.44  E-value=12  Score=30.45  Aligned_cols=77  Identities=6%  Similarity=0.024  Sum_probs=49.7

Q ss_pred             HHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHH----cCChHHHH
Q 008442          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE----LDHINEAR  237 (565)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~----~~~~~~aR  237 (565)
                      ..+.+|+.++.......++...    ++.++.... .+++|...|+++...  .+...+.....+...    .+++++|.
T Consensus         9 ~d~~~A~~~~~~aa~~g~~~a~----lg~~y~~g~-~~~~A~~~~~~Aa~~--g~~~a~~~Lg~~y~~G~g~~~d~~~A~   81 (138)
T 1klx_A            9 KDLKKAIQYYVKACELNEMFGC----LSLVSNSQI-NKQKLFQYLSKACEL--NSGNGCRFLGDFYENGKYVKKDLRKAA   81 (138)
T ss_dssp             HHHHHHHHHHHHHHHTTCTTHH----HHHHTCTTS-CHHHHHHHHHHHHHT--TCHHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             cCHHHHHHHHHHHHcCCCHhhh----HHHHHHcCC-CHHHHHHHHHHHHcC--CCHHHHHHHHHHHHcCCCCCccHHHHH
Confidence            3345555555554443333222    444444433 788899999999987  335556666666655    67999999


Q ss_pred             HHHHHHHh
Q 008442          238 SIYKRCYS  245 (565)
Q Consensus       238 ~i~~~al~  245 (565)
                      ..|+++..
T Consensus        82 ~~~~~Aa~   89 (138)
T 1klx_A           82 QYYSKACG   89 (138)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHc
Confidence            99999986

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=86.15  E-value=7.9  Score=31.58  Aligned_cols=57  Identities=7%  Similarity=0.127  Sum_probs=42.8

Q ss_pred             HHHHHHHH---cCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHH----cCChHHHHHHHHHHHh
Q 008442          187 YWAHLEQS---MGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE----LDHINEARSIYKRCYS  245 (565)
Q Consensus       187 ~~a~~e~~---~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~----~~~~~~aR~i~~~al~  245 (565)
                      .++.++..   ..+|+++|...|+++...  .+...+.....+...    .++++.|...|++|..
T Consensus        62 ~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~--g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~  125 (138)
T 1klx_A           62 FLGDFYENGKYVKKDLRKAAQYYSKACGL--NDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACR  125 (138)
T ss_dssp             HHHHHHHHCSSSCCCHHHHHHHHHHHHHT--TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCCccHHHHHHHHHHHHcC--CCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHH
Confidence            44455544   134999999999999987  335566666676666    7899999999999986

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=86.12  E-value=8.4  Score=29.59  Aligned_cols=57  Identities=9%  Similarity=0.008  Sum_probs=47.3

Q ss_pred             HHHHHHHcCCChHHHHHHHHHHHHHc-------cchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          188 WAHLEQSMGKDMVSARGVWERLLKIS-------GAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       188 ~a~~e~~~~~~~~~ar~i~e~~l~~~-------~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      .+......+ ++..|..-|+.+++..       .....++..++......|+++.|..++++++.
T Consensus        11 lG~~~~~~~-~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~   74 (104)
T 2v5f_A           11 LGKVAYTEA-DYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE   74 (104)
T ss_dssp             HHHHHHHTT-CHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcc-chHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHh
Confidence            344555666 9999999999999863       23578899999989999999999999999986

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=86.00  E-value=6.1  Score=39.81  Aligned_cols=88  Identities=8%  Similarity=0.071  Sum_probs=63.5

Q ss_pred             ChHHHHHHHHHHHHH-----ccch---HHHHHHHHHHHHHcCChHHHHHHHHHHHhc---ccCCCCcHHHHHHHHH---H
Q 008442          198 DMVSARGVWERLLKI-----SGAM---LEAWQSYISMEIELDHINEARSIYKRCYSK---RFTGTGSEDICHAWLR---F  263 (565)
Q Consensus       198 ~~~~ar~i~e~~l~~-----~~~~---~~lw~~yi~~e~~~~~~~~aR~i~~~al~~---~~~~~~~~~i~~~~~~---f  263 (565)
                      ++++|..+|+++|..     .+++   .......+..+...|+++.|..+|+++|..   .+..+.| ++...+..   .
T Consensus       313 ~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp-~~a~~l~nLa~~  391 (433)
T 3qww_A          313 SPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSL-NVASMWLKLGRL  391 (433)
T ss_dssp             CHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCH-HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCCh-HHHHHHHHHHHH
Confidence            789999999999986     2333   456666777788899999999999999854   3344444 45444544   4


Q ss_pred             HHHhCCHHHHHHHHHHHhhHHHH
Q 008442          264 EREYGTLEDFDHSVQKVTPRLEE  286 (565)
Q Consensus       264 E~~~G~~~~~~~~~~k~~~~~~~  286 (565)
                      -...|..+.+...+++++..+..
T Consensus       392 ~~~qg~~~eA~~~~~~Al~i~~~  414 (433)
T 3qww_A          392 YMGLENKAAGEKALKKAIAIMEV  414 (433)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHhccCHHHHHHHHHHHHHHHHH
Confidence            44568888888888888766554

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=82.00  E-value=13  Score=31.12  Aligned_cols=49  Identities=12%  Similarity=0.007  Sum_probs=39.8

Q ss_pred             ChHHHHHHHHHHHHHc-c-chHHHHHHHHHHHHHcCChHHHHHHHHHHHhc
Q 008442          198 DMVSARGVWERLLKIS-G-AMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       198 ~~~~ar~i~e~~l~~~-~-~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~  246 (565)
                      ++.++..+++.+++.. | ...+.+...+-...+.+++++|+..++++|..
T Consensus        50 ~~~~gI~lLe~ll~~~~p~~~rd~lY~LAv~~~kl~~Y~~A~~y~~~lL~i  100 (152)
T 1pc2_A           50 DIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQT  100 (152)
T ss_dssp             HHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            5668999999999986 6 44666666666668899999999999999973

---

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	565
d2onda1	308	a.118.8.7 (A:242-549) Cleavage stimulation factor	1e-20
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	6e-15
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	8e-13
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-11
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-10
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	6e-10
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	6e-10
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	8e-10
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-06
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-09
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-09
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-09
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-09
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	4e-09
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	5e-09
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	6e-09
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	7e-09
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	7e-09
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-09
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-08
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-08
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-08
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-08
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-08
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	6e-08
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	7e-08
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-07
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-07
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-07
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-07
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-07
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-07
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	3e-07
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-07
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	6e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	6e-07
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	7e-07
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	7e-07
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	8e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	9e-07
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-06
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-06
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-06
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	5e-06
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	9e-06
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-05
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	3e-05
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	4e-05
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-04
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-04
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.002
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	0.003

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 308

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 90.8 bits (224), Expect = 1e-20
 Identities = 51/291 (17%), Positives = 101/291 (34%), Gaps = 46/291 (15%)

Query: 19  DSEKFQQYMIYLKYEQS--------SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKT 70
           ++++   +  Y+++E+S        +    RV   YE+ +       D+W +  QYL+++
Sbjct: 4   EAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVLGHHPDIWYEAAQYLEQS 63

Query: 71  LKV-------------GNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFE 117
            K+              +   ++Y RA         L   +    E SR   E++ +++ 
Sbjct: 64  SKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYN 123

Query: 118 KSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKN 177
           + L             +                    + ++   E  +       +  ++
Sbjct: 124 RLLAIEDIDPTLVYIQY--------------------MKFARRAEGIKSGRMIFKKARED 163

Query: 178 TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEAR 237
                 +Y   A +E    KD   A  ++E  LK  G + E   +YI     L+  N  R
Sbjct: 164 ARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTR 223

Query: 238 SIYKRCYSK-RFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEEL 287
            +++R  +        S +I   +L FE   G L     S+ KV  R    
Sbjct: 224 VLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLA----SILKVEKRRFTA 270

>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 = 68.5 bits (167), Expect = 6e-15
 Identities = 28/100 (28%), Positives = 51/100 (51%)

Query: 374 KQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           K P+++ V   +    D  T F   +  +    DL  FFS VG V  +RI+ D+ + +S+
Sbjct: 1   KSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 60

Query: 434 GLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRK 473
           G+AYV+F + + +  A+    Q  LG  + +  S  ++ +
Sbjct: 61  GIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNR 100

>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 = 61.5 bits (149), Expect = 8e-13
 Identities = 19/73 (26%), Positives = 35/73 (47%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
           C  F+  ++ + T E LR +F   G V    ++ D  T +SRG  +V F+D   +   +A
Sbjct: 1   CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

Query: 452 KNKQMFLGKKLSI 464
           +++     K +  
Sbjct: 61  QSRHELDSKTIDP 73

>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 = 59.3 bits (143), Expect = 1e-11
 Identities = 21/107 (19%), Positives = 48/107 (44%), Gaps = 8/107 (7%)

Query: 365 KQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRIL 424
           ++T+E  P ++  ++    R          F+  ++ + T E LR ++   G ++   ++
Sbjct: 2   EKTLETVPLERKKREKEQFRK--------LFIGGLSFETTEESLRNYYEQWGKLTDCVVM 53

Query: 425 HDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQ 471
            D  + +SRG  +V F     + AA+A       G+ +   R+  ++
Sbjct: 54  RDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVARE 100

>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 = 55.3 bits (133), Expect = 2e-10
 Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 3/87 (3%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHD-KFTGKSRGLAYVDFIDDEHLAA 448
                 + NI  +A   ++R  FS  G + ++R+      TG  RG  +VDFI  +    
Sbjct: 7   TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKK 66

Query: 449 AVAK--NKQMFLGKKLSIARSNPKQRK 473
           A     +     G++L +  ++ +   
Sbjct: 67  AFNALCHSTHLYGRRLVLEWADSEVTV 93

>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 = 53.8 bits (129), Expect = 6e-10
 Identities = 22/89 (24%), Positives = 38/89 (42%), Gaps = 1/89 (1%)

Query: 386 KGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEH 445
           +         +  +  K T +DL+ +FS  G V  +++  D  TG S+G  +V F + E 
Sbjct: 3   RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 62

Query: 446 LAAAVAKNKQMFLGKKLSIARSNPKQRKD 474
               +   + M  G+       N KQ +D
Sbjct: 63  QVKVM-SQRHMIDGRWCDCKLPNSKQSQD 90

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 6e-10
 Identities = 23/89 (25%), Positives = 42/89 (47%), Gaps = 3/89 (3%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
            TAFL N+    T E ++ FF  +   +           + +G  Y +F D + L +A++
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 452 KNKQMFLGKKLSIARSNPKQRKD---SSG 477
            N++    K++ +  ++  Q KD   SSG
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKDSGPSSG 104

>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 = 56.2 bits (134), Expect = 8e-10
 Identities = 22/82 (26%), Positives = 36/82 (43%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  I        LR +F   G +  I I+ D+ +GK RG A+V F D + +   V +  
Sbjct: 101 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY 160

Query: 455 QMFLGKKLSIARSNPKQRKDSS 476
               G    + ++  KQ   S+
Sbjct: 161 HTVNGHNCEVRKALSKQEMASA 182

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.9 bits (110), Expect = 1e-06
 Identities = 18/79 (22%), Positives = 36/79 (45%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
             F+  ++ + T E LR  F   G ++   ++ D  T +SRG  +V +   E + AA+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 453 NKQMFLGKKLSIARSNPKQ 471
                 G+ +   R+  ++
Sbjct: 68  RPHKVDGRVVEPKRAVSRE 86

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.6 bits (128), Expect = 1e-09
 Identities = 29/92 (31%), Positives = 47/92 (51%), Gaps = 1/92 (1%)

Query: 387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHL 446
           G +     F+ N++  ++ EDL + FS  G +S +    D  T K +G A+V F+  EH 
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 447 AAAVAK-NKQMFLGKKLSIARSNPKQRKDSSG 477
             A A+ + Q+F G+ L +  S  K+    SG
Sbjct: 64  VKAYAEVDGQVFQGRMLHVLPSTIKKEASQSG 95

>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 = 52.7 bits (126), Expect = 2e-09
 Identities = 16/84 (19%), Positives = 39/84 (46%), Gaps = 1/84 (1%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
            + T ++  ++ K +   L   F   G V +  +  D+ TG+ +G  +V+F+ +E    A
Sbjct: 8   QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 67

Query: 450 VAK-NKQMFLGKKLSIARSNPKQR 472
           +   +     GK + + +++   +
Sbjct: 68  IKIMDMIKLYGKPIRVNKASAHNK 91

>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 = 51.8 bits (124), Expect = 2e-09
 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           ++ +++   T   L   FS  G + SIR+  D  T +S G AYV+F        A+   N
Sbjct: 4   YVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMN 63

Query: 454 KQMFLGKKLSIARSN 468
             +  GK + I  S 
Sbjct: 64  FDVIKGKPVRIMWSQ 78

>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 = 52.4 bits (125), Expect = 2e-09
 Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 1/87 (1%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAA 448
           T +   ++  +  +   + L   F   G ++ I+I  D  T K RG A+V+F   E  AA
Sbjct: 3   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62

Query: 449 AVAK-NKQMFLGKKLSIARSNPKQRKD 474
           A+   N+    G+ + +  + P + K+
Sbjct: 63  AIDNMNESELFGRTIRVNLAKPMRIKE 89

>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 = 51.6 bits (123), Expect = 4e-09
 Identities = 18/72 (25%), Positives = 33/72 (45%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  ++ + T E LR  F   G ++   ++ D  T +SRG  +V +   E + AA+    
Sbjct: 10  FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 69

Query: 455 QMFLGKKLSIAR 466
               G+ +   R
Sbjct: 70  HKVDGRVVEPKR 81

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 4e-09
 Identities = 16/79 (20%), Positives = 36/79 (45%), Gaps = 1/79 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+  +      + ++   +  G + +  ++ D  TG S+G A+ +++D      A+A  N
Sbjct: 5   FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 64

Query: 454 KQMFLGKKLSIARSNPKQR 472
                 KKL + R++   +
Sbjct: 65  GMQLGDKKLLVQRASVGAK 83

>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 = 50.9 bits (121), Expect = 5e-09
 Identities = 21/81 (25%), Positives = 42/81 (51%), Gaps = 2/81 (2%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGV-SSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV-AK 452
           F+ N++ +   + L   FS  G +  + +I+ D  TG S+G A+++F   +   AA+ A 
Sbjct: 2   FIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAM 61

Query: 453 NKQMFLGKKLSIARSNPKQRK 473
           N Q    + ++++ +  K  K
Sbjct: 62  NGQYLCNRPITVSYAFKKDSK 82

>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 = 51.9 bits (124), Expect = 6e-09
 Identities = 19/100 (19%), Positives = 36/100 (36%), Gaps = 4/100 (4%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
              ++ N+  K T E++   F   G +  I       T ++RG AYV + D      A  
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDAKNACD 64

Query: 452 K-NKQMFLGKKLSIARSNPKQRKDSSGERAPTEQAQSHQQ 490
             +      + L +   N  +       +   EQ +  ++
Sbjct: 65  HLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKE 104

>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 = 50.3 bits (120), Expect = 7e-09
 Identities = 18/70 (25%), Positives = 30/70 (42%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  ++     E +R +F   G V SI +  D  T K RG  ++ F ++E +   + K  
Sbjct: 3   FVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKY 62

Query: 455 QMFLGKKLSI 464
                 K  I
Sbjct: 63  HNVGLSKCEI 72

>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 = 50.8 bits (121), Expect = 7e-09
 Identities = 16/83 (19%), Positives = 29/83 (34%), Gaps = 1/83 (1%)

Query: 383 GRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFID 442
           G + G        + N+    + +++  FF     +     L     G   G A V F  
Sbjct: 1   GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 60

Query: 443 DEHLAAAVAK-NKQMFLGKKLSI 464
            +   AAV   N +    +K+ +
Sbjct: 61  RDEATAAVIDLNDRPIGSRKVKL 83

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.4 bits (120), Expect = 8e-09
 Identities = 20/72 (27%), Positives = 35/72 (48%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  ++   T +DL+ +FS  G V    +  D  TG+SRG  +V F + E +   + + +
Sbjct: 3   FIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKE 62

Query: 455 QMFLGKKLSIAR 466
               GK +   R
Sbjct: 63  HKLNGKVIDPKR 74

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.7 bits (118), Expect = 2e-08
 Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 5/82 (6%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRIL-----HDKFTGKSRGLAYVDFIDDEHLAAA 449
           ++ NI    T E +  FF+    +  +              + +  A+++F   +    A
Sbjct: 5   YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 64

Query: 450 VAKNKQMFLGKKLSIARSNPKQ 471
           +A +  +F G+ L I R +  Q
Sbjct: 65  MAFDGIIFQGQSLKIRRPHDYQ 86

>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 = 49.7 bits (118), Expect = 2e-08
 Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 1/82 (1%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           D  T  ++N++      DL+  F   G +S I +  DK TG+S+G A++ F   E  A A
Sbjct: 7   DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 66

Query: 450 VAK-NKQMFLGKKLSIARSNPK 470
           +A  +   +    L++  + P 
Sbjct: 67  IAGVSGFGYDHLILNVEWAKPS 88

>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 = 49.7 bits (118), Expect = 2e-08
 Identities = 17/88 (19%), Positives = 32/88 (36%), Gaps = 5/88 (5%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSS--IRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           C  F+  I      E++    + V       I         K+RG A+V++      A A
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 450 VAK---NKQMFLGKKLSIARSNPKQRKD 474
             K    +    G ++++  + P+   D
Sbjct: 62  RRKLMPGRIQLWGHQIAVDWAEPEIDVD 89

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.9 bits (116), Expect = 3e-08
 Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 4/82 (4%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDK---FTGKSRGLAYVDFIDDEHLAAAVA 451
           F+ N+N   T E L+  FS VG + S  I   K       S G  +V++   E    A+ 
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 452 K-NKQMFLGKKLSIARSNPKQR 472
           +       G KL +  S    +
Sbjct: 62  QLQGHTVDGHKLEVRISERATK 83

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 48.5 bits (115), Expect = 4e-08
 Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 1/79 (1%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
               ++ +    T  +L   F  +G +++ RI+ D  TG S G A+VDF  +     A+ 
Sbjct: 3   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

Query: 452 K-NKQMFLGKKLSIARSNP 469
             N      K+L ++ + P
Sbjct: 63  VLNGITVRNKRLKVSYARP 81

>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 = 48.0 bits (114), Expect = 6e-08
 Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 1/77 (1%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAA 448
             +   +++N+    T + L   F   G +    IL DK TG+ RG+A+V +   E    
Sbjct: 4   IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 63

Query: 449 AVAK-NKQMFLGKKLSI 464
           A++  N  +  G    +
Sbjct: 64  AISALNNVIPEGGSQPL 80

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 47.9 bits (113), Expect = 7e-08
 Identities = 23/80 (28%), Positives = 31/80 (38%), Gaps = 1/80 (1%)

Query: 391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAV 450
           ECT +++N     T  ++R    D+  V+    L       SR  AY+D    E     V
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 451 AK-NKQMFLGKKLSIARSNP 469
            K N     G  L    SNP
Sbjct: 61  EKLNGLKIEGYTLVTKVSNP 80

>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 = 47.6 bits (113), Expect = 1e-07
 Identities = 17/91 (18%), Positives = 33/91 (36%), Gaps = 3/91 (3%)

Query: 386 KGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEH 445
           K     CT ++ N++   T E +   FS  G +  I +  DK    + G  +V++     
Sbjct: 2   KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRAD 61

Query: 446 LAAAVAK-NKQMFLGKKLSI--ARSNPKQRK 473
              A+   N      + +         + R+
Sbjct: 62  AENAMRYINGTRLDDRIIRTDWDAGFKEGRQ 92

>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 = 47.4 bits (112), Expect = 1e-07
 Identities = 19/88 (21%), Positives = 42/88 (47%), Gaps = 1/88 (1%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAA 448
           +DE   F+  ++     + L + FS  G +S + ++ D+ T +SRG  +V F + +    
Sbjct: 3   SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 62

Query: 449 AVAK-NKQMFLGKKLSIARSNPKQRKDS 475
           A+   N +   G+++ + ++       S
Sbjct: 63  AMMAMNGKSVDGRQIRVDQAGKSSDNRS 90

>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 = 47.4 bits (112), Expect = 1e-07
 Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
           C   +  ++L  T  DLR  FS  G ++ + I++D+ + +SRG A+V F + +    A  
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 452 K-NKQMFLGKKLSI 464
           + N     G+++ +
Sbjct: 70  RANGMELDGRRIRV 83

>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 = 47.6 bits (113), Expect = 1e-07
 Identities = 22/100 (22%), Positives = 42/100 (42%), Gaps = 13/100 (13%)

Query: 383 GRTKGFTDECTAFLSNINLKATYE-DLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFI 441
           G+T   +     F+ N+N     + D+   FS  G +    +          G A+V ++
Sbjct: 7   GKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAFVQYV 58

Query: 442 DDEHLAAAV-AKNKQMFLGKKLSIARSNPKQRK---DSSG 477
           ++ +  AAV  ++ +M  G+ L I  +   +      SSG
Sbjct: 59  NERNARAAVAGEDGRMIAGQVLDINLAAEPKVNRSGPSSG 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 = 46.6 bits (110), Expect = 2e-07
 Identities = 18/93 (19%), Positives = 40/93 (43%), Gaps = 3/93 (3%)

Query: 383 GRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFID 442
           G ++  +      +SNI  +    DLR+ F   G +  + I+ ++    S+G  +V F +
Sbjct: 3   GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFEN 60

Query: 443 DEHLAAAVAK-NKQMFLGKKLSIARSNPKQRKD 474
                 A  K +  +  G+K+ +  +  +   +
Sbjct: 61  SADADRAREKLHGTVVEGRKIEVNNATARVMTN 93

>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 = 46.3 bits (109), Expect = 2e-07
 Identities = 15/72 (20%), Positives = 32/72 (44%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  +++  T ED++ +F   G V    ++ DK T + RG  +V F  ++ +      + 
Sbjct: 3   FVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHF 62

Query: 455 QMFLGKKLSIAR 466
                K +   +
Sbjct: 63  HEINNKMVECKK 74

>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 = 46.6 bits (110), Expect = 3e-07
 Identities = 22/91 (24%), Positives = 36/91 (39%), Gaps = 6/91 (6%)

Query: 387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHL 446
           G +     F+       T ++LR FFS  G V  + I            A+V F DD+  
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQI- 54

Query: 447 AAAVAKNKQMFLGKKLSIARSNPKQRKDSSG 477
           A ++     +  G  + I+ + PK   +S  
Sbjct: 55  AQSLCGEDLIIKGISVHISNAEPKHNSNSGP 85

>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 = 46.6 bits (110), Expect = 3e-07
 Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 4/82 (4%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
           ++C  ++ N+      +D+   F   G +  I + + +        A+V+F D      A
Sbjct: 13  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG---PPFAFVEFEDPRDAEDA 69

Query: 450 VAK-NKQMFLGKKLSIARSNPK 470
           V   +   + G +L +      
Sbjct: 70  VYGRDGYDYDGYRLRVEFPRSG 91

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 46.6 bits (110), Expect = 3e-07
 Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 6/90 (6%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFI 441
           P  +K      T    N++   T ++L+  F D      + I      GKS+G+AY++F 
Sbjct: 7   PCTSKKVRAARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFK 61

Query: 442 DDEHLAAAV-AKNKQMFLGKKLSIARSNPK 470
            +      +  K      G+ +S+  +  K
Sbjct: 62  SEADAEKNLEEKQGAEIDGRSVSLYYTGEK 91

>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 = 45.9 bits (108), Expect = 6e-07
 Identities = 27/96 (28%), Positives = 41/96 (42%), Gaps = 9/96 (9%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILH--------DKFTGKSRGLAYVDF 440
           +D    ++  +N   T +DL  FF   G V   +           DK TGK +G A V +
Sbjct: 6   SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSY 65

Query: 441 IDDEHLAAAVAK-NKQMFLGKKLSIARSNPKQRKDS 475
            D     AAV   + + F G KL ++ +  K   +S
Sbjct: 66  EDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 101

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 6e-07
 Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
            ++ +    T E+ R  F  +G + S +++ DK TG+S G  +V++ID +    A+   N
Sbjct: 6   IVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLN 65

Query: 454 KQMFLGKKLSIARSNP 469
                 K + ++ + P
Sbjct: 66  GLRLQTKTIKVSYARP 81

>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 = 45.4 bits (107), Expect = 7e-07
 Identities = 18/80 (22%), Positives = 37/80 (46%), Gaps = 3/80 (3%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
           F+ N++     + L   FS  G + S +++ D+    S+G  +V F   E    A+ K N
Sbjct: 12  FIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMN 69

Query: 454 KQMFLGKKLSIARSNPKQRK 473
             +   +K+ + R   ++ +
Sbjct: 70  GMLLNDRKVFVGRFKSRKER 89

>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 = 45.1 bits (106), Expect = 7e-07
 Identities = 19/73 (26%), Positives = 32/73 (43%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNK 454
           F+  I        LR +F   G +  I I+ D+ +GK RG A+V F D + +   V +  
Sbjct: 6   FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY 65

Query: 455 QMFLGKKLSIARS 467
               G    + ++
Sbjct: 66  HTVNGHNCEVRKA 78

>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 = 45.0 bits (106), Expect = 8e-07
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
            +   ++S +    T ++L + FS  G + + RIL D+ TG SRG+ ++ F        A
Sbjct: 5   RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 64

Query: 450 VAK-NKQMFLGKKLSI 464
           +   N Q   G    I
Sbjct: 65  IKGLNGQKPSGATEPI 80

>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 = 44.7 bits (105), Expect = 9e-07
 Identities = 12/83 (14%), Positives = 33/83 (39%), Gaps = 2/83 (2%)

Query: 390 DECTAFLSNINLKATYEDLRR--FFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLA 447
           +     + N++ +   E+L R  F               K    +   A++ F + +   
Sbjct: 3   EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 62

Query: 448 AAVAKNKQMFLGKKLSIARSNPK 470
            A+  N+ +   +++S++ ++ K
Sbjct: 63  RALQMNRSLLGNREISVSLADKK 85

>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 = 44.8 bits (105), Expect = 1e-06
 Identities = 17/91 (18%), Positives = 35/91 (38%), Gaps = 7/91 (7%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAA 448
           T+  T F+ N++  +  E L       G +  +R++    T  S+G A+  F+  E    
Sbjct: 6   TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 65

Query: 449 AVAK-------NKQMFLGKKLSIARSNPKQR 472
            +A              G++L +  +  +  
Sbjct: 66  CLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 96

>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 = 44.7 bits (105), Expect = 1e-06
 Identities = 19/83 (22%), Positives = 41/83 (49%), Gaps = 1/83 (1%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAA 448
            +    F+++I+ +A  ++++  F D G + +I +  D+ TG S+G A V++   +   A
Sbjct: 5   VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 64

Query: 449 AVAK-NKQMFLGKKLSIARSNPK 470
           A    N    +G+ + +     K
Sbjct: 65  AKEALNGAEIMGQTIQVDWCFVK 87

>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 = 44.8 bits (105), Expect = 1e-06
 Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 1/83 (1%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA 451
              +L N++ + T  DL   F+         I     TG+ RG A++ F + E    A+ 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 452 K-NKQMFLGKKLSIARSNPKQRK 473
             N     GK L I     K+++
Sbjct: 79  LVNGYKLYGKILVIEFGKNKKQR 101

>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 = 44.2 bits (104), Expect = 2e-06
 Identities = 18/82 (21%), Positives = 29/82 (35%), Gaps = 7/82 (8%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
             CT +   I    T + +R+ FS  G +  IR+  +K        ++V F   E  A A
Sbjct: 17  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGY------SFVRFSTHESAAHA 70

Query: 450 VAK-NKQMFLGKKLSIARSNPK 470
           +   N     G  +        
Sbjct: 71  IVSVNGTTIEGHVVKCYWGKES 92

>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 = 43.4 bits (102), Expect = 2e-06
 Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 2/71 (2%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
            +SN++   +  D++  F++ G +    + +D  +G+S G A V F        A+ + N
Sbjct: 4   LVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQYN 62

Query: 454 KQMFLGKKLSI 464
                G+ ++I
Sbjct: 63  GVPLDGRPMNI 73

>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 = 43.2 bits (101), Expect = 5e-06
 Identities = 31/93 (33%), Positives = 53/93 (56%), Gaps = 4/93 (4%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
           + F+ NI  +AT E L+  FS+VG V S R+++D+ TGK +G  + ++ D E   +A+  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 453 -NKQMFLGKKLSIARSNPKQRKD---SSGERAP 481
            N + F G+ L +  +  ++ K+   S G  AP
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102

>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 = 42.0 bits (98), Expect = 9e-06
 Identities = 17/85 (20%), Positives = 39/85 (45%), Gaps = 3/85 (3%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAA 449
              T ++ N++   T   + + FS +G   S +++ +     +    +V+F +    AAA
Sbjct: 7   QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAAA 64

Query: 450 V-AKNKQMFLGKKLSIARSNPKQRK 473
           + A N +  LGK++ +  +     +
Sbjct: 65  LAAMNGRKILGKEVKVNWATTPSSQ 89

>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 = 40.4 bits (94), Expect = 3e-05
 Identities = 18/81 (22%), Positives = 31/81 (38%), Gaps = 8/81 (9%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-- 452
           ++ N++   T +DLR+ F D                   G A+VD+ D      A+    
Sbjct: 5   YIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFVDYPDQNWAIRAIETLS 58

Query: 453 NKQMFLGKKLSIARSNPKQRK 473
            K    GK + +  S  K+ +
Sbjct: 59  GKVELHGKIMEVDYSVSKKLR 79

>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 = 41.0 bits (95), Expect = 3e-05
 Identities = 17/101 (16%), Positives = 36/101 (35%)

Query: 374 KQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           K P                  +L  +  +A  + +  FF  +  V     +     GK+ 
Sbjct: 1   KSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKAT 60

Query: 434 GLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQRKD 474
           G  +V+F ++    AA+ ++KQ    + + +     K   +
Sbjct: 61  GEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITKKGMLE 101

>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 = 40.3 bits (93), Expect = 4e-05
 Identities = 17/82 (20%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAA 448
           T     F+ N+N   +  +L+   S++   + + ++  + TG +R   YVDF   E L  
Sbjct: 11  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEK 69

Query: 449 AVAKNKQMFLGKKLSIARSNPK 470
           A+        G ++ + +   +
Sbjct: 70  ALELTGLKVFGNEIKLEKPKGR 91

>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 = 38.9 bits (90), Expect = 1e-04
 Identities = 15/81 (18%), Positives = 35/81 (43%), Gaps = 7/81 (8%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK 452
             ++ N+ L  + E + + F+++   +  R+       K R  A+V F + E    A+  
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEAMKA 63

Query: 453 -NKQMFLGKKLSIARSNPKQR 472
            N ++  G  + +  + P  +
Sbjct: 64  LNGKVLDGSPIEVTLAKPVDK 84

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 2e-04
 Identities = 15/76 (19%), Positives = 28/76 (36%), Gaps = 1/76 (1%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAA 448
               + ++      AT +D++ +  D G V +I++         +G  +V F   E    
Sbjct: 4   VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQM-RRTLHKAFKGSIFVVFDSIESAKK 62

Query: 449 AVAKNKQMFLGKKLSI 464
            V    Q +    L I
Sbjct: 63  FVETPGQKYKETDLLI 78

>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 = 37.7 bits (87), Expect = 2e-04
 Identities = 16/72 (22%), Positives = 24/72 (33%), Gaps = 7/72 (9%)

Query: 400 NLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NKQMFL 458
               T   LR  FS  G +       D      R  A+V +   E    AVA+ N     
Sbjct: 12  GEDMTPTLLRGAFSPFGNI------IDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVE 65

Query: 459 GKKLSIARSNPK 470
             +L +  +  +
Sbjct: 66  SVQLKVNIARKQ 77

>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 = 37.7 bits (87), Expect = 3e-04
 Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 8/84 (9%)

Query: 392 CTAFLSNINLKATYEDLRR----FFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLA 447
            T +++N+N K   ++L++     FS  G +  I +         RG A+V F +     
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK---MRGQAFVIFKEVSSAT 60

Query: 448 AAVAK-NKQMFLGKKLSIARSNPK 470
            A+       F  K + I  +   
Sbjct: 61  NALRSMQGFPFYDKPMRIQYAKTD 84

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 16/77 (20%), Positives = 26/77 (33%), Gaps = 3/77 (3%)

Query: 397 SNINLKATYEDLRRFFSDVGGVSSIRIL--HDKFTGKSRGLAYVDFIDDEHLAAAVAK-N 453
            +   +   ED+R   S  G V SI I    D       G  +V+F        A+    
Sbjct: 20  DDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLT 79

Query: 454 KQMFLGKKLSIARSNPK 470
            + F  + +     +P 
Sbjct: 80  GRKFANRVVVTKYCDPD 96

>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 = 35.3 bits (81), Expect = 0.003
 Identities = 14/69 (20%), Positives = 26/69 (37%), Gaps = 5/69 (7%)

Query: 405 YEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK-NKQMFLGKKLS 463
            EDLR   S  G +  + +          G+A V F D E     +   + + F G++++
Sbjct: 33  REDLRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 88

Query: 464 IARSNPKQR 472
               +    
Sbjct: 89  AQAWDGTTD 97

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	565
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.96
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.87
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.8
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.8
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.8
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.8
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.8
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.8
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.8
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.8
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.8
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.79
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.79
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.79
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.78
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.78
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.78
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.78
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.78
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.78
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.77
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.77
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.77
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.77
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.76
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.76
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.76
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.76
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.76
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.75
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.75
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.75
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.74
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.74
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.74
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.73
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.73
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.73
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.72
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.72
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.71
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.71
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.71
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.7
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.7
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.7
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.69
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.69
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.68
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.68
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.67
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.67
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.67
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.66
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.66
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.66
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.64
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.64
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.64
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.64
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.64
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.64
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.63
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.63
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.63
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.62
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.6
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.6
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.6
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.58
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.56
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.56
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.56
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.56
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.55
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.54
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.53
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.53
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.5
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.47
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	99.39
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.36
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.35
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.34
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.3
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.28
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.28
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.27
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.26
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.25
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.99
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.93
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.91
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	98.66
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.64
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.6
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	98.37
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.08
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	97.99
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.89
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.86
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.82
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.72
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.59
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.5
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	97.44
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.26
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.23
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.22
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	97.14
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.05
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	96.93
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	96.88
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	96.81
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	96.78
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	96.69
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	96.66
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.66
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.65
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	96.64
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	96.63
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	96.55
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	96.53
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.42
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	96.41
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.19
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	96.13
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	95.96
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	95.87
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	95.84
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	95.7
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	95.47
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	95.4
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	95.24
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	94.64
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	94.61
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	91.94
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	89.3
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	88.35
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	85.87

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.96  E-value=1.6e-28  Score=241.34  Aligned_cols=239  Identities=21%  Similarity=0.292  Sum_probs=191.5

Q ss_pred             hHhHHHHHHHHHHHHhcC--------CchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcc-------------hhhHHH
Q 008442           20 SEKFQQYMIYLKYEQSSG--------DPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLK-------------VGNVVR   78 (565)
Q Consensus        20 ~~~~~~W~~yi~~e~~~~--------~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~-------------~~~~~~   78 (565)
                      .+.+++|+.||+||+.++        ..++|..+|||||..+|.+++||+.|+.|+....+             ..+.++
T Consensus         5 ~~~~~~W~~yi~~E~~~~~~~~~~~~~~~Rv~~vyerAl~~~~~~~~lW~~y~~~~~~~~~~~~~~~~~~~~~~~~~~a~   84 (308)
T d2onda1           5 AQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAA   84 (308)
T ss_dssp             HHHHHHHHHHHHHHHTCTTCCCCHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCcccccccchhHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCchHHHHHHHhhcccchHHHH
Confidence            456789999999998754        24678999999999999999999999999876442             245689


Q ss_pred             HHHHHHHHc-CCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhH
Q 008442           79 DVYSRATKN-CPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDY  157 (565)
Q Consensus        79 ~v~erAl~~-~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~  157 (565)
                      .+|+||+.. +|.+..||..|+. ++...+..+.++.+|++++...+..   ...+|..++.++++..          ++
T Consensus        85 ~i~~ral~~~~p~~~~l~~~ya~-~~~~~~~~~~a~~i~~~~l~~~~~~---~~~~w~~~~~~~~~~~----------~~  150 (308)
T d2onda1          85 NIYERAISTLLKKNMLLYFAYAD-YEESRMKYEKVHSIYNRLLAIEDID---PTLVYIQYMKFARRAE----------GI  150 (308)
T ss_dssp             HHHHHHHTTTTTTCHHHHHHHHH-HHHHTTCHHHHHHHHHHHHTSSSSC---THHHHHHHHHHHHHHH----------CH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHH-HHHhcccHHHHHHHHHHHHHHhcCC---hHHHHHHHHHHHHHcC----------Ch
Confidence            999999985 6888999999998 5555788999999999999865542   1234555555554322          34


Q ss_pred             HHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHH
Q 008442          158 SLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEAR  237 (565)
Q Consensus       158 ~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR  237 (565)
                      ..++.+|++++.       ..+....+|..++.++....++++.|+.+|++++..+|++..+|+.|++|+...|++++||
T Consensus       151 ~~ar~i~~~al~-------~~~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~p~~~~~w~~y~~~~~~~g~~~~aR  223 (308)
T d2onda1         151 KSGRMIFKKARE-------DARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTR  223 (308)
T ss_dssp             HHHHHHHHHHHT-------STTCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHH
T ss_pred             HHHHHHHHHHHH-------hCCCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHcCChHHHH
Confidence            455666665544       3455567888999998877669999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcccCCC--CcHHHHHHHHHHHHHhCCHHHHHHHHHHH
Q 008442          238 SIYKRCYSKRFTGT--GSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (565)
Q Consensus       238 ~i~~~al~~~~~~~--~~~~i~~~~~~fE~~~G~~~~~~~~~~k~  280 (565)
                      .+|++|+... +.+  ....||..|+.||..||+++++..+.+++
T Consensus       224 ~~fe~ai~~~-~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~  267 (308)
T d2onda1         224 VLFERVLTSG-SLPPEKSGEIWARFLAFESNIGDLASILKVEKRR  267 (308)
T ss_dssp             HHHHHHHHSS-SSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHH
T ss_pred             HHHHHHHHhC-CCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            9999999842 222  23579999999999999999998776554

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.87  E-value=4.4e-21  Score=187.69  Aligned_cols=215  Identities=15%  Similarity=0.183  Sum_probs=172.2

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcC--------------CchhHHHHHHHHHhc-CCCCHHHHHHHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSG--------------DPGRVQLLYERAITD-FPVSSDLWLDYTQYLD   68 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~--------------~~~~~~~lyERal~~-~p~~~~lW~~Y~~~l~   68 (565)
                      .+..||.+|...|.    ..++|..|+.|+...+              ..+.++.+|+|||.. +|.+..+|..|+.++.
T Consensus        35 v~~vyerAl~~~~~----~~~lW~~y~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~  110 (308)
T d2onda1          35 VMFAYEQCLLVLGH----HPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEE  110 (308)
T ss_dssp             HHHHHHHHHHHHTT----CHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCC----CHHHHHHHHHHHHHcCchHHHHHHHhhcccchHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            55689999999988    7899999999986543              236788999999975 7899999999999877


Q ss_pred             HhcchhhHHHHHHHHHHHcCCCC-HHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhc
Q 008442           69 KTLKVGNVVRDVYSRATKNCPWV-GELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILF  147 (565)
Q Consensus        69 ~~~~~~~~~~~v~erAl~~~p~~-~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~  147 (565)
                      ..+ ..+.++.+|++++...|.. ..+|..|+.++ ...+.++.++.+|++|+...+..+..++.......     +.  
T Consensus       111 ~~~-~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~-~~~~~~~~ar~i~~~al~~~~~~~~~~~~~a~~e~-----~~--  181 (308)
T d2onda1         111 SRM-KYEKVHSIYNRLLAIEDIDPTLVYIQYMKFA-RRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEY-----YC--  181 (308)
T ss_dssp             HTT-CHHHHHHHHHHHHTSSSSCTHHHHHHHHHHH-HHHHCHHHHHHHHHHHHTSTTCCTHHHHHHHHHHH-----HT--
T ss_pred             hcc-cHHHHHHHHHHHHHHhcCChHHHHHHHHHHH-HHcCChHHHHHHHHHHHHhCCCcHHHHHHHHHHHH-----Hh--
Confidence            555 6788999999999988865 56999999844 45677899999999999876655444433221100     00  


Q ss_pred             cccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccc----hHHHHHHH
Q 008442          148 SGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA----MLEAWQSY  223 (565)
Q Consensus       148 ~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~----~~~lw~~y  223 (565)
                            ..+.+.++.+|+.++..+       +....+|..|++++...+ ++++||.+|+++++.++.    ...+|..|
T Consensus       182 ------~~~~~~a~~i~e~~l~~~-------p~~~~~w~~y~~~~~~~g-~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~  247 (308)
T d2onda1         182 ------SKDKSVAFKIFELGLKKY-------GDIPEYVLAYIDYLSHLN-EDNNTRVLFERVLTSGSLPPEKSGEIWARF  247 (308)
T ss_dssp             ------SCCHHHHHHHHHHHHHHH-------TTCHHHHHHHHHHHHTTC-CHHHHHHHHHHHHHSSSSCGGGCHHHHHHH
T ss_pred             ------ccCHHHHHHHHHHHHHhh-------hhhHHHHHHHHHHHHHcC-ChHHHHHHHHHHHHhCCCChHHHHHHHHHH
Confidence                  014566778888777653       334679999999999999 999999999999998653    45799999


Q ss_pred             HHHHHHcCChHHHHHHHHHHHh
Q 008442          224 ISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       224 i~~e~~~~~~~~aR~i~~~al~  245 (565)
                      +.||..+|+++.++++++|+..
T Consensus       248 ~~fE~~~G~~~~~~~~~~r~~~  269 (308)
T d2onda1         248 LAFESNIGDLASILKVEKRRFT  269 (308)
T ss_dssp             HHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHH
Confidence            9999999999999999999977

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=4.3e-20  Score=143.80  Aligned_cols=83  Identities=24%  Similarity=0.379  Sum_probs=78.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      ..++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.++++|..|+. +|+..|+|++|.|.+|.
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            35799999999999999999999999999999999999899999999999999999999997 89999999999999998


Q ss_pred             CCCC
Q 008442          469 PKQR  472 (565)
Q Consensus       469 ~~~~  472 (565)
                      |++.
T Consensus        84 p~~~   87 (89)
T d2cqba1          84 PMRI   87 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8654

>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=99.80  E-value=9.6e-20  Score=142.90  Aligned_cols=83  Identities=19%  Similarity=0.441  Sum_probs=78.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||.++++++|+++|++||.|.+++|+.++.+|.++|||||+|.+.++|+.|+. +++..|+|++|.|.+|
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            345899999999999999999999999999999999998899999999999999999999997 8999999999999999


Q ss_pred             CCCC
Q 008442          468 NPKQ  471 (565)
Q Consensus       468 ~~~~  471 (565)
                      .++.
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            8865

>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=99.80  E-value=1.9e-19  Score=141.14  Aligned_cols=83  Identities=18%  Similarity=0.332  Sum_probs=78.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .+++||||+|||+++++++|+++|++||.|.+|.++.++.+|.++|||||+|.+.++|..|+. ||+..++|++|.|.++
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            457899999999999999999999999999999999999899999999999999999999997 8999999999999998


Q ss_pred             CCCC
Q 008442          468 NPKQ  471 (565)
Q Consensus       468 ~~~~  471 (565)
                      .+..
T Consensus        85 ~~~~   88 (93)
T d1h2vz_          85 AGFK   88 (93)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            6543

>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=99.80  E-value=9.3e-20  Score=141.46  Aligned_cols=83  Identities=23%  Similarity=0.361  Sum_probs=78.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ..++++|||+|||+++++++|+++|+.||.|.+|+++.++.+|+++|||||+|.+.++|+.|+. +||..++|++|.|++
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            3567899999999999999999999999999999999998899999999999999999999997 899999999999999


Q ss_pred             cCCC
Q 008442          467 SNPK  470 (565)
Q Consensus       467 a~~~  470 (565)
                      |.++
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            9765

>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=99.80  E-value=6.9e-20  Score=140.56  Aligned_cols=79  Identities=25%  Similarity=0.408  Sum_probs=76.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      +++|||+|||+++++++|+++|++||.|.+++++.++.+|.++|||||+|.++++|+.|+. ||+..+.|++|.|.+|+|
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            5789999999999999999999999999999999998899999999999999999999997 899999999999999986

>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=99.80  E-value=1.4e-19  Score=141.25  Aligned_cols=83  Identities=28%  Similarity=0.431  Sum_probs=78.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .+.++|||+|||.++++++|+++|+.||.|.++.|+.++.+|.++|||||+|.+.++|..|+. ++|..++|++|.|.+|
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            356899999999999999999999999999999999998899999999999999999999998 8999999999999999


Q ss_pred             CCCC
Q 008442          468 NPKQ  471 (565)
Q Consensus       468 ~~~~  471 (565)
                      +|+.
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            9864

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=2.3e-20  Score=140.52  Aligned_cols=76  Identities=25%  Similarity=0.552  Sum_probs=73.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      |+|||+|||+++++++|+++|++||.|.+++|+.|+.+|+++|||||+|.++++|++|+.++++.|+|++|.|..|
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            7899999999999999999999999999999999998999999999999999999999999999999999999876

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=2.8e-19  Score=138.85  Aligned_cols=82  Identities=26%  Similarity=0.424  Sum_probs=76.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecCC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~~  469 (565)
                      ..++|||+|||+++++++|+++|+.||.|.+++|+.|+.+|.++|||||+|.++++|.+||. +...|+|+.|.|.++.+
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~-~~~~l~Gr~i~v~~a~~   85 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCKLPNS   85 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEECCCT
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh-cCCccCCEEeEEEeCCC
Confidence            45789999999999999999999999999999999999899999999999999999999998 34579999999999988


Q ss_pred             CCC
Q 008442          470 KQR  472 (565)
Q Consensus       470 ~~~  472 (565)
                      +..
T Consensus        86 k~~   88 (90)
T d2cqga1          86 KQS   88 (90)
T ss_dssp             TCC
T ss_pred             CCC
Confidence            754

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=1.5e-19  Score=138.75  Aligned_cols=78  Identities=23%  Similarity=0.388  Sum_probs=74.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSN  468 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~  468 (565)
                      .++|||+|||+++++++|+++|+.||.|.+++|+.++.+|+++|||||+|.++++|++|+.++++.|+|++|.|..|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            469999999999999999999999999999999999989999999999999999999999999999999999999875

>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=99.79  E-value=2.3e-19  Score=137.71  Aligned_cols=80  Identities=24%  Similarity=0.490  Sum_probs=76.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      .++|||+|||+++++++|+++|++||.|.+++++.+..+|.++|||||+|.++++|+.|+. +||..+.|++|.|.+|+|
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            3689999999999999999999999999999999998899999999999999999999997 899999999999999987


Q ss_pred             C
Q 008442          470 K  470 (565)
Q Consensus       470 ~  470 (565)
                      .
T Consensus        82 s   82 (82)
T d1fxla1          82 S   82 (82)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.79  E-value=3.1e-19  Score=142.05  Aligned_cols=84  Identities=31%  Similarity=0.494  Sum_probs=78.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||+++++++|+++|.+||.|.+++|+.++.+|+++|||||+|.+.++|+.|+. ||+..|+|++|.|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            345789999999999999999999999999999999998899999999999999999999997 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .++..
T Consensus        86 ~~~~~   90 (99)
T d1whwa_          86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCCc
Confidence            88654

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.8e-19  Score=143.68  Aligned_cols=82  Identities=21%  Similarity=0.405  Sum_probs=78.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecCCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPK  470 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~~~  470 (565)
                      .++|||+|||+++++++|+++|++||.|..+.|+.++.++.++|||||+|.+.++|.+|+.+++..|+|++|.|.+|.|+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECccc
Confidence            47999999999999999999999999999999999998999999999999999999999999999999999999999987


Q ss_pred             CC
Q 008442          471 QR  472 (565)
Q Consensus       471 ~~  472 (565)
                      ..
T Consensus       100 e~  101 (103)
T d1x4ba1         100 EE  101 (103)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.79  E-value=3.6e-19  Score=142.18  Aligned_cols=84  Identities=21%  Similarity=0.288  Sum_probs=79.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .++++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.++++|..||. +|+..|.|++|.|.++
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            456789999999999999999999999999999999998899999999999999999999997 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .|+..
T Consensus        96 ~~k~~  100 (102)
T d2cpza1          96 RSKND  100 (102)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            88754

>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=99.78  E-value=3.4e-19  Score=135.60  Aligned_cols=76  Identities=29%  Similarity=0.398  Sum_probs=73.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       393 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      +|||+|||+++++++|+++|+.||.|.+++|+.++.+|+++|||||+|.++++|..|+. ++|..+.|++|+|.+|+
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            69999999999999999999999999999999999899999999999999999999997 89999999999999985

>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=99.78  E-value=8.2e-20  Score=145.21  Aligned_cols=82  Identities=30%  Similarity=0.526  Sum_probs=77.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecC
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSN  468 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~  468 (565)
                      .+.+||||+|||+++++++|+++|+.||.|.+++|+.++.+|+++|||||+|.+.++|.+|+.+||..|+|++|.|..+.
T Consensus        16 ~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          16 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHH
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECC
Confidence            34579999999999999999999999999999999999889999999999999999999999999999999999999986


Q ss_pred             CC
Q 008442          469 PK  470 (565)
Q Consensus       469 ~~  470 (565)
                      ++
T Consensus        96 ~~   97 (101)
T d2cq4a1          96 AE   97 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>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=99.78  E-value=2.1e-19  Score=138.30  Aligned_cols=80  Identities=20%  Similarity=0.364  Sum_probs=76.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCCC
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNPK  470 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~~  470 (565)
                      ++|||+|||+++++++|+++|+.||.|.+++|+.|+.||.++|||||+|.++++|..|+. +++..|+|++|.|.+|.+.
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            579999999999999999999999999999999999899999999999999999999998 8999999999999999875


Q ss_pred             C
Q 008442          471 Q  471 (565)
Q Consensus       471 ~  471 (565)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.78  E-value=8.7e-19  Score=148.98  Aligned_cols=84  Identities=25%  Similarity=0.359  Sum_probs=78.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||+++++++|+++|+.||.|.+|+|+.++.+|+++|||||+|.+.++|..||. +|+..|+|++|.|.++
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            345789999999999999999999999999999999999899999999999999999999997 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .+...
T Consensus       120 ~~~~~  124 (139)
T d1u6fa1         120 ASGHQ  124 (139)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87644

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=9e-19  Score=140.12  Aligned_cols=84  Identities=23%  Similarity=0.409  Sum_probs=76.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecC
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSN  468 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~  468 (565)
                      ...++|||+|||+.+++++|+++|++||.|.+++|+.++.+|+++|||||+|.+.++|.+|+...+..|+|++|.|.++.
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            34578999999999999999999999999999999999989999999999999999999999943347999999999987


Q ss_pred             CCCC
Q 008442          469 PKQR  472 (565)
Q Consensus       469 ~~~~  472 (565)
                      +...
T Consensus        88 ~~~~   91 (103)
T d2cqda1          88 LGAK   91 (103)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            6543

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=2.1e-19  Score=134.70  Aligned_cols=75  Identities=27%  Similarity=0.515  Sum_probs=71.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       393 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      +|||+|||+++++++|+++|++||.|.++.|+.++.+|+++|||||+|.++++|+.|+.+++..|+|++|.|..|
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            589999999999999999999999999999999998999999999999999999999999999999999999764

>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=99.77  E-value=2.8e-19  Score=136.71  Aligned_cols=79  Identities=28%  Similarity=0.339  Sum_probs=68.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      .|||||+|||+++++++|+++|+.||.|..+.++.+..+|.++|||||+|.++++|+.|+. +|+..++|++|.|.+|+|
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            4799999999999999999999999999988888777789999999999999999999997 899999999999999987

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.6e-19  Score=134.83  Aligned_cols=75  Identities=24%  Similarity=0.402  Sum_probs=71.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       393 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      +|||+|||+++++++|+++|++||.|.+++|+.++.+|+++|||||+|.+.++|++||.++++.|+|+.|.|..|
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            599999999999999999999999999999999998999999999999999999999998888999999999865

>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=99.77  E-value=1e-18  Score=132.88  Aligned_cols=76  Identities=25%  Similarity=0.478  Sum_probs=73.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      ++|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.+++++.+|+.+++..|+|++|.|..|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            6899999999999999999999999999999999999999999999999999999999999999999999999876

>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=99.77  E-value=5.6e-19  Score=137.96  Aligned_cols=84  Identities=21%  Similarity=0.441  Sum_probs=78.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.++++|+.|+. +++..|+|++|.|.++
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            456899999999999999999999999999999999988899999999999999999999997 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .++..
T Consensus        83 ~~~~~   87 (90)
T d1x5sa1          83 GKSSD   87 (90)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            77643

>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=99.76  E-value=1.1e-18  Score=137.02  Aligned_cols=84  Identities=23%  Similarity=0.467  Sum_probs=77.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHH-c-CCcccCCeEEEEe
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDK-FTGKSRGLAYVDFIDDEHLAAAVA-K-NKQMFLGKKLSIA  465 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~-~~g~~~g~afv~f~~~~~a~~a~~-~-~~~~~~g~~l~v~  465 (565)
                      ...++|||+|||+++++++|+.+|++||.|.+++|+.++ .+|.++|||||+|.++++|..|+. | ++..|+|++|.|.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            445789999999999999999999999999999998875 379999999999999999999997 7 8999999999999


Q ss_pred             ecCCCCC
Q 008442          466 RSNPKQR  472 (565)
Q Consensus       466 ~a~~~~~  472 (565)
                      +|.+...
T Consensus        86 ~A~~~~~   92 (94)
T d2cpha1          86 WADSEVT   92 (94)
T ss_dssp             ECCCCCC
T ss_pred             EcCCCCC
Confidence            9987643

>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=99.76  E-value=1.1e-18  Score=133.99  Aligned_cols=75  Identities=27%  Similarity=0.448  Sum_probs=71.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEE
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSI  464 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v  464 (565)
                      ..++|||+|||+++++++|+++|++||.|.++.|+.++.+|+++|||||+|.+.++|..|+. +++..|+|++|.|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            35799999999999999999999999999999999998899999999999999999999997 8999999999987

>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=99.76  E-value=1.3e-18  Score=134.00  Aligned_cols=77  Identities=26%  Similarity=0.437  Sum_probs=72.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCC--eEEEEeec
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLG--KKLSIARS  467 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g--~~l~v~~a  467 (565)
                      +++|||+|||+++++++|+++|++||.|.+++++.++.+|.++|||||+|.++++|..|+. +||..+.|  ++|.|.+|
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            5789999999999999999999999999999999998899999999999999999999997 89999988  46999875

>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=99.76  E-value=5.3e-19  Score=136.49  Aligned_cols=82  Identities=17%  Similarity=0.270  Sum_probs=72.3

Q ss_pred             CCCeEEEcCCCCCCC-HHHHHHHhccCCCeeEEEEeec-CCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          390 DECTAFLSNINLKAT-YEDLRRFFSDVGGVSSIRILHD-KFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~-~~~l~~~f~~~G~i~~~~~~~~-~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      +.++|||+|||++++ +++|+++|++||.|.+++|+.+ +.+|+++|||||+|.+.++|.+|+.+|+..++|++|.|.+|
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            578999999999976 5669999999999999998764 46899999999999999999999999999999999999999


Q ss_pred             CCCC
Q 008442          468 NPKQ  471 (565)
Q Consensus       468 ~~~~  471 (565)
                      .|++
T Consensus        83 ~~kP   86 (86)
T d2ghpa3          83 DKKP   86 (86)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8763

>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=99.76  E-value=1.8e-18  Score=133.29  Aligned_cols=78  Identities=27%  Similarity=0.485  Sum_probs=73.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCC--eEEEEee
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLG--KKLSIAR  466 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g--~~l~v~~  466 (565)
                      .+++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.++++|..|+. +|+..+.|  ++|.|.+
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            45789999999999999999999999999999999998899999999999999999999998 89999876  8899987


Q ss_pred             c
Q 008442          467 S  467 (565)
Q Consensus       467 a  467 (565)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.76  E-value=9.8e-19  Score=134.28  Aligned_cols=79  Identities=24%  Similarity=0.380  Sum_probs=73.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeE-EEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCCCC
Q 008442          394 AFLSNINLKATYEDLRRFFSDVGGVSS-IRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNPKQ  471 (565)
Q Consensus       394 l~V~nl~~~~~~~~l~~~f~~~G~i~~-~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~~~  471 (565)
                      |||+|||+++++++|+++|++||.|.+ +.++.++.+|+++|||||+|.++++|..|+. +++..++|++|.|.++.|+.
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            799999999999999999999999866 4788888899999999999999999999997 89999999999999998775


Q ss_pred             C
Q 008442          472 R  472 (565)
Q Consensus       472 ~  472 (565)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.75  E-value=1.2e-18  Score=131.71  Aligned_cols=75  Identities=21%  Similarity=0.364  Sum_probs=72.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       393 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      +|||+|||+++++++|+++|++||.|.+++|+.++ +|+++|||||+|.++++|+.|+. +|+..++|++|.|.++.
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 99999999999999999999998 89999999999999875

>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=99.75  E-value=2.6e-18  Score=133.89  Aligned_cols=82  Identities=21%  Similarity=0.375  Sum_probs=74.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .+.+||||+|||.++++++|+++|+.||.|.++.++.++.+  .+|||||+|.+.++|..|+. +++..|.|++|.|.+|
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            44679999999999999999999999999999999998644  37999999999999999998 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .++..
T Consensus        84 ~~~~~   88 (90)
T d2cqia1          84 TTPSS   88 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            87654

>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=99.75  E-value=6e-19  Score=141.82  Aligned_cols=83  Identities=31%  Similarity=0.539  Sum_probs=77.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .+.+||||+|||+++++++|+++|++||.|.+|+|+.++.+|+++|||||+|.+.++|..|+. +++..|.|++|.|.++
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            345789999999999999999999999999999999998899999999999999999999997 8999999999999998


Q ss_pred             CCCC
Q 008442          468 NPKQ  471 (565)
Q Consensus       468 ~~~~  471 (565)
                      .++.
T Consensus        86 ~~~~   89 (104)
T d1p1ta_          86 ASEK   89 (104)
T ss_dssp             TCTT
T ss_pred             CCCC
Confidence            8764

>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=99.74  E-value=3e-18  Score=132.17  Aligned_cols=77  Identities=29%  Similarity=0.425  Sum_probs=71.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCC---CcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          394 AFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTG---KSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       394 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g---~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      |||+|||+++++++|+++|++||.|.++.|+.++.++   .++|||||+|.++++|..|+. +|+..++|++|.|.++.+
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            7999999999999999999999999999999887554   479999999999999999997 899999999999999865


Q ss_pred             C
Q 008442          470 K  470 (565)
Q Consensus       470 ~  470 (565)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.74  E-value=2.9e-18  Score=133.27  Aligned_cols=80  Identities=21%  Similarity=0.382  Sum_probs=74.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      ..+|||+|||+++++++|+++|+.||.|.+++|+.++  +.++|||||+|.+.++|+.|+. |||..|+|++|.|.++.+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4589999999999999999999999999999999885  4578999999999999999997 899999999999999987


Q ss_pred             CCC
Q 008442          470 KQR  472 (565)
Q Consensus       470 ~~~  472 (565)
                      ++.
T Consensus        86 ~~~   88 (89)
T d1cvja2          86 RKE   88 (89)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            654

>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=99.74  E-value=1.3e-17  Score=130.72  Aligned_cols=82  Identities=20%  Similarity=0.387  Sum_probs=75.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||+++++++|+++|+.||.|.+|.++.++  +.++|||||+|.++++|..|+. +++..++|++|.|.+|
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            446789999999999999999999999999999999885  4478999999999999999997 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .|+..
T Consensus        87 ~~r~~   91 (93)
T d2cq3a1          87 TARVM   91 (93)
T ss_dssp             CSSCC
T ss_pred             CcCCC
Confidence            88643

>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=99.73  E-value=6e-18  Score=134.58  Aligned_cols=84  Identities=20%  Similarity=0.376  Sum_probs=76.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cC------CcccCCe
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KN------KQMFLGK  460 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~------~~~~~g~  460 (565)
                      ..++++|||+|||+++++++|+++|++||.|.++.++.++.++.++|||||+|.+.++|..|+. ++      +..+.|+
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            3457899999999999999999999999999999999998899999999999999999999997 55      5678999


Q ss_pred             EEEEeecCCCC
Q 008442          461 KLSIARSNPKQ  471 (565)
Q Consensus       461 ~l~v~~a~~~~  471 (565)
                      +|.|.++.++.
T Consensus        85 ~l~v~~a~~k~   95 (98)
T d1x4ha1          85 QLKVDLAVTRD   95 (98)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEECCCCC
Confidence            99999998754

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=7.1e-18  Score=129.54  Aligned_cols=77  Identities=19%  Similarity=0.267  Sum_probs=73.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      ..++|||+|||.++++++|+++|+.||.|.+++|+.++ +|+++|||||+|.++++|.+||.+++..+.|++|.|.++
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            35799999999999999999999999999999999886 899999999999999999999999999999999999875

>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=99.73  E-value=2.5e-18  Score=129.37  Aligned_cols=75  Identities=20%  Similarity=0.442  Sum_probs=72.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       393 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      +|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|+.+|++.|+|++|.|..|
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            589999999999999999999999999999999988999999999999999999999999999999999999875

>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=99.72  E-value=8.6e-18  Score=134.40  Aligned_cols=85  Identities=33%  Similarity=0.441  Sum_probs=76.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCee--------EEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccC
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVS--------SIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFL  458 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--------~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~  458 (565)
                      +.+.++|||+|||+++++++|+++|+.||.|.        .+.+..++.+|+++|||||+|.++++|..|+. +||..|+
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            45578999999999999999999999999874        56677777889999999999999999999998 8999999


Q ss_pred             CeEEEEeecCCCCC
Q 008442          459 GKKLSIARSNPKQR  472 (565)
Q Consensus       459 g~~l~v~~a~~~~~  472 (565)
                      |++|.|.++.++..
T Consensus        85 gr~i~V~~a~~~~p   98 (101)
T d2cpea1          85 GSKLKVSLARKKPP   98 (101)
T ss_dssp             TEECEEECSSCCCC
T ss_pred             CEEEEEEEcCCCCC
Confidence            99999999987644

>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=99.72  E-value=8.2e-19  Score=136.67  Aligned_cols=81  Identities=21%  Similarity=0.408  Sum_probs=75.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecC
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSN  468 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~  468 (565)
                      ....+|||+|||+++++++|+.+|+.||.|.++.|+.++ +|+++|||||+|.+.++|+.||++++..++|++|.|.+|+
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~-~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~ak   89 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK   89 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEE-EETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecC-CCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEecC
Confidence            345799999999999999999999999999998887664 8999999999999999999999999999999999999987


Q ss_pred             CC
Q 008442          469 PK  470 (565)
Q Consensus       469 ~~  470 (565)
                      ++
T Consensus        90 ~k   91 (91)
T d1fjeb1          90 GR   91 (91)
T ss_dssp             CS
T ss_pred             CC
Confidence            63

>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=99.71  E-value=2.6e-17  Score=129.51  Aligned_cols=81  Identities=17%  Similarity=0.341  Sum_probs=73.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEe
Q 008442          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIA  465 (565)
Q Consensus       387 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~  465 (565)
                      ....+++|||+|||+++++++|+++|+.||.|..+.+..   ++.++|||||+|.++++|..|+. ||+..|.|++|.|.
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~---~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~   86 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   86 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecc---cccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            346678999999999999999999999999999988764   45678999999999999999997 89999999999999


Q ss_pred             ecCCC
Q 008442          466 RSNPK  470 (565)
Q Consensus       466 ~a~~~  470 (565)
                      ++++.
T Consensus        87 ~a~~~   91 (95)
T d1x4aa1          87 FPRSG   91 (95)
T ss_dssp             CCCCC
T ss_pred             eccCC
Confidence            98764

>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=99.71  E-value=1.1e-17  Score=133.16  Aligned_cols=80  Identities=26%  Similarity=0.414  Sum_probs=74.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .+.++|||+|||+++++++|+++|+.||.|..+.++.+. ++.++|||||+|.+.++|.+|+. +||..|.|+++.|..+
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            456899999999999999999999999999999999886 89999999999999999999997 8999999999988877


Q ss_pred             CC
Q 008442          468 NP  469 (565)
Q Consensus       468 ~~  469 (565)
                      .|
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>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=3.7e-17  Score=131.22  Aligned_cols=82  Identities=24%  Similarity=0.471  Sum_probs=73.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDK-FTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~-~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~  468 (565)
                      ..++|||+|||+++++++|+++|+.|| |..+.++.++ .+|+++|||||+|.+.++|++|+.+|+..|+|++|.|.++.
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            358999999999999999999999998 7788877664 46889999999999999999888899999999999999998


Q ss_pred             CCCC
Q 008442          469 PKQR  472 (565)
Q Consensus       469 ~~~~  472 (565)
                      ++..
T Consensus        93 ~~~~   96 (104)
T d1wi8a_          93 QAQD   96 (104)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=6.9e-17  Score=129.38  Aligned_cols=85  Identities=24%  Similarity=0.316  Sum_probs=76.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      ..+..+|||+|||+++++++|+++|..||.|....++.+..+++++|||||+|.++++|++|+.+++..|+||.|.|..+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEEC
Confidence            34566899999999999999999999999988866666666999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .+...
T Consensus        92 ~~~~~   96 (104)
T d1wg5a_          92 SRAEV   96 (104)
T ss_dssp             CTTTS
T ss_pred             CHHHh
Confidence            87754

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=3.9e-17  Score=130.23  Aligned_cols=83  Identities=23%  Similarity=0.292  Sum_probs=75.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      ....++|||+|||+++|+++|+++|..|| +..+.++.+. +|.++|||||+|.++++|++|+.+|+..|+||.|.|.++
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            35568999999999999999999999998 5578888886 899999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      .+...
T Consensus        90 ~~~~~   94 (102)
T d1weza_          90 STAGT   94 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87643

>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=99.70  E-value=2.6e-17  Score=122.93  Aligned_cols=74  Identities=12%  Similarity=0.249  Sum_probs=68.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeec
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARS  467 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a  467 (565)
                      .||||+|||+++++++|+++|+.||.|..++++.++ .+ .+|||||+|.++++|++|+.+++..|+|++|.|..+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL-KK-NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECT-TS-SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeec-cc-cceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            489999999999999999999999999999999986 33 458999999999999999999999999999999875

>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=99.69  E-value=2.5e-17  Score=129.93  Aligned_cols=80  Identities=21%  Similarity=0.380  Sum_probs=72.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ..+.++|||+|||+++++++|+++|++||.|..+..     +|.++|||||+|.+.++|..|+. +|+..|+|++|.|.+
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            455789999999999999999999999998766542     78899999999999999999997 899999999999999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +.|+..
T Consensus        88 a~~k~~   93 (96)
T d1fjca_          88 TGEKGG   93 (96)
T ss_dssp             CSSSCC
T ss_pred             eCCCCC
Confidence            998754

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=4.2e-17  Score=133.32  Aligned_cols=78  Identities=23%  Similarity=0.277  Sum_probs=72.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      .+++|||+|||.++++++|+++|++||.|.+|++..   ++.++|||||+|.+.++|..|+. |||..|+|++|.|.++.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            468999999999999999999999999999999975   56779999999999999999997 89999999999999986


Q ss_pred             CC
Q 008442          469 PK  470 (565)
Q Consensus       469 ~~  470 (565)
                      +.
T Consensus        83 ~~   84 (114)
T d2f9da1          83 AN   84 (114)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>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=99.68  E-value=8.4e-18  Score=134.65  Aligned_cols=84  Identities=25%  Similarity=0.323  Sum_probs=78.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .++++|||+|||.++++++|+++|+.||.|..+.++.+..+|+++|||||+|.++++|..|+. +||..|.|++|.|.+|
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            346899999999999999999999999999999888877789999999999999999999997 8999999999999999


Q ss_pred             CCCCC
Q 008442          468 NPKQR  472 (565)
Q Consensus       468 ~~~~~  472 (565)
                      +++..
T Consensus        96 k~k~~  100 (102)
T d2cpxa1          96 KNKKQ  100 (102)
T ss_dssp             CCCSC
T ss_pred             CCccc
Confidence            88654

>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=99.68  E-value=4e-17  Score=128.79  Aligned_cols=83  Identities=18%  Similarity=0.304  Sum_probs=73.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCC-eeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHH-cC--CcccCCeEEEEe
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGG-VSSIRILHDK-FTGKSRGLAYVDFIDDEHLAAAVA-KN--KQMFLGKKLSIA  465 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~-i~~~~~~~~~-~~g~~~g~afv~f~~~~~a~~a~~-~~--~~~~~g~~l~v~  465 (565)
                      +|+|||+|||.++++++|+++|+.||. |.++.++.+. .+|+++|||||+|.++++|..|+. |+  +..+.|++|.|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            589999999999999999999999995 9999998875 368899999999999999999997 64  455789999999


Q ss_pred             ecCCCCCC
Q 008442          466 RSNPKQRK  473 (565)
Q Consensus       466 ~a~~~~~~  473 (565)
                      +|.|+..+
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99887654

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=5.4e-17  Score=125.61  Aligned_cols=77  Identities=26%  Similarity=0.432  Sum_probs=68.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecCC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~~  469 (565)
                      ..++|||+|||+++++++|+++|++||.|.+++++     +.++|||||+|.+.++|+.|+. +++.|+|++|.|.++.|
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~~a~~   77 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG-EDLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEECCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh-CCCEECCEEeEEEeCCC
Confidence            46799999999999999999999999999998764     4568999999999999999986 77889999999999987


Q ss_pred             CCC
Q 008442          470 KQR  472 (565)
Q Consensus       470 ~~~  472 (565)
                      +..
T Consensus        78 k~~   80 (88)
T d1wf0a_          78 KHN   80 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.67  E-value=1.1e-16  Score=123.14  Aligned_cols=77  Identities=19%  Similarity=0.341  Sum_probs=70.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ...++|||+|||.++++++|+++|++||.|.+|++..+      +|||||+|.+.++|..|+. +|+..|+|++|.|.+|
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            34578999999999999999999999999999999765      4899999999999999998 8999999999999999


Q ss_pred             CCCC
Q 008442          468 NPKQ  471 (565)
Q Consensus       468 ~~~~  471 (565)
                      .++.
T Consensus        80 ~~~~   83 (86)
T d2cpja1          80 CHSA   83 (86)
T ss_dssp             SCCS
T ss_pred             CCcC
Confidence            8763

>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=99.67  E-value=1e-16  Score=125.93  Aligned_cols=75  Identities=24%  Similarity=0.400  Sum_probs=70.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      .++|||+|||.++++++|+++|++||.|.+|+++.+      +|||||+|.+.++|..|+. |++..|.|++|+|.++++
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~   91 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   91 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            579999999999999999999999999999999865      5899999999999999997 899999999999999876


Q ss_pred             CC
Q 008442          470 KQ  471 (565)
Q Consensus       470 ~~  471 (565)
                      ++
T Consensus        92 ~p   93 (96)
T d1x4ga1          92 SP   93 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.66  E-value=6.6e-17  Score=125.23  Aligned_cols=77  Identities=18%  Similarity=0.326  Sum_probs=69.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHH---HHHhccCCCeeEEEEeecCCCCCc---ceEEEEEecCHHHHHHHHH-cCCcccCCeE
Q 008442          389 TDECTAFLSNINLKATYEDL---RRFFSDVGGVSSIRILHDKFTGKS---RGLAYVDFIDDEHLAAAVA-KNKQMFLGKK  461 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l---~~~f~~~G~i~~~~~~~~~~~g~~---~g~afv~f~~~~~a~~a~~-~~~~~~~g~~  461 (565)
                      .+.++|||+|||+++++++|   .++|++||.|.+|.++.++.++.+   +|||||+|.++++|..|+. |||..++|++
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            34578999999999999999   678999999999999998766554   4999999999999999997 8999999999


Q ss_pred             EEEe
Q 008442          462 LSIA  465 (565)
Q Consensus       462 l~v~  465 (565)
                      |+|+
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9985

>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=99.66  E-value=2.6e-16  Score=124.04  Aligned_cols=75  Identities=25%  Similarity=0.508  Sum_probs=67.6

Q ss_pred             CCCCeEEEcCCC-CCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          389 TDECTAFLSNIN-LKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       389 ~~~~~l~V~nl~-~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ..+++|||+||| ..+++++|+.+|++||.|.++.|        ++|||||+|.+.++|.+||. ||+..|.|++|.|.+
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            456789999997 56889999999999999999988        36999999999999999998 899999999999999


Q ss_pred             cCCCC
Q 008442          467 SNPKQ  471 (565)
Q Consensus       467 a~~~~  471 (565)
                      +.++.
T Consensus        85 a~~~~   89 (98)
T d1wf2a_          85 AAEPK   89 (98)
T ss_dssp             TTSCC
T ss_pred             CCCCC
Confidence            97653

>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=99.66  E-value=3.6e-17  Score=121.65  Aligned_cols=70  Identities=21%  Similarity=0.311  Sum_probs=66.9

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEE
Q 008442          394 AFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLS  463 (565)
Q Consensus       394 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~  463 (565)
                      |||+|||+++++++|+++|++||.|..++++.++.++.++|||||+|.++++|++|+. +||..+.|+.|+
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            7999999999999999999999999999999998899999999999999999999997 899999998763

>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=99.64  E-value=8.4e-17  Score=121.95  Aligned_cols=75  Identities=24%  Similarity=0.354  Sum_probs=67.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCc-ccCCeEEEEeecCC
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQ-MFLGKKLSIARSNP  469 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~-~~~g~~l~v~~a~~  469 (565)
                      ++|||+|||+++++++|+++|++||.|.++.+..      ++|||||+|.++++|..|+. +||. .++|++|.|.++.|
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            4799999999999999999999999987766654      46899999999999999997 8986 59999999999998


Q ss_pred             CCC
Q 008442          470 KQR  472 (565)
Q Consensus       470 ~~~  472 (565)
                      +..
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            754

>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=99.64  E-value=4.2e-16  Score=126.26  Aligned_cols=76  Identities=26%  Similarity=0.378  Sum_probs=69.3

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          391 ECTAFLSNINL-KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       391 ~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      +++|||+|||+ .+++++|+++|+.||.|..|.|+.++     +|||||+|.+.++|.+|+. +++..|.|++|.|.++.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            57999999965 59999999999999999999998764     6899999999999999998 89999999999999987


Q ss_pred             CCC
Q 008442          469 PKQ  471 (565)
Q Consensus       469 ~~~  471 (565)
                      ...
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            553

>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=99.64  E-value=1.4e-16  Score=129.34  Aligned_cols=82  Identities=18%  Similarity=0.306  Sum_probs=73.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecC
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSN  468 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~  468 (565)
                      .+.++|||+|||+++++++|+++|+.||.+..+.++.+..+|.++|||||+|.+.++|++|+.+|+..|+|+.|.|..+.
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEEC
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEcC
Confidence            45679999999999999999999999998876555555569999999999999999999999999999999999998875


Q ss_pred             CC
Q 008442          469 PK  470 (565)
Q Consensus       469 ~~  470 (565)
                      +.
T Consensus        96 ~~   97 (112)
T d1wela1          96 KK   97 (112)
T ss_dssp             HH
T ss_pred             hH
Confidence            43

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=2e-16  Score=121.98  Aligned_cols=76  Identities=17%  Similarity=0.243  Sum_probs=68.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeE-EEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSS-IRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~-~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      .++|||+|||+++++++|+++|+.||.+.. +.+..+ .+|.++|||||+|.++++|+.|+. +|+..|.|++|.|.++
T Consensus         9 ~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~-~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           9 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeC-CCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            467999999999999999999999999876 455555 489999999999999999999997 8999999999999874

>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=99.64  E-value=1.4e-16  Score=124.21  Aligned_cols=79  Identities=24%  Similarity=0.364  Sum_probs=70.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHH----HhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEE
Q 008442          390 DECTAFLSNINLKATYEDLRR----FFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSI  464 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~----~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v  464 (565)
                      +++||||+|||+++++++|++    +|++||.|.+|.+..   ++.++|||||+|.+.++|..|+. +++..++|++|.|
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            468999999999999998864    589999999988754   67889999999999999999997 8999999999999


Q ss_pred             eecCCCC
Q 008442          465 ARSNPKQ  471 (565)
Q Consensus       465 ~~a~~~~  471 (565)
                      .+|+++.
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9998754

>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=99.64  E-value=4.5e-16  Score=118.90  Aligned_cols=74  Identities=18%  Similarity=0.274  Sum_probs=67.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCccc-CCeEEEEeec
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMF-LGKKLSIARS  467 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~-~g~~l~v~~a  467 (565)
                      ++++|||+|||.++++++|+.+|+.||.|.+++++.+     .+|||||+|.+.++|..|+. |+|..| +|++|.|.+|
T Consensus         7 P~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~a   81 (83)
T d2b0ga1           7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFA   81 (83)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEe
Confidence            3589999999999999999999999999999999754     36899999999999999998 899887 5789999998


Q ss_pred             C
Q 008442          468 N  468 (565)
Q Consensus       468 ~  468 (565)
                      +
T Consensus        82 k   82 (83)
T d2b0ga1          82 K   82 (83)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.63  E-value=3.3e-16  Score=118.40  Aligned_cols=75  Identities=21%  Similarity=0.218  Sum_probs=68.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ..++||||+|+|  +++++|+++|++||.|.++.+..+      +|||||+|.+.++|..|+. +|+..++|++|.|.++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            456899999986  899999999999999999998654      4899999999999999997 8999999999999999


Q ss_pred             CCCC
Q 008442          468 NPKQ  471 (565)
Q Consensus       468 ~~~~  471 (565)
                      +|++
T Consensus        75 ~~~P   78 (79)
T d2bz2a1          75 RKQP   78 (79)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            8764

>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=99.63  E-value=5.7e-16  Score=119.92  Aligned_cols=76  Identities=26%  Similarity=0.289  Sum_probs=68.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCccc-CCeEEEEeecC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMF-LGKKLSIARSN  468 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~-~g~~l~v~~a~  468 (565)
                      .++|||+|||+++++++|+++|+.||.|..+.+..    ++++|||||+|.+.++|..|+. |+|..| +|++|+|.+++
T Consensus        10 s~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk   85 (88)
T d2adca2          10 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK   85 (88)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECS
T ss_pred             CCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCC
Confidence            57999999999999999999999999998887654    4467899999999999999997 899887 59999999987


Q ss_pred             CC
Q 008442          469 PK  470 (565)
Q Consensus       469 ~~  470 (565)
                      +.
T Consensus        86 ~~   87 (88)
T d2adca2          86 ST   87 (88)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=99.63  E-value=7.6e-16  Score=118.64  Aligned_cols=76  Identities=20%  Similarity=0.334  Sum_probs=69.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~  469 (565)
                      .++|||+|||+++++++|+++|+.||.|..+.+.      +++|||||+|.++++|..|+. ||+..|.|++|.|.+|+|
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP   81 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   81 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccC
Confidence            4689999999999999999999999998887764      346899999999999999998 899999999999999988


Q ss_pred             CCC
Q 008442          470 KQR  472 (565)
Q Consensus       470 ~~~  472 (565)
                      +.+
T Consensus        82 ~~~   84 (86)
T d2cpda1          82 VDK   84 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>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=99.62  E-value=3.3e-16  Score=125.27  Aligned_cols=79  Identities=18%  Similarity=0.296  Sum_probs=70.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeE-EEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecCC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSS-IRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNP  469 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~-~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~~  469 (565)
                      ..+|||+|||+++++++|+++|..||.|.. +.++.+ .+|+++|||||+|.++++|+.||.+++..|+|++|.|..+.+
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~-~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~~~   86 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD-NNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVTL   86 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCC-TTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEECH
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeC-CCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEECCH
Confidence            467999999999999999999999998876 455454 599999999999999999999999999999999999998754


Q ss_pred             C
Q 008442          470 K  470 (565)
Q Consensus       470 ~  470 (565)
                      .
T Consensus        87 ~   87 (103)
T d2cpya1          87 E   87 (103)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.60  E-value=1.7e-16  Score=122.40  Aligned_cols=72  Identities=21%  Similarity=0.347  Sum_probs=66.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCCC
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNPK  470 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~~  470 (565)
                      ++|||+|||+++++++|+++|++||.|.+++++.+       |||||+|.+.++|+.||. ||+..|.|+.|.|.++.++
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            36999999999999999999999999999998643       799999999999999997 8999999999999887554

>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=99.60  E-value=4.4e-16  Score=126.65  Aligned_cols=77  Identities=13%  Similarity=0.140  Sum_probs=69.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      +.+++|||+|||+++++++|+++|+.||.|..|.|.      .++|||||+|.+.++|.+|+. |||..|.|++|.|.++
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a   81 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEEC
Confidence            345799999999999999999999999999999874      346999999999999999997 8999999999999998


Q ss_pred             CCCC
Q 008442          468 NPKQ  471 (565)
Q Consensus       468 ~~~~  471 (565)
                      ....
T Consensus        82 ~~~~   85 (111)
T d1whxa_          82 PIGV   85 (111)
T ss_dssp             ETTT
T ss_pred             CCCc
Confidence            6543

>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=9.4e-16  Score=120.76  Aligned_cols=77  Identities=13%  Similarity=0.280  Sum_probs=69.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEee
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIAR  466 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~  466 (565)
                      ....++|||+|||+++++++|+++|+.||.|.++.+..       +|||||+|.+.++|+.||. ||+..|.|+.|.|.+
T Consensus        12 ~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~   84 (98)
T d1wg4a_          12 RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSY   84 (98)
T ss_dssp             CSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            34568999999999999999999999999999999853       4899999999999999997 899999999999999


Q ss_pred             cCCCC
Q 008442          467 SNPKQ  471 (565)
Q Consensus       467 a~~~~  471 (565)
                      +++..
T Consensus        85 ~~~~~   89 (98)
T d1wg4a_          85 IRVYP   89 (98)
T ss_dssp             EEEEC
T ss_pred             EecCC
Confidence            87654

>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=99.58  E-value=3.5e-15  Score=115.04  Aligned_cols=74  Identities=14%  Similarity=0.305  Sum_probs=64.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      ...+|||+|||+++++++|+++|++|| +..+.+      +.++|||||+|.+.++|++|+. ||+..|+|++|.|.++.
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            357899999999999999999999999 333333      4567999999999999999997 89999999999999986


Q ss_pred             CC
Q 008442          469 PK  470 (565)
Q Consensus       469 ~~  470 (565)
                      ++
T Consensus        77 ~~   78 (88)
T d1wg1a_          77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.56  E-value=6.3e-15  Score=116.03  Aligned_cols=77  Identities=16%  Similarity=0.276  Sum_probs=69.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCC--eEEEEee
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLG--KKLSIAR  466 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g--~~l~v~~  466 (565)
                      +.++|||+|||+++++++|+++|++||.|..+++..+      +|||||+|.+.++|..|+. ||+..|.|  ++|.|.+
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            4589999999999999999999999999999998654      4899999999999999997 89999976  5899999


Q ss_pred             cCCCCC
Q 008442          467 SNPKQR  472 (565)
Q Consensus       467 a~~~~~  472 (565)
                      +++.+.
T Consensus        90 ak~~~~   95 (97)
T d1whya_          90 AKSGPS   95 (97)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            987543

>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=99.56  E-value=1.6e-14  Score=115.28  Aligned_cols=79  Identities=13%  Similarity=0.131  Sum_probs=69.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-c--CCcccCCeEEEE
Q 008442          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-K--NKQMFLGKKLSI  464 (565)
Q Consensus       388 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~--~~~~~~g~~l~v  464 (565)
                      ..+..+|||+|||.++++++|..+|++||.|..+.+..+      +|+|||+|.+.++|+.|+. +  ++..+.|++|.|
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            345789999999999999999999999999999998654      5899999999999999997 5  567789999999


Q ss_pred             eecCCCCC
Q 008442          465 ARSNPKQR  472 (565)
Q Consensus       465 ~~a~~~~~  472 (565)
                      .++..+..
T Consensus        86 ~~s~~~~~   93 (104)
T d1wexa_          86 NYSTSKRI   93 (104)
T ss_dssp             EECSSSSC
T ss_pred             EEcCCCcc
Confidence            99976543

>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=99.56  E-value=8.8e-15  Score=113.02  Aligned_cols=77  Identities=16%  Similarity=0.191  Sum_probs=68.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-c--CCcccCCeEEEEe
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-K--NKQMFLGKKLSIA  465 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~--~~~~~~g~~l~v~  465 (565)
                      .+.++|||+|||+++++++|+++|++||.|.++.+..+      +|||||+|.+.++|.+|+. +  ++..+.|++|.|.
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~   79 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   79 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEE
Confidence            35689999999999999999999999999999998754      4799999999999999996 4  6778999999999


Q ss_pred             ecCCCC
Q 008442          466 RSNPKQ  471 (565)
Q Consensus       466 ~a~~~~  471 (565)
                      +++.+.
T Consensus        80 ~sk~~~   85 (88)
T d2cq1a1          80 YSNHKE   85 (88)
T ss_dssp             ECSCSS
T ss_pred             ECCCCC
Confidence            997654

>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=99.56  E-value=7.6e-15  Score=109.27  Aligned_cols=70  Identities=17%  Similarity=0.306  Sum_probs=62.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecCCC
Q 008442          394 AFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSNPK  470 (565)
Q Consensus       394 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~~~  470 (565)
                      |||+|||+++++++|+++|++|| +..+.+      ++++|||||+|.+.++|.+|+. +|+..+.|++|.|.++.+.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 554443      4567999999999999999997 8999999999999998654

>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=99.55  E-value=3.9e-15  Score=119.89  Aligned_cols=78  Identities=19%  Similarity=0.152  Sum_probs=70.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCccc--CCeEEEEee
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMF--LGKKLSIAR  466 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~--~g~~l~v~~  466 (565)
                      ...+|||+|||+.+|+++|+++|++||.|.++.++.++    ++|||||+|.++++|+.|+. +|+..|  .|++|.|.+
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            34689999999999999999999999999999998764    57999999999999999998 899887  578999999


Q ss_pred             cCCCC
Q 008442          467 SNPKQ  471 (565)
Q Consensus       467 a~~~~  471 (565)
                      +++..
T Consensus        82 s~~~~   86 (108)
T d2adba1          82 SKLTS   86 (108)
T ss_dssp             CSSCS
T ss_pred             cCCcc
Confidence            87754

>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=99.54  E-value=1.1e-14  Score=114.80  Aligned_cols=77  Identities=16%  Similarity=0.202  Sum_probs=68.6

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH---cCCcccCCeEEEE
Q 008442          389 TDECTAFLSNINLK-ATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA---KNKQMFLGKKLSI  464 (565)
Q Consensus       389 ~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~---~~~~~~~g~~l~v  464 (565)
                      ..+++|||+|||.+ +++++|..+|+.||.|.++.++.+      +|||||+|.+.++|..|+.   +++..++|++|.|
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V   89 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   89 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEE
Confidence            45689999999985 899999999999999999999754      4899999999999999985   5888999999999


Q ss_pred             eecCCCC
Q 008442          465 ARSNPKQ  471 (565)
Q Consensus       465 ~~a~~~~  471 (565)
                      .+|..++
T Consensus        90 ~~s~~~~   96 (99)
T d1x4fa1          90 DLSEKYK   96 (99)
T ss_dssp             EEECSCS
T ss_pred             EEcCCcc
Confidence            9997553

>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=99.53  E-value=1.6e-14  Score=128.76  Aligned_cols=83  Identities=25%  Similarity=0.438  Sum_probs=77.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecC
Q 008442          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSN  468 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~  468 (565)
                      ...++|||+|||+.+++++|+.+|+.||.|..+.++.++.+|.++|||||+|.++++|.+|+.+++..++|++|.|.+|.
T Consensus        95 ~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~~~~~~G~~i~V~~A~  174 (183)
T d1u1qa_          95 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKAL  174 (183)
T ss_dssp             CCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSSCEEETTEEEEEEECC
T ss_pred             cccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHHhCCCeECCEEEEEEecC
Confidence            45679999999999999999999999999999999999888999999999999999999999988889999999999988


Q ss_pred             CCC
Q 008442          469 PKQ  471 (565)
Q Consensus       469 ~~~  471 (565)
                      |+.
T Consensus       175 ~k~  177 (183)
T d1u1qa_         175 SKQ  177 (183)
T ss_dssp             CHH
T ss_pred             Ccc
Confidence            753

>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=99.53  E-value=1.6e-16  Score=123.74  Aligned_cols=76  Identities=20%  Similarity=0.322  Sum_probs=66.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEe-----ecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEee
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRIL-----HDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIAR  466 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~-----~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~  466 (565)
                      ++|||+|||+++++++|+++|+.||.|..+.+.     .+..+++++|||||+|.++++|+.|+.|||..+.|++|.|..
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V~r   81 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR   81 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCCBC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEECC
Confidence            689999999999999999999999987665443     334578899999999999999999998999999999999975


Q ss_pred             c
Q 008442          467 S  467 (565)
Q Consensus       467 a  467 (565)
                      +
T Consensus        82 ~   82 (90)
T d1u2fa_          82 P   82 (90)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.50  E-value=3.5e-14  Score=109.40  Aligned_cols=77  Identities=17%  Similarity=0.218  Sum_probs=68.1

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-c--CCcccCCeEEEE
Q 008442          389 TDECTAFLSNINLK-ATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-K--NKQMFLGKKLSI  464 (565)
Q Consensus       389 ~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~--~~~~~~g~~l~v  464 (565)
                      ...++|||+|||.. +|+++|.++|++||.|.++.++.++      ++|||+|.+.++|..|+. +  ++..+.|++|.|
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            44678999999986 7899999999999999999997653      699999999999999997 4  677899999999


Q ss_pred             eecCCCC
Q 008442          465 ARSNPKQ  471 (565)
Q Consensus       465 ~~a~~~~  471 (565)
                      .+|.+.+
T Consensus        80 ~~s~~~~   86 (89)
T d1x4da1          80 HLSQKYK   86 (89)
T ss_dssp             EEECCCT
T ss_pred             EECCCcc
Confidence            9997653

>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=99.47  E-value=5.1e-14  Score=111.68  Aligned_cols=79  Identities=14%  Similarity=0.140  Sum_probs=69.0

Q ss_pred             CCCCeEEEcCCCCCC-CH----HHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEE
Q 008442          389 TDECTAFLSNINLKA-TY----EDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKL  462 (565)
Q Consensus       389 ~~~~~l~V~nl~~~~-~~----~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l  462 (565)
                      ...++|||+||+.++ ++    ++|+.+|+.||.|.++.+..      ++|||||+|.+.++|..|+. |||..|+|++|
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            346899999999986 33    56999999999999998864      45899999999999999998 89999999999


Q ss_pred             EEeecCCCCCC
Q 008442          463 SIARSNPKQRK  473 (565)
Q Consensus       463 ~v~~a~~~~~~  473 (565)
                      .|.++++....
T Consensus        77 ~v~~a~~~~~~   87 (104)
T d1weya_          77 KLYFAQTLHIG   87 (104)
T ss_dssp             EEECCCCSSCC
T ss_pred             EEeecccCCCC
Confidence            99999877553

>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=99.39  E-value=2.2e-14  Score=113.83  Aligned_cols=75  Identities=19%  Similarity=0.193  Sum_probs=70.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeec
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARS  467 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a  467 (565)
                      ..++|.+++.++++++|+++|++||.|.+|.|+.+. +|+++|||||+|.+.++|.+|+. |||..++|++|.|.++
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            357889999999999999999999999999999875 99999999999999999999998 8999999999999875

>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=99.36  E-value=1.2e-12  Score=116.45  Aligned_cols=80  Identities=23%  Similarity=0.409  Sum_probs=74.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeEEEEeecCCCC
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKKLSIARSNPKQ  471 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~~~~  471 (565)
                      ++|||+|||+++++++|+++|++||.|.++.++.+..+|.++|||||+|.+.++|.+|+.+++..+.++.+.+....+..
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~~   86 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSRE   86 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCTT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhcc
Confidence            69999999999999999999999999999999999889999999999999999999999988888999988888765543

>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=99.35  E-value=5e-13  Score=100.20  Aligned_cols=73  Identities=10%  Similarity=0.093  Sum_probs=62.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeE-EEEeecC
Q 008442          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKK-LSIARSN  468 (565)
Q Consensus       390 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~-l~v~~a~  468 (565)
                      +.+.|+|+|+|++.+++.| ..|++||.|.++++.      .++|||||+|.++++|++||.+||..|+|+. |.|..+.
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            3578999999999987655 579999999999874      3468999999999999999999999999985 5788775


Q ss_pred             C
Q 008442          469 P  469 (565)
Q Consensus       469 ~  469 (565)
                      .
T Consensus        76 ~   76 (81)
T d1wwha1          76 D   76 (81)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=1.7e-10  Score=111.66  Aligned_cols=244  Identities=11%  Similarity=-0.028  Sum_probs=167.0

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Q 008442           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER  104 (565)
Q Consensus        25 ~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~  104 (565)
                      .+..........|+++.+..+|+++|..+|.+.+.|...+.... ..+..+.+...|++|+...|....+|......+. 
T Consensus        21 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~-~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~-   98 (323)
T d1fcha_          21 QPFEEGLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQA-ENEQELLAISALRRCLELKPDNQTALMALAVSFT-   98 (323)
T ss_dssp             SHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH-HcCChHHHHHHHHhhhcccccccccccccccccc-
Confidence            35556666778899999999999999999999999999887544 4457888999999999999999999998876443 


Q ss_pred             hcCCHHHHHHHHHHHHhcccccHHHHH--HHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCc--h
Q 008442          105 SRASEEEISTVFEKSLLCAFSTFEEYL--DLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTD--G  180 (565)
Q Consensus       105 ~~~~~~~~~~if~ral~~~~~~~~~~~--~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~--~  180 (565)
                      ..+..+++...|++++...+.......  ..........    .....    .........+.++...+...+...+  .
T Consensus        99 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~----~~~~~~~~~~~~a~~~~~~al~~~p~~~  170 (323)
T d1fcha_          99 NESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLG----PSKRI----LGSLLSDSLFLEVKELFLAAVRLDPTSI  170 (323)
T ss_dssp             HTTCHHHHHHHHHHHHHTSTTTGGGCC-------------------CT----THHHHHHHHHHHHHHHHHHHHHHSTTSC
T ss_pred             ccccccccccchhhHHHhccchHHHHHhhhhhhhhcccc----cchhh----HHHHHHhhHHHHHHHHHHHHHHHhhccc
Confidence            468889999999999975433111000  0000000000    00000    0001111233334444333332111  1


Q ss_pred             hHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHH
Q 008442          181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAW  260 (565)
Q Consensus       181 ~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~  260 (565)
                      ...++...+.+....+ +++.|..+|++++...|+...+|...+.+....|+++.|...|++++..  ..+ ....|...
T Consensus       171 ~~~~~~~l~~~~~~~~-~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~-~~~a~~~l  246 (323)
T d1fcha_         171 DPDVQCGLGVLFNLSG-EYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALEL--QPG-YIRSRYNL  246 (323)
T ss_dssp             CHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT-CHHHHHHH
T ss_pred             ccccchhhHHHHHHHH-HHhhhhcccccccccccccccchhhhhhcccccccchhHHHHHHHHHHH--hhc-cHHHHHHH
Confidence            2345666777888888 9999999999999999999999999999999999999999999999973  222 33455444


Q ss_pred             HHHHHHhCCHHHHHHHHHHHhh
Q 008442          261 LRFEREYGTLEDFDHSVQKVTP  282 (565)
Q Consensus       261 ~~fE~~~G~~~~~~~~~~k~~~  282 (565)
                      ...-...|+.+.+...+.+++.
T Consensus       247 g~~~~~~g~~~~A~~~~~~al~  268 (323)
T d1fcha_         247 GISCINLGAHREAVEHFLEALN  268 (323)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHH
Confidence            5555566888877777777654

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.30  E-value=2.3e-10  Score=110.68  Aligned_cols=217  Identities=10%  Similarity=0.029  Sum_probs=156.4

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      +|...|+.+|..+|.    +..+|...+......|+.+.+...|++|+...|.+...|...+..+.. .+..+.+..+|+
T Consensus        37 ~A~~~~~~al~~~P~----~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~-~~~~~~A~~~~~  111 (323)
T d1fcha_          37 NAVLLFEAAVQQDPK----HMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTN-ESLQRQACEILR  111 (323)
T ss_dssp             HHHHHHHHHHHSCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC----CHHHHHHHHHHHHHcCChHHHHHHHHhhhccccccccccccccccccc-cccccccccchh
Confidence            477889999999987    889999999999999999999999999999999999999999876554 446778999999


Q ss_pred             HHHHcCCCCHHHHHHHHHHHH--------------HhcCCHHHHHHHHHHHHhcccc--cHHHHHHHHHHHHHHHHHHhh
Q 008442           83 RATKNCPWVGELWVRSLLSLE--------------RSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRIL  146 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le--------------~~~~~~~~~~~if~ral~~~~~--~~~~~~~~~~~~~~~~~r~~~  146 (565)
                      +++...|....++........              .......++...|.+++...+.  ....+..+-..+.        
T Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~--------  183 (323)
T d1fcha_         112 DWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFN--------  183 (323)
T ss_dssp             HHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHH--------
T ss_pred             hHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHHH--------
Confidence            999988764433221110000              0012245566777777764332  1111111111110        


Q ss_pred             ccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHH
Q 008442          147 FSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISM  226 (565)
Q Consensus       147 ~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~  226 (565)
                                   ...-+++|+.++...+...+....+|...+.++...+ ++++|...|+++++..|++...|...+..
T Consensus       184 -------------~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g-~~~~A~~~~~~al~~~p~~~~a~~~lg~~  249 (323)
T d1fcha_         184 -------------LSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGN-QSEEAVAAYRRALELQPGYIRSRYNLGIS  249 (323)
T ss_dssp             -------------HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             -------------HHHHHhhhhcccccccccccccccchhhhhhcccccc-cchhHHHHHHHHHHHhhccHHHHHHHHHH
Confidence                         0112334444444444334445677888888888888 99999999999999999999999999999


Q ss_pred             HHHcCChHHHHHHHHHHHhc
Q 008442          227 EIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       227 e~~~~~~~~aR~i~~~al~~  246 (565)
                      ....|+++.|...|++||..
T Consensus       250 ~~~~g~~~~A~~~~~~al~l  269 (323)
T d1fcha_         250 CINLGAHREAVEHFLEALNM  269 (323)
T ss_dssp             HHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHh
Confidence            99999999999999999973

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.28  E-value=1.3e-09  Score=107.06  Aligned_cols=270  Identities=13%  Similarity=0.082  Sum_probs=154.7

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...|+.+|...|.    +..+|..........|+++.+..+|+++|..+|.+...|...+...... +..+.+...|+
T Consensus        17 ~A~~~~~~~l~~~p~----~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~l~~~~~~~-g~~~~A~~~~~   91 (388)
T d1w3ba_          17 AAERHCMQLWRQEPD----NTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQNPLLAEAYSNLGNVYKER-GQLQEAIEHYR   91 (388)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC----CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHhhhh-ccccccccccc
Confidence            467889999988886    7889999999888999999999999999999999999999888765544 47778999999


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHhcCC---------------------------------HHHHHHHHHHHHhcccccHHH
Q 008442           83 RATKNCPWVGELWVRSLLSLERSRAS---------------------------------EEEISTVFEKSLLCAFSTFEE  129 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~~~~~---------------------------------~~~~~~if~ral~~~~~~~~~  129 (565)
                      +++...|.....+.............                                 .......+.+.+...+.....
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  171 (388)
T d1w3ba_          92 HALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQPNFAVA  171 (388)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHCTTCHHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhhhhHHHHHHhhccCcchhHH
Confidence            99998887766555444322221111                                 111122222222211111111


Q ss_pred             HHHHHHHH---------HHHHHHH-hhccccchhhhhHHH---HHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcC
Q 008442          130 YLDLFLTR---------IDGLRRR-ILFSGEVEGVLDYSL---IRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMG  196 (565)
Q Consensus       130 ~~~~~~~~---------~~~~~r~-~~~~~~~e~~~~~~~---~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~  196 (565)
                      +..+-..+         ..+..+. ....+..+.+.....   ....|++|+..+.......+.....+...+.+....+
T Consensus       172 ~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  251 (388)
T d1w3ba_         172 WSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQG  251 (388)
T ss_dssp             HHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             HHhhcccccccCcHHHHHHHHHHHHHhCcccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHCC
Confidence            00000000         0000000 000000000000000   0011233444443333323333344555566666666


Q ss_pred             CChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHH
Q 008442          197 KDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHS  276 (565)
Q Consensus       197 ~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~  276 (565)
                       +++.|..+|+++++..|++..+|...+......|+++.|..+|+.++..   .+....++......-...|+.+.+...
T Consensus       252 -~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~~A~~~  327 (388)
T d1w3ba_         252 -LIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRL---CPTHADSLNNLANIKREQGNIEEAVRL  327 (388)
T ss_dssp             -CHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHTTTCHHHHHHH
T ss_pred             -CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhcc---CCccchhhhHHHHHHHHCCCHHHHHHH
Confidence             7777777777777777777777777777777777777777777777652   222334454455555556776666666


Q ss_pred             HHHHh
Q 008442          277 VQKVT  281 (565)
Q Consensus       277 ~~k~~  281 (565)
                      +++++
T Consensus       328 ~~~al  332 (388)
T d1w3ba_         328 YRKAL  332 (388)
T ss_dssp             HHHHT
T ss_pred             HHHHH
Confidence            66554

>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=99.28  E-value=2.3e-12  Score=103.99  Aligned_cols=72  Identities=14%  Similarity=0.174  Sum_probs=60.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCH-HHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDD-EHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       391 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~-~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      ...+||||||+.+|+++|+.+|++||.|.+|.|+.+      +|||||.|.++ ++|..|+. +++..+.++.+.|.++.
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            345699999999999999999999999999999754      58999999986 67888887 88888777766665543

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.27  E-value=1.2e-09  Score=107.34  Aligned_cols=212  Identities=13%  Similarity=0.068  Sum_probs=155.2

Q ss_pred             HHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHH
Q 008442            6 AHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRAT   85 (565)
Q Consensus         6 ~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl   85 (565)
                      ..++..+...|.    ....|..........++.+.+...+++++...|.+...|..++..+.. .+..+.+...|++++
T Consensus       156 ~~~~~~~~~~~~----~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~-~~~~~~A~~~~~~~~  230 (388)
T d1w3ba_         156 ACYLKAIETQPN----FAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKE-ARIFDRAVAAYLRAL  230 (388)
T ss_dssp             HHHHHHHHHCTT----CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHT-TTCTTHHHHHHHHHH
T ss_pred             HHHHHhhccCcc----hhHHHHhhcccccccCcHHHHHHHHHHHHHhCcccHHHHHHHhhhhhc-cccHHHHHHHHHHhH
Confidence            344555555554    667788788888888889999999999999999999999988875553 446778899999999


Q ss_pred             HcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHH
Q 008442           86 KNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQ  165 (565)
Q Consensus        86 ~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~  165 (565)
                      ...|.....|......+ ...+..+++...|++++...+.....+..+-..+...              .++..+...|.
T Consensus       231 ~~~~~~~~~~~~l~~~~-~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~--------------~~~~~A~~~~~  295 (388)
T d1w3ba_         231 SLSPNHAVVHGNLACVY-YEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEK--------------GSVAEAEDCYN  295 (388)
T ss_dssp             HHCTTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHH--------------SCHHHHHHHHH
T ss_pred             HHhhhHHHHHHHHHHHH-HHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc--------------CCHHHHHHHHH
Confidence            98888888777655533 3467889999999999986665444433332222110              12233334444


Q ss_pred             HHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          166 RASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       166 ~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      .+.       ...+.....+...+.+....+ ++++|...|+++++.+|+...+|...+......|+++.|...|++++.
T Consensus       296 ~~~-------~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  367 (388)
T d1w3ba_         296 TAL-------RLCPTHADSLNNLANIKREQG-NIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIR  367 (388)
T ss_dssp             HHH-------HHCTTCHHHHHHHHHHHHTTT-CHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHT
T ss_pred             hhh-------ccCCccchhhhHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            333       323344556667777777777 999999999999999999999999999999999999999999999987

>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=8.3e-12  Score=97.86  Aligned_cols=80  Identities=20%  Similarity=0.325  Sum_probs=68.0

Q ss_pred             CCCCCeEEEcCC--CCCCC---------HHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCc
Q 008442          388 FTDECTAFLSNI--NLKAT---------YEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQ  455 (565)
Q Consensus       388 ~~~~~~l~V~nl--~~~~~---------~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~  455 (565)
                      ....++|+|.|+  |.++.         .++|+..|++||.|..+.+..+    .++|||||+|.++++|..|+. |||.
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~   80 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGR   80 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCc
Confidence            355789999999  55432         2689999999999999988654    467999999999999999997 8999


Q ss_pred             ccCCeEEEEeecCCCC
Q 008442          456 MFLGKKLSIARSNPKQ  471 (565)
Q Consensus       456 ~~~g~~l~v~~a~~~~  471 (565)
                      .++|++|.|.++.++.
T Consensus        81 ~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          81 WFGGRQITAQAWDGTT   96 (99)
T ss_dssp             EETTEECEEEECCSCC
T ss_pred             EECCEEEEEEEeCCcC
Confidence            9999999999988764

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.25  E-value=4.8e-12  Score=99.58  Aligned_cols=62  Identities=10%  Similarity=0.146  Sum_probs=55.1

Q ss_pred             CCCeEEEc--CCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCccc
Q 008442          390 DECTAFLS--NINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMF  457 (565)
Q Consensus       390 ~~~~l~V~--nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~  457 (565)
                      +..+|||+  |||.++|+++|+.+|++||.|..+.++.+      +|||||+|.+.++|..|+. |||..+
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            34688885  59999999999999999999999988654      4799999999999999997 899876

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.99  E-value=2e-10  Score=90.85  Aligned_cols=79  Identities=22%  Similarity=0.169  Sum_probs=66.6

Q ss_pred             CCeEEEcCC--CCCCC--------HHHHHHHhccCCCeeEEEEeecCCC--CCcceEEEEEecCHHHHHHHHH-cCCccc
Q 008442          391 ECTAFLSNI--NLKAT--------YEDLRRFFSDVGGVSSIRILHDKFT--GKSRGLAYVDFIDDEHLAAAVA-KNKQMF  457 (565)
Q Consensus       391 ~~~l~V~nl--~~~~~--------~~~l~~~f~~~G~i~~~~~~~~~~~--g~~~g~afv~f~~~~~a~~a~~-~~~~~~  457 (565)
                      .+.|.+.|+  |.++.        .++|++.|++||.|.+|.|+++..+  ....|++||+|.+.++|.+|+. |+|..+
T Consensus         4 s~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f   83 (104)
T d1o0pa_           4 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF   83 (104)
T ss_dssp             CSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCS
T ss_pred             CcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEE
Confidence            568999999  55443        3578999999999999999876533  2346999999999999999998 899999


Q ss_pred             CCeEEEEeecCC
Q 008442          458 LGKKLSIARSNP  469 (565)
Q Consensus       458 ~g~~l~v~~a~~  469 (565)
                      +||+|.|.++.+
T Consensus        84 ~gR~v~v~f~~~   95 (104)
T d1o0pa_          84 ANRVVVTKYCDP   95 (104)
T ss_dssp             SSSCCEEEEECH
T ss_pred             CCeEEEEEEcCH
Confidence            999999999864

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.93  E-value=1.6e-07  Score=90.14  Aligned_cols=204  Identities=9%  Similarity=0.027  Sum_probs=143.6

Q ss_pred             ChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHH
Q 008442           19 DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRS   98 (565)
Q Consensus        19 ~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~y   98 (565)
                      +|+..+++..+.....+.+..+++..+|++||..+|.+...|..-...+....++.+.+...|++|+...|.+..+|...
T Consensus        39 ~p~~~~a~~~~~~~~~~~e~~~~Al~~~~~ai~lnP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~~~~a~~~~  118 (315)
T d2h6fa1          39 SDKFRDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHR  118 (315)
T ss_dssp             CHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHCCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHhhhhHHHHH
Confidence            44455666655555666778899999999999999999999998887666656667889999999999999999999987


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCC
Q 008442           99 LLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNT  178 (565)
Q Consensus        99 i~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~  178 (565)
                      ...+.. .+..+++...|.+|+...+..+..|..+-..+..    .                 ..|+.|+.++...+...
T Consensus       119 ~~~~~~-l~~~~eAl~~~~kal~~dp~n~~a~~~~~~~~~~----~-----------------~~~~~Al~~~~~al~~~  176 (315)
T d2h6fa1         119 RVLVEW-LRDPSQELEFIADILNQDAKNYHAWQHRQWVIQE----F-----------------KLWDNELQYVDQLLKED  176 (315)
T ss_dssp             HHHHHH-HTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHH----H-----------------TCCTTHHHHHHHHHHHC
T ss_pred             hHHHHh-hccHHHHHHHHhhhhhhhhcchHHHHHHHHHHHH----H-----------------HhhHHHHHHHHHHHHHC
Confidence            765544 6777889999999998766654444332222210    0                 11223333333333333


Q ss_pred             chhHHHHHHHHHHHHHcCC-----ChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          179 DGLLRLYAYWAHLEQSMGK-----DMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       179 ~~~~~l~~~~a~~e~~~~~-----~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      +.....|...+.+....+.     ..++|...+.+++...|++..+|.....+.. ...++.+..+++.++.
T Consensus       177 p~n~~a~~~r~~~l~~~~~~~~~~~~~~ai~~~~~al~~~P~~~~~~~~l~~ll~-~~~~~~~~~~~~~~~~  247 (315)
T d2h6fa1         177 VRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQ-DRGLSKYPNLLNQLLD  247 (315)
T ss_dssp             TTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHT-TTCGGGCHHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHccccchhhhhHHhHHHHHHHHHhCCCchHHHHHHHHHHH-hcChHHHHHHHHHHHH
Confidence            4444455555555444442     2568889999999999999999987766644 3446788888988876

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=98.91  E-value=1.5e-07  Score=87.12  Aligned_cols=217  Identities=11%  Similarity=0.035  Sum_probs=137.7

Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHH
Q 008442            7 HLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATK   86 (565)
Q Consensus         7 ~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~   86 (565)
                      .+++.|......++....+|..........|+.+.+...|+++|..+|.++..|...+.... ..++.+.+...|++|+.
T Consensus        21 ~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~~~~a~~~lg~~~~-~~g~~~~A~~~~~~al~   99 (259)
T d1xnfa_          21 RMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLT-QAGNFDAAYEAFDSVLE   99 (259)
T ss_dssp             HHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccCCCCHHHHhhhchHHH-HHHHHHHhhhhhhHHHH
Confidence            35566666655556677788888888888999999999999999999999999998876544 45578889999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHH
Q 008442           87 NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQR  166 (565)
Q Consensus        87 ~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~  166 (565)
                      ..|.....|......+ ...+..+.+...|++++...+......+.+.....  .   .          +.......+..
T Consensus       100 ~~p~~~~a~~~lg~~~-~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~--~---~----------~~~~~~~~~~~  163 (259)
T d1xnfa_         100 LDPTYNYAHLNRGIAL-YYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQ--K---L----------DEKQAKEVLKQ  163 (259)
T ss_dssp             HCTTCTHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH--H---H----------CHHHHHHHHHH
T ss_pred             HHhhhhhhHHHHHHHH-HHHhhHHHHHHHHHHHHhhccccHHHHHHHHHHHH--H---h----------hhHHHHHHHHH
Confidence            9999888888776544 34688999999999999865543322221111111  0   0          00001111111


Q ss_pred             HHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          167 ASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       167 a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ...    .....+....+...+.......+ ....+...+...+...+.....|...+.+....|+++.|...|+++|.
T Consensus       164 ~~~----~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  237 (259)
T d1xnfa_         164 HFE----KSDKEQWGWNIVEFYLGNISEQT-LMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVA  237 (259)
T ss_dssp             HHH----HSCCCSTHHHHHHHHTTSSCHHH-HHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             Hhh----ccchhhhhhhHHHHHHHHHHHHH-HHHHHHHHHHHhhhcCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            111    11111111111111100000001 123334444444444566677888888888999999999999999997

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.66  E-value=4.9e-07  Score=87.24  Aligned_cols=232  Identities=7%  Similarity=-0.078  Sum_probs=148.0

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhc----------CCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc-
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS----------GDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL-   71 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~----------~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~-   71 (565)
                      ++...|+.+|..+|.    +..+|..--......          +....+..+|++++..+|.++.+|......+.... 
T Consensus        47 ~al~~~~~~l~~~P~----~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~pk~~~~~~~~~~~~~~~~~  122 (334)
T d1dcea1          47 SVLELTSQILGANPD----FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPE  122 (334)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCSS
T ss_pred             HHHHHHHHHHHHCCC----cHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhCCCcHHHHHHhhHHHHHhcc
Confidence            467789999998887    788885444333221          22456888999999999999999988876544333 


Q ss_pred             chhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccc
Q 008442           72 KVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEV  151 (565)
Q Consensus        72 ~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~  151 (565)
                      .+.+.+...+++|+...|.....|...+-......+..+.+...+++++...+.....+..+-..+.    ....+.+..
T Consensus       123 ~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p~~~~a~~~l~~~~~----~~~~~~~A~  198 (334)
T d1dcea1         123 PNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLP----QLHPQPDSG  198 (334)
T ss_dssp             CCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHH----HHSCCCCSS
T ss_pred             ccHHHHHHHHHHHHhhCchhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCCCCHHHHHHHHHHHH----HhcCHHHHH
Confidence            2457789999999999998887776555445555788899999999999887765554443322222    111111111


Q ss_pred             hhhhhHHHHHHHHHHHHHHHHhhh--cCCchhHHHH--------------HHHHHHHHHcCCChHHHHHHHHHHHHHccc
Q 008442          152 EGVLDYSLIRETFQRASDYLSEQM--KNTDGLLRLY--------------AYWAHLEQSMGKDMVSARGVWERLLKISGA  215 (565)
Q Consensus       152 e~~~~~~~~~~~~~~a~~~l~~~~--~~~~~~~~l~--------------~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~  215 (565)
                      ..+..   +...+.....++....  ...+.....+              ...+......+ +...|...|.+++..+|.
T Consensus       199 ~~~~~---~~~~~~~~~~~~~~~~~l~~~~~a~~~~~~~l~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~p~  274 (334)
T d1dcea1         199 PQGRL---PENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEPLFRCELSVEKSTVLQ-SELESCKELQELEPENKW  274 (334)
T ss_dssp             SCCSS---CHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCCCCSSSCCCCHHHHHHHH-HHHHHHHHHHHHCTTCHH
T ss_pred             HHHHH---hHHhHHHHHHHHHHHHHhcchhHHHHHHHHHHHhCcchhhHHHHHHHHHHHHh-hHHHHHHHHHHHHhhCch
Confidence            11001   1111111111111111  1111111000              01122223334 677888899999999999


Q ss_pred             hHHHHHHHHHHHHHcCChHHHHHHHHHHHhc
Q 008442          216 MLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       216 ~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~  246 (565)
                      +..+|...+......|+++.|.+.|++++..
T Consensus       275 ~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~l  305 (334)
T d1dcea1         275 CLLTIILLMRALDPLLYEKETLQYFSTLKAV  305 (334)
T ss_dssp             HHHHHHHHHHHHCTGGGHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999873

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.64  E-value=9.6e-07  Score=84.50  Aligned_cols=190  Identities=11%  Similarity=0.089  Sum_probs=135.1

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcC-CchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSG-DPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVY   81 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~-~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~   81 (565)
                      ++-..|+.+|.-+|.    +..+|..-.......+ +.+.+...|+++|..+|.+..+|......+. ..+..+.+...|
T Consensus        61 ~Al~~~~~ai~lnP~----~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~~~~a~~~~~~~~~-~l~~~~eAl~~~  135 (315)
T d2h6fa1          61 RAFKLTRDAIELNAA----NYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVE-WLRDPSQELEFI  135 (315)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HHTCCTTHHHHH
T ss_pred             HHHHHHHHHHHHCCC----ChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHhhhhHHHHHhHHHH-hhccHHHHHHHH
Confidence            356788888998887    8999988887766655 6899999999999999999999999876554 455778899999


Q ss_pred             HHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHH
Q 008442           82 SRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIR  161 (565)
Q Consensus        82 erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~  161 (565)
                      ++|+...|.+...|......+. ..+..+++...|++||...+.....|......+.     ..  ....    +    .
T Consensus       136 ~kal~~dp~n~~a~~~~~~~~~-~~~~~~~Al~~~~~al~~~p~n~~a~~~r~~~l~-----~~--~~~~----~----~  199 (315)
T d2h6fa1         136 ADILNQDAKNYHAWQHRQWVIQ-EFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVIS-----NT--TGYN----D----R  199 (315)
T ss_dssp             HHHHHHCTTCHHHHHHHHHHHH-HHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHH-----HT--TCSC----S----H
T ss_pred             hhhhhhhhcchHHHHHHHHHHH-HHHhhHHHHHHHHHHHHHCCccHHHHHHHHHHHH-----Hc--cccc----h----h
Confidence            9999999999999998776443 4577788999999999877654433332222111     00  0000    1    1


Q ss_pred             HHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccc
Q 008442          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA  215 (565)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~  215 (565)
                      ..+++++..+...+...+.....|.....+... . ..+.+..+++.++...++
T Consensus       200 ~~~~~ai~~~~~al~~~P~~~~~~~~l~~ll~~-~-~~~~~~~~~~~~~~l~~~  251 (315)
T d2h6fa1         200 AVLEREVQYTLEMIKLVPHNESAWNYLKGILQD-R-GLSKYPNLLNQLLDLQPS  251 (315)
T ss_dssp             HHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTT-T-CGGGCHHHHHHHHHHTTT
T ss_pred             hhhHHhHHHHHHHHHhCCCchHHHHHHHHHHHh-c-ChHHHHHHHHHHHHhCCC
Confidence            334555555555555455556667666555433 3 467888999999887554

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=98.60  E-value=1.8e-06  Score=79.56  Aligned_cols=197  Identities=11%  Similarity=0.044  Sum_probs=123.8

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...|+.+|.-+|.    +..+|..........|+.+.+...|+++|...|.+...|...+..+.. .+..+.+...|+
T Consensus        55 ~A~~~~~~al~l~p~----~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~-~g~~~~A~~~~~  129 (259)
T d1xnfa_          55 LARNDFSQALAIRPD----MPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYY-GGRDKLAQDDLL  129 (259)
T ss_dssp             HHHHHHHHHHHHCCC----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHH-TTCHHHHHHHHH
T ss_pred             HHHHHHHHhhccCCC----CHHHHhhhchHHHHHHHHHHhhhhhhHHHHHHhhhhhhHHHHHHHHHH-HhhHHHHHHHHH
Confidence            467889999998887    788999999999999999999999999999999999999998875554 446788999999


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcccccHHH-HHHHHHHHHHHHHHHhhccccchhhhhHHHHH
Q 008442           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEE-YLDLFLTRIDGLRRRILFSGEVEGVLDYSLIR  161 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~~~~-~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~  161 (565)
                      ++++..|.....+..... ........+....+...........+.. .+....            ... .       ..
T Consensus       130 ~al~~~p~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~-~-------~~  188 (259)
T d1xnfa_         130 AFYQDDPNDPFRSLWLYL-AEQKLDEKQAKEVLKQHFEKSDKEQWGWNIVEFYL------------GNI-S-------EQ  188 (259)
T ss_dssp             HHHHHCTTCHHHHHHHHH-HHHHHCHHHHHHHHHHHHHHSCCCSTHHHHHHHHT------------TSS-C-------HH
T ss_pred             HHHhhccccHHHHHHHHH-HHHHhhhHHHHHHHHHHhhccchhhhhhhHHHHHH------------HHH-H-------HH
Confidence            999999987654332221 1122232333333334333332222111 111100            000 0       01


Q ss_pred             HHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHH
Q 008442          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISME  227 (565)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e  227 (565)
                      ..+..+...+.......+.....|...+.++...| +++.|...|++++..+|++. ++..++.++
T Consensus       189 ~~~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g-~~~~A~~~~~~al~~~p~~~-~~~~~a~~~  252 (259)
T d1xnfa_         189 TLMERLKADATDNTSLAEHLSETNFYLGKYYLSLG-DLDSATALFKLAVANNVHNF-VEHRYALLE  252 (259)
T ss_dssp             HHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHTTCCTTC-HHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhcCcccHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHcCCCCH-HHHHHHHHH
Confidence            12222222221111111223445556678888888 99999999999999988764 333444444

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.37  E-value=2.5e-06  Score=82.12  Aligned_cols=207  Identities=9%  Similarity=-0.089  Sum_probs=137.3

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhc--CCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHH
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS--GDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVY   81 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~--~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~   81 (565)
                      +...|+.+|..+|.    +...|..........  ++.+.+...+++++..+|.+...|...+-......+..+.+...|
T Consensus        92 al~~~~~~l~~~pk----~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Al~~~  167 (334)
T d1dcea1          92 ELGFLESCLRVNPK----SYGTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFT  167 (334)
T ss_dssp             HHHHHHHHHHHCTT----CHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHH
T ss_pred             HHHHHHHHHHhCCC----cHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhCchhhhhhhhHHHHHHHhccccHHHHHHH
Confidence            55668888888877    888898777665554  456789999999999999999998766544555556677899999


Q ss_pred             HHHHHcCCCCHHHHHHHHHHHHHhcCCHHH-------HHHHHHHHH-------hccc-c-cHHHHHHHHHHHHHHHHHHh
Q 008442           82 SRATKNCPWVGELWVRSLLSLERSRASEEE-------ISTVFEKSL-------LCAF-S-TFEEYLDLFLTRIDGLRRRI  145 (565)
Q Consensus        82 erAl~~~p~~~~lW~~yi~~le~~~~~~~~-------~~~if~ral-------~~~~-~-~~~~~~~~~~~~~~~~~r~~  145 (565)
                      ++++...|.....|......+.. .+..++       +..++...+       .... . ..+.          +.+...
T Consensus       168 ~~~i~~~p~~~~a~~~l~~~~~~-~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~a~~~----------~~~~l~  236 (334)
T d1dcea1         168 DSLITRNFSNYSSWHYRSCLLPQ-LHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWF----------YHRWLL  236 (334)
T ss_dssp             HTTTTTTCCCHHHHHHHHHHHHH-HSCCCCSSSCCSSCHHHHHHHHHHHHHHHHHCSSCSHHHH----------HHHHHH
T ss_pred             HHHHHcCCCCHHHHHHHHHHHHH-hcCHHHHHHHHHHhHHhHHHHHHHHHHHHHhcchhHHHHH----------HHHHHH
Confidence            99999999999999775543333 222221       222222211       1110 1 0000          111111


Q ss_pred             hccccc---hhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHH
Q 008442          146 LFSGEV---EGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQS  222 (565)
Q Consensus       146 ~~~~~~---e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~  222 (565)
                      ......   ............+..++..+...+..++.....|...+......+ +.++|...|++++...|....+|..
T Consensus       237 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~~-~~~eA~~~~~~ai~ldP~~~~y~~~  315 (334)
T d1dcea1         237 GRAEPLFRCELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLL-YEKETLQYFSTLKAVDPMRAAYLDD  315 (334)
T ss_dssp             SCCCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTGG-GHHHHHHHHHHHHHHCGGGHHHHHH
T ss_pred             hCcchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHCcccHHHHHH
Confidence            111111   111122233456677888887777777777888888888888888 9999999999999999998888887


Q ss_pred             HHHH
Q 008442          223 YISM  226 (565)
Q Consensus       223 yi~~  226 (565)
                      ....
T Consensus       316 L~~~  319 (334)
T d1dcea1         316 LRSK  319 (334)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6554

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.08  E-value=8.5e-05  Score=58.97  Aligned_cols=97  Identities=18%  Similarity=0.047  Sum_probs=81.2

Q ss_pred             HHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCC
Q 008442           29 YLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRAS  108 (565)
Q Consensus        29 yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~~~~~  108 (565)
                      =.+.....|+++.+..+|+++|..+|.++.+|...+..... .++.+.+...|++|+...|.....|......+. ..+.
T Consensus         9 ~g~~~~~~g~~~eAi~~~~~al~~~p~~~~~~~~~a~~~~~-~~~~~~A~~~~~~al~~~p~~~~~~~~~g~~~~-~~~~   86 (117)
T d1elwa_           9 KGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAK-KGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALE-FLNR   86 (117)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-HTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HTTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCcchhhhhcccccccc-cccccccchhhhhHHHhccchhhHHHHHHHHHH-HccC
Confidence            34445667899999999999999999999999999875554 457788999999999999999999988877444 4788


Q ss_pred             HHHHHHHHHHHHhcccccH
Q 008442          109 EEEISTVFEKSLLCAFSTF  127 (565)
Q Consensus       109 ~~~~~~if~ral~~~~~~~  127 (565)
                      .+++...|++|+...+...
T Consensus        87 ~~~A~~~~~~a~~~~p~~~  105 (117)
T d1elwa_          87 FEEAKRTYEEGLKHEANNP  105 (117)
T ss_dssp             HHHHHHHHHHHHTTCTTCH
T ss_pred             HHHHHHHHHHHHHhCCCCH
Confidence            9999999999998766543

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=97.99  E-value=0.001  Score=62.48  Aligned_cols=121  Identities=13%  Similarity=0.081  Sum_probs=74.0

Q ss_pred             HHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccc----hHHHHHHHHHHHHHcCChHHHH
Q 008442          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA----MLEAWQSYISMEIELDHINEAR  237 (565)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~----~~~lw~~yi~~e~~~~~~~~aR  237 (565)
                      ..+.++...........+....++...+.+....+ +.+.|...+++++...+.    ....|...+......|+++.|.
T Consensus       193 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~  271 (366)
T d1hz4a_         193 SQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTG-DKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAE  271 (366)
T ss_dssp             HHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcc-cHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCHHHHH
Confidence            34444444443322222223344555666676767 899999999988876332    2445666677778899999999


Q ss_pred             HHHHHHHhcccCCCCcHHHHHHH---HHHHHHhCCHHHHHHHHHHHhhH
Q 008442          238 SIYKRCYSKRFTGTGSEDICHAW---LRFEREYGTLEDFDHSVQKVTPR  283 (565)
Q Consensus       238 ~i~~~al~~~~~~~~~~~i~~~~---~~fE~~~G~~~~~~~~~~k~~~~  283 (565)
                      .+|++++...............|   .......|+.+.+...+.+++.-
T Consensus       272 ~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~l  320 (366)
T d1hz4a_         272 IVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKL  320 (366)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            99999875321222333333333   34455668888888777776543

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.89  E-value=0.00036  Score=58.49  Aligned_cols=102  Identities=10%  Similarity=-0.099  Sum_probs=83.8

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Q 008442           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER  104 (565)
Q Consensus        25 ~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~  104 (565)
                      ....-.+...+.|+++.+...|+++|..+|.+..+|..++..+. ..+..+.+...|++||...|.....|......+. 
T Consensus        12 ~l~~~gn~~~~~~~y~~A~~~~~~al~~~p~~~~~~~~lg~~~~-~~~~~~~A~~~~~kal~~~p~~~~a~~~~g~~~~-   89 (159)
T d1a17a_          12 ELKTQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYL-RTECYGYALGDATRAIELDKKYIKGYYRRAASNM-   89 (159)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHcCCHHHHHHHhhhccccchhhhhhhhhhHHHHH-hccccchHHHHHHHHHHHcccchHHHHHHHHHHH-
Confidence            34444555567899999999999999999999999999987555 4457888999999999999999999988877444 


Q ss_pred             hcCCHHHHHHHHHHHHhcccccHH
Q 008442          105 SRASEEEISTVFEKSLLCAFSTFE  128 (565)
Q Consensus       105 ~~~~~~~~~~if~ral~~~~~~~~  128 (565)
                      ..++.+++...|++++...+....
T Consensus        90 ~~g~~~eA~~~~~~a~~~~p~~~~  113 (159)
T d1a17a_          90 ALGKFRAALRDYETVVKVKPHDKD  113 (159)
T ss_dssp             HTTCHHHHHHHHHHHHHHSTTCHH
T ss_pred             HcCCHHHHHHHHHHHHHcCCCCHH
Confidence            478899999999999986655433

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.86  E-value=0.00012  Score=57.97  Aligned_cols=95  Identities=14%  Similarity=0.090  Sum_probs=74.9

Q ss_pred             HHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHH
Q 008442          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRC  243 (565)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~a  243 (565)
                      |++|+.++...+...+....+|...+......+ +++.|...|+++++..|++...|...+......|+++.|...|+++
T Consensus        19 ~~eAi~~~~~al~~~p~~~~~~~~~a~~~~~~~-~~~~A~~~~~~al~~~p~~~~~~~~~g~~~~~~~~~~~A~~~~~~a   97 (117)
T d1elwa_          19 IDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKG-DYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRFEEAKRTYEEG   97 (117)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCcchhhhhcccccccccc-cccccchhhhhHHHhccchhhHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            455555555555545666778888888888888 9999999999999999999999999999999999999999999999


Q ss_pred             HhcccCCCCcHHHHHHHHH
Q 008442          244 YSKRFTGTGSEDICHAWLR  262 (565)
Q Consensus       244 l~~~~~~~~~~~i~~~~~~  262 (565)
                      +..  .. ....++..+-.
T Consensus        98 ~~~--~p-~~~~~~~~l~~  113 (117)
T d1elwa_          98 LKH--EA-NNPQLKEGLQN  113 (117)
T ss_dssp             HTT--CT-TCHHHHHHHHH
T ss_pred             HHh--CC-CCHHHHHHHHH
Confidence            973  22 23455554443

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=97.82  E-value=9.4e-05  Score=58.17  Aligned_cols=94  Identities=10%  Similarity=-0.034  Sum_probs=77.8

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Q 008442           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER  104 (565)
Q Consensus        25 ~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~  104 (565)
                      .|..........|++..+...|+++|..+|.++.+|........ ..+..+.+...|++|+...|.....|......+ .
T Consensus        18 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~-~~~~~~~A~~~~~~al~~~p~~~~a~~~la~~y-~   95 (112)
T d1hxia_          18 NPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQA-ENEKDGLAIIALNHARMLDPKDIAVHAALAVSH-T   95 (112)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH-H
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHhhhcccccccchhhhhhhhhhh-hhhhHHHhhcccccccccccccccchHHHHHHH-H
Confidence            45556666677899999999999999999999999999988654 445788899999999999999999998876633 3


Q ss_pred             hcCCHHHHHHHHHHHH
Q 008442          105 SRASEEEISTVFEKSL  120 (565)
Q Consensus       105 ~~~~~~~~~~if~ral  120 (565)
                      ..++.+++.+.|+|.|
T Consensus        96 ~~g~~~~A~~~l~~~l  111 (112)
T d1hxia_          96 NEHNANAALASLRAWL  111 (112)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHh
Confidence            4567888888888875

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.72  E-value=0.00017  Score=60.53  Aligned_cols=93  Identities=13%  Similarity=-0.143  Sum_probs=81.9

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...|+.+|..+|.    +...|..+.......|+.+.+...|++||..+|.+...|..++..+. ..++.+.+...|+
T Consensus        28 ~A~~~~~~al~~~p~----~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~~~~a~~~~g~~~~-~~g~~~eA~~~~~  102 (159)
T d1a17a_          28 NAIKFYSQAIELNPS----NAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNM-ALGKFRAALRDYE  102 (159)
T ss_dssp             HHHHHHHHHHHHSTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHH
T ss_pred             HHHHHhhhccccchh----hhhhhhhhHHHHHhccccchHHHHHHHHHHHcccchHHHHHHHHHHH-HcCCHHHHHHHHH
Confidence            467789999998887    88999999999999999999999999999999999999999887554 4557888999999


Q ss_pred             HHHHcCCCCHHHHHHHHH
Q 008442           83 RATKNCPWVGELWVRSLL  100 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~  100 (565)
                      +|+...|....++..+..
T Consensus       103 ~a~~~~p~~~~~~~~l~~  120 (159)
T d1a17a_         103 TVVKVKPHDKDAKMKYQE  120 (159)
T ss_dssp             HHHHHSTTCHHHHHHHHH
T ss_pred             HHHHcCCCCHHHHHHHHH
Confidence            999999999888776543

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=97.59  E-value=0.00013  Score=57.29  Aligned_cols=84  Identities=12%  Similarity=0.002  Sum_probs=44.7

Q ss_pred             HHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCCcHHHHHHHHHHHHHhCCHHH
Q 008442          193 QSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLED  272 (565)
Q Consensus       193 ~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~  272 (565)
                      ...| +++.|...|++++...|+++.+|..........++++.|...|++++..  . +.....|..+...-...|+.+.
T Consensus        27 ~~~g-~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~-p~~~~a~~~la~~y~~~g~~~~  102 (112)
T d1hxia_          27 LKLA-NLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARML--D-PKDIAVHAALAVSHTNEHNANA  102 (112)
T ss_dssp             HHTT-CHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--C-TTCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHh-hhHHHHHHHhhhcccccccchhhhhhhhhhhhhhhHHHhhccccccccc--c-cccccchHHHHHHHHHCCCHHH
Confidence            3444 5666666666666666666666666666666666666666666666552  1 1222344444444444455555


Q ss_pred             HHHHHHHH
Q 008442          273 FDHSVQKV  280 (565)
Q Consensus       273 ~~~~~~k~  280 (565)
                      +.+++++.
T Consensus       103 A~~~l~~~  110 (112)
T d1hxia_         103 ALASLRAW  110 (112)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            55555443

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.50  E-value=0.00054  Score=59.40  Aligned_cols=96  Identities=10%  Similarity=-0.089  Sum_probs=80.3

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Q 008442           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER  104 (565)
Q Consensus        25 ~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~  104 (565)
                      ....-.+-..+.|+++.|...|++||...|.++.+|...+.... ..++.+.+...|++||...|.....|......+ .
T Consensus         6 ~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~p~~~~~~~~lg~~y~-~~~~~~~Ai~~~~~al~l~p~~~~a~~~lg~~~-~   83 (201)
T d2c2la1           6 ELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYL-KMQQPEQALADCRRALELDGQSVKAHFFLGQCQ-L   83 (201)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHH-HTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHH-H
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHh-hhhhhhhhhHHHHHHHHhCCCcHHHHHHHHHHH-H
Confidence            34444555667899999999999999999999999999887554 455788899999999999999999998877644 4


Q ss_pred             hcCCHHHHHHHHHHHHhc
Q 008442          105 SRASEEEISTVFEKSLLC  122 (565)
Q Consensus       105 ~~~~~~~~~~if~ral~~  122 (565)
                      ..+.++++...|++|+..
T Consensus        84 ~l~~~~~A~~~~~~al~l  101 (201)
T d2c2la1          84 EMESYDEAIANLQRAYSL  101 (201)
T ss_dssp             HTTCHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHh
Confidence            478899999999999963

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.44  E-value=0.0063  Score=56.07  Aligned_cols=165  Identities=13%  Similarity=0.137  Sum_probs=94.0

Q ss_pred             hcchhhHHHHHHHHHHHcCC---C---CHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccc--ccHHHHHHHHHHHHHHH
Q 008442           70 TLKVGNVVRDVYSRATKNCP---W---VGELWVRSLLSLERSRASEEEISTVFEKSLLCAF--STFEEYLDLFLTRIDGL  141 (565)
Q Consensus        70 ~~~~~~~~~~v~erAl~~~p---~---~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~--~~~~~~~~~~~~~~~~~  141 (565)
                      ..++.+.+...|++|+..+.   .   ....|..... +-...+..+++...|++++....  .........+......+
T Consensus        49 ~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~-~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~  127 (290)
T d1qqea_          49 LRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYK-CFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEIL  127 (290)
T ss_dssp             HTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHH-HHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHHHHHhH
Confidence            33455666666666666321   1   1233443333 22335667777777777775321  11111111111111111


Q ss_pred             HHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccch-----
Q 008442          142 RRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM-----  216 (565)
Q Consensus       142 ~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~-----  216 (565)
                      .         ....++..+...|.+++++.... ........++...+.+....+ ++++|..+|++++...+..     
T Consensus       128 ~---------~~~~~~~~A~~~~~~A~~l~~~~-~~~~~~~~~~~~la~~~~~~g-~y~~A~~~~~~~~~~~~~~~~~~~  196 (290)
T d1qqea_         128 E---------NDLHDYAKAIDCYELAGEWYAQD-QSVALSNKCFIKCADLKALDG-QYIEASDIYSKLIKSSMGNRLSQW  196 (290)
T ss_dssp             H---------HTTCCHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHTTSSCTTTGG
T ss_pred             h---------hHHHHHHHHHHHHHHHHHHHHhc-CchhhhhhHHHHHHHHHHHcC-hHHHHHHHHHHHHHhCccchhhhh
Confidence            0         00124556666777777655331 111223455667788888888 9999999999999874432     


Q ss_pred             --HHHHHHHHHHHHHcCChHHHHHHHHHHHhc
Q 008442          217 --LEAWQSYISMEIELDHINEARSIYKRCYSK  246 (565)
Q Consensus       217 --~~lw~~yi~~e~~~~~~~~aR~i~~~al~~  246 (565)
                        ..++...+......++++.|...|++++..
T Consensus       197 ~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~  228 (290)
T d1qqea_         197 SLKDYFLKKGLCQLAATDAVAAARTLQEGQSE  228 (290)
T ss_dssp             GHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC
T ss_pred             hHHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence              235556666667789999999999999763

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.26  E-value=0.00045  Score=59.93  Aligned_cols=81  Identities=19%  Similarity=0.197  Sum_probs=68.5

Q ss_pred             HHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHH
Q 008442          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRC  243 (565)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~a  243 (565)
                      |.+|+.++...+...|....+|...+..+...+ +++.|...|+++++..|+++..|...+......|+++.|...|++|
T Consensus        20 ~~~Ai~~~~kal~~~p~~~~~~~~lg~~y~~~~-~~~~Ai~~~~~al~l~p~~~~a~~~lg~~~~~l~~~~~A~~~~~~a   98 (201)
T d2c2la1          20 YPEAAACYGRAITRNPLVAVYYTNRALCYLKMQ-QPEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRA   98 (201)
T ss_dssp             HHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHhHHHHHhhhh-hhhhhhHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            455555555555445556778888888898888 9999999999999999999999999999999999999999999999


Q ss_pred             Hh
Q 008442          244 YS  245 (565)
Q Consensus       244 l~  245 (565)
                      +.
T Consensus        99 l~  100 (201)
T d2c2la1          99 YS  100 (201)
T ss_dssp             HH
T ss_pred             HH
Confidence            86

>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=97.23  E-value=0.00024  Score=51.23  Aligned_cols=70  Identities=14%  Similarity=0.213  Sum_probs=56.3

Q ss_pred             CCeEEEcCCCCCC------CH---HHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHcCCcccCCeE
Q 008442          391 ECTAFLSNINLKA------TY---EDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAKNKQMFLGKK  461 (565)
Q Consensus       391 ~~~l~V~nl~~~~------~~---~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~~~~~~~g~~  461 (565)
                      ..||.|.=..++.      ++   .+|-+.|..||+|.-+|++.+        --.|+|.+-.+|.+|+.+++..+.|+.
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            4578775443222      22   467778899999999999875        589999999999999999999999999


Q ss_pred             EEEeecC
Q 008442          462 LSIARSN  468 (565)
Q Consensus       462 l~v~~a~  468 (565)
                      |.|....
T Consensus        87 l~It~~~   93 (95)
T d1ufwa_          87 VKISGPS   93 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEecCC
Confidence            9997643

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.22  E-value=0.0014  Score=51.95  Aligned_cols=92  Identities=10%  Similarity=-0.098  Sum_probs=70.3

Q ss_pred             HhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc--chhhHHHHHHHHHHHcCCCCH--HHHHHHHHHHHHhcCCH
Q 008442           34 QSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL--KVGNVVRDVYSRATKNCPWVG--ELWVRSLLSLERSRASE  109 (565)
Q Consensus        34 ~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~--~~~~~~~~v~erAl~~~p~~~--~lW~~yi~~le~~~~~~  109 (565)
                      ...++.+++...|+++|...|.+++++..|+..+....  .+...+..+|++++..-|...  ..|..-.. .....+++
T Consensus        10 ~~~~~l~~Ae~~Y~~aL~~~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~-~y~~~g~~   88 (122)
T d1nzna_          10 VSVEDLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAV-GNYRLKEY   88 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHH-HHHHTTCH
T ss_pred             cCHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHH-HHHHHhhh
Confidence            34457788999999999999999999999998876433  344568999999998766443  34543332 44457999


Q ss_pred             HHHHHHHHHHHhccccc
Q 008442          110 EEISTVFEKSLLCAFST  126 (565)
Q Consensus       110 ~~~~~if~ral~~~~~~  126 (565)
                      +++...|+++|...|..
T Consensus        89 ~~A~~~~~~aL~~~P~~  105 (122)
T d1nzna_          89 EKALKYVRGLLQTEPQN  105 (122)
T ss_dssp             HHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHhCcCC
Confidence            99999999999876653

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.14  E-value=0.0046  Score=53.24  Aligned_cols=99  Identities=4%  Similarity=-0.124  Sum_probs=57.6

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCC----------
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV----------   91 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~----------   91 (565)
                      +..+|..........|+.+.+...|++||..+|.+...|....... ...++.+.+...|++|+...+..          
T Consensus        35 ~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~~~~a~~~~g~~~-~~~g~~~~A~~~~~kAl~~~~~n~~~~~~~~~~  113 (192)
T d1hh8a_          35 HSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLY-YQTEKYDLAIKDLKEALIQLRGNQLIDYKILGL  113 (192)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTB
T ss_pred             CHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhhhhhHHHHHHHH-HhhccHHHHHHHHHHHHHhCccCchHHHHHhhh
Confidence            4456666666666667777777777777777777777776665533 23445566666777776643321          


Q ss_pred             ------HHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 008442           92 ------GELWVRSLLSLERSRASEEEISTVFEKSLLC  122 (565)
Q Consensus        92 ------~~lW~~yi~~le~~~~~~~~~~~if~ral~~  122 (565)
                            .++|..... +....+..+++...|.+|+..
T Consensus       114 ~~~~~~~e~~~n~a~-~~~~~~~~~~A~~~l~~A~~~  149 (192)
T d1hh8a_         114 QFKLFACEVLYNIAF-MYAKKEEWKKAEEQLALATSM  149 (192)
T ss_dssp             CCEEEHHHHHHHHHH-HHHHTTCHHHHHHHHHHHHTT
T ss_pred             hcccchHHHHHHHHH-HHHHCCCHHHHHHHHHHHHhc
Confidence                  233333333 222345666666666666653

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.05  E-value=0.0016  Score=53.48  Aligned_cols=85  Identities=9%  Similarity=-0.032  Sum_probs=41.4

Q ss_pred             hhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhc----------CCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc--
Q 008442            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS----------GDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL--   71 (565)
Q Consensus         4 ~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~----------~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~--   71 (565)
                      ++..||.+|..+|.    +.++|..+.......          +..+.+...|++||..+|.+...|......+....  
T Consensus        16 A~~~~e~al~~~P~----~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~P~~~~a~~~lG~~y~~~g~~   91 (145)
T d1zu2a1          16 IRQDAENTYKSNPL----DADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYTSFAFL   91 (145)
T ss_dssp             HHHHHHHHHHHCTT----CHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhCCc----chHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhcchhhHHHhhHHHHHHHcccc
Confidence            45556666666655    455555444433211          12244556666666666666666554433222111  


Q ss_pred             --------chhhHHHHHHHHHHHcCCCCH
Q 008442           72 --------KVGNVVRDVYSRATKNCPWVG   92 (565)
Q Consensus        72 --------~~~~~~~~v~erAl~~~p~~~   92 (565)
                              +..+.+...|++|+..-|...
T Consensus        92 ~~~~~~~~~~~~~A~~~~~kal~l~P~~~  120 (145)
T d1zu2a1          92 TPDETEAKHNFDLATQFFQQAVDEQPDNT  120 (145)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHCTTCH
T ss_pred             hhhHHHHHHhHHHhhhhhhcccccCCCHH
Confidence                    112345555555555555543

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.93  E-value=0.017  Score=48.36  Aligned_cols=89  Identities=9%  Similarity=0.107  Sum_probs=69.0

Q ss_pred             hHHHHHHHHHHHHHHHHhhhcCCch--------hHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHH
Q 008442          156 DYSLIRETFQRASDYLSEQMKNTDG--------LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISME  227 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~~~~~~--------~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e  227 (565)
                      ++..+...|.+|+.++.......+.        ...++...+..+...+ +++.|...++++|...|+++..|...+...
T Consensus        28 ~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~-~~~~A~~~~~~al~~~p~~~~a~~~~g~~~  106 (170)
T d1p5qa1          28 KYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQ-AFSAAIESCNKALELDSNNEKGLSRRGEAH  106 (170)
T ss_dssp             CHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhh-hcccccchhhhhhhccccchhhhHHHHHHH
Confidence            5556667777777766443322211        1123344566677788 999999999999999999999999999999


Q ss_pred             HHcCChHHHHHHHHHHHh
Q 008442          228 IELDHINEARSIYKRCYS  245 (565)
Q Consensus       228 ~~~~~~~~aR~i~~~al~  245 (565)
                      ...|+++.|...|++++.
T Consensus       107 ~~~g~~~~A~~~~~~al~  124 (170)
T d1p5qa1         107 LAVNDFELARADFQKVLQ  124 (170)
T ss_dssp             HHTTCHHHHHHHHHHHHH
T ss_pred             HHhhhHHHHHHHHHHHHH
Confidence            999999999999999987

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.88  E-value=0.018  Score=49.32  Aligned_cols=78  Identities=14%  Similarity=0.089  Sum_probs=65.9

Q ss_pred             HHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHH
Q 008442          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRC  243 (565)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~a  243 (565)
                      |..|++.+...   .++...+|...+.++...+ +++.|...|+++|+..|+....|..........|+++.|.+.|++|
T Consensus        21 ~~~Al~~~~~i---~~~~~~~~~nlG~~~~~~g-~~~~A~~~~~kAl~ldp~~~~a~~~~g~~~~~~g~~~~A~~~~~kA   96 (192)
T d1hh8a_          21 WKGALDAFSAV---QDPHSRICFNIGCMYTILK-NMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDLAIKDLKEA   96 (192)
T ss_dssp             HHHHHHHHHTS---SSCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhc---CCCCHHHHHHHHHHHHHcC-CchhHHHHHHHHHHHhhhhhhhHHHHHHHHHhhccHHHHHHHHHHH
Confidence            55555555432   2334567777888888889 9999999999999999999999999999999999999999999999


Q ss_pred             Hh
Q 008442          244 YS  245 (565)
Q Consensus       244 l~  245 (565)
                      +.
T Consensus        97 l~   98 (192)
T d1hh8a_          97 LI   98 (192)
T ss_dssp             HH
T ss_pred             HH
Confidence            86

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.81  E-value=0.014  Score=48.94  Aligned_cols=97  Identities=6%  Similarity=-0.089  Sum_probs=69.8

Q ss_pred             hhhHHHHHHHhcCCCCCh-----------HhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc
Q 008442            3 NARAHLEEQISRQDLSDS-----------EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL   71 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~-----------~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~   71 (565)
                      .|...|+.+|...+....           -...+|........+.|+++.+...|+++|..+|.++..|...+.... ..
T Consensus        31 ~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~-~~  109 (170)
T d1p5qa1          31 QALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHL-AV  109 (170)
T ss_dssp             HHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HT
T ss_pred             HHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhccccchhhhHHHHHHHH-Hh
Confidence            366788888866543211           012334444555567789999999999999999999999988776443 55


Q ss_pred             chhhHHHHHHHHHHHcCCCCHHHHHHHHH
Q 008442           72 KVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (565)
Q Consensus        72 ~~~~~~~~v~erAl~~~p~~~~lW~~yi~  100 (565)
                      +..+.+...|++|+..-|.+..+...+..
T Consensus       110 g~~~~A~~~~~~al~l~P~n~~~~~~l~~  138 (170)
T d1p5qa1         110 NDFELARADFQKVLQLYPNNKAAKTQLAV  138 (170)
T ss_dssp             TCHHHHHHHHHHHHHHCSSCHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            57888999999999998988877655443

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=96.78  E-value=0.0059  Score=49.82  Aligned_cols=88  Identities=9%  Similarity=-0.067  Sum_probs=62.4

Q ss_pred             CchhHHHHHHHHHhcCCCCHHHHHHHHHHHHH---------hcchhhHHHHHHHHHHHcCCCCHHHHHHHHHHHHH---h
Q 008442           38 DPGRVQLLYERAITDFPVSSDLWLDYTQYLDK---------TLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER---S  105 (565)
Q Consensus        38 ~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~---------~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~le~---~  105 (565)
                      .++.+...||+||..+|.+.++|..+...+..         ..+..+.+...|++||+..|.....|......+..   .
T Consensus        12 ~fe~A~~~~e~al~~~P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~P~~~~a~~~lG~~y~~~g~~   91 (145)
T d1zu2a1          12 LFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYTSFAFL   91 (145)
T ss_dssp             HHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhcchhhHHHhhHHHHHHHcccc
Confidence            35678999999999999999999999865432         12234679999999999999998888654332211   1


Q ss_pred             cC-------CHHHHHHHHHHHHhcccc
Q 008442          106 RA-------SEEEISTVFEKSLLCAFS  125 (565)
Q Consensus       106 ~~-------~~~~~~~if~ral~~~~~  125 (565)
                      ..       .++.+...|++|+...+.
T Consensus        92 ~~~~~~~~~~~~~A~~~~~kal~l~P~  118 (145)
T d1zu2a1          92 TPDETEAKHNFDLATQFFQQAVDEQPD  118 (145)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHCTT
T ss_pred             hhhHHHHHHhHHHhhhhhhcccccCCC
Confidence            12       245666777777765544

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=96.69  E-value=0.033  Score=46.28  Aligned_cols=89  Identities=10%  Similarity=0.150  Sum_probs=66.1

Q ss_pred             hHHHHHHHHHHHHHHHHhhhcCCch--------hHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHH
Q 008442          156 DYSLIRETFQRASDYLSEQMKNTDG--------LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISME  227 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~~~~~~--------~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e  227 (565)
                      ++..+...|.+|+.++.........        ...++...+..+...+ ++.+|...+++++..+|++...|...+...
T Consensus        30 ~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~-~~~~Ai~~~~~al~l~p~~~~a~~~~~~~~  108 (168)
T d1kt1a1          30 KYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLR-EYTKAVECCDKALGLDSANEKGLYRRGEAQ  108 (168)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhh-hcccchhhhhhhhhcccchHHHHHHHHHHH
Confidence            3445555666666655433221110        1123334566667777 999999999999999999999999999999


Q ss_pred             HHcCChHHHHHHHHHHHh
Q 008442          228 IELDHINEARSIYKRCYS  245 (565)
Q Consensus       228 ~~~~~~~~aR~i~~~al~  245 (565)
                      ...|+++.|...|.+++.
T Consensus       109 ~~l~~~~~A~~~~~~al~  126 (168)
T d1kt1a1         109 LLMNEFESAKGDFEKVLE  126 (168)
T ss_dssp             HHTTCHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHH
Confidence            999999999999999997

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=96.66  E-value=0.019  Score=47.08  Aligned_cols=61  Identities=16%  Similarity=0.056  Sum_probs=54.7

Q ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          184 LYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ++...+..+...+ +++.|...++++|...|.++..|...+......|+++.|...|++++.
T Consensus        69 ~~~Nla~~~~~l~-~~~~Al~~~~~al~~~p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~  129 (153)
T d2fbna1          69 CNLNLATCYNKNK-DYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAAS  129 (153)
T ss_dssp             HHHHHHHHHHHTT-CHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHhhHHHHHHHhc-ccchhhhhhhccccccchhhhhhHHhHHHHHHcCCHHHHHHHHHHHHH
Confidence            3444566677778 999999999999999999999999999999999999999999999997

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.66  E-value=0.0037  Score=42.56  Aligned_cols=60  Identities=18%  Similarity=0.171  Sum_probs=50.5

Q ss_pred             HHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-cCCcccCCeEEEEeecC
Q 008442          406 EDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVA-KNKQMFLGKKLSIARSN  468 (565)
Q Consensus       406 ~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-~~~~~~~g~~l~v~~a~  468 (565)
                      +.|...|..+|.|.++.+.... .|..  .|-|...+..+|.-|+. ++...|++++|.|+++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-STTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            3455678999999999987653 4443  78999999999999998 89999999999999875

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.65  E-value=0.0058  Score=48.63  Aligned_cols=98  Identities=11%  Similarity=-0.062  Sum_probs=73.4

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHH---
Q 008442           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS---  101 (565)
Q Consensus        25 ~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~---  101 (565)
                      .+..-.+.....++++.+...|+++|..+|.+..+|...+..... .++.+.+...|++||...|.....|..+...   
T Consensus         6 ~~k~~G~~~~~~~~y~~Ai~~y~~al~~~p~~~~~~~~~a~~~~~-~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~   84 (128)
T d1elra_           6 KEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFE-KGDYNKCRELCEKAIEVGRENREDYRQIAKAYAR   84 (128)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-HTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHhHHHHHHH-cCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHH
Confidence            345555556677999999999999999999999999988875544 4578889999999999776555545443221   


Q ss_pred             ---HHHhcCCHHHHHHHHHHHHhcc
Q 008442          102 ---LERSRASEEEISTVFEKSLLCA  123 (565)
Q Consensus       102 ---le~~~~~~~~~~~if~ral~~~  123 (565)
                         .....+.++++...|++++...
T Consensus        85 lg~~~~~~~~~~~A~~~~~kal~~~  109 (128)
T d1elra_          85 IGNSYFKEEKYKDAIHFYNKSLAEH  109 (128)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHhcC
Confidence               2233577888999999988643

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.64  E-value=0.12  Score=47.02  Aligned_cols=167  Identities=9%  Similarity=-0.023  Sum_probs=100.2

Q ss_pred             HhcCCHHHHHHHHHHHHhccc--ccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCchh
Q 008442          104 RSRASEEEISTVFEKSLLCAF--STFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGL  181 (565)
Q Consensus       104 ~~~~~~~~~~~if~ral~~~~--~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~~~  181 (565)
                      +..+.++++...|++|+.+..  .........+.....+...          ..++..+...|.+++.++... ......
T Consensus        48 ~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~----------~~~~~~A~~~~~~a~~~~~~~-~~~~~~  116 (290)
T d1qqea_          48 RLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKS----------GGNSVNAVDSLENAIQIFTHR-GQFRRG  116 (290)
T ss_dssp             HHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH----------TTCHHHHHHHHHHHHHHHHHT-TCHHHH
T ss_pred             HHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH----------hCCcHHHHHHHHHhhHHhhhc-ccchhH
Confidence            346788999999999987421  1122222222222211111          124556667788887776442 222222


Q ss_pred             HHHHHHHHHHHHH-cCCChHHHHHHHHHHHHHc---cc---hHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccCCCC-c
Q 008442          182 LRLYAYWAHLEQS-MGKDMVSARGVWERLLKIS---GA---MLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTG-S  253 (565)
Q Consensus       182 ~~l~~~~a~~e~~-~~~~~~~ar~i~e~~l~~~---~~---~~~lw~~yi~~e~~~~~~~~aR~i~~~al~~~~~~~~-~  253 (565)
                      ...+...+.+... .+ +++.|...|++++...   +.   ...++...+.+....|+++.|..+|++++........ .
T Consensus       117 ~~~~~~l~~~~~~~~~-~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~  195 (290)
T d1qqea_         117 ANFKFELGEILENDLH-DYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQ  195 (290)
T ss_dssp             HHHHHHHHHHHHHTTC-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTG
T ss_pred             HHHHHHHHHhHhhHHH-HHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhh
Confidence            3344445555444 45 9999999999999762   22   2457888899999999999999999999874211111 1


Q ss_pred             H---HHHHHHHHHHHHhCCHHHHHHHHHHHhh
Q 008442          254 E---DICHAWLRFEREYGTLEDFDHSVQKVTP  282 (565)
Q Consensus       254 ~---~i~~~~~~fE~~~G~~~~~~~~~~k~~~  282 (565)
                      .   .++..-.......|+.+.+..++.++..
T Consensus       196 ~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~  227 (290)
T d1qqea_         196 WSLKDYFLKKGLCQLAATDAVAAARTLQEGQS  227 (290)
T ss_dssp             GGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGC
T ss_pred             hhHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            1   1222222233456888888888887753

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=96.63  E-value=0.011  Score=49.47  Aligned_cols=63  Identities=16%  Similarity=0.009  Sum_probs=56.9

Q ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ..++...+......+ +++.|...|+++|+..|++...|...+......|+++.|...|++++.
T Consensus        77 ~~~~~nla~~~~~~~-~~~~Ai~~~~~al~~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~  139 (169)
T d1ihga1          77 LSCVLNIGACKLKMS-DWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQE  139 (169)
T ss_dssp             HHHHHHHHHHHHHTT-CHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhc-ccchhhhhhhhhhhhhhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHH
Confidence            445556677777888 999999999999999999999999999999999999999999999997

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.55  E-value=0.0028  Score=63.67  Aligned_cols=62  Identities=5%  Similarity=0.015  Sum_probs=56.0

Q ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      ..+...+.+....+ +++.|+..|.+++...|++...|...+......|+...|...|.+||.
T Consensus       153 ~~~~~LG~l~~~~~-~~~~A~~~y~~A~~l~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~  214 (497)
T d1ya0a1         153 HCLVHLGDIARYRN-QTSQAESYYRHAAQLVPSNGQPYNQLAILASSKGDHLTTIFYYCRSIA  214 (497)
T ss_dssp             HHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHcc-cHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            45556677777777 999999999999999999999999999999999999999999999986

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.53  E-value=0.0037  Score=49.43  Aligned_cols=83  Identities=8%  Similarity=-0.056  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcC--CChHHHHHHHHHHHHHccc--hHHHHHHHHHHHHHcCChHHHHH
Q 008442          163 TFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMG--KDMVSARGVWERLLKISGA--MLEAWQSYISMEIELDHINEARS  238 (565)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~--~~~~~ar~i~e~~l~~~~~--~~~lw~~yi~~e~~~~~~~~aR~  238 (565)
                      -|++|.+.+...+...+.....+..|+.......  +++.+|..+|++++...+.  ....|...+......|+++.|+.
T Consensus        14 ~l~~Ae~~Y~~aL~~~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y~~~g~~~~A~~   93 (122)
T d1nzna_          14 DLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALK   93 (122)
T ss_dssp             HHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHHHhhhHHHHH
Confidence            3444444444444444555666667776665422  1455788888888876543  35678777877888888888888


Q ss_pred             HHHHHHh
Q 008442          239 IYKRCYS  245 (565)
Q Consensus       239 i~~~al~  245 (565)
                      .|+++|.
T Consensus        94 ~~~~aL~  100 (122)
T d1nzna_          94 YVRGLLQ  100 (122)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8888887

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.42  E-value=0.01  Score=43.37  Aligned_cols=77  Identities=12%  Similarity=0.162  Sum_probs=59.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCc--ceEEEEEecCHHHHHHHHH-cCCcccCC---e--EEE
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKS--RGLAYVDFIDDEHLAAAVA-KNKQMFLG---K--KLS  463 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~--~g~afv~f~~~~~a~~a~~-~~~~~~~g---~--~l~  463 (565)
                      .+|.|++||+.+|++++.+.+...|.+.....+..+.+.+.  -.-|||.|.+.+++..-.. .+|+.+.+   .  +-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            47899999999999999999999999888777765544332  3678999999999888877 68887632   2  345


Q ss_pred             EeecC
Q 008442          464 IARSN  468 (565)
Q Consensus       464 v~~a~  468 (565)
                      |++|.
T Consensus        82 VE~AP   86 (91)
T d1uw4a_          82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            55553

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=96.41  E-value=0.33  Score=44.14  Aligned_cols=241  Identities=11%  Similarity=0.037  Sum_probs=137.3

Q ss_pred             HHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHH-----HHHHHHHHHHHhcchhhHHHHHHHHHHHcCCC---CH-HH
Q 008442           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSD-----LWLDYTQYLDKTLKVGNVVRDVYSRATKNCPW---VG-EL   94 (565)
Q Consensus        24 ~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~-----lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~---~~-~l   94 (565)
                      +...-.+......|+++.+..+|+++|...|.+..     .+..... +....++.+.+...|++|+...+.   .. .+
T Consensus        13 e~~~lrA~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~-~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~   91 (366)
T d1hz4a_          13 EFNALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGE-VLHCKGELTRSLALMQQTEQMARQHDVWHYAL   91 (366)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHH-HHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHH-HHHHCCCHHHHHHHHHHHHHHHHhhcchHHHH
Confidence            33333455556789999999999999999988754     2222232 223345778899999999985432   11 22


Q ss_pred             HHHHH-HHHHHhcCCHHHHHHHHHHHHhcc----cc--cHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHH
Q 008442           95 WVRSL-LSLERSRASEEEISTVFEKSLLCA----FS--TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRA  167 (565)
Q Consensus        95 W~~yi-~~le~~~~~~~~~~~if~ral~~~----~~--~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a  167 (565)
                      +..+. .......+....+...+.+++...    ..  .........+..+.+.            ..++......+..+
T Consensus        92 ~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~------------~~~~~~a~~~~~~~  159 (366)
T d1hz4a_          92 WSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWA------------WARLDEAEASARSG  159 (366)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHH------------TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHH------------hcchhhhHHHHHHH
Confidence            22221 122334577888888888887521    11  1111111111111000            01344455556655


Q ss_pred             HHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHcc-------chHHHHHHHHHHHHHcCChHHHHHHH
Q 008442          168 SDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG-------AMLEAWQSYISMEIELDHINEARSIY  240 (565)
Q Consensus       168 ~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~-------~~~~lw~~yi~~e~~~~~~~~aR~i~  240 (565)
                      ........  .......+...+......+ +...+...+..++....       ....++...+.+....++++.|...+
T Consensus       160 ~~~~~~~~--~~~~~~~~~~~~~~~~~~~-~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~  236 (366)
T d1hz4a_         160 IEVLSSYQ--PQQQLQCLAMLIQCSLARG-DLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWL  236 (366)
T ss_dssp             HHHTTTSC--GGGGHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHhhhhh--hhhHHHHHHHHHHHHHhhh-hHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHH
Confidence            55442211  1112223334455555667 88889999988887621       22457777788888999999999999


Q ss_pred             HHHHhcccCCCCcH--HHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          241 KRCYSKRFTGTGSE--DICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       241 ~~al~~~~~~~~~~--~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      .+++... +...+.  ..+..........|+.+.....+++++
T Consensus       237 ~~~~~~~-~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  278 (366)
T d1hz4a_         237 RHTAKPE-FANNHFLQGQWRNIARAQILLGEFEPAEIVLEELN  278 (366)
T ss_dssp             HHSCCCC-CTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHhc-cccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            9997632 222221  122222334455688777777776665

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.19  E-value=0.02  Score=45.31  Aligned_cols=81  Identities=14%  Similarity=0.153  Sum_probs=47.4

Q ss_pred             HHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHH-------HHHHHHHHHHHcCChHHH
Q 008442          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLE-------AWQSYISMEIELDHINEA  236 (565)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~-------lw~~yi~~e~~~~~~~~a  236 (565)
                      |.+|+.++...+...+....++...+..+...+ +++.|...|+++|+..|.+..       ++..........++++.|
T Consensus        20 y~~Ai~~y~~al~~~p~~~~~~~~~a~~~~~~~-~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A   98 (128)
T d1elra_          20 FDTALKHYDKAKELDPTNMTYITNQAAVYFEKG-DYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDA   98 (128)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHhCcccHHHHHhHHHHHHHcC-chHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHhCCHHHH
Confidence            334444444333333444556666677777777 777777777777776544333       333344445566677777


Q ss_pred             HHHHHHHHh
Q 008442          237 RSIYKRCYS  245 (565)
Q Consensus       237 R~i~~~al~  245 (565)
                      ..+|.+++.
T Consensus        99 ~~~~~kal~  107 (128)
T d1elra_          99 IHFYNKSLA  107 (128)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            777777765

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=96.13  E-value=0.13  Score=41.72  Aligned_cols=100  Identities=11%  Similarity=-0.138  Sum_probs=72.9

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHH----------------HHHHHHHHHHHhcchhhHHHHHHHHHHHcC
Q 008442           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSD----------------LWLDYTQYLDKTLKVGNVVRDVYSRATKNC   88 (565)
Q Consensus        25 ~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~----------------lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~   88 (565)
                      .|..=.+-..+.|++..+...|++||..++....                ++...+. .....+..+.+...|++||...
T Consensus        19 ~~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~-~~~~l~~~~~Al~~~~~al~~~   97 (153)
T d2fbna1          19 DIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLAT-CYNKNKDYPKAIDHASKVLKID   97 (153)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHH-HHHHhcccchhhhhhhcccccc
Confidence            4555555556778999999999999988765442                2222222 1223456777999999999999


Q ss_pred             CCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccccc
Q 008442           89 PWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFST  126 (565)
Q Consensus        89 p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~~~~~~  126 (565)
                      |.+...|......+.. .+.++.+...|++|+...+..
T Consensus        98 p~~~ka~~~~g~~~~~-lg~~~~A~~~~~~al~l~P~n  134 (153)
T d2fbna1          98 KNNVKALYKLGVANMY-FGFLEEAKENLYKAASLNPNN  134 (153)
T ss_dssp             TTCHHHHHHHHHHHHH-HTCHHHHHHHHHHHHHHSTTC
T ss_pred             chhhhhhHHhHHHHHH-cCCHHHHHHHHHHHHHhCCCC
Confidence            9999988887764444 688999999999999876653

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.96  E-value=0.06  Score=45.24  Aligned_cols=98  Identities=8%  Similarity=0.017  Sum_probs=73.2

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCH----------------------HHHHHHHHHHHHhcchhhHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS----------------------DLWLDYTQYLDKTLKVGNVVRD   79 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~----------------------~lW~~Y~~~l~~~~~~~~~~~~   79 (565)
                      .+..+..-..-....|+.+.+...|.+||..++...                      ..|...+..+.. .++.+.+..
T Consensus        10 ~f~~~~~~g~~~~~~g~~e~A~~~~~~AL~l~rG~~l~~~~~~~w~~~~r~~l~~~~~~a~~~la~~~~~-~g~~~~Al~   88 (179)
T d2ff4a2          10 RFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIA-CGRASAVIA   88 (179)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHH-TTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCchHHHH
Confidence            344555555555678999999999999999876442                      234444443332 346778999


Q ss_pred             HHHHHHHcCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 008442           80 VYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLL  121 (565)
Q Consensus        80 v~erAl~~~p~~~~lW~~yi~~le~~~~~~~~~~~if~ral~  121 (565)
                      .++++|...|.+..+|...+..+. ..+...++...|+++..
T Consensus        89 ~~~~al~~~P~~e~~~~~l~~al~-~~Gr~~eAl~~y~~~~~  129 (179)
T d2ff4a2          89 ELEALTFEHPYREPLWTQLITAYY-LSDRQSDALGAYRRVKT  129 (179)
T ss_dssp             HHHHHHHHSTTCHHHHHHHHHHHH-TTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCccHHHHHHHHHHHH-HhcCHHHHHHHHHHHHH
Confidence            999999999999999999998554 47888999999999753

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=95.87  E-value=0.052  Score=45.04  Aligned_cols=71  Identities=3%  Similarity=-0.103  Sum_probs=57.6

Q ss_pred             HHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHH
Q 008442           29 YLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (565)
Q Consensus        29 yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~  100 (565)
                      ......+.+++..+...|+++|..+|.+...|...+..+. ..+..+.+...|++|+...|.+..++..+-.
T Consensus        70 la~~~~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~~~~~~-~l~~~~~A~~~~~~al~l~P~n~~~~~~l~~  140 (168)
T d1kt1a1          70 LAMCYLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQL-LMNEFESAKGDFEKVLEVNPQNKAARLQIFM  140 (168)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHSCTTCHHHHHHHHH
T ss_pred             HHHHHHHhhhcccchhhhhhhhhcccchHHHHHHHHHHHH-HcCCHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            3333456789999999999999999999999998887544 4557888999999999999998888776543

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=95.84  E-value=0.02  Score=47.73  Aligned_cols=73  Identities=11%  Similarity=-0.097  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHH
Q 008442           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVR   97 (565)
Q Consensus        24 ~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~   97 (565)
                      ..|........+.++.+.+...|++||...|.+...|...+.-+. ..+..+.+...|++|+..-|....++..
T Consensus        78 ~~~~nla~~~~~~~~~~~Ai~~~~~al~~~p~~~~a~~~~g~~~~-~l~~~~~A~~~~~~al~l~p~n~~~~~~  150 (169)
T d1ihga1          78 SCVLNIGACKLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQ-GLKEYDQALADLKKAQEIAPEDKAIQAE  150 (169)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             HHHHHHHHHHHhhcccchhhhhhhhhhhhhhhhhhHHHhHHHHHH-HccCHHHHHHHHHHHHHhCCCCHHHHHH
Confidence            344444444444555555666666666666666655555544322 2334455556666666655555554433

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=95.70  E-value=0.028  Score=50.74  Aligned_cols=65  Identities=15%  Similarity=-0.030  Sum_probs=50.7

Q ss_pred             hcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHH
Q 008442           35 SSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (565)
Q Consensus        35 ~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~  100 (565)
                      ..|+++.+...|+++|..+|.+..+|..++..+...+ +.+.+...|++++...|.....|..|..
T Consensus         8 ~~G~l~eAl~~l~~al~~~P~d~~ar~~La~lL~~~G-~~e~A~~~l~~a~~l~P~~~~~~~~l~~   72 (264)
T d1zbpa1           8 SEGQLQQALELLIEAIKASPKDASLRSSFIELLCIDG-DFERADEQLMQSIKLFPEYLPGASQLRH   72 (264)
T ss_dssp             TTTCHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHCGGGHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCcHHHHHHHHH
Confidence            3577888888888888888888888888888666544 6777888888888888877777776654

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.47  E-value=0.049  Score=40.27  Aligned_cols=73  Identities=19%  Similarity=0.110  Sum_probs=55.3

Q ss_pred             hHHHHHHHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHH
Q 008442          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE  229 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~  229 (565)
                      ++..+...|++|+...............++...+..+...+ ++++|...|+++|+..|++..++.....++..
T Consensus        20 ~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g-~~~~A~~~y~~aL~l~P~~~~a~~Nl~~~~~~   92 (95)
T d1tjca_          20 DYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQG-DLDKALLLTKKLLELDPEHQRANGNLKYFEYI   92 (95)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcC-ChHHHHHHHHHHHHhCcCCHHHHHHHHHHHHH
Confidence            56667777888877765544433444566667788888888 99999999999999999999888777666543

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=95.40  E-value=0.015  Score=52.61  Aligned_cols=114  Identities=16%  Similarity=0.025  Sum_probs=81.8

Q ss_pred             hhhHHHHHHHhcCCCCChHhHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 008442            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (565)
Q Consensus         3 ~~R~~~E~~l~~~~~~~~~~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (565)
                      ++...|+.+|..+|.    +...|..++.+....|+.+++...|++++...|.+...|..|...+.... ....+...+.
T Consensus        14 eAl~~l~~al~~~P~----d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~P~~~~~~~~l~~ll~a~~-~~~~a~~~~~   88 (264)
T d1zbpa1          14 QALELLIEAIKASPK----DASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYLPGASQLRHLVKAAQ-ARKDFAQGAA   88 (264)
T ss_dssp             HHHHHHHHHHHTCTT----CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHH-HHHHHTTSCC
T ss_pred             HHHHHHHHHHHHCCC----CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhcc-ccHHHHHHhh
Confidence            467889999999998    89999999999999999999999999999999999999999988664322 1111111111


Q ss_pred             HHHHcCCCCHHHHHHHHHH--HHHhcCCHHHHHHHHHHHHhcc
Q 008442           83 RATKNCPWVGELWVRSLLS--LERSRASEEEISTVFEKSLLCA  123 (565)
Q Consensus        83 rAl~~~p~~~~lW~~yi~~--le~~~~~~~~~~~if~ral~~~  123 (565)
                      ++  .....+.-|..++..  +....++.+++..+++++....
T Consensus        89 ~~--~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~~  129 (264)
T d1zbpa1          89 TA--KVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELR  129 (264)
T ss_dssp             CE--ECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             hh--hcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC
Confidence            11  122223455554421  2334688999999999988643

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.24  E-value=0.024  Score=56.45  Aligned_cols=114  Identities=4%  Similarity=-0.124  Sum_probs=58.0

Q ss_pred             HHHHHHHHHHHhhhcCCchhHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHHcCChHHHHHHHH
Q 008442          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYK  241 (565)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~~~~~~~aR~i~~  241 (565)
                      ..|..++..+...+...+.....+..........+ +.+.|...+.+++...+  ...++...+..+..++++.|+..|.
T Consensus       100 ~~Y~~ai~~l~~~~~l~~~~~~~~~~lg~~~~~~~-~~~~A~~~~~~al~~~~--~~~~~~LG~l~~~~~~~~~A~~~y~  176 (497)
T d1ya0a1         100 GFYTQLLQELCTVFNVDLPCRVKSSQLGIISNKQT-HTSAIVKPQSSSCSYIC--QHCLVHLGDIARYRNQTSQAESYYR  176 (497)
T ss_dssp             HHHHHHHHHHTC--------------------------------CCHHHHHHH--HHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCChhhHHHHHHhHHHHHhCC-CHHHHHHHHHHHhCCCH--HHHHHHHHHHHHHcccHHHHHHHHH
Confidence            44555555554444333333344444555555556 77788888888887654  3567777888899999999999999


Q ss_pred             HHHhcccCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Q 008442          242 RCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (565)
Q Consensus       242 ~al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~k~~  281 (565)
                      +|+..   .+.....+...-..-...|+...+...+.+++
T Consensus       177 ~A~~l---~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral  213 (497)
T d1ya0a1         177 HAAQL---VPSNGQPYNQLAILASSKGDHLTTIFYYCRSI  213 (497)
T ss_dssp             HHHHH---CTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHH---CCCchHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            99973   23344566666666666788776666666654

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.64  E-value=0.17  Score=42.24  Aligned_cols=87  Identities=14%  Similarity=0.106  Sum_probs=65.6

Q ss_pred             hHHHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHHHH
Q 008442           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (565)
Q Consensus        22 ~~~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~~  101 (565)
                      ....|...++.....|+.+.+...++++|..+|.+..+|...+.-+... +..+.+..+|+++.+.+            .
T Consensus        66 ~~~a~~~la~~~~~~g~~~~Al~~~~~al~~~P~~e~~~~~l~~al~~~-Gr~~eAl~~y~~~~~~L------------~  132 (179)
T d2ff4a2          66 KVLAHTAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLS-DRQSDALGAYRRVKTTL------------A  132 (179)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHH------------H
T ss_pred             HHHHHHHHHHHHHHCCCchHHHHHHHHHHHhCCccHHHHHHHHHHHHHh-cCHHHHHHHHHHHHHHH------------H
Confidence            3467888888888899999999999999999999999999999866644 46777999999986632            1


Q ss_pred             HHHhcCCHHHHHHHHHHHHh
Q 008442          102 LERSRASEEEISTVFEKSLL  121 (565)
Q Consensus       102 le~~~~~~~~~~~if~ral~  121 (565)
                      -|....+..++..++++.+.
T Consensus       133 ~eLG~~P~~~l~~l~~~il~  152 (179)
T d2ff4a2         133 DDLGIDPGPTLRALNERILR  152 (179)
T ss_dssp             HHHSCCCCHHHHHHHHHHHT
T ss_pred             HHhCCCcCHHHHHHHHHHHh
Confidence            12223344556666666554

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.61  E-value=0.052  Score=40.13  Aligned_cols=74  Identities=14%  Similarity=-0.060  Sum_probs=53.9

Q ss_pred             HHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHH------HHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCCHHHHHHHH
Q 008442           26 YMIYLKYEQSSGDPGRVQLLYERAITDFPVSSD------LWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSL   99 (565)
Q Consensus        26 W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~------lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~~~~lW~~yi   99 (565)
                      +........+.|+...+...|++||...|.+..      -.+.++-+.....++.+.+...|++||...|.....+....
T Consensus         8 c~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~P~~~~a~~Nl~   87 (95)
T d1tjca_           8 SFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRANGNLK   87 (95)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhCcCCHHHHHHHH
Confidence            334444556788999999999999987655432      23344555555667888899999999999999988876643

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.94  E-value=0.3  Score=35.43  Aligned_cols=53  Identities=23%  Similarity=0.321  Sum_probs=44.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHc
Q 008442          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRGLAYVDFIDDEHLAAAVAK  452 (565)
Q Consensus       392 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~~  452 (565)
                      .-||.-.+|......+|.++|++||.|. |.++.+.       -|||...+.++|..++.+
T Consensus        16 dHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~~~~v~~~   68 (100)
T d1whva_          16 DHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNT   68 (100)
T ss_dssp             CSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHH
T ss_pred             ceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHHHHHHHHH
Confidence            4688889999999999999999999764 5555542       799999999999988863

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=89.30  E-value=1.7  Score=34.52  Aligned_cols=89  Identities=16%  Similarity=-0.001  Sum_probs=60.7

Q ss_pred             hHHHHHHHHHHHHHHHHhhhcCC--ch---hHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHccc-------h----HHH
Q 008442          156 DYSLIRETFQRASDYLSEQMKNT--DG---LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA-------M----LEA  219 (565)
Q Consensus       156 ~~~~~~~~~~~a~~~l~~~~~~~--~~---~~~l~~~~a~~e~~~~~~~~~ar~i~e~~l~~~~~-------~----~~l  219 (565)
                      +++.+...|.+++++........  ..   ....|...+..+..++ +++.|...+++++..++.       .    ..+
T Consensus        24 ~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~a  102 (156)
T d2hr2a1          24 EYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLR-SFDEALHSADKALHYFNRRGELNQDEGKLWISA  102 (156)
T ss_dssp             CHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcC-ccchhhHhhhhhhhcccccccccccccchhHHH
Confidence            45566677777777664433211  11   1234555666778888 999999999999976432       1    224


Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHh
Q 008442          220 WQSYISMEIELDHINEARSIYKRCYS  245 (565)
Q Consensus       220 w~~yi~~e~~~~~~~~aR~i~~~al~  245 (565)
                      +..........|+++.|...|++|+.
T Consensus       103 ~~~~g~~~~~lg~~eeA~~~~~~Al~  128 (156)
T d2hr2a1         103 VYSRALALDGLGRGAEAMPEFKKVVE  128 (156)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            45556677889999999999999986

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=88.35  E-value=1.6  Score=34.72  Aligned_cols=87  Identities=16%  Similarity=0.122  Sum_probs=57.2

Q ss_pred             HHhcCCchhHHHHHHHHHhcCCCCHH------------HHHHHHHHHHHhcchhhHHHHHHHHHHHcCC-------CCHH
Q 008442           33 EQSSGDPGRVQLLYERAITDFPVSSD------------LWLDYTQYLDKTLKVGNVVRDVYSRATKNCP-------WVGE   93 (565)
Q Consensus        33 e~~~~~~~~~~~lyERal~~~p~~~~------------lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p-------~~~~   93 (565)
                      ....|+++.+...|++||..+|..++            +|.....-+ ...+..+.+..-|++|+..+|       ....
T Consensus        19 ~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~-~~lg~~~~A~~~~~~al~~~~~~~~~~~~~~~   97 (156)
T d2hr2a1          19 QLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEAL-AGLRSFDEALHSADKALHYFNRRGELNQDEGK   97 (156)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHH-HHcCccchhhHhhhhhhhcccccccccccccc
Confidence            34568999999999999998776543            343333322 344567778888888887543       2223


Q ss_pred             HH----HHHHHHHHHhcCCHHHHHHHHHHHHh
Q 008442           94 LW----VRSLLSLERSRASEEEISTVFEKSLL  121 (565)
Q Consensus        94 lW----~~yi~~le~~~~~~~~~~~if~ral~  121 (565)
                      .|    ......+ ...+..+++...|++|+.
T Consensus        98 ~~~~a~~~~g~~~-~~lg~~eeA~~~~~~Al~  128 (156)
T d2hr2a1          98 LWISAVYSRALAL-DGLGRGAEAMPEFKKVVE  128 (156)
T ss_dssp             HHHHHHHHHHHHH-HHTTCHHHHHHHHHHHHH
T ss_pred             hhHHHHhhhHHHH-HHHHHHHHHHHHHHHHHH
Confidence            33    2222322 336788999999999986

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=85.87  E-value=9.5  Score=32.56  Aligned_cols=197  Identities=12%  Similarity=0.039  Sum_probs=105.3

Q ss_pred             HHHHHHHHHHHhcCCchhHHHHHHHHHhcCCCCHHHHHHHHHHHHH---hcchhhHHHHHHHHHHHcCCCCHHHHHHHHH
Q 008442           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDK---TLKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (565)
Q Consensus        24 ~~W~~yi~~e~~~~~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~---~~~~~~~~~~v~erAl~~~p~~~~lW~~yi~  100 (565)
                      +.|..........+|..++...|++|...  .+.+.+..+......   ..++...+...|+.+..........++..+.
T Consensus         3 ~~~~~lG~~~~~~~d~~~A~~~~~kAa~~--g~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~~~~a~~~l~~~~   80 (265)
T d1ouva_           3 KELVGLGAKSYKEKDFTQAKKYFEKACDL--KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYSNGCHLLGNLY   80 (265)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHC--CCHHHHHHHHHHHHcCCCcchhHHHHHHhhcccccccccchhhcccccc
Confidence            46666666777789999999999999875  566776666554433   1346677888999998855333333333332


Q ss_pred             HHH-HhcCCHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHHHHHHHHHHHHHhhhcCCc
Q 008442          101 SLE-RSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTD  179 (565)
Q Consensus       101 ~le-~~~~~~~~~~~if~ral~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~e~~~~~~~~~~~~~~a~~~l~~~~~~~~  179 (565)
                      ... ......+.+...|.++...........+......          .....  .+...       +...+.......+
T Consensus        81 ~~~~~~~~~~~~a~~~~~~a~~~g~~~a~~~l~~~~~~----------~~~~~--~~~~~-------a~~~~~~~~~~~~  141 (265)
T d1ouva_          81 YSGQGVSQNTNKALQYYSKACDLKYAEGCASLGGIYHD----------GKVVT--RDFKK-------AVEYFTKACDLND  141 (265)
T ss_dssp             HHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH----------CSSSC--CCHHH-------HHHHHHHHHHTTC
T ss_pred             ccccccchhhHHHHHHHhhhhhhhhhhHHHhhcccccC----------CCccc--chhHH-------HHHHhhhhhcccc
Confidence            111 1134567788888888865433222111111110          00000  01111       1222211111111


Q ss_pred             hhHHHHHHHHHHHHH---cCCChHHHHHHHHHHHHHccchHHHHHHHHHHHHH----cCChHHHHHHHHHHHh
Q 008442          180 GLLRLYAYWAHLEQS---MGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE----LDHINEARSIYKRCYS  245 (565)
Q Consensus       180 ~~~~l~~~~a~~e~~---~~~~~~~ar~i~e~~l~~~~~~~~lw~~yi~~e~~----~~~~~~aR~i~~~al~  245 (565)
                        ...+..++.+...   ...+...+...++.+....  +...+..+..+...    ..+++.|...|.++..
T Consensus       142 --~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~a~~~g--~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~  210 (265)
T d1ouva_         142 --GDGCTILGSLYDAGRGTPKDLKKALASYDKACDLK--DSPGCFNAGNMYHHGEGATKNFKEALARYSKACE  210 (265)
T ss_dssp             --HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT--CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHH
T ss_pred             --cchhhhhhhhhccCCCcccccccchhhhhcccccc--ccccccchhhhcccCcccccchhhhhhhHhhhhc
Confidence              1223333443333   2236667777777777642  23333334433332    4589999999999976