Citrus Sinensis ID: 013489

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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--
Protein Sequence
MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLPESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYTL
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHccccccccccccHHccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccEEEccccccccHHHHHHHHcccccccEEEEEEccccccccEEEEEEEEc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHcccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHccHHHHHHHcccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHcccEEEEEEEEcccccccEEEEEEEEcc
Coil and Loop (DISEMBL)
MCNARAHLEEQisrqdlsdsEKFQQYMIYLKYeqssgdpgrVQLLYERaitdfpvssdlWLDYTQYLDKTLKVGNVVRDVYSratkncpwvgELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCyskrftgtgseDICHAWLRFEreygtledfdhsvqKVTPRLEELRLFRsqqeskslpesadqkEHSVKKtgrekrksdsnisyeqspakrqkhapqkpkkvhdkEKRQVQNLAeenegretkqtveeqpkkqpikdavpgrtkgftDECTAFLSNINLKATYEDLRRFFsdvggvssirilhdkftgksrvvqsdiytl
Flexible Loop (DISEMBL)
mcnarahleeqisrqdlsdsEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYsratkncpwvgeLWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKrftgtgseDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSqqeskslpesadqkehsvkktgrekrksdsnisyeqspakrqkhapqkpkkvhdkekrqvqnlaeenegretkqtveeqpkkqpikdavpgrtkGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSsirilhdkftgksrvvqsdiytl
Low Complexity Region (SEG)
MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVrsllslersraseeeISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLPESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYTL
Disordered region (IsUnstruct)
**********************FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER******EISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV**********************************************************************************************************GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVV*******
Disordered Region (DISOPRED)
MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLP*****************************************************************************************DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYTL
Disordered Region (DISEMBL)
****************LSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFR**************************************************************************************KDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYTL
Disordered Region (DISPRO)
MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESK*******************************************************************************************TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYTL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLPESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVxxxxxxxxxxxxxxxxxxxxxQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYTL
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	442	2.2.26 [Sep-21-2011]
Q15020	963	Squamous cell carcinoma a	yes	no	0.911	0.418	0.278	5e-40
Q5REG1	981	Squamous cell carcinoma a	yes	no	0.911	0.410	0.278	6e-40
Q9JLI8	962	Squamous cell carcinoma a	yes	no	0.595	0.273	0.326	3e-38
Q9USY2	1014	Uncharacterized RNA-bindi	yes	no	0.359	0.156	0.287	7e-09
Q4PB37	781	Pre-mRNA-splicing factor	N/A	no	0.538	0.304	0.257	3e-08
Q14690	1871	Protein RRP5 homolog OS=H	no	no	0.518	0.122	0.255	1e-05
Q6NS46	1862	Protein RRP5 homolog OS=M	no	no	0.518	0.122	0.240	1e-05
P63155	690	Crooked neck-like protein	no	no	0.493	0.315	0.255	1e-05
P63154	690	Crooked neck-like protein	no	no	0.493	0.315	0.255	1e-05
Q9BZJ0	848	Crooked neck-like protein	no	no	0.490	0.255	0.249	6e-05

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

 Score =  166 bits (419), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 122/438 (27%), Positives = 208/438 (47%), Gaps = 35/438 (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 ARLCNNMQKARELWDSIMTRGNAKYANMWLEYYNLERAHGDTQHCRKALHRAV--QCTSD 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 -LRRFFSDVGGVSSIRIL 424
            LR  F   G V  IR +
Sbjct: 721 KLRPLFEACGEVVQIRPI 738

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 =  165 bits (418), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 122/438 (27%), Positives = 208/438 (47%), Gaps = 35/438 (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 ARLCNNMQKARELWDSIMTRGNAKYANMWLEYYNLERAHGDTQHCRKALHRAV--QCTSD 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 -LRRFFSDVGGVSSIRIL 424
            LR  F   G V  IR +
Sbjct: 739 KLRPLFEACGEVVQIRPI 756

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 =  159 bits (403), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 89/273 (32%), Positives = 144/273 (52%), Gaps = 10/273 (3%)

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 ARLCNNMQKARELWDSIMTRGNAKYANMWLEYYNLERAHGDTQHCRKALHRAV--QCTSD 541

Query: 252 GSEDICHAWLRFEREYGTLEDFDHSVQKVTPRL 284
             E +C   L  ER  GTLED+D ++QK   RL
Sbjct: 542 YPEHVCEVLLTMERTEGTLEDWDLAIQKTETRL 574

Mus musculus (taxid: 10090)

>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 = 62.4 bits (150), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 50/174 (28%), Positives = 78/174 (44%), Gaps = 15/174 (8%)

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-DGLLRL 184
           D F     G  +  L+    E       ++    +  DYL +  K + D  +R+
Sbjct: 382 DFF----SGFLKACLYLSSNEDK-PQEFLKHQIHKVEDYLRKNHKGSKDARMRI 430

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

>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 AF--STFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG 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|Q14690|RRP5_HUMAN Protein RRP5 homolog OS=Homo sapiens GN=PDCD11 PE=1 SV=3

 Score = 52.0 bits (123), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 70/274 (25%), Positives = 118/274 (43%), Gaps = 45/274 (16%)

Query: 31   KYEQSSGDPGRVQLL---YERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKN 87
            + E++  DPGR       ++R +   P SS LWL Y  +  +  ++    R V  RA K 
Sbjct: 1590 RIEEALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKA-RAVAERALKT 1648

Query: 88   CPWVGE-----LWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRID--- 139
              +  E     +WV +LL+LE    S+E ++ VFE+++      + E L +FL   D   
Sbjct: 1649 ISFREEQEKLNVWV-ALLNLENMYGSQESLTKVFERAV-----QYNEPLKVFLHLADIYA 1702

Query: 140  ---------GLRRRIL--FSGEVEGVLDYS--LIRET--------FQRASDYLSEQMKNT 178
                      L  R+L  F  E    + Y   L+R +         QRA + L  + ++ 
Sbjct: 1703 KSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPSK-EHV 1761

Query: 179  DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARS 238
            D    + A +A LE  +G D   A+ ++E  L       + W  YI M I+     + R 
Sbjct: 1762 D----VIAKFAQLEFQLG-DAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRD 1816

Query: 239  IYKRCYSKRFTGTGSEDICHAWLRFEREYGTLED 272
            I++R           +     +L +E+++GT +D
Sbjct: 1817 IFERVIHLSLAPKRMKFFFKRYLDYEKQHGTEKD 1850

Involved in the biogenesis of rRNA.

Homo sapiens (taxid: 9606)

>sp|Q6NS46|RRP5_MOUSE Protein RRP5 homolog OS=Mus musculus GN=Pdcd11 PE=2 SV=2

 Score = 51.2 bits (121), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 66/274 (24%), Positives = 114/274 (41%), Gaps = 45/274 (16%)

Query: 31   KYEQSSGDPGRVQLL---YERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKN 87
            + E++  DPGR       ++R +   P SS LWL Y  +  +  ++    R V  RA K 
Sbjct: 1581 RIEEALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKA-RAVAERALKT 1639

Query: 88   CPWVGE-----LWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRID--- 139
              +  E     +WV +LL+LE    S+E ++ VFE+++      + E L +FL   D   
Sbjct: 1640 ISFREEQEKLNVWV-ALLNLENMYGSQESLTKVFERAV-----QYNEPLKVFLHLADIYT 1693

Query: 140  ---------GLRRRIL------------FSGEVEGVLDYSLIRETFQRASDYLSEQMKNT 178
                      L  R+L            +   V G           QRA + L  + ++ 
Sbjct: 1694 KSEKYKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRALECLPAK-EHV 1752

Query: 179  DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARS 238
            D +++    +A LE  +G D+  A+ ++E  L       + W  YI M I+       R 
Sbjct: 1753 DVIVK----FAQLEFQLG-DVERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQTAVRD 1807

Query: 239  IYKRCYSKRFTGTGSEDICHAWLRFEREYGTLED 272
            I++R           +     +L +E+++GT +D
Sbjct: 1808 IFERVIHLSLAPKRMKFFFKRYLDYEKQHGTEKD 1841

Essential for the generation of mature 18S rRNA, specifically necessary for cleavages at sites A0, 1 and 2 of the 47S precursor. Directly interacts with U3 snoRNA.

Mus musculus (taxid: 10090)

>sp|P63155|CRNL1_RAT Crooked neck-like protein 1 OS=Rattus norvegicus GN=Crnkl1 PE=2 SV=1

 Score = 51.2 bits (121), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 71/278 (25%), Positives = 115/278 (41%), Gaps = 60/278 (21%)

Query: 10  EQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQ--------LLYERAITDFPVSSDLWL 61
           ++IS+Q+    E F+ Y I+   E+  GD   ++          YE  +   P + D W 
Sbjct: 280 DRISKQEAQ--ELFKNYTIF---EKKFGDRRGIEDIIVSKRRFQYEEEVKANPHNYDAWF 334

Query: 62  DYTQYLDKTLKVGNVVRDVYSRATKNCPWVGE---------LWVRSLLSLERSRASEEEI 112
           DY + ++   +  + VR+VY RA  N P + E         LWV   L  E      E  
Sbjct: 335 DYLRLVESDAE-ADTVREVYERAIANVPPIQEKRHWKRYIYLWVNYALYEELEAKDPERT 393

Query: 113 STVFEKSLLC------AFSTFEEYLDLFLTRIDGL---RRRI-----------LFSGEVE 152
             V++ SL         F+    Y   F  R   L   RR +           LF G +E
Sbjct: 394 RQVYQASLELIPHKKFTFAKMWLYYAQFEIRQKNLPFARRALGTSIGKCPKNKLFKGYIE 453

Query: 153 GVL---DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERL 209
             L   ++   R+ +++  ++  E   N    ++     A LE  +G D+  AR ++E  
Sbjct: 454 LELQLREFDRCRKLYEKFLEFGPE---NCTSWIKF----AELETILG-DIERARAIYE-- 503

Query: 210 LKISGAMLEA----WQSYISMEIELDHINEARSIYKRC 243
           L IS   L+     W+SYI  EIE +     R++Y++ 
Sbjct: 504 LAISQPRLDMPEVLWKSYIDFEIEQEETERTRNLYRQL 541

May be involved in pre-mRNA splicing process.

Rattus norvegicus (taxid: 10116)

>sp|P63154|CRNL1_MOUSE Crooked neck-like protein 1 OS=Mus musculus GN=Crnkl1 PE=2 SV=1

 Score = 51.2 bits (121), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 71/278 (25%), Positives = 115/278 (41%), Gaps = 60/278 (21%)

Query: 10  EQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQ--------LLYERAITDFPVSSDLWL 61
           ++IS+Q+    E F+ Y I+   E+  GD   ++          YE  +   P + D W 
Sbjct: 280 DRISKQEAQ--ELFKNYTIF---EKKFGDRRGIEDIIVSKRRFQYEEEVKANPHNYDAWF 334

Query: 62  DYTQYLDKTLKVGNVVRDVYSRATKNCPWVGE---------LWVRSLLSLERSRASEEEI 112
           DY + ++   +  + VR+VY RA  N P + E         LWV   L  E      E  
Sbjct: 335 DYLRLVESDAE-ADTVREVYERAIANVPPIQEKRHWKRYIYLWVNYALYEELEAKDPERT 393

Query: 113 STVFEKSLLC------AFSTFEEYLDLFLTRIDGL---RRRI-----------LFSGEVE 152
             V++ SL         F+    Y   F  R   L   RR +           LF G +E
Sbjct: 394 RQVYQASLELIPHKKFTFAKMWLYYAQFEIRQKNLPFARRALGTSIGKCPKNKLFKGYIE 453

Query: 153 GVL---DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERL 209
             L   ++   R+ +++  ++  E   N    ++     A LE  +G D+  AR ++E  
Sbjct: 454 LELQLREFDRCRKLYEKFLEFGPE---NCTSWIKF----AELETILG-DIERARAIYE-- 503

Query: 210 LKISGAMLEA----WQSYISMEIELDHINEARSIYKRC 243
           L IS   L+     W+SYI  EIE +     R++Y++ 
Sbjct: 504 LAISQPRLDMPEVLWKSYIDFEIEQEETERTRNLYRQL 541

Involved in pre-mRNA splicing process.

Mus musculus (taxid: 10090)

>sp|Q9BZJ0|CRNL1_HUMAN Crooked neck-like protein 1 OS=Homo sapiens GN=CRNKL1 PE=1 SV=4

 Score = 49.3 bits (116), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 69/277 (24%), Positives = 112/277 (40%), Gaps = 60/277 (21%)

Query: 10  EQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQ--------LLYERAITDFPVSSDLWL 61
           ++IS+QD    E F+ Y I+   E+  GD   ++          YE  +   P + D W 
Sbjct: 441 DRISKQDAQ--ELFKNYTIF---EKKFGDRRGIEDIIVSKRRFQYEEEVKANPHNYDAWF 495

Query: 62  DYTQYLDKTLKVGNVVRDVYSRATKNCPWVGE---------LWVRSLLSLERSRASEEEI 112
           DY + ++   +    VR+VY RA  N P + E         LW+   L  E      E  
Sbjct: 496 DYLRLVESDAE-AEAVREVYERAIANVPPIQEKRHWKRYIYLWINYALYEELEAKDPERT 554

Query: 113 STVFEKS----------------LLCAFSTFEEYLDL----FLTRIDGLRRRILFSGEVE 152
             V++ S                L   F   ++ L L      T I    +  LF   +E
Sbjct: 555 RQVYQASLELIPHKKFTFAKMWILYAQFEIRQKNLSLARRALGTSIGKCPKNKLFKVYIE 614

Query: 153 GVL---DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERL 209
             L   ++   R+ +++  ++  E   N    ++     A LE  +G D+  AR ++E  
Sbjct: 615 LELQLREFDRCRKLYEKFLEFGPE---NCTSWIKF----AELETILG-DIDRARAIYE-- 664

Query: 210 LKISGAMLEA----WQSYISMEIELDHINEARSIYKR 242
           L IS   L+     W+SYI  EIE +     R++Y+R
Sbjct: 665 LAISQPRLDMPEVLWKSYIDFEIEQEETERTRNLYRR 701

Involved in pre-mRNA splicing process.

Homo sapiens (taxid: 9606)

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	442
255573806	852	Squamous cell carcinoma antigen recogniz	0.970	0.503	0.711	1e-179
359486200	838	PREDICTED: squamous cell carcinoma antig	0.970	0.511	0.669	1e-164
297739447	819	unnamed protein product [Vitis vinifera]	0.970	0.523	0.669	1e-164
356541840	837	PREDICTED: squamous cell carcinoma antig	0.957	0.505	0.628	1e-158
449450119	800	PREDICTED: squamous cell carcinoma antig	0.959	0.53	0.618	1e-158
356560763	847	PREDICTED: squamous cell carcinoma antig	0.957	0.499	0.619	1e-155
224129810	843	predicted protein [Populus trichocarpa]	0.925	0.485	0.626	1e-152
297799572	820	RNA recognition motif-containing protein	0.947	0.510	0.588	1e-143
30686462	816	protein embryo defective 140 [Arabidopsi	0.952	0.515	0.593	1e-143
30686466	817	protein embryo defective 140 [Arabidopsi	0.952	0.515	0.593	1e-143

>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 =  634 bits (1634), Expect = e-179,   Method: Compositional matrix adjust.
 Identities = 308/433 (71%), Positives = 362/433 (83%), Gaps = 4/433 (0%)

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 IRILHDKFTGKSR 433
           IRIL DK+TGKSR
Sbjct: 705 IRILLDKYTGKSR 717

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  585 bits (1509), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 292/436 (66%), Positives = 349/436 (80%), Gaps = 7/436 (1%)

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 VSSIRILHDKFTGKSR 433
           V++IRIL DKFTGKSR
Sbjct: 679 VTAIRILKDKFTGKSR 694

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  585 bits (1508), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 292/436 (66%), Positives = 349/436 (80%), Gaps = 7/436 (1%)

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 VSSIRILHDKFTGKSR 433
           V++IRIL DKFTGKSR
Sbjct: 679 VTAIRILKDKFTGKSR 694

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 =  565 bits (1456), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 274/436 (62%), Positives = 343/436 (78%), Gaps = 13/436 (2%)

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 ESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAE--E 358
            SA++ E + K+  REKRK  S+I+ EQSP+KR +     PKK  ++ K  VQN+++  +
Sbjct: 570 -SAEESEKNTKRNAREKRKLGSDITEEQSPSKRFRDVGN-PKKAPEENKYHVQNISQVTK 627

Query: 359 NEGRETKQT-VEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGG 417
            EG   K T +++ P +Q        + +G++D+CTAFLSN++  A YE +R FFSDVGG
Sbjct: 628 VEGVNWKNTKIDDNPSEQQFSHE---KNRGYSDQCTAFLSNLHPTANYEHIRNFFSDVGG 684

Query: 418 VSSIRILHDKFTGKSR 433
           + +IRILHDKFTGKSR
Sbjct: 685 IVAIRILHDKFTGKSR 700

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 =  563 bits (1452), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 268/433 (61%), Positives = 338/433 (78%), Gaps = 9/433 (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 IRILHDKFTGKSR 433
           IRILHDKFTGKSR
Sbjct: 663 IRILHDKFTGKSR 675

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  555 bits (1430), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 270/436 (61%), Positives = 336/436 (77%), Gaps = 13/436 (2%)

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 ESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAE--E 358
            +A++ E + K+  REKRK  S+I+ EQ P KR +     PKK  ++ K Q+QN ++  +
Sbjct: 580 -TAEESEKNPKRNAREKRKLGSDITEEQYPTKRFRDVGN-PKKAPEENKYQLQNTSQVTK 637

Query: 359 NEGRETKQT-VEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGG 417
            EG   K T +++ P +Q        + + ++D+CT F+SN++  A YE +R FF D GG
Sbjct: 638 VEGANWKNTKIDDNPSEQQFNHE---KNRAYSDQCTVFISNLHPTANYEHIRNFFGDDGG 694

Query: 418 VSSIRILHDKFTGKSR 433
           + +IRILHDKFTGKSR
Sbjct: 695 IVAIRILHDKFTGKSR 710

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  543 bits (1398), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 283/452 (62%), Positives = 337/452 (74%), Gaps = 43/452 (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 KATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
            A  ED+R+FFSDVGGV+SIRILHD+ TGKSR
Sbjct: 674 -ANSEDIRKFFSDVGGVASIRILHDRNTGKSR 704

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297799572|ref|XP_002867670.1| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297313506|gb|EFH43929.1| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  516 bits (1328), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 256/435 (58%), Positives = 323/435 (74%), Gaps = 16/435 (3%)

Query: 1   MCNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLW 60
           M + RAHLEE IS +DLSD+EKFQ++M Y+K+E++SGDP RVQ +YERA+ ++PVSSDLW
Sbjct: 275 MYSERAHLEEHISNKDLSDTEKFQEFMNYIKFEKTSGDPTRVQAIYERAVAEYPVSSDLW 334

Query: 61  LDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSL 120
           +DYT YLDKTLKVG  +   YSRAT++CPW+G+LW R LL+LER  ASE+EI  +FEKSL
Sbjct: 335 IDYTMYLDKTLKVGKAITHAYSRATRSCPWIGDLWARYLLALERGSASEKEIYAIFEKSL 394

Query: 121 LCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG 180
            C FS+FEEYLDL+LTR+DGLRRR+L +  VE  LDYSLI+ETFQ+ASDYL+  M+NTD 
Sbjct: 395 QCTFSSFEEYLDLYLTRVDGLRRRMLSTRMVEA-LDYSLIKETFQQASDYLTPHMQNTDS 453

Query: 181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIY 240
           LL L+AYWA+LE ++GKD+  ARGVW+  LK SG ML AW +YI ME+ L HI EARSI+
Sbjct: 454 LLHLHAYWANLELNIGKDLAGARGVWDSFLKKSGGMLAAWHAYIDMEVHLGHIKEARSIF 513

Query: 241 KRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLP 300
           +RCY+++F GTGSEDIC  WLRFERE+G LE FD +VQKV PRLEEL+L R QQES  + 
Sbjct: 514 RRCYTRKFDGTGSEDICKGWLRFEREHGDLEGFDLAVQKVMPRLEELQLIRLQQESTPVK 573

Query: 301 ESADQKEHSVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKR--QVQNLAEE 358
            SA  KEH+      +KRK++ N+  E+S AKRQK   QK   V  +       +N+  E
Sbjct: 574 PSAGLKEHN-----SQKRKAEPNVE-EESLAKRQKRKGQKEMDVGGQSATVPNTKNVKAE 627

Query: 359 NEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGV 418
           N G+      EE       +DA P + K +TDECTAF+SN+++KA  ED+R+FF D GGV
Sbjct: 628 N-GKTADSNKEE------TEDAKPLKPKIYTDECTAFISNLSVKAQEEDIRKFFGDDGGV 680

Query: 419 SSIRILHDKFTGKSR 433
            SIRILH K TGK R
Sbjct: 681 DSIRILHHKDTGKPR 695

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  513 bits (1322), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 257/433 (59%), Positives = 323/433 (74%), Gaps = 12/433 (2%)

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 IRILHDKFTGKSR 433
           IRILH K TGK R
Sbjct: 680 IRILHHKDTGKPR 692

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 =  513 bits (1322), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 257/433 (59%), Positives = 323/433 (74%), Gaps = 12/433 (2%)

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 IRILHDKFTGKSR 433
           IRILH K TGK R
Sbjct: 680 IRILHHKDTGKPR 692

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	442
TAIR|locus:2135892	817	EMB140 "EMBRYO DEFECTIVE 140"	0.952	0.515	0.572	6.8e-127
UNIPROTKB|E1BWJ0	731	SART3 "Uncharacterized protein	0.904	0.547	0.289	7.1e-43
ZFIN|ZDB-GENE-040724-10	952	sart3 "squamous cell carcinoma	0.746	0.346	0.301	1.7e-41
UNIPROTKB|F1N0I9	655	SART3 "Uncharacterized protein	0.859	0.580	0.265	1.3e-39
UNIPROTKB|F1RGA7	959	SART3 "Uncharacterized protein	0.744	0.343	0.298	3.5e-39
UNIPROTKB|E2QXZ2	1082	SART3 "Uncharacterized protein	0.760	0.310	0.290	5.8e-39
MGI|MGI:1858230	962	Sart3 "squamous cell carcinoma	0.823	0.378	0.272	4.1e-38
UNIPROTKB|Q15020	963	SART3 "Squamous cell carcinoma	0.760	0.348	0.282	1.4e-37
RGD|1311646	960	Sart3 "squamous cell carcinoma	0.809	0.372	0.280	5.2e-37
UNIPROTKB|F8VV04	771	SART3 "Squamous cell carcinoma	0.760	0.435	0.282	2.7e-36

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

 Score = 1246 (443.7 bits), Expect = 6.8e-127, P = 6.8e-127
 Identities = 248/433 (57%), Positives = 311/433 (71%)

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 IRILHDKFTGKSR 433
             IRILH K TGK R
Sbjct:   680 IRILHHKDTGKPR 692

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

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

 Score = 458 (166.3 bits), Expect = 7.1e-43, P = 7.1e-43
 Identities = 122/421 (28%), Positives = 203/421 (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--------KDNITVFVSNLSYNMTDPEVKLKELFESCGEVSQVRPVFSNKG 676

Query:   429 T 429
             T
Sbjct:   677 T 677

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

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 = 1.7e-41, Sum P(3) = 1.7e-41
 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 = 1.3e-39, Sum P(2) = 1.3e-39
 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 = 3.5e-39, Sum P(2) = 3.5e-39
 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|E2QXZ2 SART3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 413 (150.4 bits), Expect = 5.8e-39, Sum P(2) = 5.8e-39
 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 = 4.1e-38, Sum P(2) = 4.1e-38
 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 = 1.4e-37, Sum P(2) = 1.4e-37
 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

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

 Score = 408 (148.7 bits), Expect = 5.2e-37, P = 5.2e-37
 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|F8VV04 SART3 "Squamous cell carcinoma antigen recognized by T-cells 3" [Homo sapiens (taxid:9606)]

 Score = 399 (145.5 bits), Expect = 2.7e-36, P = 2.7e-36
 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:   323 AEAPRLAEYQAYIDFEMKIGDPARIQLIFERALVENCLVPDLWIRYSQYLDRQLKVKDLV 382

Query:    78 RDVYSRATKNCPWVGELWVXXXXXXXXXXXXXXXISTVFEKSLLCAFSTFEEYLDLFLTR 137
               V++RA +NCPW   LW                IS  FEK+L   F    +Y++++   
Sbjct:   383 LSVHNRAIRNCPWTVALWSRYLLAMERHGVDHQVISVTFEKALNAGFIQATDYVEIWQAY 442

Query:   138 IDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMK---NTDG--LLRLYAYWAHLE 192
             +D LRRR+ F  +    L+   +R  F RA +YL ++++   N  G     +   WA +E
Sbjct:   443 LDYLRRRVDFKQDSSKELEE--LRAAFTRALEYLKQEVEERFNESGDPSCVIMQNWARIE 500

Query:   193 QSMGKDMVSARGVWERLLKISGAML-EAWQSYISMEIELDHINEARSIYKRCYSKRFTGT 251
               +  +M  AR +W+ ++    A     W  Y ++E         R    R    + T  
Sbjct:   501 ARLCNNMQKARELWDSIMTRGNAKYANMWLEYYNLERAHGDTQHCRKALHRAV--QCTSD 558

Query:   252 GSEDICHAWLRFEREYGTLEDFDHSVQKVTPRL---EELRLFRSQQESKSLPESADQKEH 308
               E +C   L  ER  G+LED+D +VQK   RL    E R+  +++E+  + +  ++ E 
Sbjct:   559 YPEHVCEVLLTMERTEGSLEDWDIAVQKTETRLARVNEQRMKAAEKEAALVQQEEEKAEQ 618

Query:   309 SVKKTGREKRKSDSNISYEQSPAKRQKHAPQKPKKVHDKEKRQVQNLAEEN 359
               +K  R ++K+       + P KR      + +   D+E++  +    EN
Sbjct:   619 --RKRARAEKKALKKKKKIRGPEKRGADEDDEKEWGDDEEEQPSKRRRVEN 667

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

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

---

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

Fail to connect to STRING server

---

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	442
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	7e-09
smart00360	73	smart00360, RRM, RNA recognition motif	2e-07
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	6e-07
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	9e-07
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	3e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	4e-05
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	9e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	9e-05
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-04
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	3e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	3e-04
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	4e-04
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	6e-04
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	0.001
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	0.001
smart00386	33	smart00386, HAT, HAT (Half-A-TPR) repeats	0.002
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	0.003
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	0.004
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	0.004

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

 Score = 56.5 bits (135), Expect = 7e-09
 Identities = 30/139 (21%), Positives = 56/139 (40%), Gaps = 3/139 (2%)

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 VGGVSSIRILHDKFTGKSR 433
            G V  +R++ D+ TGKSR
Sbjct: 139 FGPVKRVRLVRDRETGKSR 157

Length = 306

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

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 19/41 (46%), Positives = 26/41 (63%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           T F+ N+    T E+LR  FS  G V S+R++ DK TGKS+
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSK 41

Length = 73

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

 Score = 46.5 bits (111), Expect = 6e-07
 Identities = 15/41 (36%), Positives = 24/41 (58%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
             ++ N+    T EDL+  F   G V+S R++ D+ TG+SR
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSR 41

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|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 = 46.1 bits (110), Expect = 9e-07
 Identities = 18/39 (46%), Positives = 24/39 (61%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F+ NI   AT E L   FS+VG V S R++ D+ TGK +
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPK 40

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

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 17/41 (41%), Positives = 24/41 (58%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           T F++ +N   T   LRR F + G +  IR++ DK TGK R
Sbjct: 3   TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPR 43

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

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 15/41 (36%), Positives = 24/41 (58%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           T F+  ++LK    DL  FFS  G V  +RI+ D+ + +S+
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSK 41

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 41.0 bits (97), Expect = 5e-05
 Identities = 17/39 (43%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F+ N+    T EDL+  FS  G + SIRI+ D  TG+S+
Sbjct: 2   FVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSK 39

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

 Score = 40.4 bits (95), Expect = 9e-05
 Identities = 15/39 (38%), Positives = 24/39 (61%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F+ N++   T E+L+  F   G ++ I IL DKFTG+ +
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPK 41

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

 Score = 44.1 bits (104), Expect = 9e-05
 Identities = 28/145 (19%), Positives = 58/145 (40%), Gaps = 16/145 (11%)

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 FFSDVGGVSSIRILHDKFTGKSRVV 435
           FFS VG V  ++ + D+ + +S+ V
Sbjct: 109 FFSKVGKVRDVQCIKDRNSRRSKGV 133

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 18/39 (46%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F+ N+    T EDLR  FS  G + S+RI+ DK  GKS+
Sbjct: 2   FVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSK 39

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

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

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 13/39 (33%), Positives = 23/39 (58%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F+S ++ + T ++L   FS  G V  + ++ D  TG+SR
Sbjct: 5   FVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESR 43

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

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 15/43 (34%), Positives = 24/43 (55%)

Query: 391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
             T F+  ++L+ T E LR  FS  G +  +R++ D  TG S+
Sbjct: 3   YLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSK 45

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

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 17/39 (43%), Positives = 23/39 (58%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F+ N+    T EDL   F + G   S+R+L DK TGKS+
Sbjct: 4   FVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSK 42

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|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 = 38.6 bits (90), Expect = 4e-04
 Identities = 18/39 (46%), Positives = 27/39 (69%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F+ NI  +AT E L+  FS+VG V S R+++D+ TGK +
Sbjct: 2   FVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPK 40

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

 Score = 38.3 bits (90), Expect = 6e-04
 Identities = 18/42 (42%), Positives = 24/42 (57%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
            T F+ N+   AT E+L+  FS  G V   RI+ DK TG S+
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSK 42

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|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 = 37.2 bits (87), Expect = 0.001
 Identities = 12/36 (33%), Positives = 20/36 (55%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDK 427
            T ++ N+    T E+L+R FS  G +  +R+  DK
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK 36

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 13/33 (39%), Positives = 20/33 (60%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDK 427
           ++ N+    T EDLR FFS  G V  +R++ +K
Sbjct: 2   YVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK 34

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

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

 Score = 35.2 bits (82), 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|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 10/37 (27%), Positives = 21/37 (56%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGK 431
           F+ N++  A  + +   F + G +SS+R+  D  +G+
Sbjct: 2   FVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGR 38

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

 Score = 35.6 bits (83), Expect = 0.004
 Identities = 14/38 (36%), Positives = 23/38 (60%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTG 430
           + F+ N+      E+LR+ F D G V ++RI+ D+ TG
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTG 38

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

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 4/50 (8%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRI----LHDKFTGKSRVVQS 437
            T F+ N+ L    +DL++ F   G + S+R     + +K   K      
Sbjct: 1   RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIK 50

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	442
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	100.0
KOG1915	677	consensus Cell cycle control protein (crooked neck	100.0
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.97
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.91
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.9
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	99.9
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.89
KOG1258	577	consensus mRNA processing protein [RNA processing	99.86
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.82
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.79
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.79
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	99.72
KOG2396	568	consensus HAT (Half-A-TPR) repeat-containing prote	99.7
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	99.65
KOG1258	577	consensus mRNA processing protein [RNA processing	99.61
KOG2396	568	consensus HAT (Half-A-TPR) repeat-containing prote	99.6
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	99.53
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	99.52
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.36
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.3
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	99.3
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.3
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.29
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.28
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.25
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.25
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.22
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.2
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.17
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	99.17
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.16
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.13
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.11
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.1
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.1
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.08
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.08
KOG0122	270	consensus Translation initiation factor 3, subunit	99.07
PRK11189	296	lipoprotein NlpI; Provisional	99.06
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.06
PF08424	321	NRDE-2: NRDE-2, necessary for RNA interference; In	99.04
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.04
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.03
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.03
PRK12370	553	invasion protein regulator; Provisional	99.01
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.99
PRK11788	389	tetratricopeptide repeat protein; Provisional	98.99
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	98.97
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.97
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	98.95
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.94
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	98.92
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	98.9
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.9
PRK11189	296	lipoprotein NlpI; Provisional	98.89
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	98.85
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.85
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.85
PRK12370	553	invasion protein regulator; Provisional	98.82
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	98.82
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	98.81
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	98.8
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	98.78
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.76
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	98.74
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	98.73
COG5191	435	Uncharacterized conserved protein, contains HAT (H	98.72
KOG0547	606	consensus Translocase of outer mitochondrial membr	98.71
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.71
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.7
KOG0547	606	consensus Translocase of outer mitochondrial membr	98.7
KOG1125	579	consensus TPR repeat-containing protein [General f	98.69
PF08424	321	NRDE-2: NRDE-2, necessary for RNA interference; In	98.68
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.67
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.66
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.66
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.64
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.62
KOG2076	895	consensus RNA polymerase III transcription factor	98.62
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	98.61
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	98.6
smart00362	72	RRM_2 RNA recognition motif.	98.59
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.59
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	98.58
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	98.58
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.57
KOG2076	895	consensus RNA polymerase III transcription factor	98.55
KOG1129	478	consensus TPR repeat-containing protein [General f	98.54
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.52
smart00360	71	RRM RNA recognition motif.	98.51
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.51
PLN02789	320	farnesyltranstransferase	98.51
PLN03218	1060	maturation of RBCL 1; Provisional	98.49
KOG1126	638	consensus DNA-binding cell division cycle control	98.49
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.49
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.49
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	98.48
PLN03218	1060	maturation of RBCL 1; Provisional	98.45
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	98.45
PF08311	126	Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro	98.43
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.4
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	98.39
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	98.39
KOG1126	638	consensus DNA-binding cell division cycle control	98.38
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	98.38
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.38
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	98.37
COG5191	435	Uncharacterized conserved protein, contains HAT (H	98.35
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.33
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.33
KOG1125	579	consensus TPR repeat-containing protein [General f	98.33
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.32
PLN02789	320	farnesyltranstransferase	98.31
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.26
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	98.23
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.22
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.21
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	98.2
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.18
PRK15359	144	type III secretion system chaperone protein SscB;	98.18
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.16
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.12
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.12
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.12
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.11
PRK14574	822	hmsH outer membrane protein; Provisional	98.11
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.09
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	98.08
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.08
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.04
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.01
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	98.01
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	98.0
PLN03077	857	Protein ECB2; Provisional	97.96
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	97.95
smart00386	33	HAT HAT (Half-A-TPR) repeats. Present in several R	97.93
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.93
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	97.93
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	97.92
smart00777	125	Mad3_BUB1_I Mad3/BUB1 hoMad3/BUB1 homology region	97.91
PRK14720	906	transcript cleavage factor/unknown domain fusion p	97.91
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	97.91
PRK15359	144	type III secretion system chaperone protein SscB;	97.9
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	97.9
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.88
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	97.88
PRK14574	822	hmsH outer membrane protein; Provisional	97.88
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	97.87
PLN03077	857	Protein ECB2; Provisional	97.87
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	97.87
smart00361	70	RRM_1 RNA recognition motif.	97.86
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	97.83
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	97.81
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	97.8
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	97.8
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	97.8
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.79
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	97.79
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	97.78
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	97.75
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	97.71
PF08311	126	Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro	97.71
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	97.71
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	97.67
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.67
smart00386	33	HAT HAT (Half-A-TPR) repeats. Present in several R	97.63
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.62
KOG0226	290	consensus RNA-binding proteins [General function p	97.62
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	97.58
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.57
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	97.57
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.55
PF02184	32	HAT: HAT (Half-A-TPR) repeat; InterPro: IPR003107	97.54
PRK14720	906	transcript cleavage factor/unknown domain fusion p	97.54
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	97.54
KOG1129	478	consensus TPR repeat-containing protein [General f	97.5
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.49
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	97.45
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	97.44
PLN03213	759	repressor of silencing 3; Provisional	97.44
KOG2003	840	consensus TPR repeat-containing protein [General f	97.43
PF13428	44	TPR_14: Tetratricopeptide repeat	97.42
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.42
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	97.38
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.37
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	97.34
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.32
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.32
PF02184	32	HAT: HAT (Half-A-TPR) repeat; InterPro: IPR003107	97.3
KOG1128	777	consensus Uncharacterized conserved protein, conta	97.29
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.28
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	97.23
PF13428	44	TPR_14: Tetratricopeptide repeat	97.21
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	97.16
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	97.16
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	97.16
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.13
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.12
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.08
KOG4210	285	consensus Nuclear localization sequence binding pr	97.03
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.01
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	97.01
KOG1128	777	consensus Uncharacterized conserved protein, conta	97.01
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	96.99
KOG3785	557	consensus Uncharacterized conserved protein [Funct	96.99
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	96.98
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	96.98
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	96.95
KOG0151	877	consensus Predicted splicing regulator, contains R	96.93
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	96.93
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	96.86
KOG2003	840	consensus TPR repeat-containing protein [General f	96.86
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	96.86
PF13371	73	TPR_9: Tetratricopeptide repeat	96.86
KOG4660	549	consensus Protein Mei2, essential for commitment t	96.84
PF13371	73	TPR_9: Tetratricopeptide repeat	96.84
COG4783	484	Putative Zn-dependent protease, contains TPR repea	96.81
COG4783	484	Putative Zn-dependent protease, contains TPR repea	96.77
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	96.76
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	96.73
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	96.7
smart00777	125	Mad3_BUB1_I Mad3/BUB1 hoMad3/BUB1 homology region	96.69
PRK11906	458	transcriptional regulator; Provisional	96.66
KOG0553	304	consensus TPR repeat-containing protein [General f	96.65
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	96.64
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	96.57
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	96.56
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	96.45
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	96.41
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	96.41
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	96.38
KOG0553	304	consensus TPR repeat-containing protein [General f	96.33
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	96.21
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	96.19
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	96.16
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	96.09
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.0
PF12688	120	TPR_5: Tetratrico peptide repeat	95.94
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	95.94
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	95.94
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	95.8
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	95.73
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	95.71
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	95.69
KOG1457	284	consensus RNA binding protein (contains RRM repeat	95.65
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	95.64
PRK10803	263	tol-pal system protein YbgF; Provisional	95.63
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	95.55
PF13431	34	TPR_17: Tetratricopeptide repeat	95.55
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	95.53
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	95.3
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	95.27
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	95.17
PF03704	146	BTAD: Bacterial transcriptional activator domain;	95.15
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	95.1
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	95.08
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	95.05
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	94.99
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	94.83
PRK10803	263	tol-pal system protein YbgF; Provisional	94.82
KOG3152	278	consensus TBP-binding protein, activator of basal	94.8
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	94.77
PF13512	142	TPR_18: Tetratricopeptide repeat	94.76
PRK11906	458	transcriptional regulator; Provisional	94.75
KOG3824	472	consensus Huntingtin interacting protein HYPE [Gen	94.48
KOG1457	284	consensus RNA binding protein (contains RRM repeat	94.1
PF13431	34	TPR_17: Tetratricopeptide repeat	93.91
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	93.74
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	93.67
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	93.66
KOG1995	351	consensus Conserved Zn-finger protein [General fun	93.32
PF12688	120	TPR_5: Tetratrico peptide repeat	93.3
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	93.26
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	92.85
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	92.54
PF13512	142	TPR_18: Tetratricopeptide repeat	92.41
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	92.35
PF03704	146	BTAD: Bacterial transcriptional activator domain;	92.33
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	92.32
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	92.31
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	92.24
PF06552	186	TOM20_plant: Plant specific mitochondrial import r	92.07
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	91.69
PRK15331	165	chaperone protein SicA; Provisional	91.51
PRK15331	165	chaperone protein SicA; Provisional	91.29
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	91.08
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	90.9
KOG4555	175	consensus TPR repeat-containing protein [Function	90.73
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	90.68
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	90.58
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	90.36
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	90.1
KOG2376	652	consensus Signal recognition particle, subunit Srp	89.68
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	89.67
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	89.59
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	89.47
KOG4555	175	consensus TPR repeat-containing protein [Function	89.34
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	89.19
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	89.16
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	89.01
PF06552	186	TOM20_plant: Plant specific mitochondrial import r	88.99
KOG3824	472	consensus Huntingtin interacting protein HYPE [Gen	88.94
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	88.82
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	88.18
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	88.03
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	87.46
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	86.91
KOG2376	652	consensus Signal recognition particle, subunit Srp	86.84
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	86.41
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	86.33
KOG2314	698	consensus Translation initiation factor 3, subunit	86.19
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	85.89
KOG0530	318	consensus Protein farnesyltransferase, alpha subun	85.83
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	85.65
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	85.0
KOG4234	271	consensus TPR repeat-containing protein [General f	84.96
PF15297	353	CKAP2_C: Cytoskeleton-associated protein 2 C-termi	84.91
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	84.88
TIGR02996	42	rpt_mate_G_obs repeat-companion domain TIGR02996.	84.51
PRK04841	903	transcriptional regulator MalT; Provisional	83.29
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	83.19
KOG1166	974	consensus Mitotic checkpoint serine/threonine prot	82.99
KOG1855	484	consensus Predicted RNA-binding protein [General f	82.85
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	82.83
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	81.82
PF15297	353	CKAP2_C: Cytoskeleton-associated protein 2 C-termi	81.77

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

Probab=100.00  E-value=3e-40  Score=324.02  Aligned_cols=417  Identities=29%  Similarity=0.452  Sum_probs=299.8

Q ss_pred             hHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHH
Q 013489            5 RAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRA   84 (442)
Q Consensus         5 r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erA   84 (442)
                      +..||..++..+.    .++.|+.|++||+..|++-++..+|||++...+.+.++|+.|..|+...++.+..+..++-||
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            3456666666554    788999999999999999999999999999999999999999999998888888889999999


Q ss_pred             HHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHH
Q 013489           85 TKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETF  164 (442)
Q Consensus        85 l~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~  164 (442)
                      +++|||.+.||..|+..+++.......+-..|+++++.++.       ++..++-+.++...    +....+++.+|.+|
T Consensus       374 ~R~cp~tgdL~~rallAleR~re~~~vI~~~l~~~ls~~~~-------l~~~~~~~rr~~~~----~~~s~~~s~lr~~F  442 (881)
T KOG0128|consen  374 VRSCPWTGDLWKRALLALERNREEITVIVQNLEKDLSMTVE-------LHNDYLAYRRRCTN----IIDSQDYSSLRAAF  442 (881)
T ss_pred             hcCCchHHHHHHHHHHHHHhcCcchhhHHHHHHHHHHHHHH-------HHHHHHHHHHhhcc----cchhhhHHHHHHHH
Confidence            99999999999999999999888888899999998875443       22222222222221    12236788999999


Q ss_pred             HHHHHHHhhhhcC-chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHH-HHHHHHHHHHhcccHHHHHHHHHH
Q 013489          165 QRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLE-AWQSYISMEIELDHINEARSIYKR  242 (442)
Q Consensus       165 ~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~-~w~~~~~~e~~~g~~~~ar~i~~r  242 (442)
                      ..|..+|...+.. .++.++++..||++|+.++++++.||.||+.++........ .|+.|+++|..+|+...||.++.+
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            9999999999887 88899999999999999999999999999999998555554 999999999999999999999999


Q ss_pred             HHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhhchhHHHHHHHHHhhhhccCCCchhhhhhhcccccccccCCCC
Q 013489          243 CYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELRLFRSQQESKSLPESADQKEHSVKKTGREKRKSDS  322 (442)
Q Consensus       243 al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~krk~~~  322 (442)
                      |+.....++....|++.|..||+++|+++.+..+..+.+++.......+.+.+.+...+.+..+     +..+.+++...
T Consensus       523 ay~~~~~~~~~~ev~~~~~r~Ere~gtl~~~~~~~~~~~pr~~~~~~~~~e~~s~~v~p~~~~k-----e~~~~~~k~~~  597 (881)
T KOG0128|consen  523 AYSQVVDPEDALEVLEFFRRFEREYGTLESFDLCPEKVLPRVYEAPLERREKESTNVYPEQQKK-----EIQRRQFKGEG  597 (881)
T ss_pred             HHhcCcCchhHHHHHHHHHHHHhccccHHHHhhhHHhhcchhhhhhhhhhhhcccCCCcchhhH-----HhhHHHhhccc
Confidence            9986555555668999999999999999999999999999887666655555544422111111     11111111111


Q ss_pred             CCCccCCchhhcccCCCC-CCccchhhhhhhhhhhhhhcccCCcccccCCCCCCCCcCCCCCCCCCCCCCceEEEcCCCC
Q 013489          323 NISYEQSPAKRQKHAPQK-PKKVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINL  401 (442)
Q Consensus       323 ~~~~~~~~~k~~k~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~  401 (442)
                      +..+-..|+++.+...+. .-..-+...+..++.+++..+......++....+..+....+..+...++.+++||+||+.
T Consensus       598 ~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~pa~~~~a~~~~av~~ad~~~~~~~~kvs~n~~R~~~~~fvsnl~~  677 (881)
T KOG0128|consen  598 NVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATVPAGGALANRSAAVGLADAEEKEENFKVSPNEIRDLIKIFVSNLSP  677 (881)
T ss_pred             ccccccCccccccccccchhhhhhccccchhhcccccccccCCccccCCCCCchhhhhccCcCchHHHHHHHHHHhhcch
Confidence            111111111111111000 0000000000000111111111111111111112223344444455557788999999999


Q ss_pred             CCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          402 KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       402 ~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.+.+|...|+.+|.+..+++.....+|+.||.|||+|.
T Consensus       678 ~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~  717 (881)
T KOG0128|consen  678 KMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFL  717 (881)
T ss_pred             hhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEee
Confidence            9999999999999999988888755678999999999995

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

Probab=100.00  E-value=1.8e-31  Score=247.48  Aligned_cols=243  Identities=23%  Similarity=0.407  Sum_probs=211.4

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ..|..||..|+++..    +++.|+.|+.||..++++.+|+.+|||||.....+..||+.|+.+..++ +..+.++.|++
T Consensus        57 RkRkefEd~irrnR~----~~~~WikYaqwEesq~e~~RARSv~ERALdvd~r~itLWlkYae~Emkn-k~vNhARNv~d  131 (677)
T KOG1915|consen   57 RKRKEFEDQIRRNRL----NMQVWIKYAQWEESQKEIQRARSVFERALDVDYRNITLWLKYAEFEMKN-KQVNHARNVWD  131 (677)
T ss_pred             HHHHHHHHHHHHHHH----HHHHHHHHHHHHHhHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHhh-hhHhHHHHHHH
Confidence            478999999999876    8999999999999999999999999999999999999999999987754 56688999999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh-h-HHHHHHHHHHHHHHHHHHhhccCccchhhhHHHH
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS-T-FEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLI  160 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~-~-~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~  160 (442)
                      |||+.+|....+|..|+. +|...+++..+++||++.+...|+ . |..|+.+.+.|                 .++...
T Consensus       132 RAvt~lPRVdqlWyKY~y-mEE~LgNi~gaRqiferW~~w~P~eqaW~sfI~fElRy-----------------keiera  193 (677)
T KOG1915|consen  132 RAVTILPRVDQLWYKYIY-MEEMLGNIAGARQIFERWMEWEPDEQAWLSFIKFELRY-----------------KEIERA  193 (677)
T ss_pred             HHHHhcchHHHHHHHHHH-HHHHhcccHHHHHHHHHHHcCCCcHHHHHHHHHHHHHh-----------------hHHHHH
Confidence            999999999999999997 555689999999999999998776 2 33455544433                 355566


Q ss_pred             HHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHH---HHHHHHHHHHhcccHHHHH
Q 013489          161 RETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLE---AWQSYISMEIELDHINEAR  237 (442)
Q Consensus       161 r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~---~w~~~~~~e~~~g~~~~ar  237 (442)
                      |+.|++-.-        .++.+.-|+.||+||.++| ++..||.+|++|+...++...   +...++.||..+..+++||
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            666665433        3467889999999999999 999999999999999777643   8999999999999999999


Q ss_pred             HHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHH
Q 013489          238 SIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQ  278 (442)
Q Consensus       238 ~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~  278 (442)
                      .||+-||. .+|.+..+.|+..|..||..||+...|++++-
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 57888889999999999999999999998874

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

Probab=99.97  E-value=4.1e-28  Score=225.30  Aligned_cols=215  Identities=25%  Similarity=0.450  Sum_probs=162.2

Q ss_pred             chhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCH---------HHHHHHHHHHHHhcc
Q 013489            2 CNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS---------DLWLDYTQYLDKTLK   72 (442)
Q Consensus         2 ~~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~---------~lW~~Y~~~l~~~~~   72 (442)
                      ++.|-.||.-|+.+|.    +++.|..|+.++...|+.++++.+|||||...|...         -||++|+.|.+-..+
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            5778899999999998    999999999999999999999999999999877543         399999999887778


Q ss_pred             hhhHHHHHHHHHHHcCCCc----HHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh--hHHHHHHHHHHHHHHHHHHhh
Q 013489           73 VGNVVRDVYSRATKNCPWV----GELWVRSLLSLERSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRIL  146 (442)
Q Consensus        73 ~~~~~~~v~erAl~~~p~s----~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~--~~~~~~~~~~~~~~~l~rr~~  146 (442)
                      +.+..++||..++..+|+.    ..||..|+.+.-+ +.+...++.++-.|+...|.  .+..|+++.+..         
T Consensus       381 d~ertr~vyq~~l~lIPHkkFtFaKiWlmyA~feIR-q~~l~~ARkiLG~AIG~cPK~KlFk~YIelElqL---------  450 (677)
T KOG1915|consen  381 DVERTRQVYQACLDLIPHKKFTFAKIWLMYAQFEIR-QLNLTGARKILGNAIGKCPKDKLFKGYIELELQL---------  450 (677)
T ss_pred             hHHHHHHHHHHHHhhcCcccchHHHHHHHHHHHHHH-HcccHHHHHHHHHHhccCCchhHHHHHHHHHHHH---------
Confidence            8899999999999999985    3799999985554 78889999999999965443  234455444322         


Q ss_pred             ccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhch-hHHH-HHHHHH
Q 013489          147 FSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG-AMLE-AWQSYI  224 (442)
Q Consensus       147 ~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~-~~~~-~w~~~~  224 (442)
                                     ..|++|..+.++.+.-.|..+..|..||.+|..+| +.++||.||+-|++... +.++ +|..||
T Consensus       451 ---------------~efDRcRkLYEkfle~~Pe~c~~W~kyaElE~~Lg-dtdRaRaifelAi~qp~ldmpellwkaYI  514 (677)
T KOG1915|consen  451 ---------------REFDRCRKLYEKFLEFSPENCYAWSKYAELETSLG-DTDRARAIFELAISQPALDMPELLWKAYI  514 (677)
T ss_pred             ---------------hhHHHHHHHHHHHHhcChHhhHHHHHHHHHHHHhh-hHHHHHHHHHHHhcCcccccHHHHHHHhh
Confidence                           33444444444444445566667777777777777 77777777777776633 2232 677777


Q ss_pred             HHHHhcccHHHHHHHHHHHHhc
Q 013489          225 SMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       225 ~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      +||...|.+++||.+|++.|.+
T Consensus       515 dFEi~~~E~ekaR~LYerlL~r  536 (677)
T KOG1915|consen  515 DFEIEEGEFEKARALYERLLDR  536 (677)
T ss_pred             hhhhhcchHHHHHHHHHHHHHh
Confidence            7777777777777777776643

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

Probab=99.91  E-value=1.2e-22  Score=208.96  Aligned_cols=249  Identities=18%  Similarity=0.327  Sum_probs=203.3

Q ss_pred             hHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcC-CCCH----HHHHHHHHHHHHhcchhhHHHH
Q 013489            5 RAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDF-PVSS----DLWLDYTQYLDKTLKVGNVVRD   79 (442)
Q Consensus         5 r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~-p~~~----~lW~~Y~~~l~~~~~~~~~~~~   79 (442)
                      -+.||+.|.+.|.    ..=.|+.||.|..+.++.+.++.++||||... +.-.    .+|+.|+++....+ ..+.+..
T Consensus      1444 aeDferlvrssPN----SSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG-~eesl~k 1518 (1710)
T KOG1070|consen 1444 AEDFERLVRSSPN----SSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYG-TEESLKK 1518 (1710)
T ss_pred             HHHHHHHHhcCCC----cchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhC-cHHHHHH
Confidence            3579999999886    44489999999999999999999999999864 4332    59999999877665 4467999


Q ss_pred             HHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHH
Q 013489           80 VYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSL  159 (442)
Q Consensus        80 v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~  159 (442)
                      +|+||+++|- ...++...+.+++. .+.++.+.++|++.+..    +-.-..+|..|.+.|-|+-          +-+.
T Consensus      1519 VFeRAcqycd-~~~V~~~L~~iy~k-~ek~~~A~ell~~m~KK----F~q~~~vW~~y~~fLl~~n----------e~~a 1582 (1710)
T KOG1070|consen 1519 VFERACQYCD-AYTVHLKLLGIYEK-SEKNDEADELLRLMLKK----FGQTRKVWIMYADFLLRQN----------EAEA 1582 (1710)
T ss_pred             HHHHHHHhcc-hHHHHHHHHHHHHH-hhcchhHHHHHHHHHHH----hcchhhHHHHHHHHHhccc----------HHHH
Confidence            9999999884 24677777776666 46667788888887742    1133567777777775542          3346


Q ss_pred             HHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHH
Q 013489          160 IRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSI  239 (442)
Q Consensus       160 ~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i  239 (442)
                      .+..+.+|+.++.+     ....++...+|++|.++| +.+++|.+|+..+..+|...++|.-||++|+.+|+.+.+|.+
T Consensus      1583 a~~lL~rAL~~lPk-----~eHv~~IskfAqLEFk~G-DaeRGRtlfEgll~ayPKRtDlW~VYid~eik~~~~~~vR~l 1656 (1710)
T KOG1070|consen 1583 ARELLKRALKSLPK-----QEHVEFISKFAQLEFKYG-DAERGRTLFEGLLSAYPKRTDLWSVYIDMEIKHGDIKYVRDL 1656 (1710)
T ss_pred             HHHHHHHHHhhcch-----hhhHHHHHHHHHHHhhcC-CchhhHHHHHHHHhhCccchhHHHHHHHHHHccCCHHHHHHH
Confidence            67888899888743     235678999999999999 999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          240 YKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       240 ~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                      |+|++...++.....-+|..|++||..||+.+.++.+-.++
T Consensus      1657 feRvi~l~l~~kkmKfffKkwLeyEk~~Gde~~vE~VKarA 1697 (1710)
T KOG1070|consen 1657 FERVIELKLSIKKMKFFFKKWLEYEKSHGDEKNVEYVKARA 1697 (1710)
T ss_pred             HHHHHhcCCChhHhHHHHHHHHHHHHhcCchhhHHHHHHHH
Confidence            99999877777777889999999999999999888655444

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

Probab=99.90  E-value=1.5e-21  Score=188.08  Aligned_cols=244  Identities=19%  Similarity=0.248  Sum_probs=204.9

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (442)
                      +|.+|-.+|+..|.    +-.+|..-+.||+.+|..+....++++|+..+|..+.+|++|+.--... ++.-.++.++.+
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            68899999999886    6678999999999999999999999999999999999999999876654 455668999999


Q ss_pred             HHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHH
Q 013489           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRET  163 (442)
Q Consensus        84 Al~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~  163 (442)
                      |+...|+|.+||...+. +|..+...+.+|.+|.+|....+..     .+|+.++                 .+....+.
T Consensus       610 af~~~pnseeiwlaavK-le~en~e~eraR~llakar~~sgTe-----Rv~mKs~-----------------~~er~ld~  666 (913)
T KOG0495|consen  610 AFEANPNSEEIWLAAVK-LEFENDELERARDLLAKARSISGTE-----RVWMKSA-----------------NLERYLDN  666 (913)
T ss_pred             HHHhCCCcHHHHHHHHH-HhhccccHHHHHHHHHHHhccCCcc-----hhhHHHh-----------------HHHHHhhh
Confidence            99999999999999887 7777888899999999998754431     2232222                 22233356


Q ss_pred             HHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHH
Q 013489          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRC  243 (442)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ra  243 (442)
                      +++|+.+++.++...+....+|+...+++..++ +++.||..|..+++.+|....+|+..+++|...|.+-+||.|++++
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            677788887777778888899999999999999 9999999999999999999999999999999999999999999999


Q ss_pred             HhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHh
Q 013489          244 YSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQK  279 (442)
Q Consensus       244 l~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~  279 (442)
                      .-+   ++....+|.+-++||..+|+++..+..+.+
T Consensus       746 rlk---NPk~~~lwle~Ir~ElR~gn~~~a~~lmak  778 (913)
T KOG0495|consen  746 RLK---NPKNALLWLESIRMELRAGNKEQAELLMAK  778 (913)
T ss_pred             Hhc---CCCcchhHHHHHHHHHHcCCHHHHHHHHHH
Confidence            864   344568999999999999999877655543

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

Probab=99.90  E-value=2.6e-21  Score=183.08  Aligned_cols=278  Identities=17%  Similarity=0.258  Sum_probs=204.1

Q ss_pred             chhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchh----hHH
Q 013489            2 CNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVG----NVV   77 (442)
Q Consensus         2 ~~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~----~~~   77 (442)
                      -+.|+.||..+...|.    ...+|+.||..|....+++.+..+|.|||... ++.+||..|+.|+.+..+..    +.+
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            4689999999999887    56789999999999999999999999999875 66999999999998764332    456


Q ss_pred             HHHHHHHHHcC---CCcHHHHHHHHHHHHH--------ccCCHHHHHHHHHHHHhCChhhH----HHHHHHHHHHHHHHH
Q 013489           78 RDVYSRATKNC---PWVGELWVRSLLSLER--------SRASEEEISTVFEKSLLCAFSTF----EEYLDLFLTRIDGLR  142 (442)
Q Consensus        78 ~~v~erAl~~~---p~s~~lW~~y~~~le~--------~~~~~~~~~~i~~~al~~~~~~~----~~~~~~~~~~~~~l~  142 (442)
                      ...|+-|+..|   +.|..||..|+.|++.        .++.++.+|.+|+||+..++.+.    .+|.. |..-++.+.
T Consensus       111 ~qAy~f~l~kig~di~s~siW~eYi~FL~~vea~gk~ee~QRI~~vRriYqral~tPm~nlEkLW~DY~~-fE~~IN~~t  189 (656)
T KOG1914|consen  111 VQAYDFALEKIGMDIKSYSIWDEYINFLEGVEAVGKYEENQRITAVRRIYQRALVTPMHNLEKLWKDYEA-FEQEINIIT  189 (656)
T ss_pred             HHHHHHHHHHhccCcccchhHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHhcCccccHHHHHHHHHH-HHHHHHHHH
Confidence            78899998877   6788999999999874        23467889999999999887642    23322 211111100


Q ss_pred             -HHhhc----------------------------c---C----------ccchhhhHH----------------------
Q 013489          143 -RRILF----------------------------S---G----------EVEGVLDYS----------------------  158 (442)
Q Consensus       143 -rr~~~----------------------------~---~----------~~~~~~~~~----------------------  158 (442)
                       |++..                            .   .          .|-.+++|+                      
T Consensus       190 arK~i~e~s~~Ym~AR~~~qel~~lt~GL~r~~~~vp~~~T~~e~~qv~~W~n~I~wEksNpL~t~~~~~~~~Rv~yaye  269 (656)
T KOG1914|consen  190 ARKFIGERSPEYMNARRVYQELQNLTRGLNRNAPAVPPKGTKDEIQQVELWKNWIKWEKSNPLRTLDGTMLTRRVMYAYE  269 (656)
T ss_pred             HHHHHHhhCHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHHHHHHHHhcCCcccccccHHHHHHHHHHH
Confidence             00000                            0   0          000000000                      


Q ss_pred             -----------------------------------------HHHHHH---------------------------------
Q 013489          159 -----------------------------------------LIRETF---------------------------------  164 (442)
Q Consensus       159 -----------------------------------------~~r~~~---------------------------------  164 (442)
                                                               .++..+                                 
T Consensus       270 Q~ll~l~~~peiWy~~s~yl~~~s~l~~~~~d~~~a~~~t~e~~~~yEr~I~~l~~~~~~Ly~~~a~~eE~~~~~n~~~~  349 (656)
T KOG1914|consen  270 QCLLYLGYHPEIWYDYSMYLIEISDLLTEKGDVPDAKSLTDEAASIYERAIEGLLKENKLLYFALADYEESRYDDNKEKK  349 (656)
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHhhHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHhcccchhhh
Confidence                                                     001111                                 


Q ss_pred             ---------------------------------HHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 013489          165 ---------------------------------QRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLK  211 (442)
Q Consensus       165 ---------------------------------~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~  211 (442)
                                                       .-|..++.++-...-+..+++...|-+|+...+|...|-.||+-+|+
T Consensus       350 ~~~~~~~ll~~~~~~~tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cskD~~~AfrIFeLGLk  429 (656)
T KOG1914|consen  350 VHEIYNKLLKIEDIDLTLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCSKDKETAFRIFELGLK  429 (656)
T ss_pred             hHHHHHHHHhhhccCCceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhcCChhHHHHHHHHHHH
Confidence                                             11223333332222223467888888998888899999999999999


Q ss_pred             hchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhhchhHH
Q 013489          212 ISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLE  285 (442)
Q Consensus       212 ~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~~~~~~  285 (442)
                      .+++.+.+-..|++|....|+-.++|.+|+|++.+.++.+....||+.|++||-.+|++..+.++.++-..++.
T Consensus       430 kf~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~af~  503 (656)
T KOG1914|consen  430 KFGDSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFTAFP  503 (656)
T ss_pred             hcCCChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHHhcc
Confidence            99999999999999999999999999999999997677777889999999999999999999877766544443

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

Probab=99.89  E-value=9.9e-21  Score=182.20  Aligned_cols=235  Identities=17%  Similarity=0.295  Sum_probs=179.7

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCC--cHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPW--VGELWVRSL   99 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~--s~~lW~~y~   99 (442)
                      ++.+|..|+++|+..|.++...++|+|.|..---.|.+=++|+.||+++ .-.+.+.++|+|.+..+||  ..+||..|+
T Consensus       476 SlkiWs~y~DleEs~gtfestk~vYdriidLriaTPqii~NyAmfLEeh-~yfeesFk~YErgI~LFk~p~v~diW~tYL  554 (835)
T KOG2047|consen  476 SLKIWSMYADLEESLGTFESTKAVYDRIIDLRIATPQIIINYAMFLEEH-KYFEESFKAYERGISLFKWPNVYDIWNTYL  554 (835)
T ss_pred             hHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhh-HHHHHHHHHHHcCCccCCCccHHHHHHHHH
Confidence            3679999999999999999999999999998888999999999999976 3567799999999998854  678999999


Q ss_pred             H-HHHHccCC-HHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcC
Q 013489          100 L-SLERSRAS-EEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKN  177 (442)
Q Consensus       100 ~-~le~~~~~-~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~  177 (442)
                      . +..+.++. .+.+|.+|++||...++...-  .+|+.|...-.          +++-......++++|..-+.     
T Consensus       555 tkfi~rygg~klEraRdLFEqaL~~Cpp~~aK--tiyLlYA~lEE----------e~GLar~amsiyerat~~v~-----  617 (835)
T KOG2047|consen  555 TKFIKRYGGTKLERARDLFEQALDGCPPEHAK--TIYLLYAKLEE----------EHGLARHAMSIYERATSAVK-----  617 (835)
T ss_pred             HHHHHHhcCCCHHHHHHHHHHHHhcCCHHHHH--HHHHHHHHHHH----------HhhHHHHHHHHHHHHHhcCC-----
Confidence            6 55555443 688999999999765553222  22332321110          00111112244555544331     


Q ss_pred             chhhHHHHHHHHH-HHHHcCCCHHHHHHHHHHHHHhchhH--HHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChH
Q 013489          178 TDGLLRLYAYWAH-LEQSMGKDMVSARGVWERLLKISGAM--LEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSE  254 (442)
Q Consensus       178 ~~~~~~l~~~~a~-~e~~~~~~~~~ar~i~~~~l~~~~~~--~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~  254 (442)
                      ....+++|..|+. .....|  +...|.||+++|+..|++  .++.+.|++||.+.|.+++||.||..+-+ .+++....
T Consensus       618 ~a~~l~myni~I~kaae~yG--v~~TR~iYekaIe~Lp~~~~r~mclrFAdlEtklGEidRARaIya~~sq-~~dPr~~~  694 (835)
T KOG2047|consen  618 EAQRLDMYNIYIKKAAEIYG--VPRTREIYEKAIESLPDSKAREMCLRFADLETKLGEIDRARAIYAHGSQ-ICDPRVTT  694 (835)
T ss_pred             HHHHHHHHHHHHHHHHHHhC--CcccHHHHHHHHHhCChHHHHHHHHHHHHHhhhhhhHHHHHHHHHhhhh-cCCCcCCh
Confidence            2345778888876 444556  899999999999997765  46999999999999999999999999987 45666677


Q ss_pred             HHHHHHHHHHHHhCCHhhHHHHH
Q 013489          255 DICHAWLRFEREYGTLEDFDHSV  277 (442)
Q Consensus       255 ~i~~~~~~fE~~~G~~~~~~~~~  277 (442)
                      .+|+.|-.||-.|||.+++.+-+
T Consensus       695 ~fW~twk~FEvrHGnedT~keML  717 (835)
T KOG2047|consen  695 EFWDTWKEFEVRHGNEDTYKEML  717 (835)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHH
Confidence            89999999999999999887643

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=99.86  E-value=1.3e-19  Score=175.00  Aligned_cols=274  Identities=19%  Similarity=0.316  Sum_probs=210.0

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      .+|..|...|.+.|.    .+..|.+|+++|.+.|..+.+.++|||+|...|.+.++|++|+.++.+..++++.++..|+
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            578999999999997    8889999999999999999999999999999999999999999999988888888999999


Q ss_pred             HHHHcCC---CcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhh-------------
Q 013489           83 RATKNCP---WVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRIL-------------  146 (442)
Q Consensus        83 rAl~~~p---~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~-------------  146 (442)
                      ||+..+.   .|+.+|-.||.+. ..+.+-..+-.||+|.+..+......+.+.|...++...-++.             
T Consensus       139 ~A~~~vG~dF~S~~lWdkyie~e-n~qks~k~v~~iyeRileiP~~~~~~~f~~f~~~l~~~~~~~l~~~d~~~~l~~~~  217 (577)
T KOG1258|consen  139 RAKSYVGLDFLSDPLWDKYIEFE-NGQKSWKRVANIYERILEIPLHQLNRHFDRFKQLLNQNEEKILLSIDELIQLRSDV  217 (577)
T ss_pred             HHHHhcccchhccHHHHHHHHHH-hccccHHHHHHHHHHHHhhhhhHhHHHHHHHHHHHhcCChhhhcCHHHHHHHhhhH
Confidence            9999885   4789999999955 4577888999999999988777666666666554432100000             


Q ss_pred             cc-----------Cccc----------hhhhHH---------HHHHHH-------------HHHHHHHhhhhcC-chhhH
Q 013489          147 FS-----------GEVE----------GVLDYS---------LIRETF-------------QRASDYLSEQMKN-TDGLL  182 (442)
Q Consensus       147 ~~-----------~~~~----------~~~~~~---------~~r~~~-------------~~a~~~l~~~~~~-~~~~~  182 (442)
                      ..           +.++          ...+..         ..+.++             +..+..-...+.. ....+
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          011110         011112             1111111111222 23467


Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHH
Q 013489          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLR  262 (442)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~  262 (442)
                      ..|.+|..++...| +.+.+.-+|++++-.+..+.++|+.|+.+....|+.+-|..++.++.... .... ..|--.|..
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-VKKT-PIIHLLEAR  374 (577)
T ss_pred             HHHHHHhhhhhhcc-cHHHHHHHHHHHHhHHhhhHHHHHHHHHHHHHcCchhHHHHHHHhhhhhc-CCCC-cHHHHHHHH
Confidence            89999999999999 99999999999999999999999999999999999999999999999743 3333 357778889


Q ss_pred             HHHHhCCHhhHHHHHHhhchhH
Q 013489          263 FEREYGTLEDFDHSVQKVTPRL  284 (442)
Q Consensus       263 fE~~~G~~~~~~~~~~~~~~~~  284 (442)
                      ||+..|+..+...+++++...+
T Consensus       375 f~e~~~n~~~A~~~lq~i~~e~  396 (577)
T KOG1258|consen  375 FEESNGNFDDAKVILQRIESEY  396 (577)
T ss_pred             HHHhhccHHHHHHHHHHHHhhC
Confidence            9999999998887777765443

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

Probab=99.82  E-value=4.1e-18  Score=164.36  Aligned_cols=256  Identities=18%  Similarity=0.289  Sum_probs=185.5

Q ss_pred             HHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcc-------hhhHHH
Q 013489            6 AHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLK-------VGNVVR   78 (442)
Q Consensus         6 ~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~-------~~~~~~   78 (442)
                      .+||.-|.++|.    ++..|..||++-.. ....++..+||||++..|.+..+|.+|+..-..+.+       ..+.+.
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            379999999988    89999999997654 344677889999999999999999999976554321       224588


Q ss_pred             HHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh-----hHHHHHHHHHH-----HHHHHHHHhh--
Q 013489           79 DVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS-----TFEEYLDLFLT-----RIDGLRRRIL--  146 (442)
Q Consensus        79 ~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~-----~~~~~~~~~~~-----~~~~l~rr~~--  146 (442)
                      ..|+|++...-..+.||..|+.++-. ++.+..+|.+|.+||..-+-     .|..|+.+...     .+-.+.||.+  
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            89999999777777999999997765 68899999999999965432     23344433321     1112224443  


Q ss_pred             ccCccchhhhHHHHHHHHHHHHHHHhhhhc-------CchhhHHHHHHHHHHHHHcCCC--HHHHHHHHHHHHHhchhHH
Q 013489          147 FSGEVEGVLDYSLIRETFQRASDYLSEQMK-------NTDGLLRLYAYWAHLEQSMGKD--MVSARGVWERLLKISGAML  217 (442)
Q Consensus       147 ~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~-------~~~~~~~l~~~~a~~e~~~~~~--~~~ar~i~~~~l~~~~~~~  217 (442)
                      .+...++++++-...+..++|...+...+.       ...+...+|...-.+-..+.+.  --..-+|+..++..++++.
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            233455555554444445555444433322       1344567888776665554311  1245678888999999997


Q ss_pred             H-HHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHh
Q 013489          218 E-AWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREY  267 (442)
Q Consensus       218 ~-~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~  267 (442)
                      - +|...+++..+.|.+++||.+|+.|++....-.+...||+.|.+||+.+
T Consensus       248 g~Lw~SLAdYYIr~g~~ekarDvyeeai~~v~tvrDFt~ifd~Ya~FEE~~  298 (835)
T KOG2047|consen  248 GFLWCSLADYYIRSGLFEKARDVYEEAIQTVMTVRDFTQIFDAYAQFEESC  298 (835)
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHhheehhhHHHHHHHHHHHHHHH
Confidence            5 9999999999999999999999999987666666778999999999875

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

Probab=99.79  E-value=5.8e-17  Score=156.73  Aligned_cols=211  Identities=20%  Similarity=0.293  Sum_probs=156.3

Q ss_pred             HHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHH
Q 013489            7 HLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATK   86 (442)
Q Consensus         7 ~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~   86 (442)
                      .+..++..+|.    ....|+.|+..-...||...++.+..+|+..+|++.++|+.-+.+...+ ...+.++.+|.+|..
T Consensus       572 llqkav~~~pk----ae~lwlM~ake~w~agdv~~ar~il~~af~~~pnseeiwlaavKle~en-~e~eraR~llakar~  646 (913)
T KOG0495|consen  572 LLQKAVEQCPK----AEILWLMYAKEKWKAGDVPAARVILDQAFEANPNSEEIWLAAVKLEFEN-DELERARDLLAKARS  646 (913)
T ss_pred             HHHHHHHhCCc----chhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHhhcc-ccHHHHHHHHHHHhc
Confidence            45556666665    4558999999888899999999999999999999999999999977644 456889999999987


Q ss_pred             cCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHH
Q 013489           87 NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQR  166 (442)
Q Consensus        87 ~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~  166 (442)
                      .-| ...+|..++. +|+..+..+++.+++++||..-+.    +-.+|+..-+..          +.-.+++..|.+|..
T Consensus       647 ~sg-TeRv~mKs~~-~er~ld~~eeA~rllEe~lk~fp~----f~Kl~lmlGQi~----------e~~~~ie~aR~aY~~  710 (913)
T KOG0495|consen  647 ISG-TERVWMKSAN-LERYLDNVEEALRLLEEALKSFPD----FHKLWLMLGQIE----------EQMENIEMAREAYLQ  710 (913)
T ss_pred             cCC-cchhhHHHhH-HHHHhhhHHHHHHHHHHHHHhCCc----hHHHHHHHhHHH----------HHHHHHHHHHHHHHh
Confidence            555 5689999998 777789999999999999975332    222332211110          000122333344433


Q ss_pred             HHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          167 ASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       167 a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      +       ...+|++.-+|+..+++|.+.| ++.+||.+++++.-.+|++..+|++.|.||.+.|+.+.|+.+..+||+.
T Consensus       711 G-------~k~cP~~ipLWllLakleEk~~-~~~rAR~ildrarlkNPk~~~lwle~Ir~ElR~gn~~~a~~lmakALQe  782 (913)
T KOG0495|consen  711 G-------TKKCPNSIPLWLLLAKLEEKDG-QLVRARSILDRARLKNPKNALLWLESIRMELRAGNKEQAELLMAKALQE  782 (913)
T ss_pred             c-------cccCCCCchHHHHHHHHHHHhc-chhhHHHHHHHHHhcCCCcchhHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            3       3335666668888888888887 7888888888888888888888888888888888888888888888763

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

Probab=99.79  E-value=1.5e-17  Score=172.09  Aligned_cols=212  Identities=19%  Similarity=0.287  Sum_probs=173.2

Q ss_pred             HHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcC-CCc----HHHHHHHHHHHHHccCCHHHHHHHHH
Q 013489           43 QLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNC-PWV----GELWVRSLLSLERSRASEEEISTVFE  117 (442)
Q Consensus        43 ~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~-p~s----~~lW~~y~~~le~~~~~~~~~~~i~~  117 (442)
                      ..=|+|.+..+|++.-+|+.|+.|... ..+.+.++.+++|||..+ +.-    ..||..|+. ||...++.+.+..+|+
T Consensus      1444 aeDferlvrssPNSSi~WI~YMaf~Le-lsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lN-lEn~yG~eesl~kVFe 1521 (1710)
T KOG1070|consen 1444 AEDFERLVRSSPNSSILWIRYMAFHLE-LSEIEKARKIAERALKTINFREEEEKLNIWIAYLN-LENAYGTEESLKKVFE 1521 (1710)
T ss_pred             HHHHHHHHhcCCCcchHHHHHHHHHhh-hhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHh-HHHhhCcHHHHHHHHH
Confidence            456999999999999999999999884 456788999999999977 332    259999987 8888899999999999


Q ss_pred             HHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCC
Q 013489          118 KSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGK  197 (442)
Q Consensus       118 ~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~  197 (442)
                      ||.+..-+     +.+++..+..+                 ..-+-|+.|.+++...+....+...+|..|+.+...++ 
T Consensus      1522 RAcqycd~-----~~V~~~L~~iy-----------------~k~ek~~~A~ell~~m~KKF~q~~~vW~~y~~fLl~~n- 1578 (1710)
T KOG1070|consen 1522 RACQYCDA-----YTVHLKLLGIY-----------------EKSEKNDEADELLRLMLKKFGQTRKVWIMYADFLLRQN- 1578 (1710)
T ss_pred             HHHHhcch-----HHHHHHHHHHH-----------------HHhhcchhHHHHHHHHHHHhcchhhHHHHHHHHHhccc-
Confidence            99974322     23333332222                 22244566777777666666667889999999999998 


Q ss_pred             CHHHHHHHHHHHHHhchh--HHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHH
Q 013489          198 DMVSARGVWERLLKISGA--MLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDH  275 (442)
Q Consensus       198 ~~~~ar~i~~~~l~~~~~--~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~  275 (442)
                      .-+.||.++.+||+..|.  +.++...++++|..+||.+++|.+|+-.+.. .  +...++|..|++.|..||+.+.++.
T Consensus      1579 e~~aa~~lL~rAL~~lPk~eHv~~IskfAqLEFk~GDaeRGRtlfEgll~a-y--PKRtDlW~VYid~eik~~~~~~vR~ 1655 (1710)
T KOG1070|consen 1579 EAEAARELLKRALKSLPKQEHVEFISKFAQLEFKYGDAERGRTLFEGLLSA-Y--PKRTDLWSVYIDMEIKHGDIKYVRD 1655 (1710)
T ss_pred             HHHHHHHHHHHHHhhcchhhhHHHHHHHHHHHhhcCCchhhHHHHHHHHhh-C--ccchhHHHHHHHHHHccCCHHHHHH
Confidence            889999999999999887  7899999999999999999999999999873 2  2356899999999999999999999


Q ss_pred             HHHhhch
Q 013489          276 SVQKVTP  282 (442)
Q Consensus       276 ~~~~~~~  282 (442)
                      .++++..
T Consensus      1656 lfeRvi~ 1662 (1710)
T KOG1070|consen 1656 LFERVIE 1662 (1710)
T ss_pred             HHHHHHh
Confidence            9988643

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=99.72  E-value=8.9e-17  Score=149.70  Aligned_cols=102  Identities=28%  Similarity=0.474  Sum_probs=87.2

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCC-hHHHHHH
Q 013489          181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTG-SEDICHA  259 (442)
Q Consensus       181 ~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~-~~~i~~~  259 (442)
                      .+++|..+|.+|..++++...|++||+.+++.+|.+..+|+.|++|+...|+.++||.+|++++.. ++.+. ...||..
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            346899999999998879999999999999999999999999999999999999999999999984 56555 6789999


Q ss_pred             HHHHHHHhCCHhhHHHHHHhhchh
Q 013489          260 WLRFEREYGTLEDFDHSVQKVTPR  283 (442)
Q Consensus       260 ~~~fE~~~G~~~~~~~~~~~~~~~  283 (442)
                      |++||..||+++.+.++..++...
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            999999999999998877766543

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.

>KOG2396 consensus HAT (Half-A-TPR) repeat-containing protein [General function prediction only]

Probab=99.70  E-value=1.2e-14  Score=137.32  Aligned_cols=136  Identities=23%  Similarity=0.423  Sum_probs=104.8

Q ss_pred             chhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcC--------------------ChhhHHHHHHHHHhcCCCCHHHHH
Q 013489            2 CNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSG--------------------DPGRVQLLYERAITDFPVSSDLWL   61 (442)
Q Consensus         2 ~~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g--------------------~~~~~~~lyERal~~~p~~~~lW~   61 (442)
                      .+.|..||..|.+...    ...-+++||.+|....                    -+.+|..+|.+|+..++.++.+|.
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            4678899999987654    5667888888875421                    146788899999999999999999


Q ss_pred             HHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhh---HHHHHHHHHHHH
Q 013489           62 DYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFST---FEEYLDLFLTRI  138 (442)
Q Consensus        62 ~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~---~~~~~~~~~~~~  138 (442)
                      +|+.|..+.. ....+..||..+++..|.++.||+..+.++...+.+++.+|.+|.++|.+++..   +.+|+.+.+.++
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            9999988643 345688899999999999999999988876666777888999999999887763   446666666655


Q ss_pred             HHHH
Q 013489          139 DGLR  142 (442)
Q Consensus       139 ~~l~  142 (442)
                      .-++
T Consensus       189 ~Kl~  192 (568)
T KOG2396|consen  189 EKLR  192 (568)
T ss_pred             HHHH
Confidence            5443

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=99.65  E-value=6.1e-14  Score=130.77  Aligned_cols=267  Identities=17%  Similarity=0.221  Sum_probs=183.2

Q ss_pred             chhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchh-----hH
Q 013489            2 CNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVG-----NV   76 (442)
Q Consensus         2 ~~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~-----~~   76 (442)
                      .+.|+.||..+.-.|.    -..+|..|+.-|....++..+..+|-|||... .+.+||.-|+.|+......+     ..
T Consensus        59 ~~~re~yeq~~~pfp~----~~~aw~ly~s~ELA~~df~svE~lf~rCL~k~-l~ldLW~lYl~YIRr~n~~~tGq~r~~  133 (660)
T COG5107          59 DAEREMYEQLSSPFPI----MEHAWRLYMSGELARKDFRSVESLFGRCLKKS-LNLDLWMLYLEYIRRVNNLITGQKRFK  133 (660)
T ss_pred             HHHHHHHHHhcCCCcc----ccHHHHHHhcchhhhhhHHHHHHHHHHHHhhh-ccHhHHHHHHHHHHhhCcccccchhhh
Confidence            3579999999888776    34589999999999999999999999999874 56999999999998765332     23


Q ss_pred             HHHHHHHHHH---cCCCcHHHHHHHHHHHHH--------ccCCHHHHHHHHHHHHhCChhh---HHHHHHHHHHHHHHHH
Q 013489           77 VRDVYSRATK---NCPWVGELWVRSLLSLER--------SRASEEEISTVFEKSLLCAFST---FEEYLDLFLTRIDGLR  142 (442)
Q Consensus        77 ~~~v~erAl~---~~p~s~~lW~~y~~~le~--------~~~~~~~~~~i~~~al~~~~~~---~~~~~~~~~~~~~~l~  142 (442)
                      +.++|+-.+.   .-|.++.+|..|..+++.        .+..++.+|.+|.||+..++.+   .|.-++-|..-++.+.
T Consensus       134 i~~ayefv~~~~~~e~~s~~~W~ey~~fle~~~~~~kwEeQqrid~iR~~Y~ral~tP~~nleklW~dy~~fE~e~N~~T  213 (660)
T COG5107         134 IYEAYEFVLGCAIFEPQSENYWDEYGLFLEYIEELGKWEEQQRIDKIRNGYMRALQTPMGNLEKLWKDYENFELELNKIT  213 (660)
T ss_pred             hHHHHHHHHhcccccccccchHHHHHHHHHhccccccHHHHHHHHHHHHHHHHHHcCccccHHHHHHHHHHHHHHHHHHH
Confidence            5667776666   228899999999998875        2345678999999999988764   2322222222111111


Q ss_pred             -HHhhccC-----------------------------------------ccchh--------------------------
Q 013489          143 -RRILFSG-----------------------------------------EVEGV--------------------------  154 (442)
Q Consensus       143 -rr~~~~~-----------------------------------------~~~~~--------------------------  154 (442)
                       |++....                                         .|-.+                          
T Consensus       214 arKfvge~sp~ym~ar~~yqe~~nlt~Gl~v~~~~~~Rt~nK~~r~s~S~WlNwIkwE~en~l~L~~~~~~qRi~y~~~q  293 (660)
T COG5107         214 ARKFVGETSPIYMSARQRYQEIQNLTRGLSVKNPINLRTANKAARTSDSNWLNWIKWEMENGLKLGGRPHEQRIHYIHNQ  293 (660)
T ss_pred             HHHHhcccCHHHHHHHHHHHHHHHHhccccccCchhhhhhccccccccchhhhHhhHhhcCCcccCCCcHHHHHHHHHHH
Confidence             1110000                                         00000                          


Q ss_pred             -----------------------------------------------------hhHHHHHHHHHHHHHHHhhhhc-----
Q 013489          155 -----------------------------------------------------LDYSLIRETFQRASDYLSEQMK-----  176 (442)
Q Consensus       155 -----------------------------------------------------~~~~~~r~~~~~a~~~l~~~~~-----  176 (442)
                                                                           .|-+.++..|+.|..-|...+.     
T Consensus       294 ~~~y~~~~~evw~dys~Y~~~isd~q~al~tv~rg~~~spsL~~~lse~yel~nd~e~v~~~fdk~~q~L~r~ys~~~s~  373 (660)
T COG5107         294 ILDYFYYAEEVWFDYSEYLIGISDKQKALKTVERGIEMSPSLTMFLSEYYELVNDEEAVYGCFDKCTQDLKRKYSMGESE  373 (660)
T ss_pred             HHHHhhhhHHHHHHHHHHHhhccHHHHHHHHHHhcccCCCchheeHHHHHhhcccHHHHhhhHHHHHHHHHHHHhhhhhh
Confidence                                                                 0111122333333332211110     


Q ss_pred             ------Cch----------------------------------------------hhHHHHHHHHHHHHHcCCCHHHHHH
Q 013489          177 ------NTD----------------------------------------------GLLRLYAYWAHLEQSMGKDMVSARG  204 (442)
Q Consensus       177 ------~~~----------------------------------------------~~~~l~~~~a~~e~~~~~~~~~ar~  204 (442)
                            +++                                              ...+++++.|-+|....++...|-.
T Consensus       374 ~~s~~D~N~e~~~Ell~kr~~k~t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~~d~~ta~~  453 (660)
T COG5107         374 SASKVDNNFEYSKELLLKRINKLTFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYATGDRATAYN  453 (660)
T ss_pred             hhccccCCccccHHHHHHHHhhhhhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhcCCcchHHH
Confidence                  000                                              0112344445566665568889999


Q ss_pred             HHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHH
Q 013489          205 VWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFD  274 (442)
Q Consensus       205 i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~  274 (442)
                      ||+-++..+|+..-+-..|+.|....|+-++||.+|+.++.+ +..+....||+.|+++|-.+|++..+-
T Consensus       454 ifelGl~~f~d~~~y~~kyl~fLi~inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN~v~  522 (660)
T COG5107         454 IFELGLLKFPDSTLYKEKYLLFLIRINDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLNNVY  522 (660)
T ss_pred             HHHHHHHhCCCchHHHHHHHHHHHHhCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchHHHH
Confidence            999999999999999999999999999999999999999985 444556689999999999999997654

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=99.61  E-value=3.3e-13  Score=131.10  Aligned_cols=258  Identities=18%  Similarity=0.219  Sum_probs=185.9

Q ss_pred             hhhHHHHHHhhcC----CCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHH
Q 013489            3 NARAHLEEQISRQ----DLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVR   78 (442)
Q Consensus         3 ~~r~~yE~~l~~~----~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~   78 (442)
                      .+|+.||..|+..    .+.+..++..|+.|++|+...|+.+++..+|+||+..|.+...+|+.|+.++.+. ++.+.+.
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            5789999999875    2457778999999999999999999999999999999999999999999999977 5667789


Q ss_pred             HHHHHHHH-cCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhH
Q 013489           79 DVYSRATK-NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDY  157 (442)
Q Consensus        79 ~v~erAl~-~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~  157 (442)
                      .++.+|++ ++|..+.|...|+.+.| .++++..++.++++..+--|.    ++.+.+.+++.++|+....       + 
T Consensus       352 ~~~~~~~~i~~k~~~~i~L~~a~f~e-~~~n~~~A~~~lq~i~~e~pg----~v~~~l~~~~~e~r~~~~~-------~-  418 (577)
T KOG1258|consen  352 NVLARACKIHVKKTPIIHLLEARFEE-SNGNFDDAKVILQRIESEYPG----LVEVVLRKINWERRKGNLE-------D-  418 (577)
T ss_pred             HHHHhhhhhcCCCCcHHHHHHHHHHH-hhccHHHHHHHHHHHHhhCCc----hhhhHHHHHhHHHHhcchh-------h-
Confidence            99999999 67999999999998555 578999999999998865433    2223333333333332110       0 


Q ss_pred             HHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcc---cHH
Q 013489          158 SLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELD---HIN  234 (442)
Q Consensus       158 ~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g---~~~  234 (442)
                        . .............-.+..-...+...++++-....++.+.|+.++..++...|++..+|+++++|+..++   +++
T Consensus       419 --~-~~~~~l~s~~~~~~~~~~i~~~l~~~~~r~~~~i~~d~~~a~~~l~~~~~~~~~~k~~~~~~~~~~~~~~~~~e~d  495 (577)
T KOG1258|consen  419 --A-NYKNELYSSIYEGKENNGILEKLYVKFARLRYKIREDADLARIILLEANDILPDCKVLYLELIRFELIQPSGREYD  495 (577)
T ss_pred             --h-hHHHHHHHHhcccccCcchhHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhcCCccHHHHHHHHHHHHhCCcchhhh
Confidence              0 0011111111111111122235777789988888889999999999999999999999999999999875   344


Q ss_pred             HHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHH
Q 013489          235 EARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSV  277 (442)
Q Consensus       235 ~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~  277 (442)
                      -.-.+....+......+.+-.--+.|+.|-..+|+......+.
T Consensus       496 ~~e~~~~~~~~~~~~~~~~~~~~~k~~ef~e~~g~~~~~~~~~  538 (577)
T KOG1258|consen  496 LLEPIDWKELKMLIDFDDSRSSTDKYIEFLEWFGIDHKGAQDE  538 (577)
T ss_pred             hhhhHHHHHHhhhccccccccchHHHHHHHHhccchhHhHhhc
Confidence            4444555544432233334334467999999999876555443

>KOG2396 consensus HAT (Half-A-TPR) repeat-containing protein [General function prediction only]

Probab=99.60  E-value=1.7e-13  Score=129.64  Aligned_cols=92  Identities=14%  Similarity=0.265  Sum_probs=84.0

Q ss_pred             HHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHH
Q 013489            6 AHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRAT   85 (442)
Q Consensus         6 ~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl   85 (442)
                      ..|-.++.+.+.    +...|..|+.|.++.+.+.++-.+|..+|..+|+++++|+.-+.++..-+.+.+.++.+|-|++
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            367788877765    8899999999999999999999999999999999999999999999876666788999999999


Q ss_pred             HcCCCcHHHHHHHHHH
Q 013489           86 KNCPWVGELWVRSLLS  101 (442)
Q Consensus        86 ~~~p~s~~lW~~y~~~  101 (442)
                      |.+|.|+.||..|+++
T Consensus       168 R~npdsp~Lw~eyfrm  183 (568)
T KOG2396|consen  168 RFNPDSPKLWKEYFRM  183 (568)
T ss_pred             hcCCCChHHHHHHHHH
Confidence            9999999999999973

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=99.53  E-value=1.9e-13  Score=127.42  Aligned_cols=96  Identities=16%  Similarity=0.298  Sum_probs=51.7

Q ss_pred             HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHH
Q 013489           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER  104 (442)
Q Consensus        25 ~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~  104 (442)
                      +|+.|+.|.+..+..+.++.+|++|+...+.+..+|+.|+.+...+.++.+.+..||+++++.+|.+..+|..|+.+|..
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            46666666655555566666666665444455566666655544444555555666666666666666666666654443


Q ss_pred             ccCCHHHHHHHHHHHHh
Q 013489          105 SRASEEEISTVFEKSLL  121 (442)
Q Consensus       105 ~~~~~~~~~~i~~~al~  121 (442)
                       .++.+.+|.+|++++.
T Consensus        83 -~~d~~~aR~lfer~i~   98 (280)
T PF05843_consen   83 -LNDINNARALFERAIS   98 (280)
T ss_dssp             -TT-HHHHHHHHHHHCC
T ss_pred             -hCcHHHHHHHHHHHHH
Confidence             3444555555555553

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.

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

Probab=99.52  E-value=6.5e-12  Score=119.93  Aligned_cols=244  Identities=18%  Similarity=0.246  Sum_probs=172.7

Q ss_pred             HHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcC
Q 013489            9 EEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNC   88 (442)
Q Consensus         9 E~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~   88 (442)
                      ++.|..+|.    +.+.|...+.....+ .++.++..||+.+..+|.++..|..||.-... .++.+.+..+|.|++...
T Consensus        10 ~~rie~nP~----di~sw~~lire~qt~-~~~~~R~~YEq~~~~FP~s~r~W~~yi~~El~-skdfe~VEkLF~RCLvkv   83 (656)
T KOG1914|consen   10 RERIEENPY----DIDSWSQLIREAQTQ-PIDKVRETYEQLVNVFPSSPRAWKLYIERELA-SKDFESVEKLFSRCLVKV   83 (656)
T ss_pred             HHHHhcCCc----cHHHHHHHHHHHccC-CHHHHHHHHHHHhccCCCCcHHHHHHHHHHHH-hhhHHHHHHHHHHHHHHH
Confidence            677888887    899999999865555 88999999999999999999999999987764 357788999999999855


Q ss_pred             CCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh--hHH-HHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHH
Q 013489           89 PWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS--TFE-EYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQ  165 (442)
Q Consensus        89 p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~--~~~-~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~  165 (442)
                      -+ -+||..||.+..+..+.....+..--+|..+...  .++ ....+|..|+++|+ ..-....+++.+-++.+|..|+
T Consensus        84 Ln-lDLW~lYl~YVR~~~~~~~~~r~~m~qAy~f~l~kig~di~s~siW~eYi~FL~-~vea~gk~ee~QRI~~vRriYq  161 (656)
T KOG1914|consen   84 LN-LDLWKLYLSYVRETKGKLFGYREKMVQAYDFALEKIGMDIKSYSIWDEYINFLE-GVEAVGKYEENQRITAVRRIYQ  161 (656)
T ss_pred             hh-HhHHHHHHHHHHHHccCcchHHHHHHHHHHHHHHHhccCcccchhHHHHHHHHH-cccccccHHHHHHHHHHHHHHH
Confidence            43 6899999998877666555444443344332221  111 12356666666664 2222233344456778999999


Q ss_pred             HHHHHHhhhhcCchhhHHHHHHHHHHHHHcC------------CCHHHHHHHHHHHHHh-------ch-----------h
Q 013489          166 RASDYLSEQMKNTDGLLRLYAYWAHLEQSMG------------KDMVSARGVWERLLKI-------SG-----------A  215 (442)
Q Consensus       166 ~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~------------~~~~~ar~i~~~~l~~-------~~-----------~  215 (442)
                      +|+..      +.++.-.+|.-|..||..++            ..+..||.+++.....       .|           .
T Consensus       162 ral~t------Pm~nlEkLW~DY~~fE~~IN~~tarK~i~e~s~~Ym~AR~~~qel~~lt~GL~r~~~~vp~~~T~~e~~  235 (656)
T KOG1914|consen  162 RALVT------PMHNLEKLWKDYEAFEQEINIITARKFIGERSPEYMNARRVYQELQNLTRGLNRNAPAVPPKGTKDEIQ  235 (656)
T ss_pred             HHhcC------ccccHHHHHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCChHHHH
Confidence            98774      34556679999999998754            1234777776665532       12           2


Q ss_pred             HHHHHHHHHHHHHhcc-c-------HHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCC
Q 013489          216 MLEAWQSYISMEIELD-H-------INEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGT  269 (442)
Q Consensus       216 ~~~~w~~~~~~e~~~g-~-------~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~  269 (442)
                      ++++|..||++|+..+ .       ..++-=+|+.++..   ....++||-.+-.|-...|+
T Consensus       236 qv~~W~n~I~wEksNpL~t~~~~~~~~Rv~yayeQ~ll~---l~~~peiWy~~s~yl~~~s~  294 (656)
T KOG1914|consen  236 QVELWKNWIKWEKSNPLRTLDGTMLTRRVMYAYEQCLLY---LGYHPEIWYDYSMYLIEISD  294 (656)
T ss_pred             HHHHHHHHHHHHhcCCcccccccHHHHHHHHHHHHHHHH---HhcCHHHHHHHHHHHHHhhH
Confidence            5679999999999864 1       34666779999863   23456899999888887777

>KOG4626 consensus O-linked N-acetylglucosamine transferase OGT [Carbohydrate transport and metabolism; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=99.36  E-value=8.7e-11  Score=113.96  Aligned_cols=247  Identities=16%  Similarity=0.123  Sum_probs=159.8

Q ss_pred             chhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHH
Q 013489            2 CNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVY   81 (442)
Q Consensus         2 ~~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~   81 (442)
                      |.+-..||++++-.|.    -+++|++..+..+..+-++++...|+||+...|++....-+.+.... ..+..+.+...|
T Consensus       235 ~~aiq~y~eAvkldP~----f~dAYiNLGnV~ke~~~~d~Avs~Y~rAl~lrpn~A~a~gNla~iYy-eqG~ldlAI~~Y  309 (966)
T KOG4626|consen  235 WLAIQHYEEAVKLDPN----FLDAYINLGNVYKEARIFDRAVSCYLRALNLRPNHAVAHGNLACIYY-EQGLLDLAIDTY  309 (966)
T ss_pred             HHHHHHHHHhhcCCCc----chHHHhhHHHHHHHHhcchHHHHHHHHHHhcCCcchhhccceEEEEe-ccccHHHHHHHH
Confidence            4556678888877764    56678888887777788888888888888888877766555544333 234567788889


Q ss_pred             HHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHH----------HHHHHhhccCcc
Q 013489           82 SRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRID----------GLRRRILFSGEV  151 (442)
Q Consensus        82 erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~----------~l~rr~~~~~~~  151 (442)
                      +||+..-|+-...+...+..|.. .|+..++...|.+||...+...+.+..+-..+-+          |+..-...+.-.
T Consensus       310 kral~~~P~F~~Ay~NlanALkd-~G~V~ea~~cYnkaL~l~p~hadam~NLgni~~E~~~~e~A~~ly~~al~v~p~~a  388 (966)
T KOG4626|consen  310 KRALELQPNFPDAYNNLANALKD-KGSVTEAVDCYNKALRLCPNHADAMNNLGNIYREQGKIEEATRLYLKALEVFPEFA  388 (966)
T ss_pred             HHHHhcCCCchHHHhHHHHHHHh-ccchHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhccchHHHHHHHHHHhhChhhh
Confidence            99998888888888887776654 5788888889999887666543333222211100          000000001000


Q ss_pred             c---hhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHH
Q 013489          152 E---GVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEI  228 (442)
Q Consensus       152 ~---~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~  228 (442)
                      .   ...-+-.-++.+++|+.+...++.-.|...+.+......+..+| +++.|.+.|.++++.+|...+.....+...+
T Consensus       389 aa~nNLa~i~kqqgnl~~Ai~~YkealrI~P~fAda~~NmGnt~ke~g-~v~~A~q~y~rAI~~nPt~AeAhsNLasi~k  467 (966)
T KOG4626|consen  389 AAHNNLASIYKQQGNLDDAIMCYKEALRIKPTFADALSNMGNTYKEMG-DVSAAIQCYTRAIQINPTFAEAHSNLASIYK  467 (966)
T ss_pred             hhhhhHHHHHHhcccHHHHHHHHHHHHhcCchHHHHHHhcchHHHHhh-hHHHHHHHHHHHHhcCcHHHHHHhhHHHHhh
Confidence            0   00112223445566777666666555555566666666666667 7777777777777777777777777777777


Q ss_pred             hcccHHHHHHHHHHHHhcccCCCChHHHH
Q 013489          229 ELDHINEARSIYKRCYSKRFTGTGSEDIC  257 (442)
Q Consensus       229 ~~g~~~~ar~i~~ral~~~~~~~~~~~i~  257 (442)
                      ..|++..|..-|+.||.  +.+|.|+.-+
T Consensus       468 DsGni~~AI~sY~~aLk--lkPDfpdA~c  494 (966)
T KOG4626|consen  468 DSGNIPEAIQSYRTALK--LKPDFPDAYC  494 (966)
T ss_pred             ccCCcHHHHHHHHHHHc--cCCCCchhhh
Confidence            77777777777777775  5666665333

>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=99.30  E-value=1.3e-09  Score=113.60  Aligned_cols=239  Identities=13%  Similarity=0.093  Sum_probs=150.8

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ++-..|+.+|.... ..+.....|.....+....|+++.+...|+++|..+|.+...|+..+..+.. .++.+.+...|+
T Consensus       312 ~A~~~~~~al~~~~-~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~P~~~~~~~~la~~~~~-~g~~~eA~~~~~  389 (615)
T TIGR00990       312 EAARAFEKALDLGK-LGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELDPRVTQSYIKRASMNLE-LGDPDKAEEDFD  389 (615)
T ss_pred             HHHHHHHHHHhcCC-CChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHH-CCCHHHHHHHHH
Confidence            45567888876542 1233455677777777778888888888888888888888888877776553 345567888888


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHH---------HHHHHHHHhh-ccCccc
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLT---------RIDGLRRRIL-FSGEVE  152 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~---------~~~~l~rr~~-~~~~~~  152 (442)
                      +++...|....+|..... +....++.+++...|++++...+.....++.+-..         .+..+++-+. .+...+
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 33446778888888888887766543333221111         1111111110 111111


Q ss_pred             h---hhhHHHHHHHHHHHHHHHhhhhcCchh----h---HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHH
Q 013489          153 G---VLDYSLIRETFQRASDYLSEQMKNTDG----L---LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQS  222 (442)
Q Consensus       153 ~---~~~~~~~r~~~~~a~~~l~~~~~~~~~----~---~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~  222 (442)
                      .   ...+..-.+.+++|+..+..++...+.    .   ..++.....+....+ +++.|..++++++..+|++...|..
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            0   011111122345555555444432221    1   112222222223346 8999999999999999998889999


Q ss_pred             HHHHHHhcccHHHHHHHHHHHHh
Q 013489          223 YISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       223 ~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      .+.+....|+++.|...|++|+.
T Consensus       548 la~~~~~~g~~~eAi~~~e~A~~  570 (615)
T TIGR00990       548 MAQLLLQQGDVDEALKLFERAAE  570 (615)
T ss_pred             HHHHHHHccCHHHHHHHHHHHHH
Confidence            99999999999999999999986

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

Probab=99.30  E-value=5.9e-10  Score=111.75  Aligned_cols=215  Identities=18%  Similarity=0.164  Sum_probs=141.6

Q ss_pred             HHHHHHhhcCCCCChHhHHHHHHHHHHHH-hcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHH
Q 013489            6 AHLEEQISRQDLSDSEKFQQYMIYLKYEQ-SSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRA   84 (442)
Q Consensus         6 ~~yE~~l~~~~~~~~~~~~~w~~y~~~e~-~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erA   84 (442)
                      ..||+++...+.    +...|+.|..+.- ..+-++++..+|-|++..||...+||..|+.-+..+......+...++++
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            356777766554    4678999988764 34567788999999999999999999999977777666666677888888


Q ss_pred             HHcCCCcHHHHHHHHHHHHHccCC------HHHHHHHHHHHHhCChhhHHHHHHH-HHHHHHHHH--HHhhccCccchhh
Q 013489           85 TKNCPWVGELWVRSLLSLERSRAS------EEEISTVFEKSLLCAFSTFEEYLDL-FLTRIDGLR--RRILFSGEVEGVL  155 (442)
Q Consensus        85 l~~~p~s~~lW~~y~~~le~~~~~------~~~~~~i~~~al~~~~~~~~~~~~~-~~~~~~~l~--rr~~~~~~~~~~~  155 (442)
                      +...   ..++..|+.+..+ ..+      .+.++..|..|...    ...+... +.+.+.++.  +++          
T Consensus       409 ls~~---~~l~~~~~~~rr~-~~~~~~s~~~s~lr~~F~~A~~e----Lt~~~~~~~Dt~~~~~q~wA~~----------  470 (881)
T KOG0128|consen  409 LSMT---VELHNDYLAYRRR-CTNIIDSQDYSSLRAAFNHAWEE----LTELYGDQLDTRTEVLQLWAQV----------  470 (881)
T ss_pred             HHHH---HHHHHHHHHHHHh-hcccchhhhHHHHHHHHHHHHHH----HHHHhhhhhhhHHHHHHHHHHH----------
Confidence            8742   2366666654443 222      35577777776531    0011111 111221110  010          


Q ss_pred             hHHHHHHHHHHHHHHHhhhhcCchhhHH-HHHHHHHHHHHcCCCHHHHHHHHHHHHHh--chhH-HHHHHHHHHHHHhcc
Q 013489          156 DYSLIRETFQRASDYLSEQMKNTDGLLR-LYAYWAHLEQSMGKDMVSARGVWERLLKI--SGAM-LEAWQSYISMEIELD  231 (442)
Q Consensus       156 ~~~~~r~~~~~a~~~l~~~~~~~~~~~~-l~~~~a~~e~~~~~~~~~ar~i~~~~l~~--~~~~-~~~w~~~~~~e~~~g  231 (442)
                      ++ .+....+.|+.+....+.-....+. .|+.|+.+|..+| +...||.++.+++..  .|+. ..+...|..||+..|
T Consensus       471 E~-sl~~nmd~~R~iWn~imty~~~~iag~Wle~~~lE~~~g-~~~~~R~~~R~ay~~~~~~~~~~ev~~~~~r~Ere~g  548 (881)
T KOG0128|consen  471 EA-SLLKNMDKAREIWNFIMTYGGGSIAGKWLEAINLEREYG-DGPSARKVLRKAYSQVVDPEDALEVLEFFRRFEREYG  548 (881)
T ss_pred             HH-HHhhchhhhhHhhhccccCCcchHHHHHHHHHhHHHHhC-CchhHHHHHHHHHhcCcCchhHHHHHHHHHHHHhccc
Confidence            00 1223345565555444433444555 9999999999999 899999999999987  5654 468999999999999


Q ss_pred             cHHHHHHHHHHHH
Q 013489          232 HINEARSIYKRCY  244 (442)
Q Consensus       232 ~~~~ar~i~~ral  244 (442)
                      .++.....-.+-+
T Consensus       549 tl~~~~~~~~~~~  561 (881)
T KOG0128|consen  549 TLESFDLCPEKVL  561 (881)
T ss_pred             cHHHHhhhHHhhc
Confidence            9887766555544

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.30  E-value=4e-12  Score=108.80  Aligned_cols=55  Identities=25%  Similarity=0.402  Sum_probs=51.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       387 ~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+..-++||||+|++.++.+.|+.+|.+||.|.+..|+.|+.||+|||||||+|.
T Consensus         8 ~DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~   62 (247)
T KOG0149|consen    8 GDTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFR   62 (247)
T ss_pred             CCceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEee
Confidence            3444568999999999999999999999999999999999999999999999996

>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=99.29  E-value=5.6e-09  Score=108.95  Aligned_cols=93  Identities=9%  Similarity=-0.067  Sum_probs=73.0

Q ss_pred             hcCChhhHHHHHHHHHhcC---CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHH
Q 013489           35 SSGDPGRVQLLYERAITDF---PVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEE  111 (442)
Q Consensus        35 ~~g~~~~~~~lyERal~~~---p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~  111 (442)
                      ..+.++.+..+|++++...   |.....|.....+... .++.+.+...|++++...|.....|......+. ..++.++
T Consensus       306 ~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~-~g~~~eA~~~~~kal~l~P~~~~~~~~la~~~~-~~g~~~e  383 (615)
T TIGR00990       306 ADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCL-KGKHLEALADLSKSIELDPRVTQSYIKRASMNL-ELGDPDK  383 (615)
T ss_pred             hhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHH-HCCCHHH
Confidence            3467889999999999864   6666677776666553 456788999999999999999889988776444 4688899


Q ss_pred             HHHHHHHHHhCChhhHHH
Q 013489          112 ISTVFEKSLLCAFSTFEE  129 (442)
Q Consensus       112 ~~~i~~~al~~~~~~~~~  129 (442)
                      +...|++++...+.....
T Consensus       384 A~~~~~~al~~~p~~~~~  401 (615)
T TIGR00990       384 AEEDFDKALKLNSEDPDI  401 (615)
T ss_pred             HHHHHHHHHHhCCCCHHH
Confidence            999999999877664433

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

Probab=99.28  E-value=1.7e-11  Score=101.82  Aligned_cols=54  Identities=20%  Similarity=0.292  Sum_probs=50.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....++|||+|||+++++++|+++|.+||.|.+|.|+.|+.||+++|||||+|.
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~   84 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFN   84 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEEC
Confidence            345669999999999999999999999999999999999999999999999996

>KOG4626 consensus O-linked N-acetylglucosamine transferase OGT [Carbohydrate transport and metabolism; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=99.25  E-value=5.5e-10  Score=108.54  Aligned_cols=218  Identities=13%  Similarity=0.083  Sum_probs=148.3

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      +|-..|+.+|...|.    ...++-+.+..-..+|.++.++..|+|||...|.-++...+.++-|...+ ...++...|.
T Consensus       270 ~Avs~Y~rAl~lrpn----~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~P~F~~Ay~NlanALkd~G-~V~ea~~cYn  344 (966)
T KOG4626|consen  270 RAVSCYLRALNLRPN----HAVAHGNLACIYYEQGLLDLAIDTYKRALELQPNFPDAYNNLANALKDKG-SVTEAVDCYN  344 (966)
T ss_pred             HHHHHHHHHHhcCCc----chhhccceEEEEeccccHHHHHHHHHHHHhcCCCchHHHhHHHHHHHhcc-chHHHHHHHH
Confidence            345678888877664    44455555554566899999999999999999999999999888887654 4456889999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHH---HHHHHHH----------HHHHHHHHHhhccC
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFE---EYLDLFL----------TRIDGLRRRILFSG  149 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~---~~~~~~~----------~~~~~l~rr~~~~~  149 (442)
                      +|++.||.-..--.... ...+..+.++.+..+|.+|+...+.-..   ..-.++.          .|-..+|-.-.+.+
T Consensus       345 kaL~l~p~hadam~NLg-ni~~E~~~~e~A~~ly~~al~v~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI~P~fAd  423 (966)
T KOG4626|consen  345 KALRLCPNHADAMNNLG-NIYREQGKIEEATRLYLKALEVFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRIKPTFAD  423 (966)
T ss_pred             HHHHhCCccHHHHHHHH-HHHHHhccchHHHHHHHHHHhhChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhcCchHHH
Confidence            99999998766545533 3556678889999999999976543111   1111221          12222210000011


Q ss_pred             ccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHH
Q 013489          150 EVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISME  227 (442)
Q Consensus       150 ~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e  227 (442)
                      ....-+..-........|+.++..++.-+|...+.+...+.++...| ++..|..-|+.+|+..|+..+.....+...
T Consensus       424 a~~NmGnt~ke~g~v~~A~q~y~rAI~~nPt~AeAhsNLasi~kDsG-ni~~AI~sY~~aLklkPDfpdA~cNllh~l  500 (966)
T KOG4626|consen  424 ALSNMGNTYKEMGDVSAAIQCYTRAIQINPTFAEAHSNLASIYKDSG-NIPEAIQSYRTALKLKPDFPDAYCNLLHCL  500 (966)
T ss_pred             HHHhcchHHHHhhhHHHHHHHHHHHHhcCcHHHHHHhhHHHHhhccC-CcHHHHHHHHHHHccCCCCchhhhHHHHHH
Confidence            10000111112234466888888888878888899999999998888 999999999999999988887666555544

>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein

Probab=99.25  E-value=6.6e-09  Score=112.78  Aligned_cols=104  Identities=13%  Similarity=0.091  Sum_probs=56.5

Q ss_pred             HHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHH
Q 013489          165 QRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCY  244 (442)
Q Consensus       165 ~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral  244 (442)
                      ++|+.++.......+....+|...+......| +++.|...|++++...|++...|..++.+....|+++.|..+|++++
T Consensus       584 ~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~  662 (899)
T TIGR02917       584 KKALAILNEAADAAPDSPEAWLMLGRAQLAAG-DLNKAVSSFKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRAL  662 (899)
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34444444433333334455666666666666 66666666666666666666666666666666666666666666666


Q ss_pred             hcccCCCChHHHHHHHHHHHHHhCCHhh
Q 013489          245 SKRFTGTGSEDICHAWLRFEREYGTLED  272 (442)
Q Consensus       245 ~~~~~~~~~~~i~~~~~~fE~~~G~~~~  272 (442)
                      ..  .++.+ ..+..........|..+.
T Consensus       663 ~~--~~~~~-~~~~~l~~~~~~~~~~~~  687 (899)
T TIGR02917       663 EL--KPDNT-EAQIGLAQLLLAAKRTES  687 (899)
T ss_pred             hc--CCCCH-HHHHHHHHHHHHcCCHHH
Confidence            52  12222 333344444444454433

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.

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.22  E-value=1.2e-08  Score=106.55  Aligned_cols=78  Identities=10%  Similarity=0.078  Sum_probs=44.6

Q ss_pred             HHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          167 ASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       167 a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      |...+...+...|....++..++.+....| +.+.|...+++++...|++..++..+.......|+++.|...|++++.
T Consensus       269 A~~~~~~Al~l~P~~~~a~~~lg~~l~~~g-~~~eA~~~l~~al~l~P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~  346 (656)
T PRK15174        269 AAEHWRHALQFNSDNVRIVTLYADALIRTG-QNEKAIPLLQQSLATHPDLPYVRAMYARALRQVGQYTAASDEFVQLAR  346 (656)
T ss_pred             HHHHHHHHHhhCCCCHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            444444444444444455555555555555 566666666666666666555555555555555666666666666554

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.20  E-value=1.8e-08  Score=112.22  Aligned_cols=263  Identities=11%  Similarity=0.058  Sum_probs=172.2

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHH-------------
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDK-------------   69 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~-------------   69 (442)
                      +|...|+.+|...|.    +...+..........|+++.+...|+++|..+|.+...|......+..             
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            467788999988775    667888888888899999999999999999999999887655443210             


Q ss_pred             ----------------------------hcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHh
Q 013489           70 ----------------------------TLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLL  121 (442)
Q Consensus        70 ----------------------------~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~  121 (442)
                                                  ..+..+.+...|++|+...|.+..++...+..+. ..++.+++..+|++++.
T Consensus       445 ~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~P~~~~~~~~LA~~~~-~~G~~~~A~~~l~~al~  523 (1157)
T PRK11447        445 SASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALDPGSVWLTYRLAQDLR-QAGQRSQADALMRRLAQ  523 (1157)
T ss_pred             CHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH-HcCCHHHHHHHHHHHHH
Confidence                                        1234566889999999999999888888777454 47889999999999997


Q ss_pred             CChhhHHHHH--HHHHH-------HHHHHHHHhhccCccchh----------------hhHHHHHHHHHHHHHHHhhhhc
Q 013489          122 CAFSTFEEYL--DLFLT-------RIDGLRRRILFSGEVEGV----------------LDYSLIRETFQRASDYLSEQMK  176 (442)
Q Consensus       122 ~~~~~~~~~~--~~~~~-------~~~~l~rr~~~~~~~~~~----------------~~~~~~r~~~~~a~~~l~~~~~  176 (442)
                      ..+......+  .++..       .+..+. ++... .+...                .+.-.....++.|+.++..   
T Consensus       524 ~~P~~~~~~~a~al~l~~~~~~~~Al~~l~-~l~~~-~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~~---  598 (1157)
T PRK11447        524 QKPNDPEQVYAYGLYLSGSDRDRAALAHLN-TLPRA-QWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLRQ---  598 (1157)
T ss_pred             cCCCCHHHHHHHHHHHHhCCCHHHHHHHHH-hCCch-hcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHHh---
Confidence            6655433222  11111       111111 00000 00000                0000011224556666542   


Q ss_pred             CchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHH
Q 013489          177 NTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDI  256 (442)
Q Consensus       177 ~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i  256 (442)
                       .+....++...+.+....| +.+.|..+|++++...|++...|+..+.+....|+++.|+.+|++++..  .++.+ .+
T Consensus       599 -~p~~~~~~~~La~~~~~~g-~~~~A~~~y~~al~~~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~--~p~~~-~~  673 (1157)
T PRK11447        599 -QPPSTRIDLTLADWAQQRG-DYAAARAAYQRVLTREPGNADARLGLIEVDIAQGDLAAARAQLAKLPAT--ANDSL-NT  673 (1157)
T ss_pred             -CCCCchHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCCh-HH
Confidence             2334456677788877888 8888888888888888888888888888888888888888888887752  22333 23


Q ss_pred             HHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          257 CHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       257 ~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                      +......-...|+.+.-..+++++
T Consensus       674 ~~~la~~~~~~g~~~eA~~~~~~a  697 (1157)
T PRK11447        674 QRRVALAWAALGDTAAAQRTFNRL  697 (1157)
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHH
Confidence            333333334466665544444444

>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein

Probab=99.17  E-value=2.7e-08  Score=108.06  Aligned_cols=259  Identities=13%  Similarity=0.069  Sum_probs=160.9

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ++...|+.++...|.    +...|..++......|+++.+..+|++++...|.+...|..++...... +..+.+...|+
T Consensus       483 ~A~~~~~~a~~~~~~----~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~A~~~~~  557 (899)
T TIGR02917       483 KAREAFEKALSIEPD----FFPAAANLARIDIQEGNPDDAIQRFEKVLTIDPKNLRAILALAGLYLRT-GNEEEAVAWLE  557 (899)
T ss_pred             HHHHHHHHHHhhCCC----cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHc-CCHHHHHHHHH
Confidence            567788888877665    6667888888888888999999999999998999888888888776653 45567888888


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHH---------HHHHHHHhh-ccCccc
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTR---------IDGLRRRIL-FSGEVE  152 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~---------~~~l~rr~~-~~~~~~  152 (442)
                      +++...|.....|...+..+.. .+..+.+..++++++...+.....+..+-..+         ...+.+-+. ......
T Consensus       558 ~~~~~~~~~~~~~~~l~~~~~~-~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~  636 (899)
T TIGR02917       558 KAAELNPQEIEPALALAQYYLG-KGQLKKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQPDSAL  636 (899)
T ss_pred             HHHHhCccchhHHHHHHHHHHH-CCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChH
Confidence            8888888887888777664443 67778888888888765544322222111111         001100000 000000


Q ss_pred             hh---hhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHh
Q 013489          153 GV---LDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE  229 (442)
Q Consensus       153 ~~---~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~  229 (442)
                      .+   .........+++|..++...+...+.....|...+.+....| +++.|..+++.+....|....+|...+.....
T Consensus       637 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~  715 (899)
T TIGR02917       637 ALLLLADAYAVMKNYAKAITSLKRALELKPDNTEAQIGLAQLLLAAK-RTESAKKIAKSLQKQHPKAALGFELEGDLYLR  715 (899)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcC-CHHHHHHHHHHHHhhCcCChHHHHHHHHHHHH
Confidence            00   001111123355555555555444555556666777776666 77777777777777777666677777776667


Q ss_pred             cccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhh
Q 013489          230 LDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLED  272 (442)
Q Consensus       230 ~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~  272 (442)
                      .|+++.|...|++++... + + + ..+......-...|+.+.
T Consensus       716 ~g~~~~A~~~~~~~~~~~-~-~-~-~~~~~l~~~~~~~g~~~~  754 (899)
T TIGR02917       716 QKDYPAAIQAYRKALKRA-P-S-S-QNAIKLHRALLASGNTAE  754 (899)
T ss_pred             CCCHHHHHHHHHHHHhhC-C-C-c-hHHHHHHHHHHHCCCHHH
Confidence            777777777777777631 2 1 1 233334444444555443

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.

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=99.17  E-value=2.2e-08  Score=94.18  Aligned_cols=266  Identities=20%  Similarity=0.248  Sum_probs=172.7

Q ss_pred             HHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHc
Q 013489            8 LEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKN   87 (442)
Q Consensus         8 yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~   87 (442)
                      ..+.|+.+|.    +.-.|-..+.+...+|..+..+..||..+..+|..+..|..|+.-.. ..++...+..+|.|++..
T Consensus        31 LRerIkdNPt----nI~S~fqLiq~~~tq~s~~~~re~yeq~~~pfp~~~~aw~ly~s~EL-A~~df~svE~lf~rCL~k  105 (660)
T COG5107          31 LRERIKDNPT----NILSYFQLIQYLETQESMDAEREMYEQLSSPFPIMEHAWRLYMSGEL-ARKDFRSVESLFGRCLKK  105 (660)
T ss_pred             HHHHhhcCch----hHHHHHHHHHHHhhhhhHHHHHHHHHHhcCCCccccHHHHHHhcchh-hhhhHHHHHHHHHHHHhh
Confidence            4456666665    88899999999999999999999999999999999999999997443 234567788999999985


Q ss_pred             CCCcHHHHHHHHHHHHHccCCH-----HHHHHHHHHHHhCC-h----hh-HHHHHHHHH-----------HHHHHHHH--
Q 013489           88 CPWVGELWVRSLLSLERSRASE-----EEISTVFEKSLLCA-F----ST-FEEYLDLFL-----------TRIDGLRR--  143 (442)
Q Consensus        88 ~p~s~~lW~~y~~~le~~~~~~-----~~~~~i~~~al~~~-~----~~-~~~~~~~~~-----------~~~~~l~r--  143 (442)
                      .- +.+||..|+.++.+-+...     -.+-+.|+-.+.|. +    .. |++|..+..           .+++.+|+  
T Consensus       106 ~l-~ldLW~lYl~YIRr~n~~~tGq~r~~i~~ayefv~~~~~~e~~s~~~W~ey~~fle~~~~~~kwEeQqrid~iR~~Y  184 (660)
T COG5107         106 SL-NLDLWMLYLEYIRRVNNLITGQKRFKIYEAYEFVLGCAIFEPQSENYWDEYGLFLEYIEELGKWEEQQRIDKIRNGY  184 (660)
T ss_pred             hc-cHhHHHHHHHHHHhhCcccccchhhhhHHHHHHHHhcccccccccchHHHHHHHHHhccccccHHHHHHHHHHHHHH
Confidence            43 3689999999888755322     23555666555431 1    13 334443221           24555543  


Q ss_pred             -Hhhc--cCccc-hhhhHHHHHHH----------------HHHHHHHHhh------hhcC-----------ch-hhHHHH
Q 013489          144 -RILF--SGEVE-GVLDYSLIRET----------------FQRASDYLSE------QMKN-----------TD-GLLRLY  185 (442)
Q Consensus       144 -r~~~--~~~~~-~~~~~~~~r~~----------------~~~a~~~l~~------~~~~-----------~~-~~~~l~  185 (442)
                       |.+.  .++++ -|.|++.....                |..|...+..      .+..           .+ ....-|
T Consensus       185 ~ral~tP~~nleklW~dy~~fE~e~N~~TarKfvge~sp~ym~ar~~yqe~~nlt~Gl~v~~~~~~Rt~nK~~r~s~S~W  264 (660)
T COG5107         185 MRALQTPMGNLEKLWKDYENFELELNKITARKFVGETSPIYMSARQRYQEIQNLTRGLSVKNPINLRTANKAARTSDSNW  264 (660)
T ss_pred             HHHHcCccccHHHHHHHHHHHHHHHHHHHHHHHhcccCHHHHHHHHHHHHHHHHhccccccCchhhhhhccccccccchh
Confidence             2221  11222 11222221111                1112221111      1100           01 122358


Q ss_pred             HHHHHHHHHcC----CCH--HHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHH
Q 013489          186 AYWAHLEQSMG----KDM--VSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHA  259 (442)
Q Consensus       186 ~~~a~~e~~~~----~~~--~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~  259 (442)
                      +.|+++|...+    +++  .+.-=+|+.++..++-..++|+.|..+....++-++|.....+++.     ..| .+...
T Consensus       265 lNwIkwE~en~l~L~~~~~~qRi~y~~~q~~~y~~~~~evw~dys~Y~~~isd~q~al~tv~rg~~-----~sp-sL~~~  338 (660)
T COG5107         265 LNWIKWEMENGLKLGGRPHEQRIHYIHNQILDYFYYAEEVWFDYSEYLIGISDKQKALKTVERGIE-----MSP-SLTMF  338 (660)
T ss_pred             hhHhhHhhcCCcccCCCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhccHHHHHHHHHHhccc-----CCC-chhee
Confidence            88999987643    222  2344468888888888888999999998888898999988888875     222 36667


Q ss_pred             HHHHHHHhCCHhhHHHHHHhhchhHH
Q 013489          260 WLRFEREYGTLEDFDHSVQKVTPRLE  285 (442)
Q Consensus       260 ~~~fE~~~G~~~~~~~~~~~~~~~~~  285 (442)
                      +-.+++...+.+.+..|.++|...+.
T Consensus       339 lse~yel~nd~e~v~~~fdk~~q~L~  364 (660)
T COG5107         339 LSEYYELVNDEEAVYGCFDKCTQDLK  364 (660)
T ss_pred             HHHHHhhcccHHHHhhhHHHHHHHHH
Confidence            77888888888899999999987664

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.16  E-value=4.8e-08  Score=102.17  Aligned_cols=215  Identities=13%  Similarity=0.051  Sum_probs=143.0

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      .|...|+..+...|.    +...|...+......|+++.+...|++++..+|.+..+|...+..+.. .+..+.+..+|.
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----QPEDVLLVASVLLKSKQYATVADLAEQAWLAFSGNSQIFALHLRTLVL-MDKELQAISLAR  168 (656)
T ss_pred             HHHHHHHHHHHhCCC----ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHH-CCChHHHHHHHH
Confidence            567889999988876    777898888888889999999999999999999999999999887664 455677889999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRE  162 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~  162 (442)
                      +++...|.+...|...+. +. ..++.+++..++++++...+........ ..  ...+. ..         .++     
T Consensus       169 ~~~~~~P~~~~a~~~~~~-l~-~~g~~~eA~~~~~~~l~~~~~~~~~~~~-~l--~~~l~-~~---------g~~-----  228 (656)
T PRK15174        169 TQAQEVPPRGDMIATCLS-FL-NKSRLPEDHDLARALLPFFALERQESAG-LA--VDTLC-AV---------GKY-----  228 (656)
T ss_pred             HHHHhCCCCHHHHHHHHH-HH-HcCCHHHHHHHHHHHHhcCCCcchhHHH-HH--HHHHH-HC---------CCH-----
Confidence            999988988887765433 33 3577888888888887654321111110 00  00000 00         112     


Q ss_pred             HHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHH----HHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHH
Q 013489          163 TFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVS----ARGVWERLLKISGAMLEAWQSYISMEIELDHINEARS  238 (442)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~----ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~  238 (442)
                        +.|+..+..++...+....++..++.+....| +.+.    |...|++++..+|++..+|..++.+....|+++.|..
T Consensus       229 --~eA~~~~~~al~~~p~~~~~~~~Lg~~l~~~G-~~~eA~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~~  305 (656)
T PRK15174        229 --QEAIQTGESALARGLDGAALRRSLGLAYYQSG-RSREAKLQAAEHWRHALQFNSDNVRIVTLYADALIRTGQNEKAIP  305 (656)
T ss_pred             --HHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcC-CchhhHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHH
Confidence              22222222222223334455666666666666 4543    6677777777777666677777777666677777777


Q ss_pred             HHHHHHh
Q 013489          239 IYKRCYS  245 (442)
Q Consensus       239 i~~ral~  245 (442)
                      .|++++.
T Consensus       306 ~l~~al~  312 (656)
T PRK15174        306 LLQQSLA  312 (656)
T ss_pred             HHHHHHH
Confidence            7777665

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.13  E-value=1.7e-11  Score=100.54  Aligned_cols=55  Identities=25%  Similarity=0.401  Sum_probs=51.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       387 ~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++..|||||||+..|+.||-.+|++||.|++|.+++|+.||+|+||||+.|.
T Consensus        31 ~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYE   85 (219)
T KOG0126|consen   31 EYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYE   85 (219)
T ss_pred             hcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEec
Confidence            3456669999999999999999999999999999999999999999999999874

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.11  E-value=1.3e-10  Score=102.72  Aligned_cols=53  Identities=32%  Similarity=0.438  Sum_probs=50.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..-+||||+-|++++++..|+..|+.||+|..|+||.|+.||+++|||||+|.
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye  151 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYE  151 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEec
Confidence            44569999999999999999999999999999999999999999999999995

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.10  E-value=2.2e-07  Score=91.34  Aligned_cols=109  Identities=16%  Similarity=0.142  Sum_probs=70.1

Q ss_pred             HHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHH-HHHHHHHHHHHhcccHHHHHHHHHHH
Q 013489          165 QRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAML-EAWQSYISMEIELDHINEARSIYKRC  243 (442)
Q Consensus       165 ~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~-~~w~~~~~~e~~~g~~~~ar~i~~ra  243 (442)
                      +.|..++...+...+.....+...+.+....| +++.|.++|++++...|+.. .+|...+......|+++.|...++++
T Consensus       197 ~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g-~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~  275 (389)
T PRK11788        197 DAARALLKKALAADPQCVRASILLGDLALAQG-DYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRA  275 (389)
T ss_pred             HHHHHHHHHHHhHCcCCHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            44444444443333444556677777777777 88888888888888777654 46667777777788888888888888


Q ss_pred             HhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHH
Q 013489          244 YSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQ  278 (442)
Q Consensus       244 l~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~  278 (442)
                      +..  .++ +. ++......-...|..+.....++
T Consensus       276 ~~~--~p~-~~-~~~~la~~~~~~g~~~~A~~~l~  306 (389)
T PRK11788        276 LEE--YPG-AD-LLLALAQLLEEQEGPEAAQALLR  306 (389)
T ss_pred             HHh--CCC-ch-HHHHHHHHHHHhCCHHHHHHHHH
Confidence            763  222 22 33555666666676655444443

>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=99.10  E-value=3e-08  Score=85.91  Aligned_cols=181  Identities=17%  Similarity=0.141  Sum_probs=144.9

Q ss_pred             HhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHH
Q 013489           34 QSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEIS  113 (442)
Q Consensus        34 ~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~  113 (442)
                      ...||+..+..-+|.||...|.+...|.--+.+... .+.++.+.+-|++|+..-|..+.+-..|--||.. ++..+++.
T Consensus        46 L~~gd~~~A~~nlekAL~~DPs~~~a~~~~A~~Yq~-~Ge~~~A~e~YrkAlsl~p~~GdVLNNYG~FLC~-qg~~~eA~  123 (250)
T COG3063          46 LQQGDYAQAKKNLEKALEHDPSYYLAHLVRAHYYQK-LGENDLADESYRKALSLAPNNGDVLNNYGAFLCA-QGRPEEAM  123 (250)
T ss_pred             HHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHH-cCChhhHHHHHHHHHhcCCCccchhhhhhHHHHh-CCChHHHH
Confidence            348999999999999999999999999999887764 4567889999999999999999999999998887 46888899


Q ss_pred             HHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHH
Q 013489          114 TVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQ  193 (442)
Q Consensus       114 ~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~  193 (442)
                      .-|++|+.-+.-     .                                                .....|....-.-.
T Consensus       124 q~F~~Al~~P~Y-----~------------------------------------------------~~s~t~eN~G~Cal  150 (250)
T COG3063         124 QQFERALADPAY-----G------------------------------------------------EPSDTLENLGLCAL  150 (250)
T ss_pred             HHHHHHHhCCCC-----C------------------------------------------------CcchhhhhhHHHHh
Confidence            999998864321     0                                                00011111122224


Q ss_pred             HcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhH
Q 013489          194 SMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDF  273 (442)
Q Consensus       194 ~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~  273 (442)
                      +.| +.+.|+.+|.++|..+|+....-++.++.+..-|++-.||..+++-.++ .. ...+.||.. +++++..|+.+..
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-AQAESLLLG-IRIAKRLGDRAAA  226 (250)
T ss_pred             hcC-CchhHHHHHHHHHHhCcCCChHHHHHHHHHHhcccchHHHHHHHHHHhc-cc-ccHHHHHHH-HHHHHHhccHHHH
Confidence            567 8999999999999999999999999999999999999999999998774 23 445667755 7999999996543

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.08  E-value=1.2e-10  Score=89.92  Aligned_cols=53  Identities=23%  Similarity=0.367  Sum_probs=49.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||||||++-++++.|.++|+.||.|..|-+-.|+.+..+.|||||+|-
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy   86 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYY   86 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEe
Confidence            44679999999999999999999999999999999999999999999999983

>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B

Probab=99.08  E-value=1.4e-09  Score=101.92  Aligned_cols=248  Identities=14%  Similarity=0.089  Sum_probs=71.4

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (442)
                      |...+...+....  ++.+...|..++......++++.+...|++.+...+.++.....++.++  ..++++.+..++++
T Consensus        27 Al~~L~~~~~~~~--~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~~~~~~~~~l~~l~--~~~~~~~A~~~~~~  102 (280)
T PF13429_consen   27 ALEVLKKAAQKIA--PPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASDKANPQDYERLIQLL--QDGDPEEALKLAEK  102 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccccccccccc--ccccccccccccccccccccccccccccccccccccccccccccccccc--cccccccccccccc
Confidence            3444544444431  1235667888887777778888888888888877777777777777763  23445566677777


Q ss_pred             HHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHH
Q 013489           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRET  163 (442)
Q Consensus        84 Al~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~  163 (442)
                      +.+..+ +...|..++..+. ..+..+.+..+++++.......  .-..+|..+..+.. +.         ++.......
T Consensus       103 ~~~~~~-~~~~l~~~l~~~~-~~~~~~~~~~~l~~~~~~~~~~--~~~~~~~~~a~~~~-~~---------G~~~~A~~~  168 (280)
T PF13429_consen  103 AYERDG-DPRYLLSALQLYY-RLGDYDEAEELLEKLEELPAAP--DSARFWLALAEIYE-QL---------GDPDKALRD  168 (280)
T ss_dssp             ----------------H-HH-HTT-HHHHHHHHHHHHH-T-----T-HHHHHHHHHHHH-HC---------CHHHHHHHH
T ss_pred             cccccc-ccchhhHHHHHHH-HHhHHHHHHHHHHHHHhccCCC--CCHHHHHHHHHHHH-Hc---------CCHHHHHHH
Confidence            766543 3456666665443 3566677777777765432110  01111111111111 11         222233334


Q ss_pred             HHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHH
Q 013489          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRC  243 (442)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ra  243 (442)
                      |++|+..       .|....++..++.+....| +.+.++.++.......|++..+|..++......|+.+.|..+|+++
T Consensus       169 ~~~al~~-------~P~~~~~~~~l~~~li~~~-~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~  240 (280)
T PF13429_consen  169 YRKALEL-------DPDDPDARNALAWLLIDMG-DYDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEALEYLEKA  240 (280)
T ss_dssp             HHHHHHH--------TT-HHHHHHHHHHHCTTC-HHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHHH
T ss_pred             HHHHHHc-------CCCCHHHHHHHHHHHHHCC-ChHHHHHHHHHHHHHCcCHHHHHHHHHHHhcccccccccccccccc
Confidence            4444332       3444455656665555566 6677777777776666666667777777777777777777777777


Q ss_pred             HhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          244 YSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       244 l~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                      +..  .+++| .+...|...-...|..+.-..+..+.
T Consensus       241 ~~~--~p~d~-~~~~~~a~~l~~~g~~~~A~~~~~~~  274 (280)
T PF13429_consen  241 LKL--NPDDP-LWLLAYADALEQAGRKDEALRLRRQA  274 (280)
T ss_dssp             HHH--STT-H-HHHHHHHHHHT---------------
T ss_pred             ccc--ccccc-cccccccccccccccccccccccccc
Confidence            752  33344 35556666666666665544444443

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.07  E-value=4.6e-10  Score=96.64  Aligned_cols=55  Identities=24%  Similarity=0.326  Sum_probs=52.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       387 ~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...+.++|-|.||+.++++++|+++|.+||.|.+|.|.+|+.||.+||||||.|.
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~  239 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFE  239 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEe
Confidence            3457889999999999999999999999999999999999999999999999995

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.06  E-value=2.1e-07  Score=87.80  Aligned_cols=212  Identities=17%  Similarity=0.191  Sum_probs=143.3

Q ss_pred             HHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHH
Q 013489            6 AHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRAT   85 (442)
Q Consensus         6 ~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl   85 (442)
                      ..|...|...+..+......|..........|+...+...|+++|..+|.++..|......+.. .++.+.+...|++|+
T Consensus        47 ~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~~~~-~g~~~~A~~~~~~Al  125 (296)
T PRK11189         47 ARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALRPDMADAYNYLGIYLTQ-AGNFDAAYEAFDSVL  125 (296)
T ss_pred             HHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH-CCCHHHHHHHHHHHH
Confidence            3455566544432333466788888777888999999999999999999999999999887664 456678999999999


Q ss_pred             HcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHH
Q 013489           86 KNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQ  165 (442)
Q Consensus        86 ~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~  165 (442)
                      ...|.....|......+. ..+..+++...|++++...+...  +..+|.....   ..          .+       ++
T Consensus       126 ~l~P~~~~a~~~lg~~l~-~~g~~~eA~~~~~~al~~~P~~~--~~~~~~~l~~---~~----------~~-------~~  182 (296)
T PRK11189        126 ELDPTYNYAYLNRGIALY-YGGRYELAQDDLLAFYQDDPNDP--YRALWLYLAE---SK----------LD-------PK  182 (296)
T ss_pred             HhCCCCHHHHHHHHHHHH-HCCCHHHHHHHHHHHHHhCCCCH--HHHHHHHHHH---cc----------CC-------HH
Confidence            999999999988766444 46889999999999998776643  2223321110   00          12       23


Q ss_pred             HHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHH-------HhchhHHHHHHHHHHHHHhcccHHHHHH
Q 013489          166 RASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLL-------KISGAMLEAWQSYISMEIELDHINEARS  238 (442)
Q Consensus       166 ~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l-------~~~~~~~~~w~~~~~~e~~~g~~~~ar~  238 (442)
                      +|+..+.......++.  .|. +.......| +...+ +.++.++       ...|+..+.|..........|+++.|+.
T Consensus       183 ~A~~~l~~~~~~~~~~--~~~-~~~~~~~lg-~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~  257 (296)
T PRK11189        183 QAKENLKQRYEKLDKE--QWG-WNIVEFYLG-KISEE-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAA  257 (296)
T ss_pred             HHHHHHHHHHhhCCcc--ccH-HHHHHHHcc-CCCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHH
Confidence            3333332222111111  232 333334455 44333 2444444       3456667899999999999999999999


Q ss_pred             HHHHHHhc
Q 013489          239 IYKRCYSK  246 (442)
Q Consensus       239 i~~ral~~  246 (442)
                      .|++|+..
T Consensus       258 ~~~~Al~~  265 (296)
T PRK11189        258 LFKLALAN  265 (296)
T ss_pred             HHHHHHHh
Confidence            99999973

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.06  E-value=5.2e-10  Score=108.58  Aligned_cols=53  Identities=19%  Similarity=0.241  Sum_probs=49.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....+|||+|||+.+++++|+++|++||.|.+|+|+.|+.||++||||||+|.
T Consensus       267 ~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~  319 (352)
T TIGR01661       267 GAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMT  319 (352)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEEC
Confidence            44558999999999999999999999999999999999889999999999995

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

>PF08424 NRDE-2: NRDE-2, necessary for RNA interference; InterPro: IPR013633 This is domain is found in eukaryotic proteins of unknown function

Probab=99.04  E-value=1.9e-08  Score=95.71  Aligned_cols=114  Identities=19%  Similarity=0.261  Sum_probs=90.0

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCC------------hhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGD------------PGRVQLLYERAITDFPVSSDLWLDYTQYLDKT   70 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~------------~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~   70 (442)
                      ++...|++.|+.+|.    +.+.|+.|+.+....-.            .++-+.+|||||..+|.++.||+.|+....+.
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            456788999999887    89999999998764421            23557889999999999999999999977754


Q ss_pred             cchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccC--CHHHHHHHHHHHHh
Q 013489           71 LKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRA--SEEEISTVFEKSLL  121 (442)
Q Consensus        71 ~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~--~~~~~~~i~~~al~  121 (442)
                      . +.+.+...+++++...|.+..||..||.+......  ..+.++.+|.+||.
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            4 55678889999999999999999999987765322  35667777777664

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.04  E-value=2.1e-07  Score=103.90  Aligned_cols=239  Identities=11%  Similarity=0.016  Sum_probs=139.0

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHH--HHHHHHHH-----------HHHh
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSD--LWLDYTQY-----------LDKT   70 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~--lW~~Y~~~-----------l~~~   70 (442)
                      |...|+.+|...|.    +...|..........|+++.++.+|++++..+|.+..  .|..++..           ....
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            45566666666554    4556666666666677777777777777776665442  34322210           0011


Q ss_pred             cchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCc
Q 013489           71 LKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGE  150 (442)
Q Consensus        71 ~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~  150 (442)
                      .+..+.+...|++++...|.....|...... ....++.+++...|++++...+.....+..+...+.            
T Consensus       364 ~g~~~eA~~~~~~Al~~~P~~~~a~~~Lg~~-~~~~g~~~eA~~~y~~aL~~~p~~~~a~~~L~~l~~------------  430 (1157)
T PRK11447        364 ANNLAQAERLYQQARQVDNTDSYAVLGLGDV-AMARKDYAAAERYYQQALRMDPGNTNAVRGLANLYR------------  430 (1157)
T ss_pred             CCCHHHHHHHHHHHHHhCCCCHHHHHHHHHH-HHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH------------
Confidence            2344557777777777777666666655443 333566677777777777655543322221111110            


Q ss_pred             cchhhhHHHHHHHHHHHHHHHhhhhcCch---------hhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHH
Q 013489          151 VEGVLDYSLIRETFQRASDYLSEQMKNTD---------GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQ  221 (442)
Q Consensus       151 ~~~~~~~~~~r~~~~~a~~~l~~~~~~~~---------~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~  221 (442)
                                ....++|+.++........         -....+...+......| +.+.|..+|++++..+|++..++.
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                      0011223332221110000         00123445666667777 899999999999999999999999


Q ss_pred             HHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhH
Q 013489          222 SYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDF  273 (442)
Q Consensus       222 ~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~  273 (442)
                      ..+.+....|+++.|..+|++++..  .++.++..+ ....+....|..+..
T Consensus       500 ~LA~~~~~~G~~~~A~~~l~~al~~--~P~~~~~~~-a~al~l~~~~~~~~A  548 (1157)
T PRK11447        500 RLAQDLRQAGQRSQADALMRRLAQQ--KPNDPEQVY-AYGLYLSGSDRDRAA  548 (1157)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHH-HHHHHHHhCCCHHHH
Confidence            9999999999999999999999863  344554333 333444445554443

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.03  E-value=1.7e-07  Score=84.35  Aligned_cols=98  Identities=16%  Similarity=0.089  Sum_probs=80.5

Q ss_pred             HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHH
Q 013489           23 FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSL  102 (442)
Q Consensus        23 ~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~l  102 (442)
                      ...+...+......|+++.+...|++++...|.+...|...+..... .++.+.+...|++++...|....+|..+...+
T Consensus        31 ~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~-~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  109 (234)
T TIGR02521        31 AKIRVQLALGYLEQGDLEVAKENLDKALEHDPDDYLAYLALALYYQQ-LGELEKAEDSFRRALTLNPNNGDVLNNYGTFL  109 (234)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHH-cCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHH
Confidence            45677777777889999999999999999999999999988776664 35667899999999999999888888877644


Q ss_pred             HHccCCHHHHHHHHHHHHhC
Q 013489          103 ERSRASEEEISTVFEKSLLC  122 (442)
Q Consensus       103 e~~~~~~~~~~~i~~~al~~  122 (442)
                      . ..+..+.+...|++++..
T Consensus       110 ~-~~g~~~~A~~~~~~~~~~  128 (234)
T TIGR02521       110 C-QQGKYEQAMQQFEQAIED  128 (234)
T ss_pred             H-HcccHHHHHHHHHHHHhc
Confidence            4 467788888888887753

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.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.03  E-value=5.8e-10  Score=106.17  Aligned_cols=55  Identities=18%  Similarity=0.185  Sum_probs=51.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       387 ~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .....++|||+|||+++++++|+++|+.||.|.+|+|+.|+.||+++|||||+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~  157 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFG  157 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEc
Confidence            4456789999999999999999999999999999999999999999999999995

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).

>PRK12370 invasion protein regulator; Provisional

Probab=99.01  E-value=1.5e-07  Score=96.80  Aligned_cols=213  Identities=9%  Similarity=-0.102  Sum_probs=144.4

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHH---------hcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcch
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQ---------SSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKV   73 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~---------~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~   73 (442)
                      +|...|+.+|...|.    +...|...+....         ..++.+.+...++++|..+|.+...|..+...+.. .++
T Consensus       279 ~A~~~~~~Al~ldP~----~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~ldP~~~~a~~~lg~~~~~-~g~  353 (553)
T PRK12370        279 QALKLLTQCVNMSPN----SIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATELDHNNPQALGLLGLINTI-HSE  353 (553)
T ss_pred             HHHHHHHHHHhcCCc----cHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHH-ccC
Confidence            567788888888775    4545544433221         12347889999999999999999999988776554 345


Q ss_pred             hhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccch
Q 013489           74 GNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEG  153 (442)
Q Consensus        74 ~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~  153 (442)
                      .+.+...|++|+...|.+...|..+...+. ..+..+++...|++++...|.....+......+  +.            
T Consensus       354 ~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~-~~G~~~eAi~~~~~Al~l~P~~~~~~~~~~~~~--~~------------  418 (553)
T PRK12370        354 YIVGSLLFKQANLLSPISADIKYYYGWNLF-MAGQLEEALQTINECLKLDPTRAAAGITKLWIT--YY------------  418 (553)
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHH-HCCCHHHHHHHHHHHHhcCCCChhhHHHHHHHH--Hh------------
Confidence            677999999999999999999888776554 468889999999999988776432211111000  00            


Q ss_pred             hhhHHHHHHHHHHHHHHHhhhhcCc-hhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhccc
Q 013489          154 VLDYSLIRETFQRASDYLSEQMKNT-DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDH  232 (442)
Q Consensus       154 ~~~~~~~r~~~~~a~~~l~~~~~~~-~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~  232 (442)
                             ...+++|+..+...+... +.....+...+.+....| +.+.|+..+.+++...|.....+...+......|+
T Consensus       419 -------~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G-~~~eA~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  490 (553)
T PRK12370        419 -------HTGIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKG-KHELARKLTKEISTQEITGLIAVNLLYAEYCQNSE  490 (553)
T ss_pred             -------ccCHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCC-CHHHHHHHHHHhhhccchhHHHHHHHHHHHhccHH
Confidence                   012344444444433222 333445666777777788 89999999999888888877777666666555563


Q ss_pred             HHHHHHHHHHHHh
Q 013489          233 INEARSIYKRCYS  245 (442)
Q Consensus       233 ~~~ar~i~~ral~  245 (442)
                        .+...+++.+.
T Consensus       491 --~a~~~l~~ll~  501 (553)
T PRK12370        491 --RALPTIREFLE  501 (553)
T ss_pred             --HHHHHHHHHHH
Confidence              67776766554

>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B

Probab=98.99  E-value=3.6e-09  Score=99.22  Aligned_cols=226  Identities=16%  Similarity=0.179  Sum_probs=80.8

Q ss_pred             HHHHHHHHHHhcCChhhHHHHHHHHHhcC--CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHH
Q 013489           25 QYMIYLKYEQSSGDPGRVQLLYERAITDF--PVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSL  102 (442)
Q Consensus        25 ~w~~y~~~e~~~g~~~~~~~lyERal~~~--p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~l  102 (442)
                      ..+.++......|+++.+..++.+.+...  |.++.+|..++.... ..++.+.+..+|++.+..-+.+......++..+
T Consensus        10 ~~l~~A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~-~~~~~~~A~~ay~~l~~~~~~~~~~~~~l~~l~   88 (280)
T PF13429_consen   10 EALRLARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAW-SLGDYDEAIEAYEKLLASDKANPQDYERLIQLL   88 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccccccccccccccccccccccccc
Confidence            44577888888999999999998877664  899999999988665 345667799999999998777777777777642


Q ss_pred             HHccCCHHHHHHHHHHHHhCChhh--HHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchh
Q 013489          103 ERSRASEEEISTVFEKSLLCAFST--FEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG  180 (442)
Q Consensus       103 e~~~~~~~~~~~i~~~al~~~~~~--~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~  180 (442)
                        ..++.+.+..+++++.......  +..++.++.        +         ..++..+...++++...     ...+.
T Consensus        89 --~~~~~~~A~~~~~~~~~~~~~~~~l~~~l~~~~--------~---------~~~~~~~~~~l~~~~~~-----~~~~~  144 (280)
T PF13429_consen   89 --QDGDPEEALKLAEKAYERDGDPRYLLSALQLYY--------R---------LGDYDEAEELLEKLEEL-----PAAPD  144 (280)
T ss_dssp             -------------------------------H-HH--------H---------TT-HHHHHHHHHHHHH------T---T
T ss_pred             --ccccccccccccccccccccccchhhHHHHHHH--------H---------HhHHHHHHHHHHHHHhc-----cCCCC
Confidence              3566677777777776543221  111222211        0         13444555555554421     11345


Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHH
Q 013489          181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAW  260 (442)
Q Consensus       181 ~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~  260 (442)
                      ...+|..++.++...| +.+.|..+|++++..+|++..++..++.+....|+.+.++.+++......  .+.| .+|..+
T Consensus       145 ~~~~~~~~a~~~~~~G-~~~~A~~~~~~al~~~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~--~~~~-~~~~~l  220 (280)
T PF13429_consen  145 SARFWLALAEIYEQLG-DPDKALRDYRKALELDPDDPDARNALAWLLIDMGDYDEAREALKRLLKAA--PDDP-DLWDAL  220 (280)
T ss_dssp             -HHHHHHHHHHHHHCC-HHHHHHHHHHHHHHH-TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH---HTSC-CHCHHH
T ss_pred             CHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC--cCHH-HHHHHH
Confidence            5679999999999999 99999999999999999999999999999999999999999998877632  2233 466666


Q ss_pred             HHHHHHhCCHhhHHHHHHh
Q 013489          261 LRFEREYGTLEDFDHSVQK  279 (442)
Q Consensus       261 ~~fE~~~G~~~~~~~~~~~  279 (442)
                      .......|+.+.-...+++
T Consensus       221 a~~~~~lg~~~~Al~~~~~  239 (280)
T PF13429_consen  221 AAAYLQLGRYEEALEYLEK  239 (280)
T ss_dssp             HHHHHHHT-HHHHHHHHHH
T ss_pred             HHHhccccccccccccccc
Confidence            6666666776544444443

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=98.99  E-value=4.3e-07  Score=89.33  Aligned_cols=236  Identities=10%  Similarity=0.031  Sum_probs=149.3

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCC----HHHHHHHHHHHHHhcchhhHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVS----SDLWLDYTQYLDKTLKVGNVVR   78 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~----~~lW~~Y~~~l~~~~~~~~~~~   78 (442)
                      +|...|+.++...|.    +...|...+......|+++.+..+|++++...+..    ...|...+..+.. .++.+.+.
T Consensus        53 ~A~~~~~~al~~~p~----~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~-~g~~~~A~  127 (389)
T PRK11788         53 KAIDLFIEMLKVDPE----TVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLK-AGLLDRAE  127 (389)
T ss_pred             HHHHHHHHHHhcCcc----cHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHH-CCCHHHHH
Confidence            456778888877664    67778888888888888888888888888753332    2345555554443 34567788


Q ss_pred             HHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHH-----HHHHHHHH---------HHHHHHHH
Q 013489           79 DVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFE-----EYLDLFLT---------RIDGLRRR  144 (442)
Q Consensus        79 ~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~-----~~~~~~~~---------~~~~l~rr  144 (442)
                      .+|++++...|.....+..++..+. ..++.+++..+|++++...+....     .+..+-..         ....+.+-
T Consensus       128 ~~~~~~l~~~~~~~~~~~~la~~~~-~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a  206 (389)
T PRK11788        128 ELFLQLVDEGDFAEGALQQLLEIYQ-QEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAARALLKKA  206 (389)
T ss_pred             HHHHHHHcCCcchHHHHHHHHHHHH-HhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            8888888877777777777666444 357777888888887765432111     11111000         11111111


Q ss_pred             hh-ccCccchh---hhHHHHHHHHHHHHHHHhhhhcCchhh-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHH
Q 013489          145 IL-FSGEVEGV---LDYSLIRETFQRASDYLSEQMKNTDGL-LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEA  219 (442)
Q Consensus       145 ~~-~~~~~~~~---~~~~~~r~~~~~a~~~l~~~~~~~~~~-~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~  219 (442)
                      +. .......+   ..+......+++|..++.......+.. ..++...+..+...| +++.|..++++++...|+.. +
T Consensus       207 l~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g-~~~~A~~~l~~~~~~~p~~~-~  284 (389)
T PRK11788        207 LAADPQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALG-DEAEGLEFLRRALEEYPGAD-L  284 (389)
T ss_pred             HhHCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCch-H
Confidence            00 01111100   011111233566777776665433332 345666777778888 99999999999999988764 4


Q ss_pred             HHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          220 WQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       220 w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      ....+.+....|+++.|..+|++++..
T Consensus       285 ~~~la~~~~~~g~~~~A~~~l~~~l~~  311 (389)
T PRK11788        285 LLALAQLLEEQEGPEAAQALLREQLRR  311 (389)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHh
Confidence            478888888999999999999999973

>PF00076 RRM_1: RNA recognition motif

Probab=98.97  E-value=7.9e-10  Score=80.06  Aligned_cols=47  Identities=30%  Similarity=0.523  Sum_probs=45.1

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          394 AFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       394 v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      |||+|||.++++++|+++|++||.|..+.++.+ .+|+++|||||+|.
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~   47 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFE   47 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEES
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEc
Confidence            799999999999999999999999999999998 78999999999996

(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 ....

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.97  E-value=4.5e-07  Score=97.79  Aligned_cols=218  Identities=11%  Similarity=0.016  Sum_probs=101.8

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~  101 (442)
                      +...|..+...... +.+..+...|.+++...|.+.. .+..+..+. ..+..+.+...|++++..-|. ...|......
T Consensus       476 ~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~~Pd~~~-~L~lA~al~-~~Gr~eeAi~~~rka~~~~p~-~~a~~~la~a  551 (987)
T PRK09782        476 DAAAWNRLAKCYRD-TLPGVALYAWLQAEQRQPDAWQ-HRAVAYQAY-QVEDYATALAAWQKISLHDMS-NEDLLAAANT  551 (987)
T ss_pred             CHHHHHHHHHHHHh-CCcHHHHHHHHHHHHhCCchHH-HHHHHHHHH-HCCCHHHHHHHHHHHhccCCC-cHHHHHHHHH
Confidence            44566666655554 5555666666666666665322 221122111 233445566666666554333 2334444433


Q ss_pred             HHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHH---------HHHHHHHhhccCccchhhh---HHHHHHHHHHHHH
Q 013489          102 LERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTR---------IDGLRRRILFSGEVEGVLD---YSLIRETFQRASD  169 (442)
Q Consensus       102 le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~---------~~~l~rr~~~~~~~~~~~~---~~~~r~~~~~a~~  169 (442)
                      +.. .++.+.+...|++++...+.....+..+....         +..+++-+......+.+..   +..-...++.|+.
T Consensus       552 ll~-~Gd~~eA~~~l~qAL~l~P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~P~~~a~~~LA~~l~~lG~~deA~~  630 (987)
T PRK09782        552 AQA-AGNGAARDRWLQQAEQRGLGDNALYWWLHAQRYIPGQPELALNDLTRSLNIAPSANAYVARATIYRQRHNVPAAVS  630 (987)
T ss_pred             HHH-CCCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            332 45666666666666655443322222111000         0000000000000000000   0000112233444


Q ss_pred             HHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          170 YLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       170 ~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ++..++...|....++..++.+....| +.+.|..+|++++..+|++..+|...+......|+++.|...|++++.
T Consensus       631 ~l~~AL~l~Pd~~~a~~nLG~aL~~~G-~~eeAi~~l~~AL~l~P~~~~a~~nLA~al~~lGd~~eA~~~l~~Al~  705 (987)
T PRK09782        631 DLRAALELEPNNSNYQAALGYALWDSG-DIAQSREMLERAHKGLPDDPALIRQLAYVNQRLDDMAATQHYARLVID  705 (987)
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            444444334444455555665555555 566666666666666666666666666666666666666666666664

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=98.95  E-value=2e-06  Score=91.86  Aligned_cols=96  Identities=8%  Similarity=0.003  Sum_probs=78.5

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      +|...|+.+|...|.    +...|...+......|+++.++.++++++...|.+.. |...+..+.. .+..+.+...|+
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-LLALAYVYKR-AGRHWDELRAMT  140 (765)
T ss_pred             HHHHHHHHHHHhCCC----CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHH-HHHHHHHHHH-CCCHHHHHHHHH
Confidence            466778888877775    6677888888888889999999999999999999999 8888776654 456677999999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLLSLER  104 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~  104 (442)
                      +++...|....+|..++..+..
T Consensus       141 ~al~~~P~~~~~~~~la~~l~~  162 (765)
T PRK10049        141 QALPRAPQTQQYPTEYVQALRN  162 (765)
T ss_pred             HHHHhCCCCHHHHHHHHHHHHH
Confidence            9999999999888888775543

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=98.94  E-value=2.1e-09  Score=102.52  Aligned_cols=57  Identities=30%  Similarity=0.407  Sum_probs=52.9

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          385 TKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       385 ~~~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ++..+...+|||.|||++++++.|..+|++||.|..+.|+.++.||.++|.|||.|.
T Consensus       286 ~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fk  342 (678)
T KOG0127|consen  286 RENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFK  342 (678)
T ss_pred             cccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEec
Confidence            444566789999999999999999999999999999999999999999999999995

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

Probab=98.92  E-value=1.9e-09  Score=108.44  Aligned_cols=52  Identities=25%  Similarity=0.412  Sum_probs=49.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||||||+.+++++|+.+|..||.|.+|+|+.|+.||+++|||||+|.
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~  157 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYE  157 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeC
Confidence            4579999999999999999999999999999999999999999999999996

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.

>PF14259 RRM_6: RNA recognition motif (a

Probab=98.90  E-value=2.9e-09  Score=77.13  Aligned_cols=47  Identities=36%  Similarity=0.574  Sum_probs=42.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          394 AFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       394 v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      |||+|||+++++++|+.+|+.+|.|..+++..++. |+++|+|||+|.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~   47 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFS   47 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEES
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeC
Confidence            79999999999999999999999999999999865 999999999995

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 ....

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.90  E-value=3.7e-07  Score=98.45  Aligned_cols=197  Identities=9%  Similarity=-0.034  Sum_probs=130.0

Q ss_pred             HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHH
Q 013489           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER  104 (442)
Q Consensus        25 ~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~  104 (442)
                      .|..++......|+++.+..+|++++...|.+..+.......+. ..++.+.+...|++|+...|. ...|......+.+
T Consensus       544 a~~~la~all~~Gd~~eA~~~l~qAL~l~P~~~~l~~~La~~l~-~~Gr~~eAl~~~~~AL~l~P~-~~a~~~LA~~l~~  621 (987)
T PRK09782        544 DLLAAANTAQAAGNGAARDRWLQQAEQRGLGDNALYWWLHAQRY-IPGQPELALNDLTRSLNIAPS-ANAYVARATIYRQ  621 (987)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhcCCccHHHHHHHHHHHH-hCCCHHHHHHHHHHHHHhCCC-HHHHHHHHHHHHH
Confidence            35555555555666666666666666666665554443222111 123445566667777766664 5666665553333


Q ss_pred             ccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHH
Q 013489          105 SRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRL  184 (442)
Q Consensus       105 ~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l  184 (442)
                       .+..+++...|++++...|.....+..+-..+.                     ....++.|+.++..++...|....+
T Consensus       622 -lG~~deA~~~l~~AL~l~Pd~~~a~~nLG~aL~---------------------~~G~~eeAi~~l~~AL~l~P~~~~a  679 (987)
T PRK09782        622 -RHNVPAAVSDLRAALELEPNNSNYQAALGYALW---------------------DSGDIAQSREMLERAHKGLPDDPAL  679 (987)
T ss_pred             -CCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH---------------------HCCCHHHHHHHHHHHHHhCCCCHHH
Confidence             566666666677766665554332221111110                     0123455555555555556667788


Q ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          185 YAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       185 ~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      +...+......| +++.|...|++++...|++..+-..+..++....++.++.+.|.|+...
T Consensus       680 ~~nLA~al~~lG-d~~eA~~~l~~Al~l~P~~a~i~~~~g~~~~~~~~~~~a~~~~~r~~~~  740 (987)
T PRK09782        680 IRQLAYVNQRLD-DMAATQHYARLVIDDIDNQALITPLTPEQNQQRFNFRRLHEEVGRRWTF  740 (987)
T ss_pred             HHHHHHHHHHCC-CHHHHHHHHHHHHhcCCCCchhhhhhhHHHHHHHHHHHHHHHHHHHhhc
Confidence            999999999999 9999999999999999999999999999999999999999999999863

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.89  E-value=5e-07  Score=85.23  Aligned_cols=201  Identities=13%  Similarity=0.100  Sum_probs=138.8

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      .++..|+.+|...|.    +...|..........|+++.+...|+++|..+|.+...|...+..+.. .+..+.+...|+
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----MADAYNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAYLNRGIALYY-GGRYELAQDDLL  156 (296)
T ss_pred             HHHHHHHHHHHcCCC----CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-CCCHHHHHHHHH
Confidence            467789999988876    778999999999999999999999999999999999999998876654 456678999999


Q ss_pred             HHHHcCCCcH--HHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHH
Q 013489           83 RATKNCPWVG--ELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLI  160 (442)
Q Consensus        83 rAl~~~p~s~--~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~  160 (442)
                      +++...|...  .+|...   .+ ..+..+++...|.+++....+..+.. .+.  .+ ++             .++.. 
T Consensus       157 ~al~~~P~~~~~~~~~~l---~~-~~~~~~~A~~~l~~~~~~~~~~~~~~-~~~--~~-~l-------------g~~~~-  214 (296)
T PRK11189        157 AFYQDDPNDPYRALWLYL---AE-SKLDPKQAKENLKQRYEKLDKEQWGW-NIV--EF-YL-------------GKISE-  214 (296)
T ss_pred             HHHHhCCCCHHHHHHHHH---HH-ccCCHHHHHHHHHHHHhhCCccccHH-HHH--HH-Hc-------------cCCCH-
Confidence            9999999876  344421   22 34667888888877664322211111 000  00 00             00000 


Q ss_pred             HHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhch-hHHHHHHHHHHHHHhcc
Q 013489          161 RETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG-AMLEAWQSYISMEIELD  231 (442)
Q Consensus       161 r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~-~~~~~w~~~~~~e~~~g  231 (442)
                      ...+..+...+.......+.....|.+.+.+....| +++.|+..|++++..+| +.++.-...++++...+
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            123333333322222223445678999999999999 99999999999999975 76776666666665543

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=98.85  E-value=5.3e-09  Score=97.58  Aligned_cols=53  Identities=21%  Similarity=0.467  Sum_probs=50.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...|.||||.||.++.+++|..+|...|.|-++|||+|+.+|.+||||||+|.
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~  133 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFC  133 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEee
Confidence            45689999999999999999999999999999999999999999999999996

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=98.85  E-value=5.8e-09  Score=104.73  Aligned_cols=51  Identities=22%  Similarity=0.466  Sum_probs=48.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+++++++|+.+|+.||.|.+|+|++| .+|++||||||+|.
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~  107 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFC  107 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeC
Confidence            4589999999999999999999999999999999999 89999999999996

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.

>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=98.85  E-value=5.6e-07  Score=78.12  Aligned_cols=117  Identities=13%  Similarity=0.123  Sum_probs=100.2

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      .|+..+|.+|...|.    .+..|...+.+-...|..+.+..-|++||...|.+.++-.+|.-||-..+ .++.+..-|+
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            578899999999886    78899999999999999999999999999999999999999999999766 6788999999


Q ss_pred             HHHH--cCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh
Q 013489           83 RATK--NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus        83 rAl~--~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                      +|+.  ..|.....|...- .+-...+..+.++..|+|+|...+.
T Consensus       128 ~Al~~P~Y~~~s~t~eN~G-~Cal~~gq~~~A~~~l~raL~~dp~  171 (250)
T COG3063         128 RALADPAYGEPSDTLENLG-LCALKAGQFDQAEEYLKRALELDPQ  171 (250)
T ss_pred             HHHhCCCCCCcchhhhhhH-HHHhhcCCchhHHHHHHHHHHhCcC
Confidence            9998  5566667777743 3555568888999999999976554

>PRK12370 invasion protein regulator; Provisional

Probab=98.82  E-value=2.4e-06  Score=87.90  Aligned_cols=203  Identities=10%  Similarity=-0.079  Sum_probs=138.2

Q ss_pred             hHhHHHHHHHHHHHH--hc---CChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHH--h------cchhhHHHHHHHHHHH
Q 013489           20 SEKFQQYMIYLKYEQ--SS---GDPGRVQLLYERAITDFPVSSDLWLDYTQYLDK--T------LKVGNVVRDVYSRATK   86 (442)
Q Consensus        20 ~~~~~~w~~y~~~e~--~~---g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~--~------~~~~~~~~~v~erAl~   86 (442)
                      +++++.|..|+.-..  ..   ++.+.+..+|++|+..+|.+...|...+.....  .      .+....+...+++|+.
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            346777777766431  11   245789999999999999999888655432211  1      1234678999999999


Q ss_pred             cCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHH
Q 013489           87 NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQR  166 (442)
Q Consensus        87 ~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~  166 (442)
                      .-|.....|..+...+. ..++.+++...|++|+...|.....+..+-..+.                     ..+.+++
T Consensus       333 ldP~~~~a~~~lg~~~~-~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~---------------------~~G~~~e  390 (553)
T PRK12370        333 LDHNNPQALGLLGLINT-IHSEYIVGSLLFKQANLLSPISADIKYYYGWNLF---------------------MAGQLEE  390 (553)
T ss_pred             cCCCCHHHHHHHHHHHH-HccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH---------------------HCCCHHH
Confidence            99999999988766444 4678899999999999988775544332221110                     0122344


Q ss_pred             HHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh-chhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          167 ASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI-SGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       167 a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~-~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      |+..+..++...|.....+...+......| +++.|...+++++.. .|+.+..+.....+....|+++.|+..+.+.+.
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            444444444333333222222333344567 799999999999988 477777888888888889999999999998765

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

Probab=98.82  E-value=7.8e-09  Score=104.00  Aligned_cols=52  Identities=8%  Similarity=0.132  Sum_probs=49.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+++++++|+.+|+.||.|.+|+|+.|+.+|++||||||+|.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe  254 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYN  254 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEEC
Confidence            3469999999999999999999999999999999999889999999999995

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.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=98.81  E-value=7.6e-09  Score=98.58  Aligned_cols=51  Identities=25%  Similarity=0.417  Sum_probs=48.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||..+++++|+++|+.||.|..|+|+.|+.+|+++|||||+|.
T Consensus       193 ~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~  243 (346)
T TIGR01659       193 DTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFN  243 (346)
T ss_pred             cceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEEC
Confidence            458999999999999999999999999999999999889999999999995

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).

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=98.80  E-value=1.2e-08  Score=91.68  Aligned_cols=51  Identities=24%  Similarity=0.286  Sum_probs=45.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|+|+||||...+.||+.+|.+||.|.+|.|+.+ +.| |||||||+|.
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN-ERG-SKGFGFVTme  144 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN-ERG-SKGFGFVTME  144 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec-cCC-CCccceEEec
Confidence            44569999999999999999999999999999999997 444 7999999984

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=98.78  E-value=1.2e-08  Score=102.73  Aligned_cols=55  Identities=31%  Similarity=0.442  Sum_probs=51.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       387 ~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...+.++|||+|||..+++.+|+.+|+.||.|.+|+|+.|+.+|+++|||||+|.
T Consensus        85 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~  139 (457)
T TIGR01622        85 AERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFY  139 (457)
T ss_pred             cccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEC
Confidence            3455779999999999999999999999999999999999999999999999995

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=98.76  E-value=8.6e-09  Score=84.99  Aligned_cols=53  Identities=23%  Similarity=0.334  Sum_probs=50.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +...|||||||+..++++-|.++|-++|+|.++++++|+.++.++|||||+|-
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~   59 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFR   59 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEe
Confidence            44569999999999999999999999999999999999999999999999994

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=98.74  E-value=3.2e-05  Score=82.77  Aligned_cols=232  Identities=11%  Similarity=0.028  Sum_probs=149.7

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (442)
                      +...|+..+...|.    ....|...+......|++..+..+|+++|...|.++.+|...+..+... +..+.+...+++
T Consensus        34 A~~~~~~~~~~~~~----~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~l~~~-g~~~eA~~~l~~  108 (765)
T PRK10049         34 VITVYNRYRVHMQL----PARGYAAVAVAYRNLKQWQNSLTLWQKALSLEPQNDDYQRGLILTLADA-GQYDEALVKAKQ  108 (765)
T ss_pred             HHHHHHHHHhhCCC----CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHC-CCHHHHHHHHHH
Confidence            34556666653333    4557888998889999999999999999999999999999888876644 456779999999


Q ss_pred             HHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHH---------HHHHHHHhhcc-C---c
Q 013489           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTR---------IDGLRRRILFS-G---E  150 (442)
Q Consensus        84 Al~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~---------~~~l~rr~~~~-~---~  150 (442)
                      ++...|.... |......+. ..+..+.+...|++++...|......+.+-...         +..+. ++... .   .
T Consensus       109 ~l~~~P~~~~-~~~la~~l~-~~g~~~~Al~~l~~al~~~P~~~~~~~~la~~l~~~~~~e~Al~~l~-~~~~~p~~~~~  185 (765)
T PRK10049        109 LVSGAPDKAN-LLALAYVYK-RAGRHWDELRAMTQALPRAPQTQQYPTEYVQALRNNRLSAPALGAID-DANLTPAEKRD  185 (765)
T ss_pred             HHHhCCCCHH-HHHHHHHHH-HCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCChHHHHHHHH-hCCCCHHHHHH
Confidence            9999999999 888776555 468889999999999988776544332211111         00111 00000 0   0


Q ss_pred             cchhhhHHHHH-------------HHHHHHHHHHhhhhc---Cchh----hHHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 013489          151 VEGVLDYSLIR-------------ETFQRASDYLSEQMK---NTDG----LLRLYAYWAHLEQSMGKDMVSARGVWERLL  210 (442)
Q Consensus       151 ~~~~~~~~~~r-------------~~~~~a~~~l~~~~~---~~~~----~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l  210 (442)
                      .+.......++             ...++|+..+...+.   ..+.    .........-.....+ +++.|+..|++++
T Consensus       186 l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll~~g-~~~eA~~~~~~ll  264 (765)
T PRK10049        186 LEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLGALLARD-RYKDVISEYQRLK  264 (765)
T ss_pred             HHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHHHHhh-hHHHHHHHHHHhh
Confidence            00000001111             111445554443332   1111    1111111111224456 8999999999999


Q ss_pred             Hhc---hhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          211 KIS---GAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       211 ~~~---~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      ...   |.....|+  +......|++++|..+|++++..
T Consensus       265 ~~~~~~P~~a~~~l--a~~yl~~g~~e~A~~~l~~~l~~  301 (765)
T PRK10049        265 AEGQIIPPWAQRWV--ASAYLKLHQPEKAQSILTELFYH  301 (765)
T ss_pred             ccCCCCCHHHHHHH--HHHHHhcCCcHHHHHHHHHHhhc
Confidence            874   66677775  66777789999999999998863

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.73  E-value=1.6e-08  Score=88.43  Aligned_cols=51  Identities=25%  Similarity=0.391  Sum_probs=49.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...||||.|...++.++|++.|.+||.|.+++|++|..|+|+||||||.|-
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~  112 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFP  112 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEecc
Confidence            568999999999999999999999999999999999999999999999984

>COG5191 Uncharacterized conserved protein, contains HAT (Half-A-TPR) repeat [General function prediction only]

Probab=98.72  E-value=4.5e-08  Score=88.00  Aligned_cols=135  Identities=22%  Similarity=0.370  Sum_probs=107.7

Q ss_pred             chhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhc-------------C---------ChhhHHHHHHHHHhcCCCCHHH
Q 013489            2 CNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS-------------G---------DPGRVQLLYERAITDFPVSSDL   59 (442)
Q Consensus         2 ~~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~-------------g---------~~~~~~~lyERal~~~p~~~~l   59 (442)
                      .+.|..||..|.+...    .+.-++.||.+|-..             |         -|.++..+|.|+...+|.++.+
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            4679999999988765    677899999987532             1         1345566789999999999999


Q ss_pred             HHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh---hHHHHHHHHHH
Q 013489           60 WLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS---TFEEYLDLFLT  136 (442)
Q Consensus        60 W~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~---~~~~~~~~~~~  136 (442)
                      |.+|+.|+.+.. ....+-.||..+++..|...+||.....+....+++++..|.+|.+++.+.+.   .|.+|+.+.+.
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            999999998654 44568899999999999999999986655555578999999999999987665   35567777776


Q ss_pred             HHHHH
Q 013489          137 RIDGL  141 (442)
Q Consensus       137 ~~~~l  141 (442)
                      ++.-|
T Consensus       189 yiTKL  193 (435)
T COG5191         189 YITKL  193 (435)
T ss_pred             HHHHH
Confidence            66544

>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.71  E-value=3.4e-06  Score=80.65  Aligned_cols=218  Identities=14%  Similarity=0.155  Sum_probs=155.7

Q ss_pred             hcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHH
Q 013489           35 SSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEIST  114 (442)
Q Consensus        35 ~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~  114 (442)
                      -.|+...++..|..+|..+|..+.+++.-...+. ..++.+.....|..|.+..|..+.+|..... +..-.+.++++-.
T Consensus       338 L~g~~~~a~~d~~~~I~l~~~~~~lyI~~a~~y~-d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQ-m~flL~q~e~A~a  415 (606)
T KOG0547|consen  338 LKGDSLGAQEDFDAAIKLDPAFNSLYIKRAAAYA-DENQSEKMWKDFNKAEDLDPENPDVYYHRGQ-MRFLLQQYEEAIA  415 (606)
T ss_pred             hcCCchhhhhhHHHHHhcCcccchHHHHHHHHHh-hhhccHHHHHHHHHHHhcCCCCCchhHhHHH-HHHHHHHHHHHHH
Confidence            3578888999999999999999998665554333 3345677889999999999999888887765 2222466788999


Q ss_pred             HHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHH
Q 013489          115 VFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQS  194 (442)
Q Consensus       115 i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~  194 (442)
                      -|++|+...+.++-.|+.+....  |   |.         ..+......|++++.       ..|.+++++.+++++...
T Consensus       416 DF~Kai~L~pe~~~~~iQl~~a~--Y---r~---------~k~~~~m~~Fee~kk-------kFP~~~Evy~~fAeiLtD  474 (606)
T KOG0547|consen  416 DFQKAISLDPENAYAYIQLCCAL--Y---RQ---------HKIAESMKTFEEAKK-------KFPNCPEVYNLFAEILTD  474 (606)
T ss_pred             HHHHHhhcChhhhHHHHHHHHHH--H---HH---------HHHHHHHHHHHHHHH-------hCCCCchHHHHHHHHHhh
Confidence            99999999888766666543211  1   11         123344456666655       457778899999999999


Q ss_pred             cCCCHHHHHHHHHHHHHhchh------HHHHHHHHHHHHHh-cccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHh
Q 013489          195 MGKDMVSARGVWERLLKISGA------MLEAWQSYISMEIE-LDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREY  267 (442)
Q Consensus       195 ~~~~~~~ar~i~~~~l~~~~~------~~~~w~~~~~~e~~-~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~  267 (442)
                      .+ +++.|.+.|..++...|.      +.-..+.=+-+..+ .+++..|..++.+|+.  ++ +..+.-+....+||-..
T Consensus       475 qq-qFd~A~k~YD~ai~LE~~~~~~~v~~~plV~Ka~l~~qwk~d~~~a~~Ll~KA~e--~D-pkce~A~~tlaq~~lQ~  550 (606)
T KOG0547|consen  475 QQ-QFDKAVKQYDKAIELEPREHLIIVNAAPLVHKALLVLQWKEDINQAENLLRKAIE--LD-PKCEQAYETLAQFELQR  550 (606)
T ss_pred             HH-hHHHHHHHHHHHHhhccccccccccchhhhhhhHhhhchhhhHHHHHHHHHHHHc--cC-chHHHHHHHHHHHHHHH
Confidence            99 999999999999999776      33222222222222 2799999999999997  33 34566777888999998


Q ss_pred             CCHhhHHHHHHh
Q 013489          268 GTLEDFDHSVQK  279 (442)
Q Consensus       268 G~~~~~~~~~~~  279 (442)
                      |+++.--+.+++
T Consensus       551 ~~i~eAielFEk  562 (606)
T KOG0547|consen  551 GKIDEAIELFEK  562 (606)
T ss_pred             hhHHHHHHHHHH
Confidence            987654334433

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.71  E-value=8.2e-09  Score=87.38  Aligned_cols=54  Identities=19%  Similarity=0.161  Sum_probs=51.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEeeC
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYTL  442 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~  442 (442)
                      ...+++|||+|..++++.-|...|-+||.|.+|.++.|-.++++||||||+|.+
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~   61 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEE   61 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeec
Confidence            556799999999999999999999999999999999999999999999999964

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=98.70  E-value=2.5e-08  Score=92.78  Aligned_cols=54  Identities=30%  Similarity=0.382  Sum_probs=51.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +.+..++|||.+|..++|.||+.+|.+||.|.+|.|++|+.||.++|+|||.|.
T Consensus        31 d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~   84 (510)
T KOG0144|consen   31 DGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYY   84 (510)
T ss_pred             CchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEec
Confidence            456679999999999999999999999999999999999999999999999985

>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.70  E-value=2.9e-06  Score=81.07  Aligned_cols=221  Identities=13%  Similarity=0.119  Sum_probs=148.0

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      .+...|..+|.-.|.    ..+.|+..........+.......|..|...+|.+++++.+-.+...- ....+.+..=|+
T Consensus       344 ~a~~d~~~~I~l~~~----~~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~fl-L~q~e~A~aDF~  418 (606)
T KOG0547|consen  344 GAQEDFDAAIKLDPA----FNSLYIKRAAAYADENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFL-LQQYEEAIADFQ  418 (606)
T ss_pred             hhhhhHHHHHhcCcc----cchHHHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHH-HHHHHHHHHHHH
Confidence            345667777766654    333355555555566778888999999999999999999988765442 345577899999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRE  162 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~  162 (442)
                      +|++.-|.+.--++.....+++ ...+++....|+.+...-|. -.+.+.+|   .+.|-          +-.++...-.
T Consensus       419 Kai~L~pe~~~~~iQl~~a~Yr-~~k~~~~m~~Fee~kkkFP~-~~Evy~~f---AeiLt----------DqqqFd~A~k  483 (606)
T KOG0547|consen  419 KAISLDPENAYAYIQLCCALYR-QHKIAESMKTFEEAKKKFPN-CPEVYNLF---AEILT----------DQQQFDKAVK  483 (606)
T ss_pred             HHhhcChhhhHHHHHHHHHHHH-HHHHHHHHHHHHHHHHhCCC-CchHHHHH---HHHHh----------hHHhHHHHHH
Confidence            9999999887777776665665 45788999999998853222 11222222   11111          1134444445


Q ss_pred             HHHHHHHHHhhhhcCc-hhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHH
Q 013489          163 TFQRASDYLSEQMKNT-DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYK  241 (442)
Q Consensus       163 ~~~~a~~~l~~~~~~~-~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~  241 (442)
                      .|+.|+.+-....... ..-.-++...+.+-.+ + ++..|.+++.++++.+|..-......++|+...|++++|..+|+
T Consensus       484 ~YD~ai~LE~~~~~~~v~~~plV~Ka~l~~qwk-~-d~~~a~~Ll~KA~e~Dpkce~A~~tlaq~~lQ~~~i~eAielFE  561 (606)
T KOG0547|consen  484 QYDKAIELEPREHLIIVNAAPLVHKALLVLQWK-E-DINQAENLLRKAIELDPKCEQAYETLAQFELQRGKIDEAIELFE  561 (606)
T ss_pred             HHHHHHhhccccccccccchhhhhhhHhhhchh-h-hHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            5555555321100000 0111122223323233 4 89999999999999999988899999999999999999999999


Q ss_pred             HHHh
Q 013489          242 RCYS  245 (442)
Q Consensus       242 ral~  245 (442)
                      +++.
T Consensus       562 ksa~  565 (606)
T KOG0547|consen  562 KSAQ  565 (606)
T ss_pred             HHHH
Confidence            9985

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.69  E-value=2.1e-06  Score=83.64  Aligned_cols=237  Identities=12%  Similarity=0.081  Sum_probs=155.4

Q ss_pred             HhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHH
Q 013489           34 QSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEIS  113 (442)
Q Consensus        34 ~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~  113 (442)
                      ++.|++..+..+||-|+..+|.+.+.|.....--.... ....+...+.||+..-|....+-...+- .....+....+-
T Consensus       296 m~nG~L~~A~LafEAAVkqdP~haeAW~~LG~~qaENE-~E~~ai~AL~rcl~LdP~NleaLmaLAV-SytNeg~q~~Al  373 (579)
T KOG1125|consen  296 MKNGDLSEAALAFEAAVKQDPQHAEAWQKLGITQAENE-NEQNAISALRRCLELDPTNLEALMALAV-SYTNEGLQNQAL  373 (579)
T ss_pred             HhcCCchHHHHHHHHHHhhChHHHHHHHHhhhHhhhcc-chHHHHHHHHHHHhcCCccHHHHHHHHH-HHhhhhhHHHHH
Confidence            34677888888888888888888888887654333222 2234777888888888877655444332 222233334566


Q ss_pred             HHHHHHHhCChh--------------------hHHHHHHHHHHHHHHHHHHhhccCccchhhhH-------HHHHHHHHH
Q 013489          114 TVFEKSLLCAFS--------------------TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDY-------SLIRETFQR  166 (442)
Q Consensus       114 ~i~~~al~~~~~--------------------~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~-------~~~r~~~~~  166 (442)
                      ..+.+.+...|.                    ....+..+-..+++..+  .... ..+  -|+       -.+-.-|++
T Consensus       374 ~~L~~Wi~~~p~y~~l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~--~~~~-~~D--pdvQ~~LGVLy~ls~efdr  448 (579)
T KOG1125|consen  374 KMLDKWIRNKPKYVHLVSAGENEDFENTKSFLDSSHLAHIQELFLEAAR--QLPT-KID--PDVQSGLGVLYNLSGEFDR  448 (579)
T ss_pred             HHHHHHHHhCccchhccccCccccccCCcCCCCHHHHHHHHHHHHHHHH--hCCC-CCC--hhHHhhhHHHHhcchHHHH
Confidence            666666543221                    11112222222222221  1111 011  111       124467899


Q ss_pred             HHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          167 ASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       167 a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      |++++..++...|..+.+|..+.-....-. ....|.+.|.+|++..|..+.+|....--.+..|.+..|.+.|=.||.-
T Consensus       449 aiDcf~~AL~v~Pnd~~lWNRLGAtLAN~~-~s~EAIsAY~rALqLqP~yVR~RyNlgIS~mNlG~ykEA~~hlL~AL~m  527 (579)
T KOG1125|consen  449 AVDCFEAALQVKPNDYLLWNRLGATLANGN-RSEEAISAYNRALQLQPGYVRVRYNLGISCMNLGAYKEAVKHLLEALSM  527 (579)
T ss_pred             HHHHHHHHHhcCCchHHHHHHhhHHhcCCc-ccHHHHHHHHHHHhcCCCeeeeehhhhhhhhhhhhHHHHHHHHHHHHHh
Confidence            999999999888889999999987766544 7889999999999999999999999999999999999999999999853


Q ss_pred             ccC----CCC---hHHHHHHHHHHHHHhCCHhhHHHHHH
Q 013489          247 RFT----GTG---SEDICHAWLRFEREYGTLEDFDHSVQ  278 (442)
Q Consensus       247 ~~~----~~~---~~~i~~~~~~fE~~~G~~~~~~~~~~  278 (442)
                      .-.    .+.   .+.||.....+-...|..+.+..+..
T Consensus       528 q~ks~~~~~~~~~se~iw~tLR~als~~~~~D~l~~a~~  566 (579)
T KOG1125|consen  528 QRKSRNHNKAPMASENIWQTLRLALSAMNRSDLLQEAAP  566 (579)
T ss_pred             hhcccccccCCcchHHHHHHHHHHHHHcCCchHHHHhcc
Confidence            111    112   25799888877777787775554443

>PF08424 NRDE-2: NRDE-2, necessary for RNA interference; InterPro: IPR013633 This is domain is found in eukaryotic proteins of unknown function

Probab=98.68  E-value=4.5e-06  Score=79.51  Aligned_cols=168  Identities=15%  Similarity=0.203  Sum_probs=118.2

Q ss_pred             HHHHHHHhcCCCCHHHHHHHHHHHHHhcc-----------hhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHH
Q 013489           44 LLYERAITDFPVSSDLWLDYTQYLDKTLK-----------VGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEI  112 (442)
Q Consensus        44 ~lyERal~~~p~~~~lW~~Y~~~l~~~~~-----------~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~  112 (442)
                      .-|+|.|..+|.+.+.|+.|+.|-.....           ..+.-..||+||+++.|.+..||..|+..... ..+.+.+
T Consensus         6 ~el~~~v~~~P~di~~Wl~li~~Qd~~~~~~~~~~~~~~a~~E~klsilerAL~~np~~~~L~l~~l~~~~~-~~~~~~l   84 (321)
T PF08424_consen    6 AELNRRVRENPHDIEAWLELIEFQDELFRLQSSSKAERRALAERKLSILERALKHNPDSERLLLGYLEEGEK-VWDSEKL   84 (321)
T ss_pred             HHHHHHHHhCcccHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-hCCHHHH
Confidence            45899999999999999999998775432           12346689999999999999999999996665 4577888


Q ss_pred             HHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHH
Q 013489          113 STVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLE  192 (442)
Q Consensus       113 ~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e  192 (442)
                      ...+++++...+.    ...+|..|+++...++..       -.+..++.+|.+|+..+.......             .
T Consensus        85 ~~~we~~l~~~~~----~~~LW~~yL~~~q~~~~~-------f~v~~~~~~y~~~l~~L~~~~~~~-------------~  140 (321)
T PF08424_consen   85 AKKWEELLFKNPG----SPELWREYLDFRQSNFAS-------FTVSDVRDVYEKCLRALSRRRSGR-------------M  140 (321)
T ss_pred             HHHHHHHHHHCCC----ChHHHHHHHHHHHHHhcc-------CcHHHHHHHHHHHHHHHHHhhccc-------------c
Confidence            9999998876443    346777777666544321       246677888888888764332110             0


Q ss_pred             HHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcc
Q 013489          193 QSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKR  247 (442)
Q Consensus       193 ~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~  247 (442)
                      .... +..          ......+.+.+.++.|++..|..++|..+++-.+.-+
T Consensus       141 ~~~~-~~~----------~~e~~~l~v~~r~~~fl~~aG~~E~Ava~~Qa~lE~n  184 (321)
T PF08424_consen  141 TSHP-DLP----------ELEEFMLYVFLRLCRFLRQAGYTERAVALWQALLEFN  184 (321)
T ss_pred             cccc-chh----------hHHHHHHHHHHHHHHHHHHCCchHHHHHHHHHHHHHH
Confidence            0000 100          1122335577788888888999999999988888654

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=98.67  E-value=3e-08  Score=83.38  Aligned_cols=53  Identities=25%  Similarity=0.393  Sum_probs=49.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....+|-|-||.+.++.++|+.+|..||.|.+|.|+.|+.|+.++|||||-|.
T Consensus        11 ~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~   63 (256)
T KOG4207|consen   11 EGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFH   63 (256)
T ss_pred             ccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEee
Confidence            44568999999999999999999999999999999999999999999999995

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.66  E-value=2e-05  Score=70.63  Aligned_cols=196  Identities=13%  Similarity=0.032  Sum_probs=133.5

Q ss_pred             HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHH
Q 013489           57 SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLT  136 (442)
Q Consensus        57 ~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~  136 (442)
                      ...+...+..+.. .++.+.+...|++++...|.....|......+. ..++.+.+...|++++...+.....+..+-..
T Consensus        31 ~~~~~~la~~~~~-~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~-~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~  108 (234)
T TIGR02521        31 AKIRVQLALGYLE-QGDLEVAKENLDKALEHDPDDYLAYLALALYYQ-QLGELEKAEDSFRRALTLNPNNGDVLNNYGTF  108 (234)
T ss_pred             HHHHHHHHHHHHH-CCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHH-HcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHH
Confidence            4566665554443 356678999999999999998888888766444 46888999999999998765533222211111


Q ss_pred             HHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH
Q 013489          137 RIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM  216 (442)
Q Consensus       137 ~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~  216 (442)
                      +.     ..         .++......|.+++...     ..+.....+...+.+....| +++.|...+.+++...|+.
T Consensus       109 ~~-----~~---------g~~~~A~~~~~~~~~~~-----~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~~~~  168 (234)
T TIGR02521       109 LC-----QQ---------GKYEQAMQQFEQAIEDP-----LYPQPARSLENAGLCALKAG-DFDKAEKYLTRALQIDPQR  168 (234)
T ss_pred             HH-----Hc---------ccHHHHHHHHHHHHhcc-----ccccchHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCcCC
Confidence            10     00         22333333444443310     12233456777788888888 9999999999999999998


Q ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHH
Q 013489          217 LEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSV  277 (442)
Q Consensus       217 ~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~  277 (442)
                      ...|..++.+....|+++.|..++++++..  ..+.+. .+..........|+.+......
T Consensus       169 ~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--~~~~~~-~~~~~~~~~~~~~~~~~a~~~~  226 (234)
T TIGR02521       169 PESLLELAELYYLRGQYKDARAYLERYQQT--YNQTAE-SLWLGIRIARALGDVAAAQRYG  226 (234)
T ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHH-HHHHHHHHHHHHhhHHHHHHHH
Confidence            889999999999999999999999999973  333444 3335566667777776655443

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.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=98.66  E-value=4.6e-08  Score=99.84  Aligned_cols=52  Identities=15%  Similarity=0.301  Sum_probs=49.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||||||+.+++++|+.+|..||.|..+.|+.++.+|+++|||||+|.
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~  345 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYK  345 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEEC
Confidence            4569999999999999999999999999999999999889999999999995

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.64  E-value=2.9e-08  Score=95.98  Aligned_cols=50  Identities=34%  Similarity=0.456  Sum_probs=49.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +.|||||+|+++++++|..+|+..|.|.+++++.|+.||+++||||++|.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~   68 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFT   68 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecC
Confidence            79999999999999999999999999999999999999999999999996

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=98.62  E-value=2.1e-08  Score=91.16  Aligned_cols=51  Identities=25%  Similarity=0.445  Sum_probs=49.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      -|+||||.+.++..++.|+..|.+||+|+++.+.-|+.||+++|||||+|.
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYE  163 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYE  163 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEe
Confidence            479999999999999999999999999999999999999999999999995

>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]

Probab=98.62  E-value=0.00013  Score=74.90  Aligned_cols=253  Identities=16%  Similarity=0.146  Sum_probs=155.0

Q ss_pred             ChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcH------
Q 013489           19 DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVG------   92 (442)
Q Consensus        19 ~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~------   92 (442)
                      +|.+.+.|....++-.+.|++++++-+|.|||..+|.+..+-..++.++.+.+ +...+...|.+.++.+|.+.      
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            34477899999999999999999999999999999999888888888777554 45568899999999999443      


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCh-----hhHHHHHHHHHHHHHH------HHHHhh---ccC---------
Q 013489           93 ELWVRSLLSLERSRASEEEISTVFEKSLLCAF-----STFEEYLDLFLTRIDG------LRRRIL---FSG---------  149 (442)
Q Consensus        93 ~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~-----~~~~~~~~~~~~~~~~------l~rr~~---~~~---------  149 (442)
                      .+|.. +.+... ....+.+-.+++.++..+.     +....+..+++..-.+      +.+...   ..+         
T Consensus       282 ~i~~~-~~~~~~-~~~~e~a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~  359 (895)
T KOG2076|consen  282 LIRRV-AHYFIT-HNERERAAKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDER  359 (895)
T ss_pred             HHHHH-HHHHHH-hhHHHHHHHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhh
Confidence            34432 332222 2333778888888886332     2344555555542221      111110   000         


Q ss_pred             ---------ccchh--hhHHHHHHHH----------HHHHH-HHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHH
Q 013489          150 ---------EVEGV--LDYSLIRETF----------QRASD-YLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWE  207 (442)
Q Consensus       150 ---------~~~~~--~~~~~~r~~~----------~~a~~-~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~  207 (442)
                               ...+.  .++..++...          ..++. ++...........+++...++.....| .+..|..+|.
T Consensus       360 ~~~~~~~~~~~~~~~s~~l~v~rl~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~-~~~~Al~~l~  438 (895)
T KOG2076|consen  360 RREEPNALCEVGKELSYDLRVIRLMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIG-KYKEALRLLS  438 (895)
T ss_pred             ccccccccccCCCCCCccchhHhHhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcc-cHHHHHHHHH
Confidence                     00000  1111111111          11111 111111112234567777888888888 8999999999


Q ss_pred             HHHHhchhH-HHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHH
Q 013489          208 RLLKISGAM-LEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQ  278 (442)
Q Consensus       208 ~~l~~~~~~-~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~  278 (442)
                      .++...+.+ ..+|...+.+++..|.++.|-..|++++..  .++. .++-.....+-...|+.+....+++
T Consensus       439 ~i~~~~~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~--~p~~-~D~Ri~Lasl~~~~g~~EkalEtL~  507 (895)
T KOG2076|consen  439 PITNREGYQNAFVWYKLARCYMELGEYEEAIEFYEKVLIL--APDN-LDARITLASLYQQLGNHEKALETLE  507 (895)
T ss_pred             HHhcCccccchhhhHHHHHHHHHHhhHHHHHHHHHHHHhc--CCCc-hhhhhhHHHHHHhcCCHHHHHHHHh
Confidence            998886544 468999999999999999999999999963  3332 2333333445555566654444443

>KOG1155 consensus Anaphase-promoting complex (APC), Cdc23 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=98.61  E-value=9.4e-06  Score=77.23  Aligned_cols=183  Identities=17%  Similarity=0.203  Sum_probs=108.2

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhc-------------------------------CChhhHHHHHHHHHh
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS-------------------------------GDPGRVQLLYERAIT   51 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~-------------------------------g~~~~~~~lyERal~   51 (442)
                      .+-..||..++..|+ ..++++.+.+-+-.....                               ++.+.+..+|.|||.
T Consensus       280 ~a~s~Feei~knDPY-Rl~dmdlySN~LYv~~~~skLs~LA~~v~~idKyR~ETCCiIaNYYSlr~eHEKAv~YFkRALk  358 (559)
T KOG1155|consen  280 QAESVFEEIRKNDPY-RLDDMDLYSNVLYVKNDKSKLSYLAQNVSNIDKYRPETCCIIANYYSLRSEHEKAVMYFKRALK  358 (559)
T ss_pred             HHHHHHHHHHhcCCC-cchhHHHHhHHHHHHhhhHHHHHHHHHHHHhccCCccceeeehhHHHHHHhHHHHHHHHHHHHh
Confidence            355689999988886 344565555444322110                               123456667777777


Q ss_pred             cCCCCHHHHHHHHH-HHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHH
Q 013489           52 DFPVSSDLWLDYTQ-YLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEY  130 (442)
Q Consensus        52 ~~p~~~~lW~~Y~~-~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~  130 (442)
                      .||....+|.--.. |++  .++...+...|.|||..||.+...|...-...+.. +=..-+.--               
T Consensus       359 LNp~~~~aWTLmGHEyvE--mKNt~AAi~sYRrAvdi~p~DyRAWYGLGQaYeim-~Mh~YaLyY---------------  420 (559)
T KOG1155|consen  359 LNPKYLSAWTLMGHEYVE--MKNTHAAIESYRRAVDINPRDYRAWYGLGQAYEIM-KMHFYALYY---------------  420 (559)
T ss_pred             cCcchhHHHHHhhHHHHH--hcccHHHHHHHHHHHhcCchhHHHHhhhhHHHHHh-cchHHHHHH---------------
Confidence            77777777765442 222  23344566777777777777777776644433321 001111222               


Q ss_pred             HHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 013489          131 LDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLL  210 (442)
Q Consensus       131 ~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l  210 (442)
                                                       |++|..+       -|...++|...++.+.+++ .++.|.+.|.+++
T Consensus       421 ---------------------------------fqkA~~~-------kPnDsRlw~aLG~CY~kl~-~~~eAiKCykrai  459 (559)
T KOG1155|consen  421 ---------------------------------FQKALEL-------KPNDSRLWVALGECYEKLN-RLEEAIKCYKRAI  459 (559)
T ss_pred             ---------------------------------HHHHHhc-------CCCchHHHHHHHHHHHHhc-cHHHHHHHHHHHH
Confidence                                             3333332       2344467777777777777 7777777777777


Q ss_pred             HhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          211 KISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       211 ~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      .............+++....++.+.|-..|++.+.
T Consensus       460 ~~~dte~~~l~~LakLye~l~d~~eAa~~yek~v~  494 (559)
T KOG1155|consen  460 LLGDTEGSALVRLAKLYEELKDLNEAAQYYEKYVE  494 (559)
T ss_pred             hccccchHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            66544455666677777777777777777777775

>KOG1155 consensus Anaphase-promoting complex (APC), Cdc23 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=98.60  E-value=4.3e-05  Score=72.89  Aligned_cols=243  Identities=14%  Similarity=0.065  Sum_probs=147.6

Q ss_pred             hhhHHHHHHhhc-CCCCChHhHHHHHHHHHHH-HhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHH
Q 013489            3 NARAHLEEQISR-QDLSDSEKFQQYMIYLKYE-QSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDV   80 (442)
Q Consensus         3 ~~r~~yE~~l~~-~~~~~~~~~~~w~~y~~~e-~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v   80 (442)
                      +++..+|..+.. .|.     ......++.-. ....|++.+..+||..+..+|...+----|-+.|..... ...+.-+
T Consensus       245 e~~~k~e~l~~~gf~~-----~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~-~skLs~L  318 (559)
T KOG1155|consen  245 EALQKKERLSSVGFPN-----SMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKND-KSKLSYL  318 (559)
T ss_pred             HHHHHHHHHHhccCCc-----cHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhh-hHHHHHH
Confidence            466777777766 332     22344444433 245689999999999999999876655556555543321 1222222


Q ss_pred             HHHHHH---cCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh--hHHHHHHHHHHHHHHHHHHhhccCccchhh
Q 013489           81 YSRATK---NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRILFSGEVEGVL  155 (442)
Q Consensus        81 ~erAl~---~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~--~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~  155 (442)
                      -+....   .-|..+-|-..|-. +   .+..+.+-.-|+|||..++.  .+|-.+.-     +++.-           .
T Consensus       319 A~~v~~idKyR~ETCCiIaNYYS-l---r~eHEKAv~YFkRALkLNp~~~~aWTLmGH-----EyvEm-----------K  378 (559)
T KOG1155|consen  319 AQNVSNIDKYRPETCCIIANYYS-L---RSEHEKAVMYFKRALKLNPKYLSAWTLMGH-----EYVEM-----------K  378 (559)
T ss_pred             HHHHHHhccCCccceeeehhHHH-H---HHhHHHHHHHHHHHHhcCcchhHHHHHhhH-----HHHHh-----------c
Confidence            222222   22554444444422 2   24567888899999988765  22221110     01100           0


Q ss_pred             hHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHH
Q 013489          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINE  235 (442)
Q Consensus       156 ~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~  235 (442)
                      +-...-..|.+|+++       +|..++.|--..+.+..++ -.-=|.=.|++++..-|+...+|....++..+.+..+.
T Consensus       379 Nt~AAi~sYRrAvdi-------~p~DyRAWYGLGQaYeim~-Mh~YaLyYfqkA~~~kPnDsRlw~aLG~CY~kl~~~~e  450 (559)
T KOG1155|consen  379 NTHAAIESYRRAVDI-------NPRDYRAWYGLGQAYEIMK-MHFYALYYFQKALELKPNDSRLWVALGECYEKLNRLEE  450 (559)
T ss_pred             ccHHHHHHHHHHHhc-------CchhHHHHhhhhHHHHHhc-chHHHHHHHHHHHhcCCCchHHHHHHHHHHHHhccHHH
Confidence            111122445555553       6777888988888887777 67788889999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhhch
Q 013489          236 ARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTP  282 (442)
Q Consensus       236 ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~~~  282 (442)
                      |.++|++|+.-   ++....++-....+-+..++..+-..+.++|..
T Consensus       451 AiKCykrai~~---~dte~~~l~~LakLye~l~d~~eAa~~yek~v~  494 (559)
T KOG1155|consen  451 AIKCYKRAILL---GDTEGSALVRLAKLYEELKDLNEAAQYYEKYVE  494 (559)
T ss_pred             HHHHHHHHHhc---cccchHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            99999999962   333333333333343344444443334444433

>smart00362 RRM_2 RNA recognition motif

Probab=98.59  E-value=1.1e-07  Score=68.62  Aligned_cols=47  Identities=34%  Similarity=0.517  Sum_probs=44.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +|||+|||..++.++|+.+|.++|.|..+.++.++  |.++|+|||+|.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~   47 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFE   47 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeC
Confidence            58999999999999999999999999999999875  889999999995

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=98.59  E-value=1.1e-07  Score=88.86  Aligned_cols=51  Identities=35%  Similarity=0.524  Sum_probs=49.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||||||+.+++++|..+|..||.|..+.++.++.+|+++|||||+|.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~  165 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFE  165 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEec
Confidence            689999999999999999999999999999999999889999999999995

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=98.58  E-value=1.2e-07  Score=95.45  Aligned_cols=51  Identities=20%  Similarity=0.382  Sum_probs=49.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||+.+++++|+.+|+.||.|..|.++.++.+|+++|||||+|.
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~  236 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFH  236 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEEC
Confidence            569999999999999999999999999999999999889999999999996

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.

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.58  E-value=1e-07  Score=83.49  Aligned_cols=48  Identities=21%  Similarity=0.340  Sum_probs=44.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|+|||||++..++++.+++.|++||+|.+||+..+      +||+||-|.
T Consensus       161 sp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~  208 (321)
T KOG0148|consen  161 SPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFE  208 (321)
T ss_pred             CCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEec
Confidence            457899999999999999999999999999999999998      499999995

>TIGR00540 hemY_coli hemY protein

Probab=98.57  E-value=0.00012  Score=72.59  Aligned_cols=246  Identities=12%  Similarity=0.031  Sum_probs=157.9

Q ss_pred             HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCH-HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHH
Q 013489           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS-DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLE  103 (442)
Q Consensus        25 ~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~-~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le  103 (442)
                      .+.--+......|+++.+..+|++++...|.+. .+-..++...... +..+.+...+++.+..-|.+..++..+...+.
T Consensus       120 ~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~-~~~~~Al~~l~~l~~~~P~~~~~l~ll~~~~~  198 (409)
T TIGR00540       120 NLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQ-NELHAARHGVDKLLEMAPRHKEVLKLAEEAYI  198 (409)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHC-CCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            455556666778999999999999999999885 6888787766644 45678999999999999999988888776444


Q ss_pred             HccCCHHHHHHHHHHHHhCChhhHHHHH----HHHHHHHH---------HHHHHhh-cc----Cccc---hhhhHHHHHH
Q 013489          104 RSRASEEEISTVFEKSLLCAFSTFEEYL----DLFLTRID---------GLRRRIL-FS----GEVE---GVLDYSLIRE  162 (442)
Q Consensus       104 ~~~~~~~~~~~i~~~al~~~~~~~~~~~----~~~~~~~~---------~l~rr~~-~~----~~~~---~~~~~~~~r~  162 (442)
                       ..++.+.+..++++.+..+......+.    ..+...++         .+..-.. .+    +...   .....-...+
T Consensus       199 -~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g  277 (409)
T TIGR00540       199 -RSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCD  277 (409)
T ss_pred             -HHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCC
Confidence             468888899999998865332222221    11211110         1100000 00    0000   0000011112


Q ss_pred             HHHHHHHHHhhhhcCchhhHH----HHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHH--HHHHHHHHHHHhcccHHHH
Q 013489          163 TFQRASDYLSEQMKNTDGLLR----LYAYWAHLEQSMGKDMVSARGVWERLLKISGAML--EAWQSYISMEIELDHINEA  236 (442)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~~~~----l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~--~~w~~~~~~e~~~g~~~~a  236 (442)
                      .++.|...+...+...+....    ++..+..+  ..+ +...+.+.++++++.+|+++  .+...+..+....|++++|
T Consensus       278 ~~~~A~~~l~~~l~~~pd~~~~~~~~l~~~~~l--~~~-~~~~~~~~~e~~lk~~p~~~~~~ll~sLg~l~~~~~~~~~A  354 (409)
T TIGR00540       278 DHDSAQEIIFDGLKKLGDDRAISLPLCLPIPRL--KPE-DNEKLEKLIEKQAKNVDDKPKCCINRALGQLLMKHGEFIEA  354 (409)
T ss_pred             ChHHHHHHHHHHHhhCCCcccchhHHHHHhhhc--CCC-ChHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHcccHHHH
Confidence            346677777666654333321    22223322  234 78889999999999999888  8888899988889999999


Q ss_pred             HHHHHH--HHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHh
Q 013489          237 RSIYKR--CYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQK  279 (442)
Q Consensus       237 r~i~~r--al~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~  279 (442)
                      +..|++  ++..  . +.++. +..+...-...|+.+.-.+...+
T Consensus       355 ~~~le~a~a~~~--~-p~~~~-~~~La~ll~~~g~~~~A~~~~~~  395 (409)
T TIGR00540       355 ADAFKNVAACKE--Q-LDAND-LAMAADAFDQAGDKAEAAAMRQD  395 (409)
T ss_pred             HHHHHHhHHhhc--C-CCHHH-HHHHHHHHHHcCCHHHHHHHHHH
Confidence            999994  5542  2 33444 45778888888887766655544

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.

>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]

Probab=98.55  E-value=2e-05  Score=80.67  Aligned_cols=236  Identities=14%  Similarity=0.075  Sum_probs=143.9

Q ss_pred             chhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHH-----HHHHHHHhcchhhH
Q 013489            2 CNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLD-----YTQYLDKTLKVGNV   76 (442)
Q Consensus         2 ~~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~-----Y~~~l~~~~~~~~~   76 (442)
                      ..||-.|-++|+..|.    +++...+++.+..+.|+..+++.-|.+++..+|...-.|+.     ++.+..... ..+.
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----NWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHN-ERER  298 (895)
T ss_pred             HHHHHHHHHHHhcCCc----chHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhh-HHHH
Confidence            3688899999999987    78877889999999999999999999999999944433332     344444333 3377


Q ss_pred             HHHHHHHHHHcCCC--cHHHHHHHHHHHHHccCCHHHHHHHHHHHH-hCCh----------------------hhHHHHH
Q 013489           77 VRDVYSRATKNCPW--VGELWVRSLLSLERSRASEEEISTVFEKSL-LCAF----------------------STFEEYL  131 (442)
Q Consensus        77 ~~~v~erAl~~~p~--s~~lW~~y~~~le~~~~~~~~~~~i~~~al-~~~~----------------------~~~~~~~  131 (442)
                      +.++++-++..+-.  +..-...|+..+-.........+.|-...- ....                      ....--+
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            88899999884421  111112222212211111122222222111 0000                      0000001


Q ss_pred             HH-----HHHHH------HHHHHHhhccCc------cchhhhHHHH---HHHHHHHHHHHhhhhcC-chhhHHHHHHHHH
Q 013489          132 DL-----FLTRI------DGLRRRILFSGE------VEGVLDYSLI---RETFQRASDYLSEQMKN-TDGLLRLYAYWAH  190 (442)
Q Consensus       132 ~~-----~~~~~------~~l~rr~~~~~~------~~~~~~~~~~---r~~~~~a~~~l~~~~~~-~~~~~~l~~~~a~  190 (442)
                      .+     .+..+      +.+- .++...+      ++-+.|+...   .+.|..|+.++...... ..+..-+|...++
T Consensus       379 ~v~rl~icL~~L~~~e~~e~ll-~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~  457 (895)
T KOG2076|consen  379 RVIRLMICLVHLKERELLEALL-HFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLAR  457 (895)
T ss_pred             hhHhHhhhhhcccccchHHHHH-HHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHH
Confidence            11     11100      0010 0011111      1111121111   13356788888766542 2233569999999


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHH
Q 013489          191 LEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCY  244 (442)
Q Consensus       191 ~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral  244 (442)
                      .+..++ ..+.|.+.|+++|...|++.++-+..+.+....|+.++|..++...+
T Consensus       458 c~~~l~-e~e~A~e~y~kvl~~~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~  510 (895)
T KOG2076|consen  458 CYMELG-EYEEAIEFYEKVLILAPDNLDARITLASLYQQLGNHEKALETLEQII  510 (895)
T ss_pred             HHHHHh-hHHHHHHHHHHHHhcCCCchhhhhhHHHHHHhcCCHHHHHHHHhccc
Confidence            999999 99999999999999999999999999999999999999999988855

>KOG1129 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.54  E-value=6.8e-06  Score=74.84  Aligned_cols=199  Identities=18%  Similarity=0.195  Sum_probs=120.8

Q ss_pred             hcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHH
Q 013489           35 SSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEIST  114 (442)
Q Consensus        35 ~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~  114 (442)
                      ..|-+.++...++-+|...|.-.. .+-... +....+.++.+..+|...+..+|....+-..-++..|. .+..+.+-+
T Consensus       235 rLgm~r~AekqlqssL~q~~~~dT-fllLsk-vY~ridQP~~AL~~~~~gld~fP~~VT~l~g~ARi~ea-m~~~~~a~~  311 (478)
T KOG1129|consen  235 RLGMPRRAEKQLQSSLTQFPHPDT-FLLLSK-VYQRIDQPERALLVIGEGLDSFPFDVTYLLGQARIHEA-MEQQEDALQ  311 (478)
T ss_pred             HhcChhhhHHHHHHHhhcCCchhH-HHHHHH-HHHHhccHHHHHHHHhhhhhcCCchhhhhhhhHHHHHH-HHhHHHHHH
Confidence            346666676777777766654322 111111 22223345566667777777777666655555554443 344455666


Q ss_pred             HHHHHHhCChhhHHHHH------------HHHHHHHHHHHHHhhccCc--cchh----------hhHHHHHHHHHHHHHH
Q 013489          115 VFEKSLLCAFSTFEEYL------------DLFLTRIDGLRRRILFSGE--VEGV----------LDYSLIRETFQRASDY  170 (442)
Q Consensus       115 i~~~al~~~~~~~~~~~------------~~~~~~~~~l~rr~~~~~~--~~~~----------~~~~~~r~~~~~a~~~  170 (442)
                      +|..++...+.+++...            ++-+.   |. ||++....  .+-+          ..++.+-..|++|+..
T Consensus       312 lYk~vlk~~~~nvEaiAcia~~yfY~~~PE~Alr---yY-RRiLqmG~~speLf~NigLCC~yaqQ~D~~L~sf~RAlst  387 (478)
T KOG1129|consen  312 LYKLVLKLHPINVEAIACIAVGYFYDNNPEMALR---YY-RRILQMGAQSPELFCNIGLCCLYAQQIDLVLPSFQRALST  387 (478)
T ss_pred             HHHHHHhcCCccceeeeeeeeccccCCChHHHHH---HH-HHHHHhcCCChHHHhhHHHHHHhhcchhhhHHHHHHHHhh
Confidence            66666654333221100            11111   11 23322111  1100          2333445667777665


Q ss_pred             HhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          171 LSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       171 l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ...    .+...++|-....+....| |+..|...|.-+|..++++.+.....+-++.+.|+++.||.+|..|-+
T Consensus       388 at~----~~~aaDvWYNlg~vaV~iG-D~nlA~rcfrlaL~~d~~h~ealnNLavL~~r~G~i~~Arsll~~A~s  457 (478)
T KOG1129|consen  388 ATQ----PGQAADVWYNLGFVAVTIG-DFNLAKRCFRLALTSDAQHGEALNNLAVLAARSGDILGARSLLNAAKS  457 (478)
T ss_pred             ccC----cchhhhhhhccceeEEecc-chHHHHHHHHHHhccCcchHHHHHhHHHHHhhcCchHHHHHHHHHhhh
Confidence            421    2345689998888888889 999999999999999999999999999999999999999999999976

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.52  E-value=0.00018  Score=71.02  Aligned_cols=243  Identities=11%  Similarity=0.031  Sum_probs=156.7

Q ss_pred             HHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHH-HHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHH
Q 013489           26 YMIYLKYEQSSGDPGRVQLLYERAITDFPVSSD-LWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER  104 (442)
Q Consensus        26 w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~-lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~  104 (442)
                      +..-+......|+++.+..+|+++....|.+.- ..+.-..+.. ..++.+.+...+++++...|.+..+....+..+. 
T Consensus       121 ~llaA~aA~~~g~~~~A~~~l~~A~~~~~~~~~~~~l~~a~l~l-~~g~~~~Al~~l~~~~~~~P~~~~al~ll~~~~~-  198 (398)
T PRK10747        121 YLLAAEAAQQRGDEARANQHLERAAELADNDQLPVEITRVRIQL-ARNENHAARHGVDKLLEVAPRHPEVLRLAEQAYI-  198 (398)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHH-HCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHH-
Confidence            444455557789999999999999999888753 3233233333 3456788999999999999999877766665343 


Q ss_pred             ccCCHHHHHHHHHHHHhCChhhHHHHHHHH-HHHHHHHHHHhhccC--c----cc----hhh-hH---------HHHHHH
Q 013489          105 SRASEEEISTVFEKSLLCAFSTFEEYLDLF-LTRIDGLRRRILFSG--E----VE----GVL-DY---------SLIRET  163 (442)
Q Consensus       105 ~~~~~~~~~~i~~~al~~~~~~~~~~~~~~-~~~~~~l~rr~~~~~--~----~~----~~~-~~---------~~~r~~  163 (442)
                      ..++.+.+..++.+..........+.-.+. ..++..+.......+  .    +.    ... +.         ....+.
T Consensus       199 ~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~  278 (398)
T PRK10747        199 RTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRKTRHQVALQVAMAEHLIECDD  278 (398)
T ss_pred             HHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCCC
Confidence            457888899888887765433222221111 111111110000000  0    00    000 00         001122


Q ss_pred             HHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHH
Q 013489          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRC  243 (442)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ra  243 (442)
                      .+.|...+...+. .+....+...|+++.  .+ +++.+.+..++.++.+|+++.+.+.+..+....|++..|+..|+++
T Consensus       279 ~~~A~~~L~~~l~-~~~~~~l~~l~~~l~--~~-~~~~al~~~e~~lk~~P~~~~l~l~lgrl~~~~~~~~~A~~~le~a  354 (398)
T PRK10747        279 HDTAQQIILDGLK-RQYDERLVLLIPRLK--TN-NPEQLEKVLRQQIKQHGDTPLLWSTLGQLLMKHGEWQEASLAFRAA  354 (398)
T ss_pred             HHHHHHHHHHHHh-cCCCHHHHHHHhhcc--CC-ChHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            3566677766665 333445666676653  25 8999999999999999999999999999999999999999999999


Q ss_pred             HhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHH
Q 013489          244 YSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQ  278 (442)
Q Consensus       244 l~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~  278 (442)
                      +..  .++ . ..+..+....+..|..+.-..+..
T Consensus       355 l~~--~P~-~-~~~~~La~~~~~~g~~~~A~~~~~  385 (398)
T PRK10747        355 LKQ--RPD-A-YDYAWLADALDRLHKPEEAAAMRR  385 (398)
T ss_pred             Hhc--CCC-H-HHHHHHHHHHHHcCCHHHHHHHHH
Confidence            973  222 3 334567788888898766554444

>smart00360 RRM RNA recognition motif

Probab=98.51  E-value=1.8e-07  Score=67.15  Aligned_cols=46  Identities=35%  Similarity=0.515  Sum_probs=43.4

Q ss_pred             EcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          396 LSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       396 v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      |+|||..+++++|+.+|.+||.|..+.+..++.+++++|+|||+|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~   46 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFE   46 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeC
Confidence            6899999999999999999999999999998778999999999995

>TIGR00540 hemY_coli hemY protein

Probab=98.51  E-value=3.6e-05  Score=76.26  Aligned_cols=218  Identities=13%  Similarity=0.022  Sum_probs=134.8

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHH---
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRD---   79 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~---   79 (442)
                      .+...|+.++...|..   ...+...++......|+++.+...+++.+...|.++.++..++...... ++.+.+..   
T Consensus       136 ~A~~~l~~a~~~~p~~---~l~~~~~~a~l~l~~~~~~~Al~~l~~l~~~~P~~~~~l~ll~~~~~~~-~d~~~a~~~l~  211 (409)
T TIGR00540       136 RANQHLEEAAELAGND---NILVEIARTRILLAQNELHAARHGVDKLLEMAPRHKEVLKLAEEAYIRS-GAWQALDDIID  211 (409)
T ss_pred             HHHHHHHHHHHhCCcC---chHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHH-hhHHHHHHHHH
Confidence            3556677776665531   2345555677677788888888888888888888887766665544322 22222222   


Q ss_pred             -----------------------------------HHHHHHHcCC----CcHHHHHHHHHHHHHccCCHHHHHHHHHHHH
Q 013489           80 -----------------------------------VYSRATKNCP----WVGELWVRSLLSLERSRASEEEISTVFEKSL  120 (442)
Q Consensus        80 -----------------------------------v~erAl~~~p----~s~~lW~~y~~~le~~~~~~~~~~~i~~~al  120 (442)
                                                         .+..+....|    .+..++..++..+. ..+..+.+..++++++
T Consensus       212 ~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~-~~g~~~~A~~~l~~~l  290 (409)
T TIGR00540       212 NMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLI-DCDDHDSAQEIIFDGL  290 (409)
T ss_pred             HHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHH-HCCChHHHHHHHHHHH
Confidence                                               3333344445    35666666666333 3566677777777777


Q ss_pred             hCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhH--HHHHHHHHHHHHcCCC
Q 013489          121 LCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLL--RLYAYWAHLEQSMGKD  198 (442)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~--~l~~~~a~~e~~~~~~  198 (442)
                      ...++.....+..+..+.     .+ ..      .+.       ..+...++.+....+...  .+...++.+....+ +
T Consensus       291 ~~~pd~~~~~~~~l~~~~-----~l-~~------~~~-------~~~~~~~e~~lk~~p~~~~~~ll~sLg~l~~~~~-~  350 (409)
T TIGR00540       291 KKLGDDRAISLPLCLPIP-----RL-KP------EDN-------EKLEKLIEKQAKNVDDKPKCCINRALGQLLMKHG-E  350 (409)
T ss_pred             hhCCCcccchhHHHHHhh-----hc-CC------CCh-------HHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHcc-c
Confidence            654443211111110000     00 00      112       223333333333344444  78888999999988 9


Q ss_pred             HHHHHHHHH--HHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          199 MVSARGVWE--RLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       199 ~~~ar~i~~--~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      +++|++.|+  .+++..|+... +..++.+....|+.+.|+.+|++++.-
T Consensus       351 ~~~A~~~le~a~a~~~~p~~~~-~~~La~ll~~~g~~~~A~~~~~~~l~~  399 (409)
T TIGR00540       351 FIEAADAFKNVAACKEQLDAND-LAMAADAFDQAGDKAEAAAMRQDSLGL  399 (409)
T ss_pred             HHHHHHHHHHhHHhhcCCCHHH-HHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            999999999  57777888766 559999999999999999999999864

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.

>PLN02789 farnesyltranstransferase

Probab=98.51  E-value=0.00013  Score=69.27  Aligned_cols=198  Identities=11%  Similarity=0.003  Sum_probs=133.4

Q ss_pred             HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHH
Q 013489           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER  104 (442)
Q Consensus        25 ~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~  104 (442)
                      +|.-+-......+..+++..+++.+|..+|.+..+|..-...+...+...+.+...+++++...|.+..+|......++.
T Consensus        39 a~~~~ra~l~~~e~serAL~lt~~aI~lnP~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npknyqaW~~R~~~l~~  118 (320)
T PLN02789         39 AMDYFRAVYASDERSPRALDLTADVIRLNPGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPKNYQIWHHRRWLAEK  118 (320)
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCcchHHhHHHHHHHHH
Confidence            34333333345668899999999999999999999998877776544345678899999999999999999987655554


Q ss_pred             ccCC-HHHHHHHHHHHHhCChhhHH--HHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhh
Q 013489          105 SRAS-EEEISTVFEKSLLCAFSTFE--EYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGL  181 (442)
Q Consensus       105 ~~~~-~~~~~~i~~~al~~~~~~~~--~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~  181 (442)
                      .... .+.....+++++...+.++.  .+..+.+...                       ..+++++.+....+..++..
T Consensus       119 l~~~~~~~el~~~~kal~~dpkNy~AW~~R~w~l~~l-----------------------~~~~eeL~~~~~~I~~d~~N  175 (320)
T PLN02789        119 LGPDAANKELEFTRKILSLDAKNYHAWSHRQWVLRTL-----------------------GGWEDELEYCHQLLEEDVRN  175 (320)
T ss_pred             cCchhhHHHHHHHHHHHHhCcccHHHHHHHHHHHHHh-----------------------hhHHHHHHHHHHHHHHCCCc
Confidence            3322 24567778888887766433  2222221111                       22556666666665544444


Q ss_pred             HHHHHHHHHHHHHc---CC---CHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhc----ccHHHHHHHHHHHHh
Q 013489          182 LRLYAYWAHLEQSM---GK---DMVSARGVWERLLKISGAMLEAWQSYISMEIEL----DHINEARSIYKRCYS  245 (442)
Q Consensus       182 ~~l~~~~a~~e~~~---~~---~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~----g~~~~ar~i~~ral~  245 (442)
                      ...|..-.-+....   ++   ..+....+..++|...|++...|.....+....    +....|...+..++.
T Consensus       176 ~sAW~~R~~vl~~~~~l~~~~~~~e~el~y~~~aI~~~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~  249 (320)
T PLN02789        176 NSAWNQRYFVITRSPLLGGLEAMRDSELKYTIDAILANPRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLS  249 (320)
T ss_pred             hhHHHHHHHHHHhccccccccccHHHHHHHHHHHHHhCCCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhc
Confidence            55666544333332   21   135677778899999999999998888877663    334557777888775

>PLN03218 maturation of RBCL 1; Provisional

Probab=98.49  E-value=0.00021  Score=78.13  Aligned_cols=266  Identities=8%  Similarity=-0.011  Sum_probs=159.2

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDF-PVSSDLWLDYTQYLDKTLKVGNVVRDVY   81 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~-p~~~~lW~~Y~~~l~~~~~~~~~~~~v~   81 (442)
                      .++..|+........  + +...|...|...-+.|+++.+..+|++..... ..+...|...|..+.+. +..+.+..+|
T Consensus       490 ~A~~vf~eM~~~Gv~--P-dvvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~-G~~deA~~lf  565 (1060)
T PLN03218        490 AMFEVFHEMVNAGVE--A-NVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQS-GAVDRAFDVL  565 (1060)
T ss_pred             HHHHHHHHHHHcCCC--C-CHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHC-CCHHHHHHHH
Confidence            567788887765421  1 56688888888888899999999998887652 34567787777766644 4567788888


Q ss_pred             HHHHHc----CCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh----hHHHHHHHHHHHH--H---HHHHHhhcc
Q 013489           82 SRATKN----CPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS----TFEEYLDLFLTRI--D---GLRRRILFS  148 (442)
Q Consensus        82 erAl~~----~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~----~~~~~~~~~~~~~--~---~l~rr~~~~  148 (442)
                      ++....    .|. ...|...|..+-+ .+..+.+..+|+.+...+..    .+...+..+...-  +   .+-..+...
T Consensus       566 ~eM~~~~~gi~PD-~vTynaLI~ay~k-~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~  643 (1060)
T PLN03218        566 AEMKAETHPIDPD-HITVGALMKACAN-AGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKK  643 (1060)
T ss_pred             HHHHHhcCCCCCc-HHHHHHHHHHHHH-CCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Confidence            888752    243 4566666664444 67788888899888876542    1222222221100  0   000011000


Q ss_pred             CccchhhhHHHHH------HHHHHHHHHHhhhhcC-chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh-chhHHHHH
Q 013489          149 GEVEGVLDYSLIR------ETFQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI-SGAMLEAW  220 (442)
Q Consensus       149 ~~~~~~~~~~~~r------~~~~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~-~~~~~~~w  220 (442)
                      ...-+..-+..+.      ..++.|..++...... ..+....|...+..+.+.| +++.|.++|+.+... ...+...|
T Consensus       644 Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tynsLI~ay~k~G-~~eeA~~lf~eM~~~g~~Pdvvty  722 (1060)
T PLN03218        644 GVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAK-NWKKALELYEDIKSIKLRPTVSTM  722 (1060)
T ss_pred             CCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCC-CHHHHHHHHHHHHHcCCCCCHHHH
Confidence            0000000011111      1234455555444432 2334456777777778888 899999999888765 22235678


Q ss_pred             HHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHH
Q 013489          221 QSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSV  277 (442)
Q Consensus       221 ~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~  277 (442)
                      ...+......|+++.|..+|+.+....+.++  ...|...+.-....|.++....++
T Consensus       723 N~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd--~~Ty~sLL~a~~k~G~le~A~~l~  777 (1060)
T PLN03218        723 NALITALCEGNQLPKALEVLSEMKRLGLCPN--TITYSILLVASERKDDADVGLDLL  777 (1060)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHHCCCHHHHHHHH
Confidence            8888888888999999999998776433322  234555555555566655544433

>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]

Probab=98.49  E-value=1.7e-05  Score=78.77  Aligned_cols=82  Identities=9%  Similarity=0.077  Sum_probs=41.3

Q ss_pred             HHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHH
Q 013489          163 TFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKR  242 (442)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~r  242 (442)
                      .|+.|..++..++...+..+..|-=..-++.+.+ ..+.|.-.|++|+..+|.+..+...+..++...|..++|..+|++
T Consensus       470 e~d~a~~~fr~Al~~~~rhYnAwYGlG~vy~Kqe-k~e~Ae~~fqkA~~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~  548 (638)
T KOG1126|consen  470 EFDKAMKSFRKALGVDPRHYNAWYGLGTVYLKQE-KLEFAEFHFQKAVEINPSNSVILCHIGRIQHQLKRKDKALQLYEK  548 (638)
T ss_pred             HHHhHHHHHHhhhcCCchhhHHHHhhhhheeccc-hhhHHHHHHHhhhcCCccchhHHhhhhHHHHHhhhhhHHHHHHHH
Confidence            3444444444444444444444444444444444 455555555555555555555555555555555555555555555


Q ss_pred             HHh
Q 013489          243 CYS  245 (442)
Q Consensus       243 al~  245 (442)
                      |+.
T Consensus       549 A~~  551 (638)
T KOG1126|consen  549 AIH  551 (638)
T ss_pred             HHh
Confidence            554

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=98.49  E-value=5.5e-08  Score=90.51  Aligned_cols=52  Identities=25%  Similarity=0.362  Sum_probs=49.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.+++|||.|+..+++.+++.+|++||.|.+|.|++| ..|.+||+|||.|.
T Consensus       122 ~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd-~~~~sRGcaFV~fs  173 (510)
T KOG0144|consen  122 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRD-PDGLSRGCAFVKFS  173 (510)
T ss_pred             ccchhhhhhhccccccHHHHHHHHHhhCccchhhheec-ccccccceeEEEEe
Confidence            44679999999999999999999999999999999999 69999999999996

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.49  E-value=3.8e-05  Score=75.74  Aligned_cols=212  Identities=13%  Similarity=0.097  Sum_probs=137.2

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      .++..|+.+...+|..   .......-+......|+++.+...+++.+...|.++.+....+...... ++.+.+..++.
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            4667788888776641   1223333356667789999999999999999999987665555544322 33344444444


Q ss_pred             HHHHcC------------------------------------------CCcHHHHHHHHHHHHHccCCHHHHHHHHHHHH
Q 013489           83 RATKNC------------------------------------------PWVGELWVRSLLSLERSRASEEEISTVFEKSL  120 (442)
Q Consensus        83 rAl~~~------------------------------------------p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al  120 (442)
                      +..+..                                          |....++..|+..+.. .+..+.+..++++++
T Consensus       212 ~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~-~g~~~~A~~~L~~~l  290 (398)
T PRK10747        212 SMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRKTRHQVALQVAMAEHLIE-CDDHDTAQQIILDGL  290 (398)
T ss_pred             HHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHH-CCCHHHHHHHHHHHH
Confidence            444333                                          3344455555553333 344455555555555


Q ss_pred             hCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHH
Q 013489          121 LCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMV  200 (442)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~  200 (442)
                      ..+++.  ..+.++   .     ++              ....+++++..++......|....+...++++....+ +..
T Consensus       291 ~~~~~~--~l~~l~---~-----~l--------------~~~~~~~al~~~e~~lk~~P~~~~l~l~lgrl~~~~~-~~~  345 (398)
T PRK10747        291 KRQYDE--RLVLLI---P-----RL--------------KTNNPEQLEKVLRQQIKQHGDTPLLWSTLGQLLMKHG-EWQ  345 (398)
T ss_pred             hcCCCH--HHHHHH---h-----hc--------------cCCChHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCC-CHH
Confidence            432221  000011   0     00              0022345556665555556777789999999999999 999


Q ss_pred             HHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          201 SARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       201 ~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      .|++.|++++...|+... +..++.+....|+.+.|..+|++++.
T Consensus       346 ~A~~~le~al~~~P~~~~-~~~La~~~~~~g~~~~A~~~~~~~l~  389 (398)
T PRK10747        346 EASLAFRAALKQRPDAYD-YAWLADALDRLHKPEEAAAMRRDGLM  389 (398)
T ss_pred             HHHHHHHHHHhcCCCHHH-HHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            999999999999998654 66788999999999999999999986

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

Probab=98.48  E-value=2.2e-07  Score=95.85  Aligned_cols=50  Identities=26%  Similarity=0.428  Sum_probs=47.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||..+++++|+++|+.||.|.+|+++.| .+|+++|||||+|.
T Consensus       285 ~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~  334 (562)
T TIGR01628       285 GVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFS  334 (562)
T ss_pred             CCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeC
Confidence            458999999999999999999999999999999999 79999999999996

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>PLN03218 maturation of RBCL 1; Provisional

Probab=98.45  E-value=0.00048  Score=75.39  Aligned_cols=268  Identities=9%  Similarity=-0.011  Sum_probs=144.4

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDF-PVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~-p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ++..|+..+.....   .+...|...|...-+.|+++.+..+|+++.... ..+...|...|..+.+. +..+.+..+|+
T Consensus       456 A~~lf~~M~~~Gl~---pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~-G~~eeAl~lf~  531 (1060)
T PLN03218        456 ALRVLRLVQEAGLK---ADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARA-GQVAKAFGAYG  531 (1060)
T ss_pred             HHHHHHHHHHcCCC---CCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHC-cCHHHHHHHHH
Confidence            45556555544321   134466777777777777777777777777653 23667777777655543 34556777777


Q ss_pred             HHHHc-CCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHh--CC--hh--hHHHHHHHHHHHH--H---HHHHHhhccCc
Q 013489           83 RATKN-CPWVGELWVRSLLSLERSRASEEEISTVFEKSLL--CA--FS--TFEEYLDLFLTRI--D---GLRRRILFSGE  150 (442)
Q Consensus        83 rAl~~-~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~--~~--~~--~~~~~~~~~~~~~--~---~l~rr~~~~~~  150 (442)
                      +.... +.-+...|...|..+-+ .+..+.+..+|+.+..  .+  ++  .+...+..+...-  +   .+-+.+.....
T Consensus       532 ~M~~~Gv~PD~vTYnsLI~a~~k-~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi  610 (1060)
T PLN03218        532 IMRSKNVKPDRVVFNALISACGQ-SGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNI  610 (1060)
T ss_pred             HHHHcCCCCCHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCC
Confidence            77652 22234566666665544 4667777777777654  11  22  1111222211000  0   00000000000


Q ss_pred             cchhhhHHHHH------HHHHHHHHHHhhhhcC-chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh-chhHHHHHHH
Q 013489          151 VEGVLDYSLIR------ETFQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI-SGAMLEAWQS  222 (442)
Q Consensus       151 ~~~~~~~~~~r------~~~~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~-~~~~~~~w~~  222 (442)
                      .....-+..+-      ..++.|..++...... ..+....|...+......| +++.|.++|+.+.+. .+.+...|..
T Consensus       611 ~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G-~~eeA~~l~~eM~k~G~~pd~~tyns  689 (1060)
T PLN03218        611 KGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAG-DLDKAFEILQDARKQGIKLGTVSYSS  689 (1060)
T ss_pred             CCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCC-CHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            00000011111      1124455544433322 1223345566666666667 788888888887776 3344567778


Q ss_pred             HHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHh
Q 013489          223 YISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQK  279 (442)
Q Consensus       223 ~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~  279 (442)
                      .+....+.|+++.|..+|+......+.++  ...|...+.--...|..+.....+..
T Consensus       690 LI~ay~k~G~~eeA~~lf~eM~~~g~~Pd--vvtyN~LI~gy~k~G~~eeAlelf~e  744 (1060)
T PLN03218        690 LMGACSNAKNWKKALELYEDIKSIKLRPT--VSTMNALITALCEGNQLPKALEVLSE  744 (1060)
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            88888888888888888887765333222  34577777777777777666655554

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.45  E-value=7.3e-07  Score=66.59  Aligned_cols=49  Identities=24%  Similarity=0.364  Sum_probs=43.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++.+||.|||+.+|.++..++|..||+|..|+|-..+.   .+|-|||.|.
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYe   65 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYE   65 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEeh
Confidence            456899999999999999999999999999999876544   5799999984

>PF08311 Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro: IPR013212 Proteins containing this domain are checkpoint proteins involved in cell division

Probab=98.43  E-value=2.9e-06  Score=68.75  Aligned_cols=110  Identities=17%  Similarity=0.348  Sum_probs=84.4

Q ss_pred             chhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhc----CChhhHHHHHHHHHhcCCCC---------HHHHHHHHHHHH
Q 013489            2 CNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS----GDPGRVQLLYERAITDFPVS---------SDLWLDYTQYLD   68 (442)
Q Consensus         2 ~~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~----g~~~~~~~lyERal~~~p~~---------~~lW~~Y~~~l~   68 (442)
                      -+.|..||..|.... ...+-++.|..||.|....    +.......++|||+..+..+         ..+|+.|+.+..
T Consensus         2 ~~~r~~~e~~i~~~~-~~dDPL~~w~~yI~w~~~~~p~~~~~~~L~~lLer~~~~f~~~~~Y~nD~RylkiWi~ya~~~~   80 (126)
T PF08311_consen    2 EQQRQEFEEQIRSYE-EGDDPLDPWLRYIKWIEENYPSGGKQSGLLELLERCIRKFKDDERYKNDERYLKIWIKYADLSS   80 (126)
T ss_dssp             HHHHHHHHHHHHCCG-GSS-CHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHTTSGGGTT-HHHHHHHHHHHTTBS
T ss_pred             HHHHHHHHHHHHHcc-CCCCChHHHHHHHHHHHHHCCCCCchhHHHHHHHHHHHHHhhhHhhcCCHHHHHHHHHHHHHcc
Confidence            467999999998876 1234578899999998854    34567788999999976554         369999998643


Q ss_pred             HhcchhhHHHHHHHHHHH--cCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHH
Q 013489           69 KTLKVGNVVRDVYSRATK--NCPWVGELWVRSLLSLERSRASEEEISTVFEKSL  120 (442)
Q Consensus        69 ~~~~~~~~~~~v~erAl~--~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al  120 (442)
                             ....||.....  ..-....+|..|+.+++. .++...+..||++++
T Consensus        81 -------~~~~if~~l~~~~IG~~~A~fY~~wA~~le~-~~~~~~A~~I~~~Gi  126 (126)
T PF08311_consen   81 -------DPREIFKFLYSKGIGTKLALFYEEWAEFLEK-RGNFKKADEIYQLGI  126 (126)
T ss_dssp             -------HHHHHHHHHHHHTTSTTBHHHHHHHHHHHHH-TT-HHHHHHHHHHHH
T ss_pred             -------CHHHHHHHHHHcCccHHHHHHHHHHHHHHHH-cCCHHHHHHHHHhhC
Confidence                   25678887776  346678999999998887 688999999999875

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.

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.40  E-value=4e-07  Score=71.29  Aligned_cols=56  Identities=23%  Similarity=0.319  Sum_probs=52.0

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          386 KGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       386 ~~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..+.+...|||.++...++++++.+.|..||.|+.+.+-.|+.||-.+|||.|+|.
T Consensus        67 qrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYe  122 (170)
T KOG0130|consen   67 QRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYE  122 (170)
T ss_pred             ccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehH
Confidence            34466789999999999999999999999999999999999999999999999985

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

Probab=98.39  E-value=4.3e-07  Score=93.77  Aligned_cols=50  Identities=24%  Similarity=0.284  Sum_probs=47.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..+|||+|||.++++++|+++|+.||.|.+|+++.+ .+|+++|||||+|.
T Consensus        88 ~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~-~~g~skg~afV~F~  137 (562)
T TIGR01628        88 VGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFE  137 (562)
T ss_pred             CCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeec-CCCCcccEEEEEEC
Confidence            458999999999999999999999999999999998 69999999999995

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=98.39  E-value=8.5e-07  Score=77.27  Aligned_cols=53  Identities=23%  Similarity=0.393  Sum_probs=49.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...+.+.|.-||.++|+++++.+|+..|.|.+|++++|+-+|++-|||||-|.
T Consensus        39 ~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv   91 (360)
T KOG0145|consen   39 ESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYV   91 (360)
T ss_pred             cccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeec
Confidence            44568999999999999999999999999999999999999999999999874

>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]

Probab=98.38  E-value=5e-05  Score=75.45  Aligned_cols=197  Identities=11%  Similarity=0.071  Sum_probs=140.3

Q ss_pred             HHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhh
Q 013489           47 ERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFST  126 (442)
Q Consensus        47 ERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~  126 (442)
                      .-.|..+|++|+-|....+++- ..++.+.+...|+||++.-|.....+...- ........++.+...|..||.+.+..
T Consensus       411 q~Li~~~~~sPesWca~GNcfS-LQkdh~~Aik~f~RAiQldp~faYayTLlG-hE~~~~ee~d~a~~~fr~Al~~~~rh  488 (638)
T KOG1126|consen  411 QDLIDTDPNSPESWCALGNCFS-LQKDHDTAIKCFKRAIQLDPRFAYAYTLLG-HESIATEEFDKAMKSFRKALGVDPRH  488 (638)
T ss_pred             HHHHhhCCCCcHHHHHhcchhh-hhhHHHHHHHHHHHhhccCCccchhhhhcC-ChhhhhHHHHhHHHHHHhhhcCCchh
Confidence            4456678888888888888655 446677788888888888885433332211 11112344677888888888877766


Q ss_pred             HHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHH
Q 013489          127 FEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVW  206 (442)
Q Consensus       127 ~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~  206 (442)
                      +..++.+-+.|.                     -.+-++.|.-++.+++.-+|....+...+..++.+.+ ..++|..+|
T Consensus       489 YnAwYGlG~vy~---------------------Kqek~e~Ae~~fqkA~~INP~nsvi~~~~g~~~~~~k-~~d~AL~~~  546 (638)
T KOG1126|consen  489 YNAWYGLGTVYL---------------------KQEKLEFAEFHFQKAVEINPSNSVILCHIGRIQHQLK-RKDKALQLY  546 (638)
T ss_pred             hHHHHhhhhhee---------------------ccchhhHHHHHHHhhhcCCccchhHHhhhhHHHHHhh-hhhHHHHHH
Confidence            555555444332                     1256889999999999888888888888999999999 899999999


Q ss_pred             HHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCH
Q 013489          207 ERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTL  270 (442)
Q Consensus       207 ~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~  270 (442)
                      ++|+..+|.++-.-..-+......+++..|...++..-. ..+ +.. .++-.....-+.+|..
T Consensus       547 ~~A~~ld~kn~l~~~~~~~il~~~~~~~eal~~LEeLk~-~vP-~es-~v~~llgki~k~~~~~  607 (638)
T KOG1126|consen  547 EKAIHLDPKNPLCKYHRASILFSLGRYVEALQELEELKE-LVP-QES-SVFALLGKIYKRLGNT  607 (638)
T ss_pred             HHHHhcCCCCchhHHHHHHHHHhhcchHHHHHHHHHHHH-hCc-chH-HHHHHHHHHHHHHccc
Confidence            999999999887777777777778999999999998654 222 222 3444445555555653

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=98.38  E-value=6.9e-07  Score=86.68  Aligned_cols=51  Identities=27%  Similarity=0.375  Sum_probs=48.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||..+++++|+.+|++||.|..++++.+..+|.++|||||+|.
T Consensus        89 ~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~  139 (352)
T TIGR01661        89 GANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFD  139 (352)
T ss_pred             cceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEEC
Confidence            458999999999999999999999999999999999889999999999995

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

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.38  E-value=1.7e-05  Score=70.04  Aligned_cols=117  Identities=13%  Similarity=0.040  Sum_probs=93.8

Q ss_pred             hHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcch--hhHHHHHHH
Q 013489            5 RAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKV--GNVVRDVYS   82 (442)
Q Consensus         5 r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~--~~~~~~v~e   82 (442)
                      -..|+.+|..+|.    +.+.|..........|+++.+...|++++...|.+..+|..|+..+....+.  .+.+..+|+
T Consensus        59 i~~l~~~L~~~P~----~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~  134 (198)
T PRK10370         59 LQALQDKIRANPQ----NSEQWALLGEYYLWRNDYDNALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQTREMID  134 (198)
T ss_pred             HHHHHHHHHHCCC----CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHH
Confidence            3456777777765    7889999999888999999999999999999999999999999854323222  467899999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhh
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFST  126 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~  126 (442)
                      ++++..|.....|......+. ..++.+++...|++++...++.
T Consensus       135 ~al~~dP~~~~al~~LA~~~~-~~g~~~~Ai~~~~~aL~l~~~~  177 (198)
T PRK10370        135 KALALDANEVTALMLLASDAF-MQADYAQAIELWQKVLDLNSPR  177 (198)
T ss_pred             HHHHhCCCChhHHHHHHHHHH-HcCCHHHHHHHHHHHHhhCCCC
Confidence            999999998888877665443 4788899999999998776653

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=98.37  E-value=8.8e-07  Score=77.21  Aligned_cols=55  Identities=22%  Similarity=0.276  Sum_probs=50.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       387 ~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .......|||-||.+++.+.-|.++|.+||.|..|++++|..|.+.+|||||..+
T Consensus       274 ~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMt  328 (360)
T KOG0145|consen  274 GPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMT  328 (360)
T ss_pred             CCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEec
Confidence            3455679999999999999999999999999999999999888999999999864

>COG5191 Uncharacterized conserved protein, contains HAT (Half-A-TPR) repeat [General function prediction only]

Probab=98.35  E-value=5e-07  Score=81.42  Aligned_cols=82  Identities=13%  Similarity=0.304  Sum_probs=74.7

Q ss_pred             HhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHH
Q 013489           21 EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (442)
Q Consensus        21 ~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~  100 (442)
                      +++..|..|+.+..+.|....+-.+|-.||..+|+++++|+--+.|......+.+.++.+|.+++|..|.++.||..|.+
T Consensus       105 ~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         105 NDPKIWSQYAAYVIKKKMYGEMKNIFAECLTKHPLNVDLWIYCCAFELFEIANIESSRAMFLKGLRMNSRSPRIWIEYFR  184 (435)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCceeeeeeccchhhhhccHHHHHHHHHhhhccCCCCchHHHHHHH
Confidence            47889999999999999999999999999999999999999878877766667788999999999999999999999998


Q ss_pred             HHH
Q 013489          101 SLE  103 (442)
Q Consensus       101 ~le  103 (442)
                       +|
T Consensus       185 -~E  186 (435)
T COG5191         185 -ME  186 (435)
T ss_pred             -HH
Confidence             44

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=98.33  E-value=3.1e-07  Score=88.38  Aligned_cols=48  Identities=21%  Similarity=0.407  Sum_probs=46.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          394 AFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       394 v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +|||||.+++++++|+.+|.+||.|..|.++.|..||+++|||||+|.
T Consensus       281 l~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~  328 (549)
T KOG0147|consen  281 LYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFV  328 (549)
T ss_pred             hhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEe
Confidence            999999999999999999999999999999999889999999999996

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=98.33  E-value=1.3e-06  Score=63.18  Aligned_cols=48  Identities=40%  Similarity=0.536  Sum_probs=43.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +|+|+|||..+++++|+.+|..+|.|..+.+..++ .+.++|+|||+|.
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~-~~~~~~~~~v~f~   48 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDK-DTKSKGFAFVEFE   48 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCC-CCCcceEEEEEEC
Confidence            58999999999999999999999999999999885 4478999999995

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).

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.33  E-value=8.5e-05  Score=72.78  Aligned_cols=215  Identities=15%  Similarity=0.142  Sum_probs=138.4

Q ss_pred             CHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHH
Q 013489           56 SSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFL  135 (442)
Q Consensus        56 ~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~  135 (442)
                      .++-...=+.++. .+. ...+.=.||-||..-|...+.|...-. ....++....+...+.+|+...+.+...+..+-.
T Consensus       285 ~pdPf~eG~~lm~-nG~-L~~A~LafEAAVkqdP~haeAW~~LG~-~qaENE~E~~ai~AL~rcl~LdP~NleaLmaLAV  361 (579)
T KOG1125|consen  285 HPDPFKEGCNLMK-NGD-LSEAALAFEAAVKQDPQHAEAWQKLGI-TQAENENEQNAISALRRCLELDPTNLEALMALAV  361 (579)
T ss_pred             CCChHHHHHHHHh-cCC-chHHHHHHHHHHhhChHHHHHHHHhhh-HhhhccchHHHHHHHHHHHhcCCccHHHHHHHHH
Confidence            4444555555554 333 556778999999999999999998543 5555677777888999999988875444332222


Q ss_pred             H---------HHHHHHH--Hhhc------c---C-------ccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHH
Q 013489          136 T---------RIDGLRR--RILF------S---G-------EVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYW  188 (442)
Q Consensus       136 ~---------~~~~l~r--r~~~------~---~-------~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~  188 (442)
                      .         .|.+|..  +..+      .   .       ...+...+..+...|-.|.....     ....+++..-.
T Consensus       362 SytNeg~q~~Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~~~~-----~~~DpdvQ~~L  436 (579)
T KOG1125|consen  362 SYTNEGLQNQALKMLDKWIRNKPKYVHLVSAGENEDFENTKSFLDSSHLAHIQELFLEAARQLP-----TKIDPDVQSGL  436 (579)
T ss_pred             HHhhhhhHHHHHHHHHHHHHhCccchhccccCccccccCCcCCCCHHHHHHHHHHHHHHHHhCC-----CCCChhHHhhh
Confidence            2         1222211  0000      0   0       00111123334444444433221     11234566666


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhC
Q 013489          189 AHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYG  268 (442)
Q Consensus       189 a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G  268 (442)
                      .-++...+ ++++|...|+.||+..|+++.+|-.+.--...-.....|..-|.||++  +.+...    ..+.++--.|=
T Consensus       437 GVLy~ls~-efdraiDcf~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALq--LqP~yV----R~RyNlgIS~m  509 (579)
T KOG1125|consen  437 GVLYNLSG-EFDRAVDCFEAALQVKPNDYLLWNRLGATLANGNRSEEAISAYNRALQ--LQPGYV----RVRYNLGISCM  509 (579)
T ss_pred             HHHHhcch-HHHHHHHHHHHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHh--cCCCee----eeehhhhhhhh
Confidence            65555555 999999999999999999999999999988776788999999999997  443333    45566666677


Q ss_pred             CHhhHHHHHHhhchhHH
Q 013489          269 TLEDFDHSVQKVTPRLE  285 (442)
Q Consensus       269 ~~~~~~~~~~~~~~~~~  285 (442)
                      ++..+.+|+.-...++.
T Consensus       510 NlG~ykEA~~hlL~AL~  526 (579)
T KOG1125|consen  510 NLGAYKEAVKHLLEALS  526 (579)
T ss_pred             hhhhHHHHHHHHHHHHH
Confidence            78888888877665553

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.32  E-value=6.7e-07  Score=78.20  Aligned_cols=56  Identities=16%  Similarity=0.306  Sum_probs=53.0

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          386 KGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       386 ~~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....+.|++||-+||.+.++.+|-.+|-+||.|.+.++..|+.|+.||+||||.|.
T Consensus       280 reGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfD  335 (371)
T KOG0146|consen  280 REGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFD  335 (371)
T ss_pred             hcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecC
Confidence            34678999999999999999999999999999999999999999999999999995

>PLN02789 farnesyltranstransferase

Probab=98.31  E-value=0.00019  Score=68.09  Aligned_cols=201  Identities=10%  Similarity=-0.008  Sum_probs=131.6

Q ss_pred             HHHHHHhhcCCCCChHhHHHHHHHHHHHHhcC-ChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcch-hhHHHHHHHH
Q 013489            6 AHLEEQISRQDLSDSEKFQQYMIYLKYEQSSG-DPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKV-GNVVRDVYSR   83 (442)
Q Consensus         6 ~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g-~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~-~~~~~~v~er   83 (442)
                      ..++.+|..+|.    ++.+|..-.......| +++.++..++++|..+|.+..+|..-.-.+...+.. .+.....+++
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            345566666654    8899987776666666 578999999999999999999999776555543321 2456789999


Q ss_pred             HHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhH--HHHHHHHHHHHHHHHHHhhccCccchhhhHHHHH
Q 013489           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTF--EEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIR  161 (442)
Q Consensus        84 Al~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~--~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r  161 (442)
                      ++..-|.....|....-.+.. .+..++....+++++...+.+.  |.+..+.+..       ...   .   ...   .
T Consensus       134 al~~dpkNy~AW~~R~w~l~~-l~~~~eeL~~~~~~I~~d~~N~sAW~~R~~vl~~-------~~~---l---~~~---~  196 (320)
T PLN02789        134 ILSLDAKNYHAWSHRQWVLRT-LGGWEDELEYCHQLLEEDVRNNSAWNQRYFVITR-------SPL---L---GGL---E  196 (320)
T ss_pred             HHHhCcccHHHHHHHHHHHHH-hhhHHHHHHHHHHHHHHCCCchhHHHHHHHHHHh-------ccc---c---ccc---c
Confidence            999999999999997765555 4667788888999998766643  3332221111       100   0   000   1


Q ss_pred             HHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCC---CHHHHHHHHHHHHHhchhHHHHHHHHHHHH
Q 013489          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGK---DMVSARGVWERLLKISGAMLEAWQSYISME  227 (442)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~---~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e  227 (442)
                      ..++..+.+...++...+.....|.+..-+....+.   ....|..++..++...+++....-..+++.
T Consensus       197 ~~~e~el~y~~~aI~~~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~~~s~~al~~l~d~~  265 (320)
T PLN02789        197 AMRDSELKYTIDAILANPRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKDSNHVFALSDLLDLL  265 (320)
T ss_pred             ccHHHHHHHHHHHHHhCCCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhcccCCcHHHHHHHHHHH
Confidence            123445566555555556666688887776665321   334588888888887776655444444433

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.26  E-value=4.5e-05  Score=67.31  Aligned_cols=82  Identities=15%  Similarity=0.065  Sum_probs=41.5

Q ss_pred             hhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCC--HHHHHHHHH
Q 013489           40 GRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRAS--EEEISTVFE  117 (442)
Q Consensus        40 ~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~--~~~~~~i~~  117 (442)
                      +.+...++++|..+|.+.+.|......+.. .++.+.+...|++|++..|....+|..|+..+....+.  .+.+..+++
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 EAQLQALQDKIRANPQNSEQWALLGEYYLW-RNDYDNALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQTREMID  134 (198)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHH
Confidence            444455555566666666666655554432 23344455566666665565555555555433222222  244555555


Q ss_pred             HHHhC
Q 013489          118 KSLLC  122 (442)
Q Consensus       118 ~al~~  122 (442)
                      +++..
T Consensus       135 ~al~~  139 (198)
T PRK10370        135 KALAL  139 (198)
T ss_pred             HHHHh
Confidence            54443

>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional

Probab=98.23  E-value=0.00018  Score=76.43  Aligned_cols=258  Identities=10%  Similarity=0.043  Sum_probs=153.9

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (442)
                      ++..+...++....   .+...|...++...+.|+++.|..+|++..   +.+...|...+..+... +..+.+..+|++
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---GDTFVSCALIDMYSKCGDIEDARCVFDGMP---EKTTVAWNSMLAGYALH-GYSEEALCLYYE  315 (697)
T ss_pred             HHHHHHHHHHhCCC---ccceeHHHHHHHHHHCCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhC-CCHHHHHHHHHH
Confidence            34455555544321   134467777888888888888888888764   34667788777766544 455678888888


Q ss_pred             HHHc-CCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh----hHHHHHHHHHHH--HHHHH---HHhhccCccch
Q 013489           84 ATKN-CPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS----TFEEYLDLFLTR--IDGLR---RRILFSGEVEG  153 (442)
Q Consensus        84 Al~~-~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~----~~~~~~~~~~~~--~~~l~---rr~~~~~~~~~  153 (442)
                      .... +.-+...+...+..+-+ .+..+.+..++..++..++.    .+...++.|...  ++...   ..+...+    
T Consensus       316 M~~~g~~pd~~t~~~ll~a~~~-~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~d----  390 (697)
T PLN03081        316 MRDSGVSIDQFTFSIMIRIFSR-LALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKN----  390 (697)
T ss_pred             HHHcCCCCCHHHHHHHHHHHHh-ccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCCCC----
Confidence            8763 32233456665654443 56778888888888876543    223333333210  00000   0110000    


Q ss_pred             hhhHHHHHHH------HHHHHHHHhhhhcC-chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchh--HHHHHHHHH
Q 013489          154 VLDYSLIRET------FQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA--MLEAWQSYI  224 (442)
Q Consensus       154 ~~~~~~~r~~------~~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~--~~~~w~~~~  224 (442)
                      ..-|..+-..      .++|+.++...... ..+....+...+.-....| .++.|.++|+.+.+.++-  ....|...+
T Consensus       391 ~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g-~~~~a~~~f~~m~~~~g~~p~~~~y~~li  469 (697)
T PLN03081        391 LISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSG-LSEQGWEIFQSMSENHRIKPRAMHYACMI  469 (697)
T ss_pred             eeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCC-cHHHHHHHHHHHHHhcCCCCCccchHhHH
Confidence            0112222222      24566655544332 2222334555555556667 899999999998875332  245677888


Q ss_pred             HHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHh
Q 013489          225 SMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQK  279 (442)
Q Consensus       225 ~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~  279 (442)
                      +...+.|.++.|..+++++-   +  .....+|...+.-...+|+.+....+.++
T Consensus       470 ~~l~r~G~~~eA~~~~~~~~---~--~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~  519 (697)
T PLN03081        470 ELLGREGLLDEAYAMIRRAP---F--KPTVNMWAALLTACRIHKNLELGRLAAEK  519 (697)
T ss_pred             HHHHhcCCHHHHHHHHHHCC---C--CCCHHHHHHHHHHHHHcCCcHHHHHHHHH
Confidence            88888999999999987742   1  22346788888888899988776665554

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=98.22  E-value=1.7e-06  Score=78.90  Aligned_cols=50  Identities=8%  Similarity=0.159  Sum_probs=47.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+|||..+.++.+++||+.+|.-||.|..|.+.+++.++.+||||||+|.
T Consensus       211 nRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~  260 (544)
T KOG0124|consen  211 NRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYN  260 (544)
T ss_pred             heEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEec
Confidence            48999999999999999999999999999999999888889999999995

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.21  E-value=2.5e-06  Score=72.25  Aligned_cols=52  Identities=19%  Similarity=0.271  Sum_probs=47.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccC-CCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDV-GGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~-G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...-++|+.+|+.+.+..+..+|.++ |.|..+++-+.+.||.|+|||||+|.
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFE  100 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFE  100 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEec
Confidence            34479999999999999999999998 78888899899999999999999995

>KOG1173 consensus Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=98.20  E-value=0.00053  Score=67.18  Aligned_cols=202  Identities=13%  Similarity=0.064  Sum_probs=114.7

Q ss_pred             HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHH
Q 013489           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER  104 (442)
Q Consensus        25 ~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~  104 (442)
                      .|..-..+-..-|...+|+.+|-.|...+|.-..-|+.|..-+- ..+..+.+...|.+|-+.+|.+..- ..|+.....
T Consensus       314 sW~aVg~YYl~i~k~seARry~SKat~lD~~fgpaWl~fghsfa-~e~EhdQAmaaY~tAarl~~G~hlP-~LYlgmey~  391 (611)
T KOG1173|consen  314 SWFAVGCYYLMIGKYSEARRYFSKATTLDPTFGPAWLAFGHSFA-GEGEHDQAMAAYFTAARLMPGCHLP-SLYLGMEYM  391 (611)
T ss_pred             chhhHHHHHHHhcCcHHHHHHHHHHhhcCccccHHHHHHhHHhh-hcchHHHHHHHHHHHHHhccCCcch-HHHHHHHHH
Confidence            45555555444455566666666666666666666666665433 2233455666666666666554321 122322222


Q ss_pred             ccCCHHHHHHHHHHHHhCChhhHH--HHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhH
Q 013489          105 SRASEEEISTVFEKSLLCAFSTFE--EYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLL  182 (442)
Q Consensus       105 ~~~~~~~~~~i~~~al~~~~~~~~--~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~  182 (442)
                      ...+.+.+..-|..|+...|...-  ..+.+..    +            .+.++......|..++..+...........
T Consensus       392 ~t~n~kLAe~Ff~~A~ai~P~Dplv~~Elgvva----y------------~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~  455 (611)
T KOG1173|consen  392 RTNNLKLAEKFFKQALAIAPSDPLVLHELGVVA----Y------------TYEEYPEALKYFQKALEVIKSVLNEKIFWE  455 (611)
T ss_pred             HhccHHHHHHHHHHHHhcCCCcchhhhhhhhee----e------------hHhhhHHHHHHHHHHHHHhhhccccccchh
Confidence            245555566666666654433111  1111000    0            012222333344444433322221112233


Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      .+|...+....+++ ..+.|...|+++|...|.++..+...+-..-..|+++.|...|.+||-
T Consensus       456 p~~~NLGH~~Rkl~-~~~eAI~~~q~aL~l~~k~~~~~asig~iy~llgnld~Aid~fhKaL~  517 (611)
T KOG1173|consen  456 PTLNNLGHAYRKLN-KYEEAIDYYQKALLLSPKDASTHASIGYIYHLLGNLDKAIDHFHKALA  517 (611)
T ss_pred             HHHHhHHHHHHHHh-hHHHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcChHHHHHHHHHHHh
Confidence            46777888888888 899999999999999999888776666666678999999999999996

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.18  E-value=0.0014  Score=58.13  Aligned_cols=225  Identities=15%  Similarity=0.108  Sum_probs=154.4

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCC---CCHHHHHHHHHHHHHhc--chhhHHHHHHHHHHHcCCCcHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFP---VSSDLWLDYTQYLDKTL--KVGNVVRDVYSRATKNCPWVGELWV   96 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p---~~~~lW~~Y~~~l~~~~--~~~~~~~~v~erAl~~~p~s~~lW~   96 (442)
                      .+..|.++     ..-+++.+..+++..+...+   .-++.|.-|=.......  +....+..++.+--..+|.|..+=.
T Consensus        16 ~~~~wr~~-----~~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~fp~S~RV~~   90 (289)
T KOG3060|consen   16 QMRKWREE-----TVRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRFPGSKRVGK   90 (289)
T ss_pred             HHHHHHhc-----cccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhCCCChhHHH
Confidence            45577543     44578889888888887654   45789988855444322  2234577888887778899999888


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhc
Q 013489           97 RSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMK  176 (442)
Q Consensus        97 ~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~  176 (442)
                      .++..+|. .+..+++.++|++.+.-++.+...+.    ..+..++.+-   .      ..    .+++.-.++++.   
T Consensus        91 lkam~lEa-~~~~~~A~e~y~~lL~ddpt~~v~~K----RKlAilka~G---K------~l----~aIk~ln~YL~~---  149 (289)
T KOG3060|consen   91 LKAMLLEA-TGNYKEAIEYYESLLEDDPTDTVIRK----RKLAILKAQG---K------NL----EAIKELNEYLDK---  149 (289)
T ss_pred             HHHHHHHH-hhchhhHHHHHHHHhccCcchhHHHH----HHHHHHHHcC---C------cH----HHHHHHHHHHHH---
Confidence            88887776 68889999999999977665433322    2222222110   0      00    333334444443   


Q ss_pred             CchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcc---cHHHHHHHHHHHHhcccCCCCh
Q 013489          177 NTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELD---HINEARSIYKRCYSKRFTGTGS  253 (442)
Q Consensus       177 ~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g---~~~~ar~i~~ral~~~~~~~~~  253 (442)
                       +....+.|...++++...+ ++.+|-=+|+.++-..|.++-+...|++.....|   +++-+|+.|.+|+..  .+   
T Consensus       150 -F~~D~EAW~eLaeiY~~~~-~f~kA~fClEE~ll~~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl--~~---  222 (289)
T KOG3060|consen  150 -FMNDQEAWHELAEIYLSEG-DFEKAAFCLEELLLIQPFNPLYFQRLAEVLYTQGGAENLELARKYYERALKL--NP---  222 (289)
T ss_pred             -hcCcHHHHHHHHHHHHhHh-HHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHh--Ch---
Confidence             3455679999999999999 9999999999999999999999999999887776   678899999999973  22   


Q ss_pred             HHHHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          254 EDICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       254 ~~i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                       .=+.+|.-.-...-.+.++.+...+-
T Consensus       223 -~~~ral~GI~lc~~~la~~sk~~~k~  248 (289)
T KOG3060|consen  223 -KNLRALFGIYLCGSALAQISKAELKR  248 (289)
T ss_pred             -HhHHHHHHHHHHHHHHHHHhHHHHhh
Confidence             22234444444555566555555543

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.18  E-value=0.00013  Score=60.97  Aligned_cols=112  Identities=12%  Similarity=0.011  Sum_probs=91.7

Q ss_pred             HHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHH
Q 013489            6 AHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRAT   85 (442)
Q Consensus         6 ~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl   85 (442)
                      ..|+.+|...|.    +   |..........|+++.+...|.+++..+|.+...|...+..+... +..+.+...|++|+
T Consensus        14 ~~~~~al~~~p~----~---~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~-g~~~~A~~~y~~Al   85 (144)
T PRK15359         14 DILKQLLSVDPE----T---VYASGYASWQEGDYSRAVIDFSWLVMAQPWSWRAHIALAGTWMML-KEYTTAINFYGHAL   85 (144)
T ss_pred             HHHHHHHHcCHH----H---HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHH-hhHHHHHHHHHHHH
Confidence            456777766653    3   445555567789999999999999999999999999999877644 45677999999999


Q ss_pred             HcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhh
Q 013489           86 KNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFST  126 (442)
Q Consensus        86 ~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~  126 (442)
                      ...|.....|......+.. .+..+++...|++++...+..
T Consensus        86 ~l~p~~~~a~~~lg~~l~~-~g~~~eAi~~~~~Al~~~p~~  125 (144)
T PRK15359         86 MLDASHPEPVYQTGVCLKM-MGEPGLAREAFQTAIKMSYAD  125 (144)
T ss_pred             hcCCCCcHHHHHHHHHHHH-cCCHHHHHHHHHHHHHhCCCC
Confidence            9999999999988775554 688999999999999877664

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=98.16  E-value=3.4e-06  Score=81.09  Aligned_cols=50  Identities=24%  Similarity=0.294  Sum_probs=45.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .-.+.|.||||.+...+|..+|+.||.|.+|.|++. ..|+-.|||||.|+
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k-~dgklcGFaFV~fk  166 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRK-KDGKLCGFAFVQFK  166 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccC-CCCCccceEEEEEe
Confidence            448999999999999999999999999999999986 56777799999996

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.12  E-value=0.0014  Score=58.07  Aligned_cols=158  Identities=19%  Similarity=0.125  Sum_probs=84.2

Q ss_pred             hhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHH
Q 013489           39 PGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEK  118 (442)
Q Consensus        39 ~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~  118 (442)
                      ...|+.++.+.-..+|.+..+=..++.+++..+. ...+.++|++-+.-.|....++..-+-.+...+.+.+.++.+-+-
T Consensus        68 ~~lAq~C~~~L~~~fp~S~RV~~lkam~lEa~~~-~~~A~e~y~~lL~ddpt~~v~~KRKlAilka~GK~l~aIk~ln~Y  146 (289)
T KOG3060|consen   68 DDLAQKCINQLRDRFPGSKRVGKLKAMLLEATGN-YKEAIEYYESLLEDDPTDTVIRKRKLAILKAQGKNLEAIKELNEY  146 (289)
T ss_pred             hHHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhc-hhhHHHHHHHHhccCcchhHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence            3444555555555666666666666666664432 244666677666666666666665555444444444433333221


Q ss_pred             HHhCC--hhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcC
Q 013489          119 SLLCA--FSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMG  196 (442)
Q Consensus       119 al~~~--~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~  196 (442)
                      .-.|.  ...|++.-++|.                        ....|.+|.=+++..+-..|..+-++..++++.+..|
T Consensus       147 L~~F~~D~EAW~eLaeiY~------------------------~~~~f~kA~fClEE~ll~~P~n~l~f~rlae~~Yt~g  202 (289)
T KOG3060|consen  147 LDKFMNDQEAWHELAEIYL------------------------SEGDFEKAAFCLEELLLIQPFNPLYFQRLAEVLYTQG  202 (289)
T ss_pred             HHHhcCcHHHHHHHHHHHH------------------------hHhHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHh
Confidence            11111  112222223331                        1255666666666665555555566666666666655


Q ss_pred             C--CHHHHHHHHHHHHHhchhHHHHHH
Q 013489          197 K--DMVSARGVWERLLKISGAMLEAWQ  221 (442)
Q Consensus       197 ~--~~~~ar~i~~~~l~~~~~~~~~w~  221 (442)
                      +  |+..+|+.|.++++.+|.+.--|.
T Consensus       203 g~eN~~~arkyy~~alkl~~~~~ral~  229 (289)
T KOG3060|consen  203 GAENLELARKYYERALKLNPKNLRALF  229 (289)
T ss_pred             hHHHHHHHHHHHHHHHHhChHhHHHHH
Confidence            3  455667777777766665444443

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.12  E-value=0.00096  Score=60.60  Aligned_cols=186  Identities=15%  Similarity=0.015  Sum_probs=124.4

Q ss_pred             hHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCH---HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHH--
Q 013489           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS---DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGEL--   94 (442)
Q Consensus        20 ~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~---~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~l--   94 (442)
                      ....+.+...+......|+++.+...|++++..+|.++   ..|...+..+.. .++.+.+...|+++++..|.+..+  
T Consensus        30 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~-~~~~~~A~~~~~~~l~~~p~~~~~~~  108 (235)
T TIGR03302        30 EWPAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYK-SGDYAEAIAAADRFIRLHPNHPDADY  108 (235)
T ss_pred             cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHh-cCCHHHHHHHHHHHHHHCcCCCchHH
Confidence            44566788887777789999999999999999999876   455666555553 356788999999999999976653  


Q ss_pred             -HHHHHHHHHHc-------cCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHH
Q 013489           95 -WVRSLLSLERS-------RASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQR  166 (442)
Q Consensus        95 -W~~y~~~le~~-------~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~  166 (442)
                       |..........       .+..+.+...|++++...+.+......++  .+                          ..
T Consensus       109 a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~--~~--------------------------~~  160 (235)
T TIGR03302       109 AYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPNSEYAPDAKK--RM--------------------------DY  160 (235)
T ss_pred             HHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCCCChhHHHHHH--HH--------------------------HH
Confidence             32222222111       13345677777777765444211110000  00                          00


Q ss_pred             HHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchh---HHHHHHHHHHHHHhcccHHHHHHHHHHH
Q 013489          167 ASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA---MLEAWQSYISMEIELDHINEARSIYKRC  243 (442)
Q Consensus       167 a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~---~~~~w~~~~~~e~~~g~~~~ar~i~~ra  243 (442)
                      ....+          .......+.+....| +...|...|+.++..+|+   ..+.|...+......|+++.|..+++..
T Consensus       161 ~~~~~----------~~~~~~~a~~~~~~g-~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l  229 (235)
T TIGR03302       161 LRNRL----------AGKELYVARFYLKRG-AYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVL  229 (235)
T ss_pred             HHHHH----------HHHHHHHHHHHHHcC-ChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            00000          011224556667778 999999999999999765   3579999999999999999999988886


Q ss_pred             Hh
Q 013489          244 YS  245 (442)
Q Consensus       244 l~  245 (442)
                      ..
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).

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=98.12  E-value=7.7e-06  Score=82.52  Aligned_cols=48  Identities=15%  Similarity=0.245  Sum_probs=43.4

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINL-KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+ .+++++|+.+|+.||.|.+|+++.++     +|||||+|.
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~  321 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMA  321 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEEC
Confidence            4567999999998 69999999999999999999999873     699999996

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.11  E-value=3.4e-06  Score=73.87  Aligned_cols=52  Identities=21%  Similarity=0.402  Sum_probs=48.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.+++|||-|...-+|+|++.+|..||.|.+|.+.+. ..|.+||++||.|.
T Consensus        17 ~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg-~dg~sKGCAFVKf~   68 (371)
T KOG0146|consen   17 GDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRG-PDGNSKGCAFVKFS   68 (371)
T ss_pred             ccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecC-CCCCCCCceEEEec
Confidence            36779999999999999999999999999999999998 58999999999995

>PRK14574 hmsH outer membrane protein; Provisional

Probab=98.11  E-value=0.012  Score=62.87  Aligned_cols=63  Identities=16%  Similarity=0.054  Sum_probs=50.2

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      .+.....+......| ++..|.++++.++...|.+..+++.++++++..|...+|..+++.++.
T Consensus       416 ~~~~~l~a~~~~~~g-dl~~Ae~~le~l~~~aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~  478 (822)
T PRK14574        416 IEGQTLLVQSLVALN-DLPTAQKKLEDLSSTAPANQNLRIALASIYLARDLPRKAEQELKAVES  478 (822)
T ss_pred             HHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Confidence            344444566666667 888888888888888888888888888888888888888888877775

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=98.09  E-value=0.00025  Score=58.29  Aligned_cols=114  Identities=14%  Similarity=0.087  Sum_probs=93.9

Q ss_pred             HHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHH
Q 013489            6 AHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRAT   85 (442)
Q Consensus         6 ~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl   85 (442)
                      +.|+.+|...|.    +......++......|+.+.+...|++++..+|.++.+|...+..+... ++.+.+..+|++++
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            467888877765    5666667777777889999999999999999999999999998877644 45677899999999


Q ss_pred             HcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh
Q 013489           86 KNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus        86 ~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                      ...|.....|......+. ..++.+.+...|++++...+.
T Consensus        79 ~~~p~~~~~~~~la~~~~-~~g~~~~A~~~~~~al~~~p~  117 (135)
T TIGR02552        79 ALDPDDPRPYFHAAECLL-ALGEPESALKALDLAIEICGE  117 (135)
T ss_pred             hcCCCChHHHHHHHHHHH-HcCCHHHHHHHHHHHHHhccc
Confidence            999999898887666444 468899999999999987665

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]

Probab=98.08  E-value=0.0008  Score=69.87  Aligned_cols=237  Identities=13%  Similarity=0.129  Sum_probs=134.6

Q ss_pred             hhhHHHHHHhhcCC-CCChHh---HH--HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhH
Q 013489            3 NARAHLEEQISRQD-LSDSEK---FQ--QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNV   76 (442)
Q Consensus         3 ~~r~~yE~~l~~~~-~~~~~~---~~--~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~   76 (442)
                      +|+..|..++.... ..+++.   ..  .--+.+...+..+++..+...|--.|..+|...+-.+..+.+....+. ...
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 KALEHFKSALGKLLEVANKDEGKSTNLTLKYNLARLLEELHDTEVAEEMYKSILKEHPGYIDAYLRLGCMARDKNN-LYE  548 (1018)
T ss_pred             HHHHHHHHHhhhhhhhcCccccccchhHHHHHHHHHHHhhhhhhHHHHHHHHHHHHCchhHHHHHHhhHHHHhccC-cHH
Confidence            57778888886621 112222   11  122344455667889999999999999999999988888765554433 345


Q ss_pred             HHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHH--HHHHHHHHHHHHHHhhccCccchh
Q 013489           77 VRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEY--LDLFLTRIDGLRRRILFSGEVEGV  154 (442)
Q Consensus        77 ~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~--~~~~~~~~~~l~rr~~~~~~~~~~  154 (442)
                      +...+..++........+|..+-. +.........+..-|+.+++......+.|  +.+-..++..+.   ......   
T Consensus       549 a~~~lk~~l~~d~~np~arsl~G~-~~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~---~~~rn~---  621 (1018)
T KOG2002|consen  549 ASLLLKDALNIDSSNPNARSLLGN-LHLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGNVYIQALH---NPSRNP---  621 (1018)
T ss_pred             HHHHHHHHHhcccCCcHHHHHHHH-HHHhhhhhcccccHHHHHHhhhccCCchhHHHHhhHHHHHHhc---ccccCh---
Confidence            888999999988777889887653 44333444445555555554332221222  222222222111   111110   


Q ss_pred             hhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHH--HHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhccc
Q 013489          155 LDYSLIRETFQRASDYLSEQMKNTDGLLRLYAY--WAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDH  232 (442)
Q Consensus       155 ~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~--~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~  232 (442)
                         ..-+..+++|+.++.+.+...|..  +|-.  .+-+....| .+..|+.||.+....-.+..++|+..+.+...+|.
T Consensus       622 ---ek~kk~~~KAlq~y~kvL~~dpkN--~yAANGIgiVLA~kg-~~~~A~dIFsqVrEa~~~~~dv~lNlah~~~e~~q  695 (1018)
T KOG2002|consen  622 ---EKEKKHQEKALQLYGKVLRNDPKN--MYAANGIGIVLAEKG-RFSEARDIFSQVREATSDFEDVWLNLAHCYVEQGQ  695 (1018)
T ss_pred             ---HHHHHHHHHHHHHHHHHHhcCcch--hhhccchhhhhhhcc-CchHHHHHHHHHHHHHhhCCceeeeHHHHHHHHHH
Confidence               223345566666655555443332  2221  233344445 66677777766666554556667777776666677


Q ss_pred             HHHHHHHHHHHHhcccCCCCh
Q 013489          233 INEARSIYKRCYSKRFTGTGS  253 (442)
Q Consensus       233 ~~~ar~i~~ral~~~~~~~~~  253 (442)
                      +..|.++|+.++....+.+.+
T Consensus       696 y~~AIqmYe~~lkkf~~~~~~  716 (1018)
T KOG2002|consen  696 YRLAIQMYENCLKKFYKKNRS  716 (1018)
T ss_pred             HHHHHHHHHHHHHHhcccCCH
Confidence            777777777776654443433

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=98.08  E-value=3e-06  Score=70.23  Aligned_cols=50  Identities=24%  Similarity=0.271  Sum_probs=46.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEE-EEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSI-RILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~-~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||||.+.+.+..|.++|+.||.+.+. .+++++.||.++|||||.|+
T Consensus        97 anlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~  147 (203)
T KOG0131|consen   97 ANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYA  147 (203)
T ss_pred             ccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEech
Confidence            589999999999999999999999988654 78999999999999999885

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.04  E-value=4.4e-06  Score=76.10  Aligned_cols=50  Identities=28%  Similarity=0.349  Sum_probs=48.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .-+||..|.+-++.++|.-+|+.||.|.+|.+++|..||-+-.||||+|.
T Consensus       240 NVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFe  289 (479)
T KOG0415|consen  240 NVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFE  289 (479)
T ss_pred             ceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeec
Confidence            38999999999999999999999999999999999999999999999995

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.01  E-value=1.1e-05  Score=74.80  Aligned_cols=52  Identities=23%  Similarity=0.382  Sum_probs=49.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....||||.||.++++.++++.|.++|.|..+.++.|..+++++|||||+|.
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~  147 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFD  147 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEec
Confidence            3558999999999999999999999999999999999999999999999984

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=98.01  E-value=0.0052  Score=61.51  Aligned_cols=241  Identities=15%  Similarity=0.152  Sum_probs=143.6

Q ss_pred             ChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhc--------CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcC--
Q 013489           19 DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITD--------FPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNC--   88 (442)
Q Consensus        19 ~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~--------~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~--   88 (442)
                      +|.-..............|+++.+..+|++||..        +|.-..+=..++.++... +....+..+|++|+...  
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 DPERLRTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSL-GKYDEAVNLYEEALTIREE  273 (508)
T ss_pred             CchHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHh-ccHHHHHHHHHHHHHHHHH
Confidence            3445555666666666789999999999999987        444444444466655544 44567899999999843  


Q ss_pred             ------CCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh-------hHHH-HHHHHHHHHHHHHHHhhccCccchh
Q 013489           89 ------PWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS-------TFEE-YLDLFLTRIDGLRRRILFSGEVEGV  154 (442)
Q Consensus        89 ------p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~-------~~~~-~~~~~~~~~~~l~rr~~~~~~~~~~  154 (442)
                            |....+...... +.-..+.+.+++..+++|+..--.       .+.. +..+....  ...            
T Consensus       274 ~~G~~h~~va~~l~nLa~-ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~--~~~------------  338 (508)
T KOG1840|consen  274 VFGEDHPAVAATLNNLAV-LYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAIL--QSM------------  338 (508)
T ss_pred             hcCCCCHHHHHHHHHHHH-HHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHH--HHh------------
Confidence                  334445554333 334578888999888888853111       1111 11111100  000            


Q ss_pred             hhHHHHHHHHHHHHHHHhhhhcCch-hhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc----h-----hHHHHHHHHH
Q 013489          155 LDYSLIRETFQRASDYLSEQMKNTD-GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS----G-----AMLEAWQSYI  224 (442)
Q Consensus       155 ~~~~~~r~~~~~a~~~l~~~~~~~~-~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~----~-----~~~~~w~~~~  224 (442)
                      .+++..-..+.+++..+...+...+ ....+...++.+....| .++.|+++|+++++..    .     ....+|.--.
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            1233344455566666655554433 44578888999999999 8999999999999873    2     1234776666


Q ss_pred             HHHHhcccHHHHHHHHHHHHhc--ccCCCChHHHHHHHHHHHHHhCCHhhHHHHHH
Q 013489          225 SMEIELDHINEARSIYKRCYSK--RFTGTGSEDICHAWLRFEREYGTLEDFDHSVQ  278 (442)
Q Consensus       225 ~~e~~~g~~~~ar~i~~ral~~--~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~  278 (442)
                      .++ ..+.+..|-.+|.+++.-  .+.++.| .+...|.++-..|-.+..++.|++
T Consensus       418 ~~~-~~k~~~~a~~l~~~~~~i~~~~g~~~~-~~~~~~~nL~~~Y~~~g~~e~a~~  471 (508)
T KOG1840|consen  418 AYE-ELKKYEEAEQLFEEAKDIMKLCGPDHP-DVTYTYLNLAALYRAQGNYEAAEE  471 (508)
T ss_pred             HHH-HhcccchHHHHHHHHHHHHHHhCCCCC-chHHHHHHHHHHHHHcccHHHHHH
Confidence            663 445566666666665532  1223334 455566777666644444444443

>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]

Probab=98.00  E-value=0.007  Score=63.19  Aligned_cols=235  Identities=11%  Similarity=0.022  Sum_probs=127.5

Q ss_pred             hhHHHHHHhhcCCCCChH-hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcc--hhhHHHHH
Q 013489            4 ARAHLEEQISRQDLSDSE-KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLK--VGNVVRDV   80 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~-~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~--~~~~~~~v   80 (442)
                      +-..|-.+|..+|..-++ ....|..+..    .|+.+.|...|+|++..+|.++..-+....+......  ....+...
T Consensus       183 al~yyk~al~inp~~~aD~rIgig~Cf~k----l~~~~~a~~a~~ralqLdp~~v~alv~L~~~~l~~~d~~s~~~~~~l  258 (1018)
T KOG2002|consen  183 ALKYYKKALRINPACKADVRIGIGHCFWK----LGMSEKALLAFERALQLDPTCVSALVALGEVDLNFNDSDSYKKGVQL  258 (1018)
T ss_pred             HHHHHHHHHhcCcccCCCccchhhhHHHh----ccchhhHHHHHHHHHhcChhhHHHHHHHHHHHHHccchHHHHHHHHH
Confidence            345677777776632111 1234433333    5667778888888888888887766665554443321  22346677


Q ss_pred             HHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhh---HHHHHHHHHH----------HHHHHHHHhhc
Q 013489           81 YSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFST---FEEYLDLFLT----------RIDGLRRRILF  147 (442)
Q Consensus        81 ~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~---~~~~~~~~~~----------~~~~l~rr~~~  147 (442)
                      +.+|....|.++.+-...+..+. ..++...+-.+.+-++......   ...|+.+-..          ..-|.......
T Consensus       259 l~~ay~~n~~nP~~l~~LAn~fy-fK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~~  337 (1018)
T KOG2002|consen  259 LQRAYKENNENPVALNHLANHFY-FKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKAD  337 (1018)
T ss_pred             HHHHHhhcCCCcHHHHHHHHHHh-hcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccC
Confidence            78887766665555444444332 2466666766666666543221   1112211111          11111111111


Q ss_pred             cCc-cc---hhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcC---CCHHHHHHHHHHHHHhchhHHHHH
Q 013489          148 SGE-VE---GVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMG---KDMVSARGVWERLLKISGAMLEAW  220 (442)
Q Consensus       148 ~~~-~~---~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~---~~~~~ar~i~~~~l~~~~~~~~~w  220 (442)
                      .+. +-   ..+.+...+..++.+..+++..+...+..++.....+.++...+   ...+.|..+..+++...|..++.|
T Consensus       338 ~d~~~l~~~GlgQm~i~~~dle~s~~~fEkv~k~~p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~K~~~~~~~d~~a~  417 (1018)
T KOG2002|consen  338 NDNFVLPLVGLGQMYIKRGDLEESKFCFEKVLKQLPNNYETMKILGCLYAHSAKKQEKRDKASNVLGKVLEQTPVDSEAW  417 (1018)
T ss_pred             CCCccccccchhHHHHHhchHHHHHHHHHHHHHhCcchHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHHHhcccccHHHH
Confidence            111 00   11223333455666777776666655555555444444443331   135788888999998888888999


Q ss_pred             HHHHHHHHhcccHHHHHHHHHHHH
Q 013489          221 QSYISMEIELDHINEARSIYKRCY  244 (442)
Q Consensus       221 ~~~~~~e~~~g~~~~ar~i~~ral  244 (442)
                      +..+.+... ++...+...|.+|+
T Consensus       418 l~laql~e~-~d~~~sL~~~~~A~  440 (1018)
T KOG2002|consen  418 LELAQLLEQ-TDPWASLDAYGNAL  440 (1018)
T ss_pred             HHHHHHHHh-cChHHHHHHHHHHH
Confidence            888887654 44444466666666

>PLN03077 Protein ECB2; Provisional

Probab=97.96  E-value=0.0028  Score=69.13  Aligned_cols=110  Identities=10%  Similarity=0.047  Sum_probs=69.1

Q ss_pred             HHHHHHHhhhhcC-chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhch--hHHHHHHHHHHHHHhcccHHHHHHHHH
Q 013489          165 QRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG--AMLEAWQSYISMEIELDHINEARSIYK  241 (442)
Q Consensus       165 ~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~--~~~~~w~~~~~~e~~~g~~~~ar~i~~  241 (442)
                      ++|+.++...... ..+....+...+......| .++.|..+|+.+...++  .+...+...+++..+.|++++|..+++
T Consensus       571 ~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g-~v~ea~~~f~~M~~~~gi~P~~~~y~~lv~~l~r~G~~~eA~~~~~  649 (857)
T PLN03077        571 SMAVELFNRMVESGVNPDEVTFISLLCACSRSG-MVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFIN  649 (857)
T ss_pred             HHHHHHHHHHHHcCCCCCcccHHHHHHHHhhcC-hHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHhCCCHHHHHHHHH
Confidence            4555555544332 1122223333344445556 78888888888885422  234677888888888888888888888


Q ss_pred             HHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          242 RCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       242 ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                      ..-   +.+  ...+|...+.-.+.||+++--+.+.++.
T Consensus       650 ~m~---~~p--d~~~~~aLl~ac~~~~~~e~~e~~a~~l  683 (857)
T PLN03077        650 KMP---ITP--DPAVWGALLNACRIHRHVELGELAAQHI  683 (857)
T ss_pred             HCC---CCC--CHHHHHHHHHHHHHcCChHHHHHHHHHH
Confidence            752   222  2467888888888889887666555443

>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional

Probab=97.95  E-value=0.0043  Score=66.00  Aligned_cols=262  Identities=11%  Similarity=0.026  Sum_probs=159.4

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDF-PVSSDLWLDYTQYLDKTLKVGNVVRDVY   81 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~-p~~~~lW~~Y~~~l~~~~~~~~~~~~v~   81 (442)
                      +|...|+..+.....  + +...|...+......|....+..++..++... ..+..++...+..+.+. +..+.+..+|
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 EAFALFREMWEDGSD--A-EPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKC-GDIEDARCVF  282 (697)
T ss_pred             HHHHHHHHHHHhCCC--C-ChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHC-CCHHHHHHHH
Confidence            567788888766432  1 33456666776677888899999998887753 44667777778776654 4567789999


Q ss_pred             HHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh-hHHHHHHHHHHHH------------HHHHHHhhcc
Q 013489           82 SRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS-TFEEYLDLFLTRI------------DGLRRRILFS  148 (442)
Q Consensus        82 erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~-~~~~~~~~~~~~~------------~~l~rr~~~~  148 (442)
                      ++..   +.+...|...|..+-+ .+..+++..+|++....+.. +..-|..+...++            ..+.+.-...
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 DGMP---EKTTVAWNSMLAGYAL-HGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPL  358 (697)
T ss_pred             HhCC---CCChhHHHHHHHHHHh-CCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCC
Confidence            8763   3355788888875554 68889999999998765432 2222222221111            0010110000


Q ss_pred             Cc--cchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh--chhHHHHHHHHH
Q 013489          149 GE--VEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI--SGAMLEAWQSYI  224 (442)
Q Consensus       149 ~~--~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~--~~~~~~~w~~~~  224 (442)
                      +.  .+...+.---.+.++.|..++.....   +....|...+.-+...| +.+.|.++|++++..  .|+ ...+...+
T Consensus       359 d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~---~d~~t~n~lI~~y~~~G-~~~~A~~lf~~M~~~g~~Pd-~~T~~~ll  433 (697)
T PLN03081        359 DIVANTALVDLYSKWGRMEDARNVFDRMPR---KNLISWNALIAGYGNHG-RGTKAVEMFERMIAEGVAPN-HVTFLAVL  433 (697)
T ss_pred             CeeehHHHHHHHHHCCCHHHHHHHHHhCCC---CCeeeHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCCC-HHHHHHHH
Confidence            00  00000100001223556666654432   23346777788778888 899999999998876  455 44566777


Q ss_pred             HHHHhcccHHHHHHHHHHHHhc-ccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHh
Q 013489          225 SMEIELDHINEARSIYKRCYSK-RFTGTGSEDICHAWLRFEREYGTLEDFDHSVQK  279 (442)
Q Consensus       225 ~~e~~~g~~~~ar~i~~ral~~-~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~  279 (442)
                      ......|.++.|..+|+.+... .+.+  ....|...+..--..|.+++..+.+++
T Consensus       434 ~a~~~~g~~~~a~~~f~~m~~~~g~~p--~~~~y~~li~~l~r~G~~~eA~~~~~~  487 (697)
T PLN03081        434 SACRYSGLSEQGWEIFQSMSENHRIKP--RAMHYACMIELLGREGLLDEAYAMIRR  487 (697)
T ss_pred             HHHhcCCcHHHHHHHHHHHHHhcCCCC--CccchHhHHHHHHhcCCHHHHHHHHHH
Confidence            7777788999999999988752 1111  123455566666667777666555544

>smart00386 HAT HAT (Half-A-TPR) repeats

Probab=97.93  E-value=1.5e-05  Score=47.75  Aligned_cols=32  Identities=44%  Similarity=0.949  Sum_probs=23.0

Q ss_pred             CChhhHHHHHHHHHhcCCCCHHHHHHHHHHHH
Q 013489           37 GDPGRVQLLYERAITDFPVSSDLWLDYTQYLD   68 (442)
Q Consensus        37 g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~   68 (442)
                      |+++.++.+|+|+|..+|.++.+|+.|+.|+.
T Consensus         1 ~~~~~~r~i~e~~l~~~~~~~~~W~~y~~~e~   32 (33)
T smart00386        1 GDIERARKIYERALEKFPKSVELWLKYAEFEE   32 (33)
T ss_pred             CcHHHHHHHHHHHHHHCCCChHHHHHHHHHHh
Confidence            35667777777777777777777777777653

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

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.93  E-value=0.0028  Score=66.30  Aligned_cols=81  Identities=11%  Similarity=0.084  Sum_probs=61.4

Q ss_pred             HHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHH
Q 013489          165 QRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCY  244 (442)
Q Consensus       165 ~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral  244 (442)
                      ++|+......+...+.........+.....+| ..++|..+|++++..+|+....|+.|....+..|+.+.|...|++|+
T Consensus       137 eeA~~~~~~~l~~~p~~~~~~~~~a~~l~~~g-~~~~A~~~y~~~~~~~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~  215 (694)
T PRK15179        137 EAGRAEIELYFSGGSSSAREILLEAKSWDEIG-QSEQADACFERLSRQHPEFENGYVGWAQSLTRRGALWRARDVLQAGL  215 (694)
T ss_pred             HHHHHHHHHHhhcCCCCHHHHHHHHHHHHHhc-chHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            33333333333334444555666676777788 89999999999999888888999999999999999999999999998


Q ss_pred             hc
Q 013489          245 SK  246 (442)
Q Consensus       245 ~~  246 (442)
                      ..
T Consensus       216 ~~  217 (694)
T PRK15179        216 DA  217 (694)
T ss_pred             Hh
Confidence            74

>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=97.93  E-value=0.01  Score=59.86  Aligned_cols=73  Identities=14%  Similarity=0.155  Sum_probs=51.7

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc----chhhHHHHHHHHHHHcCCCcHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL----KVGNVVRDVYSRATKNCPWVGEL   94 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~----~~~~~~~~v~erAl~~~p~s~~l   94 (442)
                      .......-+.+..+.|..+.|..+|...|..||.+......|...+....    ...+....+|+.--..+|.+..+
T Consensus        37 k~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNPdn~~Yy~~L~~~~g~~~~~~~~~~~~~~~~y~~l~~~yp~s~~~  113 (517)
T PF12569_consen   37 KLAVLEKRAELLLKLGRKEEAEKIYRELIDRNPDNYDYYRGLEEALGLQLQLSDEDVEKLLELYDELAEKYPRSDAP  113 (517)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHhCccccch
Confidence            34445555666677888899999999999999998888888877662211    23455778888777788876433

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 [], [].

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=97.92  E-value=5.7e-05  Score=77.20  Aligned_cols=51  Identities=18%  Similarity=0.221  Sum_probs=39.3

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccC------------CCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          385 TKGFTDECTAFLSNINLKATYEDLRRFFSDV------------GGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       385 ~~~~~~~~~v~v~nl~~~~~~~~l~~~f~~~------------G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +......++|||||||+.+++++|..+|..+            +.|..+.      .++.+|||||+|.
T Consensus       169 ~~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~------~~~~kg~afVeF~  231 (509)
T TIGR01642       169 QQATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVN------INKEKNFAFLEFR  231 (509)
T ss_pred             ccCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEE------ECCCCCEEEEEeC
Confidence            3445667899999999999999999999975            2333333      3456899999995

Members of this subfamily are found in plants, metazoa and fungi.

>smart00777 Mad3_BUB1_I Mad3/BUB1 hoMad3/BUB1 homology region 1

Probab=97.91  E-value=0.00019  Score=57.52  Aligned_cols=108  Identities=17%  Similarity=0.301  Sum_probs=77.8

Q ss_pred             chhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhc---C-ChhhHHHHHHHHHhcCC---------CCHHHHHHHHHHHH
Q 013489            2 CNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS---G-DPGRVQLLYERAITDFP---------VSSDLWLDYTQYLD   68 (442)
Q Consensus         2 ~~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~---g-~~~~~~~lyERal~~~p---------~~~~lW~~Y~~~l~   68 (442)
                      ...|..||..|..... ..+-++.|..||.|....   | .-.....++|||+..+-         .-..+|+.|+.+..
T Consensus         2 ~~~r~~~e~~i~~~~~-~dDPL~~w~~yI~W~~~~~p~g~~~s~L~~lLerc~~~f~~~~~YknD~RyLkiWi~ya~~~~   80 (125)
T smart00777        2 EQQRQAFEQELQDLYE-GDDPLDLWLRYIKWTEENYPQGGKESGLLTLLERCIRYFEDDERYKNDPRYLKIWLKYADNCD   80 (125)
T ss_pred             hHHHHHHHHHHHhccc-CCCChHHHHHHHHHHHHhCCCCCchhhHHHHHHHHHHHhhhhhhhcCCHHHHHHHHHHHHhcC
Confidence            3578999999943221 123478899999998743   3 33467888999998643         33479999998742


Q ss_pred             HhcchhhHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHccCCHHHHHHHHHH
Q 013489           69 KTLKVGNVVRDVYSRATKN--CPWVGELWVRSLLSLERSRASEEEISTVFEK  118 (442)
Q Consensus        69 ~~~~~~~~~~~v~erAl~~--~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~  118 (442)
                          +   ...+|.-..++  .-....+|..|+.++|. .+....+..||+.
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   34677776663  24567899999998987 6888999999875

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.

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=97.91  E-value=0.0074  Score=64.19  Aligned_cols=233  Identities=9%  Similarity=-0.003  Sum_probs=133.1

Q ss_pred             ChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcH------
Q 013489           19 DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVG------   92 (442)
Q Consensus        19 ~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~------   92 (442)
                      ++.+.++|...+......++++.+..+.+.++..+|....+|...+-....... .+.+.-+  +++..++...      
T Consensus        27 ~p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~P~~i~~yy~~G~l~~q~~~-~~~~~lv--~~l~~~~~~~~~~~ve  103 (906)
T PRK14720         27 SLSKFKELDDLIDAYKSENLTDEAKDICEEHLKEHKKSISALYISGILSLSRRP-LNDSNLL--NLIDSFSQNLKWAIVE  103 (906)
T ss_pred             CcchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCcceehHHHHHHHHHhhcc-hhhhhhh--hhhhhcccccchhHHH
Confidence            466889999999988899999999999999999999999998877764433322 2223223  5555554332      


Q ss_pred             -------------HHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHH--HHHHHHHHHHHHHHHhhccCccchhhhH
Q 013489           93 -------------ELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEE--YLDLFLTRIDGLRRRILFSGEVEGVLDY  157 (442)
Q Consensus        93 -------------~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~--~~~~~~~~~~~l~rr~~~~~~~~~~~~~  157 (442)
                                   ......+. +....+..+++..+|++++...+.++..  .+..+..-                 .++
T Consensus       104 ~~~~~i~~~~~~k~Al~~LA~-~Ydk~g~~~ka~~~yer~L~~D~~n~~aLNn~AY~~ae-----------------~dL  165 (906)
T PRK14720        104 HICDKILLYGENKLALRTLAE-AYAKLNENKKLKGVWERLVKADRDNPEIVKKLATSYEE-----------------EDK  165 (906)
T ss_pred             HHHHHHHhhhhhhHHHHHHHH-HHHHcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHH-----------------hhH
Confidence                         33333333 3333577788999999999887654321  11111100                 011


Q ss_pred             HHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh--chhHHHHHHHHHHHHHhcccHHH
Q 013489          158 SLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI--SGAMLEAWQSYISMEIELDHINE  235 (442)
Q Consensus       158 ~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~--~~~~~~~w~~~~~~e~~~g~~~~  235 (442)
                      ......+.+|+..+   +. ......+...|..+......+++-=-.+.++++..  +..-..+|.-........++++.
T Consensus       166 ~KA~~m~~KAV~~~---i~-~kq~~~~~e~W~k~~~~~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~y~~~~~~~~  241 (906)
T PRK14720        166 EKAITYLKKAIYRF---IK-KKQYVGIEEIWSKLVHYNSDDFDFFLRIERKVLGHREFTRLVGLLEDLYEPYKALEDWDE  241 (906)
T ss_pred             HHHHHHHHHHHHHH---Hh-hhcchHHHHHHHHHHhcCcccchHHHHHHHHHHhhhccchhHHHHHHHHHHHhhhhhhhH
Confidence            22223333333221   10 11112233333333333332445444555555554  44445566666666666678889


Q ss_pred             HHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHH
Q 013489          236 ARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQ  278 (442)
Q Consensus       236 ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~  278 (442)
                      +-.+++.+|..  .++.......--..|-..|++-..+++++.
T Consensus       242 ~i~iLK~iL~~--~~~n~~a~~~l~~~y~~kY~~~~~~ee~l~  282 (906)
T PRK14720        242 VIYILKKILEH--DNKNNKAREELIRFYKEKYKDHSLLEDYLK  282 (906)
T ss_pred             HHHHHHHHHhc--CCcchhhHHHHHHHHHHHccCcchHHHHHH
Confidence            99999999973  333333444444455566776555555554

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=97.91  E-value=0.014  Score=55.51  Aligned_cols=219  Identities=13%  Similarity=0.058  Sum_probs=111.8

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHH--------------------
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVY--------------------   81 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~--------------------   81 (442)
                      +.......++.+...|+...+...||.+...+|.+..----|+-++...++ -+.+..+-                    
T Consensus       231 NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~dpy~i~~MD~Ya~LL~~eg~-~e~~~~L~~~Lf~~~~~ta~~wfV~~~~  309 (564)
T KOG1174|consen  231 NEHLMMALGKCLYYNGDYFQAEDIFSSTLCANPDNVEAMDLYAVLLGQEGG-CEQDSALMDYLFAKVKYTASHWFVHAQL  309 (564)
T ss_pred             cHHHHHHHhhhhhhhcCchHHHHHHHHHhhCChhhhhhHHHHHHHHHhccC-HhhHHHHHHHHHhhhhcchhhhhhhhhh
Confidence            667788888888888888888888888888888877766667665554332 22233333                    


Q ss_pred             --------------HHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhc
Q 013489           82 --------------SRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILF  147 (442)
Q Consensus        82 --------------erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~  147 (442)
                                    +++++.-|.+..-++.--. +-...+..+++--.|..|...-|.....|..++..|+         
T Consensus       310 l~~~K~~~rAL~~~eK~I~~~~r~~~alilKG~-lL~~~~R~~~A~IaFR~Aq~Lap~rL~~Y~GL~hsYL---------  379 (564)
T KOG1174|consen  310 LYDEKKFERALNFVEKCIDSEPRNHEALILKGR-LLIALERHTQAVIAFRTAQMLAPYRLEIYRGLFHSYL---------  379 (564)
T ss_pred             hhhhhhHHHHHHHHHHHhccCcccchHHHhccH-HHHhccchHHHHHHHHHHHhcchhhHHHHHHHHHHHH---------
Confidence                          3333333333222222111 1111233333333344443333332333333333332         


Q ss_pred             cCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHH
Q 013489          148 SGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISME  227 (442)
Q Consensus       148 ~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e  227 (442)
                              -...++++.-.|...+. .+......+.++-.-.-++.-.+  -++|.++++++|+..|.+...-...+++.
T Consensus       380 --------A~~~~kEA~~~An~~~~-~~~~sA~~LtL~g~~V~~~dp~~--rEKAKkf~ek~L~~~P~Y~~AV~~~AEL~  448 (564)
T KOG1174|consen  380 --------AQKRFKEANALANWTIR-LFQNSARSLTLFGTLVLFPDPRM--REKAKKFAEKSLKINPIYTPAVNLIAELC  448 (564)
T ss_pred             --------hhchHHHHHHHHHHHHH-HhhcchhhhhhhcceeeccCchh--HHHHHHHHHhhhccCCccHHHHHHHHHHH
Confidence                    11122222222222211 11111111111111111111122  46899999999999999888777778877


Q ss_pred             HhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHH
Q 013489          228 IELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFERE  266 (442)
Q Consensus       228 ~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~  266 (442)
                      ...|....+.+++++++.. ++ |.  .+.....+|-.-
T Consensus       449 ~~Eg~~~D~i~LLe~~L~~-~~-D~--~LH~~Lgd~~~A  483 (564)
T KOG1174|consen  449 QVEGPTKDIIKLLEKHLII-FP-DV--NLHNHLGDIMRA  483 (564)
T ss_pred             HhhCccchHHHHHHHHHhh-cc-cc--HHHHHHHHHHHH
Confidence            7778888888999998862 22 22  234444455444

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.90  E-value=0.0002  Score=59.79  Aligned_cols=93  Identities=9%  Similarity=-0.073  Sum_probs=80.1

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ++...|..+|...|.    +...|...+......|+++.+...|++++..+|.++..|......+.. .+..+.+...|.
T Consensus        42 ~A~~~~~~al~~~P~----~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~~~~a~~~lg~~l~~-~g~~~eAi~~~~  116 (144)
T PRK15359         42 RAVIDFSWLVMAQPW----SWRAHIALAGTWMMLKEYTTAINFYGHALMLDASHPEPVYQTGVCLKM-MGEPGLAREAFQ  116 (144)
T ss_pred             HHHHHHHHHHHcCCC----cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHH-cCCHHHHHHHHH
Confidence            356678888877776    888999999999999999999999999999999999999999987764 456678999999


Q ss_pred             HHHHcCCCcHHHHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLL  100 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~  100 (442)
                      +|+...|.....|.....
T Consensus       117 ~Al~~~p~~~~~~~~~~~  134 (144)
T PRK15359        117 TAIKMSYADASWSEIRQN  134 (144)
T ss_pred             HHHHhCCCChHHHHHHHH
Confidence            999999999888866443

>KOG1173 consensus Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=97.90  E-value=0.0063  Score=59.93  Aligned_cols=227  Identities=11%  Similarity=0.099  Sum_probs=125.6

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~  101 (442)
                      +.....-+|......|+..+...+=-+.+...|..+--|..-..|..--+ ....++.-|.+|+..-|.-+.-|+.|...
T Consensus       277 h~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~yP~~a~sW~aVg~YYl~i~-k~seARry~SKat~lD~~fgpaWl~fghs  355 (611)
T KOG1173|consen  277 HLPCLPLHIACLYELGKSNKLFLLSHKLVDLYPSKALSWFAVGCYYLMIG-KYSEARRYFSKATTLDPTFGPAWLAFGHS  355 (611)
T ss_pred             CcchHHHHHHHHHHhcccchHHHHHHHHHHhCCCCCcchhhHHHHHHHhc-CcHHHHHHHHHHhhcCccccHHHHHHhHH
Confidence            44444444444445555544444445556666776667776666555332 33456777777777666666677776654


Q ss_pred             HHHccCCHHHHHHHHHHHHhCChh--hHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCch
Q 013489          102 LERSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTD  179 (442)
Q Consensus       102 le~~~~~~~~~~~i~~~al~~~~~--~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~  179 (442)
                      +-. .+..+.+...|.+|-+.-+.  ....|+.+.-.+                       ...++.|..++..++.-.|
T Consensus       356 fa~-e~EhdQAmaaY~tAarl~~G~hlP~LYlgmey~~-----------------------t~n~kLAe~Ff~~A~ai~P  411 (611)
T KOG1173|consen  356 FAG-EGEHDQAMAAYFTAARLMPGCHLPSLYLGMEYMR-----------------------TNNLKLAEKFFKQALAIAP  411 (611)
T ss_pred             hhh-cchHHHHHHHHHHHHHhccCCcchHHHHHHHHHH-----------------------hccHHHHHHHHHHHHhcCC
Confidence            432 23445555556555543222  122333222111                       1334555566655554444


Q ss_pred             hhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhch-------hHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCC
Q 013489          180 GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG-------AMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTG  252 (442)
Q Consensus       180 ~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~-------~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~  252 (442)
                      ..+-+....+-+-...+ .+..|..+|+.++..-+       ....+|.......++.+.++.|...|++||.. .+.+ 
T Consensus       412 ~Dplv~~Elgvvay~~~-~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l-~~k~-  488 (611)
T KOG1173|consen  412 SDPLVLHELGVVAYTYE-EYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKALLL-SPKD-  488 (611)
T ss_pred             CcchhhhhhhheeehHh-hhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHHHHc-CCCc-
Confidence            33323333333334445 78899999999994421       23457888889999999999999999999973 2333 


Q ss_pred             hHHHHHHHHHHHHHhCCHhhHHHHH
Q 013489          253 SEDICHAWLRFEREYGTLEDFDHSV  277 (442)
Q Consensus       253 ~~~i~~~~~~fE~~~G~~~~~~~~~  277 (442)
                      + ..+..-.-.-...|+++..-+.+
T Consensus       489 ~-~~~asig~iy~llgnld~Aid~f  512 (611)
T KOG1173|consen  489 A-STHASIGYIYHLLGNLDKAIDHF  512 (611)
T ss_pred             h-hHHHHHHHHHHHhcChHHHHHHH
Confidence            2 23322222223457765433333

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.88  E-value=1.1e-05  Score=71.98  Aligned_cols=53  Identities=19%  Similarity=0.451  Sum_probs=49.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+...|||||+.+.++.+++..+|..||.|..+.++.|+.+|.++||+||+|.
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~  151 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFS  151 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecc
Confidence            44569999999999999999999999999999999999999999999999996

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=97.88  E-value=2.9e-05  Score=74.92  Aligned_cols=55  Identities=20%  Similarity=0.186  Sum_probs=46.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       387 ~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ......+|||+|||++++...|+++|..||.|...+|......++..+||||+|.
T Consensus       284 ~~~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~  338 (419)
T KOG0116|consen  284 PRADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFE  338 (419)
T ss_pred             eeecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEe
Confidence            3444567999999999999999999999999999998775445666699999984

>PRK14574 hmsH outer membrane protein; Provisional

Probab=97.88  E-value=0.0026  Score=67.81  Aligned_cols=183  Identities=13%  Similarity=0.063  Sum_probs=120.6

Q ss_pred             HHHhcCChhhHHHHHHHHHhcCCCCH-HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHH
Q 013489           32 YEQSSGDPGRVQLLYERAITDFPVSS-DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEE  110 (442)
Q Consensus        32 ~e~~~g~~~~~~~lyERal~~~p~~~-~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~  110 (442)
                      ..-..|++..+...|+.++..+|.+. .+. +++.++... +..+.+...+++++...|.....-...+. +....++.+
T Consensus        43 i~~r~Gd~~~Al~~L~qaL~~~P~~~~av~-dll~l~~~~-G~~~~A~~~~eka~~p~n~~~~~llalA~-ly~~~gdyd  119 (822)
T PRK14574         43 IRARAGDTAPVLDYLQEESKAGPLQSGQVD-DWLQIAGWA-GRDQEVIDVYERYQSSMNISSRGLASAAR-AYRNEKRWD  119 (822)
T ss_pred             HHHhCCCHHHHHHHHHHHHhhCccchhhHH-HHHHHHHHc-CCcHHHHHHHHHhccCCCCCHHHHHHHHH-HHHHcCCHH
Confidence            34568999999999999999999995 444 777766544 44567999999999433433333332232 334468889


Q ss_pred             HHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHH
Q 013489          111 EISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAH  190 (442)
Q Consensus       111 ~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~  190 (442)
                      .+..+|++++...+.+...+..+...+.                 +.    ...++|+..+.......+. ...++..+.
T Consensus       120 ~Aiely~kaL~~dP~n~~~l~gLa~~y~-----------------~~----~q~~eAl~~l~~l~~~dp~-~~~~l~lay  177 (822)
T PRK14574        120 QALALWQSSLKKDPTNPDLISGMIMTQA-----------------DA----GRGGVVLKQATELAERDPT-VQNYMTLSY  177 (822)
T ss_pred             HHHHHHHHHHhhCCCCHHHHHHHHHHHh-----------------hc----CCHHHHHHHHHHhcccCcc-hHHHHHHHH
Confidence            9999999999988876555543332221                 11    2234444444444333332 223344455


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHH
Q 013489          191 LEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIY  240 (442)
Q Consensus       191 ~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~  240 (442)
                      +....+ +...|.+.|++++..+|++.+++..|+......|-...|-.+.
T Consensus       178 L~~~~~-~~~~AL~~~ekll~~~P~n~e~~~~~~~~l~~~~~~~~a~~l~  226 (822)
T PRK14574        178 LNRATD-RNYDALQASSEAVRLAPTSEEVLKNHLEILQRNRIVEPALRLA  226 (822)
T ss_pred             HHHhcc-hHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCcHHHHHHH
Confidence            554455 5556999999999999999999999999888887655444443

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=97.87  E-value=1.7e-05  Score=76.28  Aligned_cols=46  Identities=22%  Similarity=0.329  Sum_probs=43.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .|||.||+..++..+|.++|+.||.|.+|+++.+ ..| ++|| ||+|.
T Consensus        78 ~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~-~~g-~kg~-FV~f~  123 (369)
T KOG0123|consen   78 LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATD-ENG-SKGY-FVQFE  123 (369)
T ss_pred             eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEc-CCC-ceee-EEEeC
Confidence            3999999999999999999999999999999999 577 9999 99996

>PLN03077 Protein ECB2; Provisional

Probab=97.87  E-value=0.0038  Score=68.14  Aligned_cols=113  Identities=5%  Similarity=-0.125  Sum_probs=71.1

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      .+++.|+..++....   .+...|...++...+.|+++.|..+|++...   .+...|...+.-+... +..+.+..+|.
T Consensus       407 ~a~~l~~~~~~~g~~---~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~---~d~vs~~~mi~~~~~~-g~~~eA~~lf~  479 (857)
T PLN03077        407 VGVKLHELAERKGLI---SYVVVANALIEMYSKCKCIDKALEVFHNIPE---KDVISWTSIIAGLRLN-NRCFEALIFFR  479 (857)
T ss_pred             HHHHHHHHHHHhCCC---cchHHHHHHHHHHHHcCCHHHHHHHHHhCCC---CCeeeHHHHHHHHHHC-CCHHHHHHHHH
Confidence            467778888766432   1455788888888888999999999988654   3456787777655543 34466788888


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCC
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA  123 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~  123 (442)
                      +.+..++-+...+...+..+-+ .+..+..+.++..++..+
T Consensus       480 ~m~~~~~pd~~t~~~lL~a~~~-~g~l~~~~~i~~~~~~~g  519 (857)
T PLN03077        480 QMLLTLKPNSVTLIAALSACAR-IGALMCGKEIHAHVLRTG  519 (857)
T ss_pred             HHHhCCCCCHhHHHHHHHHHhh-hchHHHhHHHHHHHHHhC
Confidence            8877553333444444443332 344455555555555433

>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals

Probab=97.87  E-value=0.0022  Score=62.08  Aligned_cols=203  Identities=9%  Similarity=-0.088  Sum_probs=122.8

Q ss_pred             ChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCH---HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHH
Q 013489           19 DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS---DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELW   95 (442)
Q Consensus        19 ~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~---~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW   95 (442)
                      ||+..-.|...+.+....|++..+...|.++....|.+.   ..+.-.+.... ..++.+.+..++++++...|.+...|
T Consensus         2 dp~~~~a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~-~~g~~~~A~~~~~~~l~~~P~~~~a~   80 (355)
T cd05804           2 DPDFALGHAAAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEALSAW-IAGDLPKALALLEQLLDDYPRDLLAL   80 (355)
T ss_pred             CCccHHHHHHHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHH-HcCCHHHHHHHHHHHHHHCCCcHHHH
Confidence            344555666666666677888888888888888777553   33332222222 33456778999999999999888776


Q ss_pred             HH---HHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHh
Q 013489           96 VR---SLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLS  172 (442)
Q Consensus        96 ~~---y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~  172 (442)
                      ..   +.. +....+....+..++.......+..+.....+  ..   +.                ...+.+++|...+.
T Consensus        81 ~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~--a~---~~----------------~~~G~~~~A~~~~~  138 (355)
T cd05804          81 KLHLGAFG-LGDFSGMRDHVARVLPLWAPENPDYWYLLGML--AF---GL----------------EEAGQYDRAEEAAR  138 (355)
T ss_pred             HHhHHHHH-hcccccCchhHHHHHhccCcCCCCcHHHHHHH--HH---HH----------------HHcCCHHHHHHHHH
Confidence            62   222 11112333444444443222222211111000  00   00                00122333444444


Q ss_pred             hhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH----HHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          173 EQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM----LEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       173 ~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~----~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ..+...+....++..++.+....| +++.|..++++++...|..    ...|..++.+....|+++.|..+|++++.
T Consensus       139 ~al~~~p~~~~~~~~la~i~~~~g-~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~  214 (355)
T cd05804         139 RALELNPDDAWAVHAVAHVLEMQG-RFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIA  214 (355)
T ss_pred             HHHhhCCCCcHHHHHHHHHHHHcC-CHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhc
Confidence            443334444557777888888888 8999999999999885432    24677888899999999999999999874

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.

>smart00361 RRM_1 RNA recognition motif

Probab=97.86  E-value=2.2e-05  Score=56.60  Aligned_cols=37  Identities=30%  Similarity=0.299  Sum_probs=32.2

Q ss_pred             HHHHHHHhc----cCCCeeEEE-EeeCCCC--CCCcceEEEEee
Q 013489          405 YEDLRRFFS----DVGGVSSIR-ILHDKFT--GKSRVVQSDIYT  441 (442)
Q Consensus       405 ~~~l~~~f~----~~G~i~~~~-~~~~~~~--g~~~g~~fv~f~  441 (442)
                      +++|+++|+    .||.|.+|. ++.++.+  |+++|||||+|.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~   45 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFE   45 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEEC
Confidence            578899998    999999995 7777666  999999999995

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=97.83  E-value=0.019  Score=57.62  Aligned_cols=233  Identities=16%  Similarity=0.123  Sum_probs=131.7

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~  101 (442)
                      +.-.|.-|.-.-+...+++.++..|.+||...|+|..+|.+... +..+.++.+-...+-.+-++..|....-|..|+..
T Consensus        74 S~vCwHv~gl~~R~dK~Y~eaiKcy~nAl~~~~dN~qilrDlsl-LQ~QmRd~~~~~~tr~~LLql~~~~ra~w~~~Avs  152 (700)
T KOG1156|consen   74 SHVCWHVLGLLQRSDKKYDEAIKCYRNALKIEKDNLQILRDLSL-LQIQMRDYEGYLETRNQLLQLRPSQRASWIGFAVA  152 (700)
T ss_pred             cchhHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcHHHHHHHHH-HHHHHHhhhhHHHHHHHHHHhhhhhHHHHHHHHHH
Confidence            44478888887777778888888888888888888888888764 33344454545566666677778777888888763


Q ss_pred             HHHccCCHHHHHHH---HHHHHhCChhhH-HHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcC
Q 013489          102 LERSRASEEEISTV---FEKSLLCAFSTF-EEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKN  177 (442)
Q Consensus       102 le~~~~~~~~~~~i---~~~al~~~~~~~-~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~  177 (442)
                      .-. .++...+..+   |++....+++.. -......+.....+                 .-.+.++.|.+.+...-..
T Consensus       153 ~~L-~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~-----------------~E~g~~q~ale~L~~~e~~  214 (700)
T KOG1156|consen  153 QHL-LGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQIL-----------------IEAGSLQKALEHLLDNEKQ  214 (700)
T ss_pred             HHH-HHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHH-----------------HHcccHHHHHHHHHhhhhH
Confidence            332 3444444433   333332222211 11111111111111                 0012244454444221111


Q ss_pred             chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHH-hcccHHHHHHHHHHHHhc----------
Q 013489          178 TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEI-ELDHINEARSIYKRCYSK----------  246 (442)
Q Consensus       178 ~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~-~~g~~~~ar~i~~ral~~----------  246 (442)
                      .-..+.+-..-+.++..++ .++.|..+|...+..+|++...+..+....- ..+..+....+|...-+.          
T Consensus       215 i~Dkla~~e~ka~l~~kl~-~lEeA~~~y~~Ll~rnPdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~y~r~e~p~Rl  293 (700)
T KOG1156|consen  215 IVDKLAFEETKADLLMKLG-QLEEAVKVYRRLLERNPDNLDYYEGLEKALGKIKDMLEALKALYAILSEKYPRHECPRRL  293 (700)
T ss_pred             HHHHHHHhhhHHHHHHHHh-hHHhHHHHHHHHHhhCchhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhcCcccccchhc
Confidence            1112223444577888889 8999999999999999998875555544442 223444454666665432          


Q ss_pred             ---ccCCCChHHHHHHHHHHHHHhCCHhhHH
Q 013489          247 ---RFTGTGSEDICHAWLRFEREYGTLEDFD  274 (442)
Q Consensus       247 ---~~~~~~~~~i~~~~~~fE~~~G~~~~~~  274 (442)
                         .+..+.-..+...|+.-+-..|-+.-+.
T Consensus       294 plsvl~~eel~~~vdkyL~~~l~Kg~p~vf~  324 (700)
T KOG1156|consen  294 PLSVLNGEELKEIVDKYLRPLLSKGVPSVFK  324 (700)
T ss_pred             cHHHhCcchhHHHHHHHHHHHhhcCCCchhh
Confidence               0111222356667777777776554433

>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]

Probab=97.81  E-value=0.025  Score=52.18  Aligned_cols=219  Identities=9%  Similarity=0.100  Sum_probs=125.1

Q ss_pred             CChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCc---HHHHHHHH--HHHHHccCCHHH
Q 013489           37 GDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV---GELWVRSL--LSLERSRASEEE  111 (442)
Q Consensus        37 g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s---~~lW~~y~--~~le~~~~~~~~  111 (442)
                      ..++++..+|-..+...|...++-+...++...- +..+.+..|..--+. -|.-   ..+...+-  +-+ ...|-.+.
T Consensus        49 ~Q~dKAvdlF~e~l~~d~~t~e~~ltLGnLfRsR-GEvDRAIRiHQ~L~~-spdlT~~qr~lAl~qL~~Dy-m~aGl~DR  125 (389)
T COG2956          49 NQPDKAVDLFLEMLQEDPETFEAHLTLGNLFRSR-GEVDRAIRIHQTLLE-SPDLTFEQRLLALQQLGRDY-MAAGLLDR  125 (389)
T ss_pred             cCcchHHHHHHHHHhcCchhhHHHHHHHHHHHhc-chHHHHHHHHHHHhc-CCCCchHHHHHHHHHHHHHH-HHhhhhhH
Confidence            3577888888888888888888888777765543 344555555443333 2321   11111111  100 01344566


Q ss_pred             HHHHHHHHHhCChh---hHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHH
Q 013489          112 ISTVFEKSLLCAFS---TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYW  188 (442)
Q Consensus       112 ~~~i~~~al~~~~~---~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~  188 (442)
                      ++.+|......+--   .....+.+|..-                 .||   ..+++-|..+....  ..+..+.|-.+|
T Consensus       126 AE~~f~~L~de~efa~~AlqqLl~IYQ~t-----------------reW---~KAId~A~~L~k~~--~q~~~~eIAqfy  183 (389)
T COG2956         126 AEDIFNQLVDEGEFAEGALQQLLNIYQAT-----------------REW---EKAIDVAERLVKLG--GQTYRVEIAQFY  183 (389)
T ss_pred             HHHHHHHHhcchhhhHHHHHHHHHHHHHh-----------------hHH---HHHHHHHHHHHHcC--CccchhHHHHHH
Confidence            77777765542211   111122222110                 122   23333343333211  112233343333


Q ss_pred             ---HHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHH
Q 013489          189 ---AHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFER  265 (442)
Q Consensus       189 ---a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~  265 (442)
                         |+-..... ++++|+.++.++++.+|+.+..=+...+++...|+++.|...+++++..  ..+....|......--+
T Consensus       184 CELAq~~~~~~-~~d~A~~~l~kAlqa~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQ--n~~yl~evl~~L~~~Y~  260 (389)
T COG2956         184 CELAQQALASS-DVDRARELLKKALQADKKCVRASIILGRVELAKGDYQKAVEALERVLEQ--NPEYLSEVLEMLYECYA  260 (389)
T ss_pred             HHHHHHHhhhh-hHHHHHHHHHHHHhhCccceehhhhhhHHHHhccchHHHHHHHHHHHHh--ChHHHHHHHHHHHHHHH
Confidence               43333334 7899999999999999999888888899999999999999999999874  33444455555555556


Q ss_pred             HhCCHhhHHHHHHhhchh
Q 013489          266 EYGTLEDFDHSVQKVTPR  283 (442)
Q Consensus       266 ~~G~~~~~~~~~~~~~~~  283 (442)
                      ..|.+++....+.+++..
T Consensus       261 ~lg~~~~~~~fL~~~~~~  278 (389)
T COG2956         261 QLGKPAEGLNFLRRAMET  278 (389)
T ss_pred             HhCCHHHHHHHHHHHHHc
Confidence            668888777666665443

>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]

Probab=97.80  E-value=0.028  Score=51.83  Aligned_cols=239  Identities=15%  Similarity=0.131  Sum_probs=139.1

Q ss_pred             hHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCH--HHHHHH--H-HHHHHhcchhhHHHH
Q 013489            5 RAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS--DLWLDY--T-QYLDKTLKVGNVVRD   79 (442)
Q Consensus         5 r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~--~lW~~Y--~-~~l~~~~~~~~~~~~   79 (442)
                      -..|=..+...    ++.++.-....++-...|..++++.+.+-.+..-....  .+-.-+  . +|+.  .+..+.+..
T Consensus        55 vdlF~e~l~~d----~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~--aGl~DRAE~  128 (389)
T COG2956          55 VDLFLEMLQED----PETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMA--AGLLDRAED  128 (389)
T ss_pred             HHHHHHHHhcC----chhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHH--hhhhhHHHH
Confidence            33444444433    44788888888888889999999999887765422222  111110  0 1111  112233444


Q ss_pred             HHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHH
Q 013489           80 VYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSL  159 (442)
Q Consensus        80 v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~  159 (442)
                      +|..-+..--.-...-...+. ++.....-+.+-.+-++..+.+...+..-+..  .||+...              -..
T Consensus       129 ~f~~L~de~efa~~AlqqLl~-IYQ~treW~KAId~A~~L~k~~~q~~~~eIAq--fyCELAq--------------~~~  191 (389)
T COG2956         129 IFNQLVDEGEFAEGALQQLLN-IYQATREWEKAIDVAERLVKLGGQTYRVEIAQ--FYCELAQ--------------QAL  191 (389)
T ss_pred             HHHHHhcchhhhHHHHHHHHH-HHHHhhHHHHHHHHHHHHHHcCCccchhHHHH--HHHHHHH--------------HHh
Confidence            444433311111122222222 33333444455555555444444432222222  2332221              112


Q ss_pred             HHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHH-HHHHHHHHHHhcccHHHHHH
Q 013489          160 IRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLE-AWQSYISMEIELDHINEARS  238 (442)
Q Consensus       160 ~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~-~w~~~~~~e~~~g~~~~ar~  238 (442)
                      ....+++|...+.+++..++.+++.-+...+++...| ++..|.+.|+++++.+|..+. +-..........|+.+....
T Consensus       192 ~~~~~d~A~~~l~kAlqa~~~cvRAsi~lG~v~~~~g-~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~  270 (389)
T COG2956         192 ASSDVDRARELLKKALQADKKCVRASIILGRVELAKG-DYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLN  270 (389)
T ss_pred             hhhhHHHHHHHHHHHHhhCccceehhhhhhHHHHhcc-chHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence            3355666777777777777888888888999999999 999999999999999999875 56666667778899999999


Q ss_pred             HHHHHHhcccCCCChHHHHHHHHHHHHHhCCH
Q 013489          239 IYKRCYSKRFTGTGSEDICHAWLRFEREYGTL  270 (442)
Q Consensus       239 i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~  270 (442)
                      .+.+++.. .+...++  ..-+--.|...|..
T Consensus       271 fL~~~~~~-~~g~~~~--l~l~~lie~~~G~~  299 (389)
T COG2956         271 FLRRAMET-NTGADAE--LMLADLIELQEGID  299 (389)
T ss_pred             HHHHHHHc-cCCccHH--HHHHHHHHHhhChH
Confidence            99999974 3433343  33333445555653

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=97.80  E-value=3.3e-05  Score=72.80  Aligned_cols=54  Identities=20%  Similarity=0.247  Sum_probs=44.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEeeCC-CCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVG-GVSSIRILHDK-FTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~-~~g~~~g~~fv~f~  441 (442)
                      +.++|++||||+|.+.+++++.+.|++.+ .|.+|-+..++ .+.|+||||||+|-
T Consensus       161 Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe  216 (506)
T KOG0117|consen  161 SVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYE  216 (506)
T ss_pred             eeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEee
Confidence            45678999999999999999999999888 45666665543 35789999999984

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=97.80  E-value=3.3e-05  Score=77.94  Aligned_cols=50  Identities=24%  Similarity=0.303  Sum_probs=42.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCC--eeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGG--VSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~--i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...+|||+|||.++++++|+++|+.||.  |..+++... .++ .+|||||+|.
T Consensus       393 ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~-~~~-~~~~gfVeF~  444 (481)
T TIGR01649       393 PSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPK-DNE-RSKMGLLEWE  444 (481)
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecC-CCC-cceeEEEEcC
Confidence            3469999999999999999999999998  888887654 344 5899999995

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).

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.79  E-value=0.0017  Score=67.93  Aligned_cols=97  Identities=9%  Similarity=-0.001  Sum_probs=54.2

Q ss_pred             HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHH
Q 013489           23 FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSL  102 (442)
Q Consensus        23 ~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~l  102 (442)
                      .+.....+..+...|..+.+..++++++...|.+...+..|+.-|..... .+.+...+++++..-|.+.......+..|
T Consensus        86 ~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~Pd~~~a~~~~a~~L~~~~~-~eeA~~~~~~~l~~~p~~~~~~~~~a~~l  164 (694)
T PRK15179         86 ELFQVLVARALEAAHRSDEGLAVWRGIHQRFPDSSEAFILMLRGVKRQQG-IEAGRAEIELYFSGGSSSAREILLEAKSW  164 (694)
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhcc-HHHHHHHHHHHhhcCCCCHHHHHHHHHHH
Confidence            34444455555555666666666666666666666666666665554332 34456666666666666655555555434


Q ss_pred             HHccCCHHHHHHHHHHHHh
Q 013489          103 ERSRASEEEISTVFEKSLL  121 (442)
Q Consensus       103 e~~~~~~~~~~~i~~~al~  121 (442)
                      .. .+..+++..+|++++.
T Consensus       165 ~~-~g~~~~A~~~y~~~~~  182 (694)
T PRK15179        165 DE-IGQSEQADACFERLSR  182 (694)
T ss_pred             HH-hcchHHHHHHHHHHHh
Confidence            33 4555556666666554

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.79  E-value=3.4e-05  Score=70.45  Aligned_cols=49  Identities=27%  Similarity=0.323  Sum_probs=43.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       387 ~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+....++|||+|-..+++.+|+++|.+||.|.+++++..      +|+|||+|+
T Consensus       224 eD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ft  272 (377)
T KOG0153|consen  224 EDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFT  272 (377)
T ss_pred             cccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeeh
Confidence            3455669999999999999999999999999999998876      479999996

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=97.78  E-value=3.5e-05  Score=72.25  Aligned_cols=50  Identities=26%  Similarity=0.435  Sum_probs=46.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhc-cCCCeeEEEEeeCCCCCCCcceEEEEeeC
Q 013489          392 CTAFLSNINLKATYEDLRRFFS-DVGGVSSIRILHDKFTGKSRVVQSDIYTL  442 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~-~~G~i~~~~~~~~~~~g~~~g~~fv~f~~  442 (442)
                      +.|||.|+|+++.+.+|+++|. ..|.|.-|.+..| .+||+||+|.|+|++
T Consensus        45 R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~   95 (608)
T KOG4212|consen   45 RSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKD   95 (608)
T ss_pred             ceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeC
Confidence            4699999999999999999998 6899999999999 799999999999974

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.75  E-value=1.5e-05  Score=79.23  Aligned_cols=51  Identities=22%  Similarity=0.327  Sum_probs=46.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.|.|.|||+..+-.+++.+|..||.|.+|+|+.-...+.+||||||+|-
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~  663 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFL  663 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeecc
Confidence            358999999999999999999999999999999987566778999999984

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=97.71  E-value=9.2e-05  Score=71.71  Aligned_cols=54  Identities=17%  Similarity=0.206  Sum_probs=48.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..-.+++||++|+..+...+|+.+|+.||.|+-..+|.+..+.-.|+||||+..
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMS  455 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMS  455 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEec
Confidence            455679999999999999999999999999999999998778888999999864

>PF08311 Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro: IPR013212 Proteins containing this domain are checkpoint proteins involved in cell division

Probab=97.71  E-value=0.00071  Score=54.80  Aligned_cols=79  Identities=15%  Similarity=0.277  Sum_probs=59.4

Q ss_pred             HHHHHHHHHHHHHhh--hhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh--chhHHHHHHHHHHHHHhcccHH
Q 013489          159 LIRETFQRASDYLSE--QMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI--SGAMLEAWQSYISMEIELDHIN  234 (442)
Q Consensus       159 ~~r~~~~~a~~~l~~--~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~--~~~~~~~w~~~~~~e~~~g~~~  234 (442)
                      .+..++++|+..+..  .+.+....+++|+.||++.       +.++.+|.-+...  .-..+.+|..|+.+....|++.
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            344667777776643  3445566788999998542       2889999999887  3455779999999999999999


Q ss_pred             HHHHHHHHHH
Q 013489          235 EARSIYKRCY  244 (442)
Q Consensus       235 ~ar~i~~ral  244 (442)
                      +|..||+.+|
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.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=97.71  E-value=6.7e-05  Score=75.92  Aligned_cols=43  Identities=19%  Similarity=0.247  Sum_probs=38.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccC--CCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDV--GGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~--G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..+|||+|||.++++++|+++|+.|  |.|.+|.++        +|||||+|.
T Consensus       233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~  277 (578)
T TIGR01648       233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFE  277 (578)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeC
Confidence            4589999999999999999999999  999998765        369999995

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=97.67  E-value=1.3e-05  Score=77.49  Aligned_cols=59  Identities=25%  Similarity=0.328  Sum_probs=54.1

Q ss_pred             CCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          383 GRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       383 ~~~~~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....+.++.+|||+-.|+..++.-+|.+||+.+|.|.+|+++.|+.+++++|.|||+|.
T Consensus       171 ~l~~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~  229 (549)
T KOG0147|consen  171 ILSPEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFC  229 (549)
T ss_pred             cCCchHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEe
Confidence            34445678899999999999999999999999999999999999999999999999994

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=97.67  E-value=0.00087  Score=55.00  Aligned_cols=81  Identities=9%  Similarity=-0.034  Sum_probs=65.7

Q ss_pred             HHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHH
Q 013489          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRC  243 (442)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ra  243 (442)
                      ++.|...+.......+....+|...+.+....+ +++.|..+|++++..+|+...+|.....+....|+.+.|...|+++
T Consensus        33 ~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~~-~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~a  111 (135)
T TIGR02552        33 YDEALKLFQLLAAYDPYNSRYWLGLAACCQMLK-EYEEAIDAYALAAALDPDDPRPYFHAAECLLALGEPESALKALDLA  111 (135)
T ss_pred             HHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHH-HHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            344444444443334556678888899888888 8999999999999999999999999999888899999999999999


Q ss_pred             Hh
Q 013489          244 YS  245 (442)
Q Consensus       244 l~  245 (442)
                      +.
T Consensus       112 l~  113 (135)
T TIGR02552       112 IE  113 (135)
T ss_pred             HH
Confidence            97

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=97.63  E-value=9.1e-05  Score=44.18  Aligned_cols=31  Identities=32%  Similarity=0.527  Sum_probs=28.2

Q ss_pred             CHHHHHHHHHHHHHhchhHHHHHHHHHHHHH
Q 013489          198 DMVSARGVWERLLKISGAMLEAWQSYISMEI  228 (442)
Q Consensus       198 ~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~  228 (442)
                      +++.||.+|++++..+|.+..+|+.|++|+.
T Consensus         2 ~~~~~r~i~e~~l~~~~~~~~~W~~y~~~e~   32 (33)
T smart00386        2 DIERARKIYERALEKFPKSVELWLKYAEFEE   32 (33)
T ss_pred             cHHHHHHHHHHHHHHCCCChHHHHHHHHHHh
Confidence            6889999999999999998999999999985

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

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.62  E-value=0.00036  Score=49.25  Aligned_cols=58  Identities=24%  Similarity=0.239  Sum_probs=51.9

Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          188 WAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       188 ~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      .+......| +++.|..+|+.++..+|++..+|..+..+....|+++.|...|++++..
T Consensus         3 ~a~~~~~~g-~~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen    3 LARALYQQG-DYDEAIAAFEQALKQDPDNPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHHCT-HHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHcC-CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            355667778 9999999999999999999999999999999999999999999999973

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=97.62  E-value=9.8e-05  Score=64.66  Aligned_cols=56  Identities=20%  Similarity=0.242  Sum_probs=50.9

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          386 KGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       386 ~~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +-+.+...||.|.|..+++.+.|...|..|-.-...++++|+.||+++|||||.|.
T Consensus       185 ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~  240 (290)
T KOG0226|consen  185 EWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFR  240 (290)
T ss_pred             cCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeec
Confidence            33456789999999999999999999999988888899999999999999999995

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=97.58  E-value=0.00014  Score=62.98  Aligned_cols=47  Identities=28%  Similarity=0.418  Sum_probs=41.7

Q ss_pred             ceEEEcCCCCCCCHHHHHH----HhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRR----FFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~----~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .|+||.||+..+..++|+.    +|++||.|.+|...   .|++.||-|||.|.
T Consensus        10 ~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~---kt~KmRGQA~VvFk   60 (221)
T KOG4206|consen   10 GTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF---KTPKMRGQAFVVFK   60 (221)
T ss_pred             ceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec---CCCCccCceEEEec
Confidence            4999999999999999888    99999999887543   37899999999996

>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=97.57  E-value=0.0018  Score=48.25  Aligned_cols=97  Identities=18%  Similarity=0.107  Sum_probs=76.1

Q ss_pred             HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHH
Q 013489           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER  104 (442)
Q Consensus        25 ~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~  104 (442)
                      .|...+......|+++.+..+|++++...|.+..+|..++..+... ++.+.+...|++++...|....+|...+..+..
T Consensus         2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (100)
T cd00189           2 ALLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKL-GKYEEALEDYEKALELDPDNAKAYYNLGLAYYK   80 (100)
T ss_pred             HHHHHHHHHHHHhcHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhCCCcchhHHHHHHHHHHH
Confidence            3555566666788999999999999999999998888888776643 456778999999999999888888877764443


Q ss_pred             ccCCHHHHHHHHHHHHhCC
Q 013489          105 SRASEEEISTVFEKSLLCA  123 (442)
Q Consensus       105 ~~~~~~~~~~i~~~al~~~  123 (442)
                       .++.+.+...|.+++...
T Consensus        81 -~~~~~~a~~~~~~~~~~~   98 (100)
T cd00189          81 -LGKYEEALEAYEKALELD   98 (100)
T ss_pred             -HHhHHHHHHHHHHHHccC
Confidence             566778888888877543

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=97.57  E-value=0.011  Score=53.53  Aligned_cols=175  Identities=13%  Similarity=-0.050  Sum_probs=105.7

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHH---HHHHHHHHHHh-------cc
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDL---WLDYTQYLDKT-------LK   72 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~l---W~~Y~~~l~~~-------~~   72 (442)
                      .+...|+..+...|. ++.....|...+......|+++.+...|++++..+|.++.+   |..-.......       .+
T Consensus        51 ~A~~~~~~~~~~~p~-~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~g~~~~~~~~~~~~~~~  129 (235)
T TIGR03302        51 EAIKYFEALESRYPF-SPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYLRGLSNYNQIDRVDRDQT  129 (235)
T ss_pred             HHHHHHHHHHHhCCC-chhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHHHHHHHHHHhcccccCCHH
Confidence            456778888877764 22234577888888888999999999999999999988763   33322222211       13


Q ss_pred             hhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccc
Q 013489           73 VGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVE  152 (442)
Q Consensus        73 ~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~  152 (442)
                      ..+.+...|++++...|.+...|..+......        ........       ...-.++...               
T Consensus       130 ~~~~A~~~~~~~~~~~p~~~~~~~a~~~~~~~--------~~~~~~~~-------~~~a~~~~~~---------------  179 (235)
T TIGR03302       130 AAREAFEAFQELIRRYPNSEYAPDAKKRMDYL--------RNRLAGKE-------LYVARFYLKR---------------  179 (235)
T ss_pred             HHHHHHHHHHHHHHHCCCChhHHHHHHHHHHH--------HHHHHHHH-------HHHHHHHHHc---------------
Confidence            45678999999999999987777554432111        00000000       0000011000               


Q ss_pred             hhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchh
Q 013489          153 GVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA  215 (442)
Q Consensus       153 ~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~  215 (442)
                        .++......|++++...    .+.+...+.|...+..+...| +.+.|..+++.+...+|+
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              12222223333333321    112334578888888888889 999999999888877763

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).

>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=97.55  E-value=0.00047  Score=49.29  Aligned_cols=68  Identities=16%  Similarity=0.082  Sum_probs=53.6

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCC
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCP   89 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p   89 (442)
                      +...|...+......|+++.+...|+++|..+|.++.+|..........++....+...|++|+...|
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            45678888888888888888888899999888888888888887666443256678888888887665

...

>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=97.54  E-value=0.00012  Score=42.68  Aligned_cols=30  Identities=23%  Similarity=0.577  Sum_probs=24.8

Q ss_pred             CHHHHHHHHHHHHHhchhHHHHHHHHHHHHH
Q 013489          198 DMVSARGVWERLLKISGAMLEAWQSYISMEI  228 (442)
Q Consensus       198 ~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~  228 (442)
                      .+++||.||++.+..+|+ +..|+.|+.||.
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            478889999998888865 788999988885

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

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=97.54  E-value=0.013  Score=62.38  Aligned_cols=153  Identities=14%  Similarity=0.126  Sum_probs=94.8

Q ss_pred             HHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh
Q 013489           46 YERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus        46 yERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                      |-.+|...|.+-..-...+..+. ..+..+.+..+|+|+++.-|....+-..|+.++...  +.+.+...+.+|+..-..
T Consensus       105 ~~~~i~~~~~~k~Al~~LA~~Yd-k~g~~~ka~~~yer~L~~D~~n~~aLNn~AY~~ae~--dL~KA~~m~~KAV~~~i~  181 (906)
T PRK14720        105 ICDKILLYGENKLALRTLAEAYA-KLNENKKLKGVWERLVKADRDNPEIVKKLATSYEEE--DKEKAITYLKKAIYRFIK  181 (906)
T ss_pred             HHHHHHhhhhhhHHHHHHHHHHH-HcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHh--hHHHHHHHHHHHHHHHHh
Confidence            33333334444344444444333 345667799999999999999999989988877765  889999999999965332


Q ss_pred             --hHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHH---------HHHHHHHHhhhhcCchhhHHHHHHHHHHHHH
Q 013489          126 --TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRET---------FQRASDYLSEQMKNTDGLLRLYAYWAHLEQS  194 (442)
Q Consensus       126 --~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~---------~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~  194 (442)
                        .+.....+|..+|.+.-            .++..+-..         |.++..+          ...+|..|    ..
T Consensus       182 ~kq~~~~~e~W~k~~~~~~------------~d~d~f~~i~~ki~~~~~~~~~~~~----------~~~l~~~y----~~  235 (906)
T PRK14720        182 KKQYVGIEEIWSKLVHYNS------------DDFDFFLRIERKVLGHREFTRLVGL----------LEDLYEPY----KA  235 (906)
T ss_pred             hhcchHHHHHHHHHHhcCc------------ccchHHHHHHHHHHhhhccchhHHH----------HHHHHHHH----hh
Confidence              45566778877764431            111111111         2222222          12244444    23


Q ss_pred             cCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHH
Q 013489          195 MGKDMVSARGVWERLLKISGAMLEAWQSYISMEI  228 (442)
Q Consensus       195 ~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~  228 (442)
                      .. +++.+-.++..+|...|++...-...+++.+
T Consensus       236 ~~-~~~~~i~iLK~iL~~~~~n~~a~~~l~~~y~  268 (906)
T PRK14720        236 LE-DWDEVIYILKKILEHDNKNNKAREELIRFYK  268 (906)
T ss_pred             hh-hhhHHHHHHHHHHhcCCcchhhHHHHHHHHH
Confidence            33 7889999999999998877665556666554

>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals

Probab=97.54  E-value=0.058  Score=52.16  Aligned_cols=208  Identities=12%  Similarity=-0.024  Sum_probs=118.4

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcH----HHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVG----ELWVR   97 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~----~lW~~   97 (442)
                      ....+..........|+++.+...|++++...|.+...+..+...+.. .+..+.+...+++++...|...    ..|..
T Consensus       113 ~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~p~~~~~~~~la~i~~~-~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~  191 (355)
T cd05804         113 YWYLLGMLAFGLEEAGQYDRAEEAARRALELNPDDAWAVHAVAHVLEM-QGRFKEGIAFMESWRDTWDCSSMLRGHNWWH  191 (355)
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHH-cCCHHHHHHHHHhhhhccCCCcchhHHHHHH
Confidence            333344444455678889999999999999999998888888776664 3456778889999998776432    24445


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHhCCh--hhHHHHHHH-HHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhh
Q 013489           98 SLLSLERSRASEEEISTVFEKSLLCAF--STFEEYLDL-FLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQ  174 (442)
Q Consensus        98 y~~~le~~~~~~~~~~~i~~~al~~~~--~~~~~~~~~-~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~  174 (442)
                      .+. +....++.+.+..+|++++...+  ..+...... +..+      +............|..   .......    .
T Consensus       192 la~-~~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~------~~~~~g~~~~~~~w~~---~~~~~~~----~  257 (355)
T cd05804         192 LAL-FYLERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLW------RLELAGHVDVGDRWED---LADYAAW----H  257 (355)
T ss_pred             HHH-HHHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHH------HHHhcCCCChHHHHHH---HHHHHHh----h
Confidence            555 33346888889999998874433  112111111 1111      1111010100011111   1111111    1


Q ss_pred             hcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-h---h-----HHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          175 MKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS-G---A-----MLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       175 ~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~-~---~-----~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      .. .+.........+......+ +.+.|..+++.+.... .   .     .+.+.+-.+-.....|+.+.|..++..|+.
T Consensus       258 ~~-~~~~~~~~~~~a~~~~~~~-~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l~A~~~~~~g~~~~A~~~L~~al~  335 (355)
T cd05804         258 FP-DHGLAFNDLHAALALAGAG-DKDALDKLLAALKGRASSADDNKQPARDVGLPLAEALYAFAEGNYATALELLGPVRD  335 (355)
T ss_pred             cC-cccchHHHHHHHHHHhcCC-CHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            00 0111112223555556667 8999999998887642 1   1     123444444555567999999999999986


Q ss_pred             c
Q 013489          246 K  246 (442)
Q Consensus       246 ~  246 (442)
                      .
T Consensus       336 ~  336 (355)
T cd05804         336 D  336 (355)
T ss_pred             H
Confidence            3

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.

>KOG1129 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.50  E-value=0.0012  Score=60.51  Aligned_cols=204  Identities=16%  Similarity=0.184  Sum_probs=123.8

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (442)
                      |-..+...|+..+.     .+.+.-....-..-..|.++..+|-..|..+|.++.+-..-+...+. .+..+.+.++|.+
T Consensus       242 AekqlqssL~q~~~-----~dTfllLskvY~ridQP~~AL~~~~~gld~fP~~VT~l~g~ARi~ea-m~~~~~a~~lYk~  315 (478)
T KOG1129|consen  242 AEKQLQSSLTQFPH-----PDTFLLLSKVYQRIDQPERALLVIGEGLDSFPFDVTYLLGQARIHEA-MEQQEDALQLYKL  315 (478)
T ss_pred             hHHHHHHHhhcCCc-----hhHHHHHHHHHHHhccHHHHHHHHhhhhhcCCchhhhhhhhHHHHHH-HHhHHHHHHHHHH
Confidence            44566777777664     33444333333344578889999999999999998887777765543 2344567888888


Q ss_pred             HHHcCCCcHH----HHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHH-----HH----HHHHHhhccCc
Q 013489           84 ATKNCPWVGE----LWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTR-----ID----GLRRRILFSGE  150 (442)
Q Consensus        84 Al~~~p~s~~----lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~-----~~----~l~rr~~~~~~  150 (442)
                      ++..-|...+    |=..|.     ..++.+.+...|.|.|+.+..+.+.|..+-++.     +|    +..|-......
T Consensus       316 vlk~~~~nvEaiAcia~~yf-----Y~~~PE~AlryYRRiLqmG~~speLf~NigLCC~yaqQ~D~~L~sf~RAlstat~  390 (478)
T KOG1129|consen  316 VLKLHPINVEAIACIAVGYF-----YDNNPEMALRYYRRILQMGAQSPELFCNIGLCCLYAQQIDLVLPSFQRALSTATQ  390 (478)
T ss_pred             HHhcCCccceeeeeeeeccc-----cCCChHHHHHHHHHHHHhcCCChHHHhhHHHHHHhhcchhhhHHHHHHHHhhccC
Confidence            8887665432    222221     246667788888888887766555554444331     11    11121111110


Q ss_pred             ----cchhhhHH---HHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHH
Q 013489          151 ----VEGVLDYS---LIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEA  219 (442)
Q Consensus       151 ----~~~~~~~~---~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~  219 (442)
                          .+.|-++.   .-...|.-|..++..++.+++...+.+...+-++...| +++.||.+++.+-...|+..+.
T Consensus       391 ~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~h~ealnNLavL~~r~G-~i~~Arsll~~A~s~~P~m~E~  465 (478)
T KOG1129|consen  391 PGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQHGEALNNLAVLAARSG-DILGARSLLNAAKSVMPDMAEV  465 (478)
T ss_pred             cchhhhhhhccceeEEeccchHHHHHHHHHHhccCcchHHHHHhHHHHHhhcC-chHHHHHHHHHhhhhCcccccc
Confidence                01111100   01123444555555555555666678888898999999 9999999999999988886653

>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=97.49  E-value=0.001  Score=47.52  Aligned_cols=62  Identities=15%  Similarity=0.179  Sum_probs=57.9

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcc-cHHHHHHHHHHHHh
Q 013489          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELD-HINEARSIYKRCYS  245 (442)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g-~~~~ar~i~~ral~  245 (442)
                      .+|...+......+ +++.|...|.+++..+|+++.+|..........| ++..|...|++|+.
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            47888888888888 9999999999999999999999999999999999 79999999999996

...

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=97.45  E-value=0.071  Score=54.63  Aligned_cols=94  Identities=12%  Similarity=0.134  Sum_probs=70.5

Q ss_pred             HHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHH--HHHHHHHHHHhchhHHHHHHHHHHHHHhcccHH
Q 013489          157 YSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVS--ARGVWERLLKISGAMLEAWQSYISMEIELDHIN  234 (442)
Q Consensus       157 ~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~--ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~  234 (442)
                      ...+++.+++|...+..++.-+|..+......+.+....| +...  .|.++..+++.+|.+.+.|.......+..|+.+
T Consensus       693 ~~~~~~~~~EA~~af~~Al~ldP~hv~s~~Ala~~lle~G-~~~la~~~~~L~dalr~dp~n~eaW~~LG~v~k~~Gd~~  771 (799)
T KOG4162|consen  693 LLEVKGQLEEAKEAFLVALALDPDHVPSMTALAELLLELG-SPRLAEKRSLLSDALRLDPLNHEAWYYLGEVFKKLGDSK  771 (799)
T ss_pred             HHHHHHhhHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhC-CcchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHccchH
Confidence            3345566677777766666656666677777888887777 5544  444899999999999999999999988999999


Q ss_pred             HHHHHHHHHHhcccCCCCh
Q 013489          235 EARSIYKRCYSKRFTGTGS  253 (442)
Q Consensus       235 ~ar~i~~ral~~~~~~~~~  253 (442)
                      .|-.+|..|++  +....|
T Consensus       772 ~Aaecf~aa~q--Le~S~P  788 (799)
T KOG4162|consen  772 QAAECFQAALQ--LEESNP  788 (799)
T ss_pred             HHHHHHHHHHh--hccCCC
Confidence            99999999986  344444

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=97.44  E-value=0.00018  Score=69.24  Aligned_cols=50  Identities=24%  Similarity=0.430  Sum_probs=47.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..+|||.|++..++.+.|+.+|+.+|.|.+++|+.+ ..|+++|||||.|.
T Consensus       270 ~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~-~~g~skG~gfV~fs  319 (369)
T KOG0123|consen  270 GANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVD-ENGKSKGFGFVEFS  319 (369)
T ss_pred             ccccccccCccccchhHHHHHHhcccceeeEEEEec-cCCCccceEEEEcC
Confidence            348999999999999999999999999999999999 79999999999996

>PLN03213 repressor of silencing 3; Provisional

Probab=97.44  E-value=0.00019  Score=68.52  Aligned_cols=36  Identities=17%  Similarity=0.357  Sum_probs=33.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeC
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHD  426 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~  426 (442)
                      ..+||||||++.+++++|+.+|+.||.|.+|.|++.
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE   45 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT   45 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc
Confidence            469999999999999999999999999999999943

>KOG2003 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.43  E-value=0.057  Score=51.93  Aligned_cols=79  Identities=18%  Similarity=0.229  Sum_probs=50.6

Q ss_pred             HHHHHHHHHHHHHhchhHHHHHHHH-HHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCH--hhHHH
Q 013489          199 MVSARGVWERLLKISGAMLEAWQSY-ISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTL--EDFDH  275 (442)
Q Consensus       199 ~~~ar~i~~~~l~~~~~~~~~w~~~-~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~--~~~~~  275 (442)
                      .+++.++|+++.-..|+... |.-+ +.+.++.|++++|..+|+.... .||.+.  +.+.-.+...-+.|-.  .++.+
T Consensus       642 ~ekai~y~ekaaliqp~~~k-wqlmiasc~rrsgnyqka~d~yk~~hr-kfpedl--dclkflvri~~dlgl~d~key~~  717 (840)
T KOG2003|consen  642 SEKAINYFEKAALIQPNQSK-WQLMIASCFRRSGNYQKAFDLYKDIHR-KFPEDL--DCLKFLVRIAGDLGLKDAKEYAD  717 (840)
T ss_pred             HHHHHHHHHHHHhcCccHHH-HHHHHHHHHHhcccHHHHHHHHHHHHH-hCccch--HHHHHHHHHhccccchhHHHHHH
Confidence            47888889998888888666 5444 4466778999999999988654 565432  3344445555555533  34544


Q ss_pred             HHHhhc
Q 013489          276 SVQKVT  281 (442)
Q Consensus       276 ~~~~~~  281 (442)
                      -+++..
T Consensus       718 klek~e  723 (840)
T KOG2003|consen  718 KLEKAE  723 (840)
T ss_pred             HHHHHH
Confidence            455543

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=97.42  E-value=0.00047  Score=44.43  Aligned_cols=42  Identities=19%  Similarity=0.360  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHH
Q 013489           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQ   65 (442)
Q Consensus        24 ~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~   65 (442)
                      ..|..++......|+++++..+|+++|..+|.++.+|..++.
T Consensus         2 ~~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~~~a~~~La~   43 (44)
T PF13428_consen    2 AAWLALARAYRRLGQPDEAERLLRRALALDPDDPEAWRALAQ   43 (44)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCHHHHHHhhh
Confidence            468889999999999999999999999999999999998764

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.42  E-value=0.018  Score=58.41  Aligned_cols=178  Identities=11%  Similarity=0.023  Sum_probs=113.0

Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHcc----CCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHH
Q 013489           83 RATKNCPWVGELWVRSLLSLERSR----ASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYS  158 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~----~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~  158 (442)
                      ++.+.-|.+...|..|++......    +....+..+|++|+...|.....+..+...+  ..+... ..  .. ..++.
T Consensus       328 ~~~~~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ldP~~a~a~A~la~~~--~~~~~~-~~--~~-~~~l~  401 (517)
T PRK10153        328 RLQQGLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSEPDFTYAQAEKALAD--IVRHSQ-QP--LD-EKQLA  401 (517)
T ss_pred             HHhccCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHH--HHHHhc-CC--cc-HHHHH
Confidence            344455777788888887544321    2256788999999998877544443332222  121111 11  00 01222


Q ss_pred             HHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHH
Q 013489          159 LIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARS  238 (442)
Q Consensus       159 ~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~  238 (442)
                      .......++....     ..+....++...+-.....| +++.|...+++++...|+ ...|..+..+....|+.+.|..
T Consensus       402 ~a~~~~~~a~al~-----~~~~~~~~~~ala~~~~~~g-~~~~A~~~l~rAl~L~ps-~~a~~~lG~~~~~~G~~~eA~~  474 (517)
T PRK10153        402 ALSTELDNIVALP-----ELNVLPRIYEILAVQALVKG-KTDEAYQAINKAIDLEMS-WLNYVLLGKVYELKGDNRLAAD  474 (517)
T ss_pred             HHHHHHHHhhhcc-----cCcCChHHHHHHHHHHHhcC-CHHHHHHHHHHHHHcCCC-HHHHHHHHHHHHHcCCHHHHHH
Confidence            3333333332220     12222356666666666666 999999999999999985 6788888999999999999999


Q ss_pred             HHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHH
Q 013489          239 IYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQ  278 (442)
Q Consensus       239 i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~  278 (442)
                      .|.+|+.  +.+..|...|..=+-|   |-|+++|.-+.-
T Consensus       475 ~~~~A~~--L~P~~pt~~~~~~~~f---~~~~~~~~~~~~  509 (517)
T PRK10153        475 AYSTAFN--LRPGENTLYWIENLVF---QTSVETVVPYLY  509 (517)
T ss_pred             HHHHHHh--cCCCCchHHHHHhccc---cccHHHHHHHHH
Confidence            9999996  5666777666666666   667777765443

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=97.38  E-value=0.098  Score=52.67  Aligned_cols=215  Identities=14%  Similarity=0.143  Sum_probs=118.9

Q ss_pred             HHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcc
Q 013489           27 MIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSR  106 (442)
Q Consensus        27 ~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~  106 (442)
                      ..=++++.+.+.++.+..+|.+.|..+|++.+....|...+.......+.+..+|.+.-...|.+..+-..=+.++..  
T Consensus       223 e~ka~l~~kl~~lEeA~~~y~~Ll~rnPdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~y~r~e~p~Rlplsvl~~--  300 (700)
T KOG1156|consen  223 ETKADLLMKLGQLEEAVKVYRRLLERNPDNLDYYEGLEKALGKIKDMLEALKALYAILSEKYPRHECPRRLPLSVLNG--  300 (700)
T ss_pred             hhHHHHHHHHhhHHhHHHHHHHHHhhCchhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhcCcccccchhccHHHhCc--
Confidence            334455566778899999999999999999988888877664222233445578888777777654433322332321  


Q ss_pred             CCH-HHHHHHHHHHHhCChh-hHHHHHHHHHH--HHHHHHHHhh------ccC-cc--------ch--hhhH--------
Q 013489          107 ASE-EEISTVFEKSLLCAFS-TFEEYLDLFLT--RIDGLRRRIL------FSG-EV--------EG--VLDY--------  157 (442)
Q Consensus       107 ~~~-~~~~~i~~~al~~~~~-~~~~~~~~~~~--~~~~l~rr~~------~~~-~~--------~~--~~~~--------  157 (442)
                      .++ +.+...+...++.|.+ ...+...++..  .++.+.+-+.      .+. ..        +.  ..-|        
T Consensus       301 eel~~~vdkyL~~~l~Kg~p~vf~dl~SLyk~p~k~~~le~Lvt~y~~~L~~~~~f~~~D~~~~E~PttllWt~y~laqh  380 (700)
T KOG1156|consen  301 EELKEIVDKYLRPLLSKGVPSVFKDLRSLYKDPEKVAFLEKLVTSYQHSLSGTGMFNFLDDGKQEPPTTLLWTLYFLAQH  380 (700)
T ss_pred             chhHHHHHHHHHHHhhcCCCchhhhhHHHHhchhHhHHHHHHHHHHHhhcccccCCCcccccccCCchHHHHHHHHHHHH
Confidence            111 2233333333333322 12223333321  1112221111      000 00        00  0000        


Q ss_pred             HHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHH
Q 013489          158 SLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEAR  237 (442)
Q Consensus       158 ~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar  237 (442)
                      -...+.++.|..+++.+++..|+.+++++.-|++....| +++.|-.+++.+-..+..+.-+=..++.+-.+-+.++.|-
T Consensus       381 ~D~~g~~~~A~~yId~AIdHTPTliEly~~KaRI~kH~G-~l~eAa~~l~ea~elD~aDR~INsKcAKYmLrAn~i~eA~  459 (700)
T KOG1156|consen  381 YDKLGDYEVALEYIDLAIDHTPTLIELYLVKARIFKHAG-LLDEAAAWLDEAQELDTADRAINSKCAKYMLRANEIEEAE  459 (700)
T ss_pred             HHHcccHHHHHHHHHHHhccCchHHHHHHHHHHHHHhcC-ChHHHHHHHHHHHhccchhHHHHHHHHHHHHHccccHHHH
Confidence            112344566777777777777777777777777776666 7777777777777665443444445666666667777776


Q ss_pred             HHHHHHH
Q 013489          238 SIYKRCY  244 (442)
Q Consensus       238 ~i~~ral  244 (442)
                      .+...-.
T Consensus       460 ~~~skFT  466 (700)
T KOG1156|consen  460 EVLSKFT  466 (700)
T ss_pred             HHHHHhh
Confidence            6655543

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.37  E-value=0.00091  Score=47.14  Aligned_cols=61  Identities=18%  Similarity=0.168  Sum_probs=49.8

Q ss_pred             HHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCc
Q 013489           30 LKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV   91 (442)
Q Consensus        30 ~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s   91 (442)
                      +......|+++.+..+|+++|..+|.++..|..+...+... +..+.+...|++++...|.+
T Consensus         4 a~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~~-g~~~~A~~~~~~a~~~~P~~   64 (65)
T PF13432_consen    4 ARALYQQGDYDEAIAAFEQALKQDPDNPEAWYLLGRILYQQ-GRYDEALAYYERALELDPDN   64 (65)
T ss_dssp             HHHHHHCTHHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHHT-T-HHHHHHHHHHHHHHSTT-
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHCcCC
Confidence            34456688999999999999999999999999999887744 55677889999999988875

>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=97.34  E-value=0.19  Score=50.92  Aligned_cols=217  Identities=16%  Similarity=0.156  Sum_probs=132.2

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhc-----CChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchh-hH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS-----GDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVG-NV   76 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~-----g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~-~~   76 (442)
                      +|...|...|..+|.    +...+..|.......     .+......+|+..-..+|.+...=.-=+.|+.  +... ..
T Consensus        56 eA~~~y~~Li~rNPd----n~~Yy~~L~~~~g~~~~~~~~~~~~~~~~y~~l~~~yp~s~~~~rl~L~~~~--g~~F~~~  129 (517)
T PF12569_consen   56 EAEKIYRELIDRNPD----NYDYYRGLEEALGLQLQLSDEDVEKLLELYDELAEKYPRSDAPRRLPLDFLE--GDEFKER  129 (517)
T ss_pred             HHHHHHHHHHHHCCC----cHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHhCccccchhHhhcccCC--HHHHHHH
Confidence            577889999999886    787888888866322     24677788999888888875433222223222  1111 22


Q ss_pred             HHHHHHHHHH-cCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhC-----ChhhH------HHHHHHHHHHHHHHHHH
Q 013489           77 VRDVYSRATK-NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLC-----AFSTF------EEYLDLFLTRIDGLRRR  144 (442)
Q Consensus        77 ~~~v~erAl~-~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~-----~~~~~------~~~~~~~~~~~~~l~rr  144 (442)
                      +.....+.++ .+|   .+... +..+........-+..+++..+..     .+...      ....-+|..++  +-..
T Consensus       130 ~~~yl~~~l~KgvP---slF~~-lk~Ly~d~~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~--lAqh  203 (517)
T PF12569_consen  130 LDEYLRPQLRKGVP---SLFSN-LKPLYKDPEKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYF--LAQH  203 (517)
T ss_pred             HHHHHHHHHhcCCc---hHHHH-HHHHHcChhHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHH--HHHH
Confidence            4444455554 334   33333 233433222233455555543321     00000      00111221110  0000


Q ss_pred             hhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHH
Q 013489          145 ILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYI  224 (442)
Q Consensus       145 ~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~  224 (442)
                      .             ...+.+++|+.+++.++...|+.++++..-|++....| ++..|-..++.+-..++.+=-+=...+
T Consensus       204 y-------------d~~g~~~~Al~~Id~aI~htPt~~ely~~KarilKh~G-~~~~Aa~~~~~Ar~LD~~DRyiNsK~a  269 (517)
T PF12569_consen  204 Y-------------DYLGDYEKALEYIDKAIEHTPTLVELYMTKARILKHAG-DLKEAAEAMDEARELDLADRYINSKCA  269 (517)
T ss_pred             H-------------HHhCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHCC-CHHHHHHHHHHHHhCChhhHHHHHHHH
Confidence            0             11234678888888888888889999999999999889 999999999999988776655666778


Q ss_pred             HHHHhcccHHHHHHHHHHHHh
Q 013489          225 SMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       225 ~~e~~~g~~~~ar~i~~ral~  245 (442)
                      .+..+.|.++.|..++..-..
T Consensus       270 Ky~LRa~~~e~A~~~~~~Ftr  290 (517)
T PF12569_consen  270 KYLLRAGRIEEAEKTASLFTR  290 (517)
T ss_pred             HHHHHCCCHHHHHHHHHhhcC
Confidence            888889999999988877543

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 [], [].

>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=97.32  E-value=0.00083  Score=47.78  Aligned_cols=64  Identities=20%  Similarity=0.100  Sum_probs=53.9

Q ss_pred             hcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHH
Q 013489           35 SSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSL   99 (442)
Q Consensus        35 ~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~   99 (442)
                      ..|+++.|..+|++++..+|.+.++|+.++..+... +..+.+..++++++...|....+|....
T Consensus         3 ~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~-g~~~~A~~~l~~~~~~~~~~~~~~~l~a   66 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQRNPDNPEARLLLAQCYLKQ-GQYDEAEELLERLLKQDPDNPEYQQLLA   66 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHT-T-HHHHHHHHHCCHGGGTTHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHCcCHHHHHHHHh
Confidence            568899999999999999999999999999888755 5667899999999999998777766544

...

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=97.32  E-value=0.00086  Score=61.49  Aligned_cols=50  Identities=18%  Similarity=0.330  Sum_probs=43.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeE--------EEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSS--------IRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~--------~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +..|||+|||.++|-+++..+|+.||.|.+        |.|-++ ..|+.+|=|.|.|.
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd-~~G~lKGDaLc~y~  191 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRD-NQGKLKGDALCCYI  191 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEec-CCCCccCceEEEee
Confidence            457999999999999999999999997754        677787 56999999998885

>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=97.30  E-value=0.0003  Score=40.99  Aligned_cols=30  Identities=23%  Similarity=0.615  Sum_probs=22.6

Q ss_pred             ChhhHHHHHHHHHhcCCCCHHHHHHHHHHHH
Q 013489           38 DPGRVQLLYERAITDFPVSSDLWLDYTQYLD   68 (442)
Q Consensus        38 ~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~   68 (442)
                      .+++|+.+|||.|..+| ++..|+.|+.|.+
T Consensus         2 E~dRAR~IyeR~v~~hp-~~k~WikyAkFEe   31 (32)
T PF02184_consen    2 EFDRARSIYERFVLVHP-EVKNWIKYAKFEE   31 (32)
T ss_pred             hHHHHHHHHHHHHHhCC-CchHHHHHHHhhc
Confidence            35788888888888775 4788888888753

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

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=97.29  E-value=0.015  Score=59.09  Aligned_cols=115  Identities=15%  Similarity=0.162  Sum_probs=93.5

Q ss_pred             HHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHH
Q 013489          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYK  241 (442)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~  241 (442)
                      ..|..+...++..+.-++.....|..+.-.....+ +...|-+.|.++++..|++.+.|..+.....+.|+-.+|+..+.
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            45666666666666556666778888777777777 89999999999999999999999999999999999999999999


Q ss_pred             HHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          242 RCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       242 ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                      +|+..  . ..+-.||+.|+-.-.+.|..++.-.|..+.
T Consensus       578 EAlKc--n-~~~w~iWENymlvsvdvge~eda~~A~~rl  613 (777)
T KOG1128|consen  578 EALKC--N-YQHWQIWENYMLVSVDVGEFEDAIKAYHRL  613 (777)
T ss_pred             HHhhc--C-CCCCeeeechhhhhhhcccHHHHHHHHHHH
Confidence            99973  3 345579999999999999887776666543

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.28  E-value=0.0066  Score=58.84  Aligned_cols=95  Identities=19%  Similarity=0.056  Sum_probs=79.8

Q ss_pred             HHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCH
Q 013489           30 LKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASE  109 (442)
Q Consensus        30 ~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~  109 (442)
                      +.-....|+++.++.+|++||..+|.+..+|...+..+.. .+..+.+...+++|+...|.....|......+. ..+..
T Consensus         9 a~~a~~~~~~~~Ai~~~~~Al~~~P~~~~a~~~~a~~~~~-~g~~~eAl~~~~~Al~l~P~~~~a~~~lg~~~~-~lg~~   86 (356)
T PLN03088          9 AKEAFVDDDFALAVDLYTQAIDLDPNNAELYADRAQANIK-LGNFTEAVADANKAIELDPSLAKAYLRKGTACM-KLEEY   86 (356)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHH-HhCCH
Confidence            3334567899999999999999999999999999887764 456677999999999999999999888776444 47889


Q ss_pred             HHHHHHHHHHHhCChhh
Q 013489          110 EEISTVFEKSLLCAFST  126 (442)
Q Consensus       110 ~~~~~i~~~al~~~~~~  126 (442)
                      +.+...|++++...+..
T Consensus        87 ~eA~~~~~~al~l~P~~  103 (356)
T PLN03088         87 QTAKAALEKGASLAPGD  103 (356)
T ss_pred             HHHHHHHHHHHHhCCCC
Confidence            99999999999877664

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=97.23  E-value=0.23  Score=49.96  Aligned_cols=172  Identities=15%  Similarity=0.111  Sum_probs=111.2

Q ss_pred             HHHHHHhcchhhHHHHHHHHHHHc--------CCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCh---hhHHHHHH
Q 013489           64 TQYLDKTLKVGNVVRDVYSRATKN--------CPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAF---STFEEYLD  132 (442)
Q Consensus        64 ~~~l~~~~~~~~~~~~v~erAl~~--------~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~---~~~~~~~~  132 (442)
                      +.-+....+..+.+..+|++|++.        +|.....-..+.. +....+.+.++..+|++|+...-   ......+.
T Consensus       205 La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~-~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h~~va  283 (508)
T KOG1840|consen  205 LAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILAL-VYRSLGKYDEAVNLYEEALTIREEVFGEDHPAVA  283 (508)
T ss_pred             HHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHH-HHHHhccHHHHHHHHHHHHHHHHHhcCCCCHHHH
Confidence            333333446678899999999997        4544333333333 45557888999999999995321   11111111


Q ss_pred             HHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhh-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 013489          133 LFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGL-LRLYAYWAHLEQSMGKDMVSARGVWERLLK  211 (442)
Q Consensus       133 ~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~-~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~  211 (442)
                      ..+..+..+.         ....++...+..+++|..+....+...++. ...+...+.++...+ .++.|..++.++++
T Consensus       284 ~~l~nLa~ly---------~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~-~~Eea~~l~q~al~  353 (508)
T KOG1840|consen  284 ATLNNLAVLY---------YKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMN-EYEEAKKLLQKALK  353 (508)
T ss_pred             HHHHHHHHHH---------hccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhc-chhHHHHHHHHHHH
Confidence            1111111111         011456677788889988887754444443 345555666666677 89999999999987


Q ss_pred             hch--------hHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          212 ISG--------AMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       212 ~~~--------~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      ..-        .-..+...+..+....|.++.|+.+|+.|++.
T Consensus       354 i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~  396 (508)
T KOG1840|consen  354 IYLDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQI  396 (508)
T ss_pred             HHHhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHH
Confidence            721        22358888899999999999999999999976

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=97.21  E-value=0.00091  Score=43.09  Aligned_cols=42  Identities=19%  Similarity=0.260  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHH
Q 013489          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYIS  225 (442)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~  225 (442)
                      .+|..+++.+...| +++.|+.+|+++++.+|++..+|..++.
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            36888899999999 9999999999999999999999988865

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=97.16  E-value=0.00039  Score=70.09  Aligned_cols=44  Identities=23%  Similarity=0.292  Sum_probs=40.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEe
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIY  440 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f  440 (442)
                      ++|||||+|+.++++.||..+|..||.|.+|.++..      ||+|||..
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M  464 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKM  464 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEE
Confidence            579999999999999999999999999999987764      69999864

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=97.16  E-value=0.00038  Score=62.19  Aligned_cols=42  Identities=24%  Similarity=0.294  Sum_probs=39.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+++||||.+.++.++|+..|..+|+|.+|+|++|        |+||-|.
T Consensus        79 tkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d  120 (346)
T KOG0109|consen   79 TKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFD  120 (346)
T ss_pred             cccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEe
Confidence            48999999999999999999999999999999987        9999885

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=97.16  E-value=0.39  Score=49.51  Aligned_cols=246  Identities=13%  Similarity=0.089  Sum_probs=136.4

Q ss_pred             HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcC--CCcHHHHHHHHH
Q 013489           23 FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNC--PWVGELWVRSLL  100 (442)
Q Consensus        23 ~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~--p~s~~lW~~y~~  100 (442)
                      ..+|.-..-.....|.+..+...||+++...-.....|..+..-+...+.+ ..+..+.+..+..-  |........-..
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 AAIFDHLTFALSRCGQFEVLAEQFEQALPFSFGEHERWYQLALSYSAAGSD-SKAVNLLRESLKKSEQPSDISVLLMASK  401 (799)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhHHHHHHHHHHHHHhccc-hHHHHHHHhhcccccCCCcchHHHHHHH
Confidence            335555555555566677777777777766666667777776555444332 34566666666544  433333222222


Q ss_pred             HHHHccCCHHHHHHHHHHHHhCChh-----hHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHH-HHHHHHHHHhhh
Q 013489          101 SLERSRASEEEISTVFEKSLLCAFS-----TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRE-TFQRASDYLSEQ  174 (442)
Q Consensus       101 ~le~~~~~~~~~~~i~~~al~~~~~-----~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~-~~~~a~~~l~~~  174 (442)
                      .+....+..+++...-.+++...-.     ....+.-+-.+|  ....+.    ..   .+  ..|. .-.++++.++.+
T Consensus       402 lc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y--~~~A~~----a~---~~--seR~~~h~kslqale~a  470 (799)
T KOG4162|consen  402 LCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAY--GFQARQ----AN---LK--SERDALHKKSLQALEEA  470 (799)
T ss_pred             HHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHH--HhHhhc----CC---Ch--HHHHHHHHHHHHHHHHH
Confidence            2333344444544545555541100     000111111111  010010    00   00  1111 123344455544


Q ss_pred             hcCchhhHHHHHHHHHHH-HHcCCCHHHHHHHHHHHHHh-chhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCC
Q 013489          175 MKNTDGLLRLYAYWAHLE-QSMGKDMVSARGVWERLLKI-SGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTG  252 (442)
Q Consensus       175 ~~~~~~~~~l~~~~a~~e-~~~~~~~~~ar~i~~~~l~~-~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~  252 (442)
                      +.-.++.+ ..++|..++ .... +++.|.....+++.. .+++...|.-++-+....+++..|..+.+.++.. ++.+ 
T Consensus       471 v~~d~~dp-~~if~lalq~A~~R-~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~E-~~~N-  546 (799)
T KOG4162|consen  471 VQFDPTDP-LVIFYLALQYAEQR-QLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALEE-FGDN-  546 (799)
T ss_pred             HhcCCCCc-hHHHHHHHHHHHHH-hHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHH-hhhh-
Confidence            43223333 333444444 4455 899999999999999 6788899999999999999999999999999984 2221 


Q ss_pred             hHHHHHHHHHHHHHhCCHhhHHHHHHhhchhHHHHH
Q 013489          253 SEDICHAWLRFEREYGTLEDFDHSVQKVTPRLEELR  288 (442)
Q Consensus       253 ~~~i~~~~~~fE~~~G~~~~~~~~~~~~~~~~~~~~  288 (442)
                       -.+..--+..|..+|+.   +.++..|.+.++-++
T Consensus       547 -~~l~~~~~~i~~~~~~~---e~~l~t~~~~L~~we  578 (799)
T KOG4162|consen  547 -HVLMDGKIHIELTFNDR---EEALDTCIHKLALWE  578 (799)
T ss_pred             -hhhchhhhhhhhhcccH---HHHHHHHHHHHHHHH
Confidence             23455567778887775   456777777776665

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.13  E-value=0.0076  Score=58.39  Aligned_cols=90  Identities=12%  Similarity=-0.018  Sum_probs=76.8

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      .|...|+.+|...|.    +...|...+......|+++.+...++++|..+|.+...|...+..+.. .+..+.+...|+
T Consensus        20 ~Ai~~~~~Al~~~P~----~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~~~a~~~lg~~~~~-lg~~~eA~~~~~   94 (356)
T PLN03088         20 LAVDLYTQAIDLDPN----NAELYADRAQANIKLGNFTEAVADANKAIELDPSLAKAYLRKGTACMK-LEEYQTAKAALE   94 (356)
T ss_pred             HHHHHHHHHHHhCCC----CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHH-hCCHHHHHHHHH
Confidence            467789999988876    778899999988999999999999999999999999999998876664 456678999999


Q ss_pred             HHHHcCCCcHHHHHH
Q 013489           83 RATKNCPWVGELWVR   97 (442)
Q Consensus        83 rAl~~~p~s~~lW~~   97 (442)
                      +|+...|....++..
T Consensus        95 ~al~l~P~~~~~~~~  109 (356)
T PLN03088         95 KGASLAPGDSRFTKL  109 (356)
T ss_pred             HHHHhCCCCHHHHHH
Confidence            999999987764333

>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=97.12  E-value=0.0022  Score=45.59  Aligned_cols=52  Identities=19%  Similarity=0.179  Sum_probs=46.7

Q ss_pred             HcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          194 SMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       194 ~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      ..| +++.|..+|++++..+|++.++++.++.+....|+++.|+.++++++..
T Consensus         3 ~~~-~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~   54 (68)
T PF14559_consen    3 KQG-DYDEAIELLEKALQRNPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQ   54 (68)
T ss_dssp             HTT-HHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG
T ss_pred             hcc-CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            345 8999999999999999999999999999999999999999999999873

...

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=97.08  E-value=0.0016  Score=49.63  Aligned_cols=50  Identities=20%  Similarity=0.054  Sum_probs=43.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhcc--CCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSD--VGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~--~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +||.|.|+|...+.++|.+++..  .|...-+-++.|..++.+.|||||-|.
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~   53 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFT   53 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcC
Confidence            59999999999999999988774  456666788999889999999999885

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.03  E-value=0.00036  Score=64.64  Aligned_cols=54  Identities=22%  Similarity=0.380  Sum_probs=49.1

Q ss_pred             CCCCceEE-EcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAF-LSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~-v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .....++| |+++++.++.++|+.+|..||.|..++++.++.+|.++|||||.|.
T Consensus       181 ~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~  235 (285)
T KOG4210|consen  181 SGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFS  235 (285)
T ss_pred             cCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhh
Confidence            34455666 9999999999999999999999999999999999999999999985

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=97.01  E-value=0.0011  Score=59.30  Aligned_cols=52  Identities=19%  Similarity=0.305  Sum_probs=47.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....+|+|.|||+.+++.||+++|..||.+..+-+..+ .+|++.|.|-|.|.
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~-~~G~s~Gta~v~~~  132 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYD-RAGRSLGTADVSFN  132 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccC-CCCCCCccceeeec
Confidence            34468999999999999999999999999999988888 69999999999985

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=97.01  E-value=0.033  Score=51.12  Aligned_cols=86  Identities=9%  Similarity=-0.017  Sum_probs=68.7

Q ss_pred             hhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCC--HHHHHHHH
Q 013489           39 PGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRAS--EEEISTVF  116 (442)
Q Consensus        39 ~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~--~~~~~~i~  116 (442)
                      ++....-.|.-|..+|.+.+=|.......... ++...+...|.+|++.-|.+..+|..|...+....+.  ...++.+|
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 MEALIARLETHLQQNPGDAEGWDLLGRAYMAL-GRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALL  216 (287)
T ss_pred             HHHHHHHHHHHHHhCCCCchhHHHHHHHHHHh-cchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccHHHHHHH
Confidence            45667778999999999999999999877654 4556789999999999999999999999888765443  24577788


Q ss_pred             HHHHhCChh
Q 013489          117 EKSLLCAFS  125 (442)
Q Consensus       117 ~~al~~~~~  125 (442)
                      .+++..++.
T Consensus       217 ~~al~~D~~  225 (287)
T COG4235         217 RQALALDPA  225 (287)
T ss_pred             HHHHhcCCc
Confidence            887765544

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=97.01  E-value=0.024  Score=57.63  Aligned_cols=77  Identities=10%  Similarity=0.146  Sum_probs=64.4

Q ss_pred             HHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          169 DYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       169 ~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      +.+..++.-.|....-|..++..+..++ ...+|+..+.++++.+-.+..+|..|.-.-...|+.+.|...|.+.+.-
T Consensus       540 ~aF~rcvtL~Pd~~eaWnNls~ayi~~~-~k~ra~~~l~EAlKcn~~~w~iWENymlvsvdvge~eda~~A~~rll~~  616 (777)
T KOG1128|consen  540 KAFHRCVTLEPDNAEAWNNLSTAYIRLK-KKKRAFRKLKEALKCNYQHWQIWENYMLVSVDVGEFEDAIKAYHRLLDL  616 (777)
T ss_pred             HHHHHHhhcCCCchhhhhhhhHHHHHHh-hhHHHHHHHHHHhhcCCCCCeeeechhhhhhhcccHHHHHHHHHHHHHh
Confidence            3333333335566778999999999999 8899999999999998778899999999999999999999999998853

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=96.99  E-value=0.07  Score=47.87  Aligned_cols=49  Identities=16%  Similarity=0.004  Sum_probs=30.0

Q ss_pred             HHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHH
Q 013489          193 QSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKR  242 (442)
Q Consensus       193 ~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~r  242 (442)
                      .-.| +.+.|+.++..+...-+....+-...+-.....|++..|+.|-..
T Consensus       179 ~L~g-d~~~A~~lll~a~l~~~ad~~v~~NLAl~~~~~g~~~~A~~i~~~  227 (257)
T COG5010         179 LLRG-DLEDAETLLLPAYLSPAADSRVRQNLALVVGLQGDFREAEDIAVQ  227 (257)
T ss_pred             HHcC-CHHHHHHHHHHHHhCCCCchHHHHHHHHHHhhcCChHHHHhhccc
Confidence            3444 677777777776666555555555555556666676666666544

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.99  E-value=0.066  Score=50.04  Aligned_cols=171  Identities=16%  Similarity=0.083  Sum_probs=99.7

Q ss_pred             cCChhhHHHHHHHHHhcCC---CCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHH
Q 013489           36 SGDPGRVQLLYERAITDFP---VSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEI  112 (442)
Q Consensus        36 ~g~~~~~~~lyERal~~~p---~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~  112 (442)
                      ..|+..++.+.|-.+...-   .+.++|+.|+.|   +.++.+.+..+|.-+...---.+++|...+- +.-..+...++
T Consensus        35 ~rDytGAislLefk~~~~~EEE~~~~lWia~C~f---hLgdY~~Al~~Y~~~~~~~~~~~el~vnLAc-c~FyLg~Y~eA  110 (557)
T KOG3785|consen   35 NRDYTGAISLLEFKLNLDREEEDSLQLWIAHCYF---HLGDYEEALNVYTFLMNKDDAPAELGVNLAC-CKFYLGQYIEA  110 (557)
T ss_pred             cccchhHHHHHHHhhccchhhhHHHHHHHHHHHH---hhccHHHHHHHHHHHhccCCCCcccchhHHH-HHHHHHHHHHH
Confidence            4466667777666654321   355788888887   4466677888887777633223467766442 22222334455


Q ss_pred             HHHHHHHHhCChhh------------HHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchh
Q 013489          113 STVFEKSLLCAFST------------FEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG  180 (442)
Q Consensus       113 ~~i~~~al~~~~~~------------~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~  180 (442)
                      .++-.+|-..+...            -.....+....-+.+..++       ....+.-+|..|++|+++....+.+++.
T Consensus       111 ~~~~~ka~k~pL~~RLlfhlahklndEk~~~~fh~~LqD~~EdqL-------SLAsvhYmR~HYQeAIdvYkrvL~dn~e  183 (557)
T KOG3785|consen  111 KSIAEKAPKTPLCIRLLFHLAHKLNDEKRILTFHSSLQDTLEDQL-------SLASVHYMRMHYQEAIDVYKRVLQDNPE  183 (557)
T ss_pred             HHHHhhCCCChHHHHHHHHHHHHhCcHHHHHHHHHHHhhhHHHHH-------hHHHHHHHHHHHHHHHHHHHHHHhcChh
Confidence            55544443332210            0000011111111111111       1124566889999999999888777666


Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHH
Q 013489          181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLE  218 (442)
Q Consensus       181 ~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~  218 (442)
                      ..-+-.+.|-.++++. -++-+.+++.-.++.+|+++-
T Consensus       184 y~alNVy~ALCyyKlD-Yydvsqevl~vYL~q~pdSti  220 (557)
T KOG3785|consen  184 YIALNVYMALCYYKLD-YYDVSQEVLKVYLRQFPDSTI  220 (557)
T ss_pred             hhhhHHHHHHHHHhcc-hhhhHHHHHHHHHHhCCCcHH
Confidence            6556666666667777 788999999999999998763

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=96.98  E-value=0.056  Score=45.09  Aligned_cols=102  Identities=9%  Similarity=-0.068  Sum_probs=86.2

Q ss_pred             hHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHH
Q 013489           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSL   99 (442)
Q Consensus        20 ~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~   99 (442)
                      ++.++..-.|+......|+++.+..+|+-.+...|.+...|.....-.. ..++.+.+...|.+|+..-|+++.......
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 TQPLNTLYRYAMQLMEVKEFAGAARLFQLLTIYDAWSFDYWFRLGECCQ-AQKHWGEAIYAYGRAAQIKIDAPQAPWAAA  110 (157)
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHH-HHhhHHHHHHHHHHHHhcCCCCchHHHHHH
Confidence            5677777788888889999999999999999999999999999997655 345667899999999999998888777655


Q ss_pred             HHHHHccCCHHHHHHHHHHHHhCC
Q 013489          100 LSLERSRASEEEISTVFEKSLLCA  123 (442)
Q Consensus       100 ~~le~~~~~~~~~~~i~~~al~~~  123 (442)
                      . +....++.+.++..|+.++...
T Consensus       111 ~-c~L~lG~~~~A~~aF~~Ai~~~  133 (157)
T PRK15363        111 E-CYLACDNVCYAIKALKAVVRIC  133 (157)
T ss_pred             H-HHHHcCCHHHHHHHHHHHHHHh
Confidence            4 4455799999999999999643

>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=96.98  E-value=0.0061  Score=45.21  Aligned_cols=81  Identities=16%  Similarity=0.197  Sum_probs=52.9

Q ss_pred             HHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHH
Q 013489          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRC  243 (442)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ra  243 (442)
                      ++.|..++...+...+....++...+.+....+ +++.|..+|+.++...|....+|...+.+....|+.+.|..++.++
T Consensus        16 ~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~   94 (100)
T cd00189          16 YDEALEYYEKALELDPDNADAYYNLAAAYYKLG-KYEEALEDYEKALELDPDNAKAYYNLGLAYYKLGKYEEALEAYEKA   94 (100)
T ss_pred             HHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHH-HHHHHHHHHHHHHhCCCcchhHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            344444444433333333356666666666666 7777888888877777776677777777777777777777777777


Q ss_pred             Hh
Q 013489          244 YS  245 (442)
Q Consensus       244 l~  245 (442)
                      +.
T Consensus        95 ~~   96 (100)
T cd00189          95 LE   96 (100)
T ss_pred             Hc
Confidence            64

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=96.95  E-value=0.051  Score=45.28  Aligned_cols=91  Identities=12%  Similarity=0.045  Sum_probs=72.0

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHH
Q 013489          187 YWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFERE  266 (442)
Q Consensus       187 ~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~  266 (442)
                      .++-.....| +++.|..+|+-++..+|.+...|..+.-.....|++..|...|.+|+.  +.++.|.-.+.. -.---.
T Consensus        40 ~~A~~ly~~G-~l~~A~~~f~~L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~--L~~ddp~~~~~a-g~c~L~  115 (157)
T PRK15363         40 RYAMQLMEVK-EFAGAARLFQLLTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQ--IKIDAPQAPWAA-AECYLA  115 (157)
T ss_pred             HHHHHHHHCC-CHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHh--cCCCCchHHHHH-HHHHHH
Confidence            3455556777 999999999999999999999999999999999999999999999997  566777655543 333344


Q ss_pred             hCCHhhHHHHHHhhc
Q 013489          267 YGTLEDFDHSVQKVT  281 (442)
Q Consensus       267 ~G~~~~~~~~~~~~~  281 (442)
                      .|+++.-..++..++
T Consensus       116 lG~~~~A~~aF~~Ai  130 (157)
T PRK15363        116 CDNVCYAIKALKAVV  130 (157)
T ss_pred             cCCHHHHHHHHHHHH
Confidence            688776666665543

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=96.93  E-value=0.0019  Score=64.69  Aligned_cols=54  Identities=17%  Similarity=0.233  Sum_probs=46.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCC---CCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDK---FTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~---~~g~~~g~~fv~f~  441 (442)
                      +...+++|||||++.+++..|-..|..||+|.+++|+..+   ...+.+.+|||.|.
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafm  227 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFM  227 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeeh
Confidence            4556789999999999999999999999999999998764   24567789999884

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=96.93  E-value=0.032  Score=51.18  Aligned_cols=113  Identities=13%  Similarity=0.097  Sum_probs=91.8

Q ss_pred             HHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc--chhhHHHHHHHHH
Q 013489            7 HLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL--KVGNVVRDVYSRA   84 (442)
Q Consensus         7 ~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~--~~~~~~~~v~erA   84 (442)
                      ..|..|..+|.    +.+.|.-....-...|+...+..-|.+|+...|.++++|..|..-+....  .....+..+|.+|
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            45777777776    88899999999999999999999999999999999999999998776543  3445689999999


Q ss_pred             HHcCCCcHH-HHHHHHHHHHHccCCHHHHHHHHHHHHhCChh
Q 013489           85 TKNCPWVGE-LWVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus        85 l~~~p~s~~-lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                      ++.-|.... +|..-+..++  .++..++...|+..+...+.
T Consensus       220 l~~D~~~iral~lLA~~afe--~g~~~~A~~~Wq~lL~~lp~  259 (287)
T COG4235         220 LALDPANIRALSLLAFAAFE--QGDYAEAAAAWQMLLDLLPA  259 (287)
T ss_pred             HhcCCccHHHHHHHHHHHHH--cccHHHHHHHHHHHHhcCCC
Confidence            999987654 4444344444  58899999999999976554

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=96.86  E-value=0.0013  Score=54.46  Aligned_cols=37  Identities=24%  Similarity=0.469  Sum_probs=33.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeC
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHD  426 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~  426 (442)
                      -.+.||||||+..+++.+|+..|..||.|.+|=|-..
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn   45 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN   45 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec
Confidence            3679999999999999999999999999999866554

>KOG2003 consensus TPR repeat-containing protein [General function prediction only]

Probab=96.86  E-value=0.49  Score=45.76  Aligned_cols=189  Identities=13%  Similarity=0.038  Sum_probs=119.2

Q ss_pred             HHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHH
Q 013489           31 KYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEE  110 (442)
Q Consensus        31 ~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~  110 (442)
                      .|.....++..+..+-..||...-.++..-.+-.+... ..++.+++...|..|+++-..|.+.....-...+ ..++.+
T Consensus       464 ~flqggk~~~~aqqyad~aln~dryn~~a~~nkgn~~f-~ngd~dka~~~ykeal~ndasc~ealfniglt~e-~~~~ld  541 (840)
T KOG2003|consen  464 RFLQGGKDFADAQQYADIALNIDRYNAAALTNKGNIAF-ANGDLDKAAEFYKEALNNDASCTEALFNIGLTAE-ALGNLD  541 (840)
T ss_pred             HHHhcccchhHHHHHHHHHhcccccCHHHhhcCCceee-ecCcHHHHHHHHHHHHcCchHHHHHHHHhcccHH-HhcCHH
Confidence            33333446777887888888876666665555544443 2356788999999999987766654443222233 367888


Q ss_pred             HHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHH
Q 013489          111 EISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAH  190 (442)
Q Consensus       111 ~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~  190 (442)
                      ++...|-+.-..-..++.-.+.+-..|                     .+.+.-.+|++++.+.....+....+....+.
T Consensus       542 eald~f~klh~il~nn~evl~qianiy---------------------e~led~aqaie~~~q~~slip~dp~ilskl~d  600 (840)
T KOG2003|consen  542 EALDCFLKLHAILLNNAEVLVQIANIY---------------------ELLEDPAQAIELLMQANSLIPNDPAILSKLAD  600 (840)
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHH---------------------HHhhCHHHHHHHHHHhcccCCCCHHHHHHHHH
Confidence            888888774433333333333222111                     01122234566666655555666678889999


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHhchhHHHH--HHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          191 LEQSMGKDMVSARGVWERLLKISGAMLEA--WQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       191 ~e~~~~~~~~~ar~i~~~~l~~~~~~~~~--w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ++-.-| +..+|-+++-.....+|.+.+.  |+..+-++  ..-.+++...|++|.-
T Consensus       601 lydqeg-dksqafq~~ydsyryfp~nie~iewl~ayyid--tqf~ekai~y~ekaal  654 (840)
T KOG2003|consen  601 LYDQEG-DKSQAFQCHYDSYRYFPCNIETIEWLAAYYID--TQFSEKAINYFEKAAL  654 (840)
T ss_pred             Hhhccc-chhhhhhhhhhcccccCcchHHHHHHHHHHHh--hHHHHHHHHHHHHHHh
Confidence            988888 8999999999988889998773  55433322  2234677788888763

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.86  E-value=0.0017  Score=65.21  Aligned_cols=48  Identities=33%  Similarity=0.401  Sum_probs=41.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCC----CcceEEEEee
Q 013489          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGK----SRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~----~~g~~fv~f~  441 (442)
                      ++||.||+++++.+++..+|...|.|.++.|...+ .+.    |.|||||+|.
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkk-d~~~k~lSmGfgFVEF~  568 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKK-DPANKYLSMGFGFVEFA  568 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccc-cccccccccceeEEEec
Confidence            49999999999999999999999999999887653 332    5599999996

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.86  E-value=0.0092  Score=42.94  Aligned_cols=55  Identities=22%  Similarity=0.191  Sum_probs=50.5

Q ss_pred             HHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          191 LEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       191 ~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      +....+ +++.|.+++++++..+|+++.+|..++.+....|++..|...|++++..
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            345566 8999999999999999999999999999999999999999999999973

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=96.84  E-value=0.0016  Score=63.50  Aligned_cols=52  Identities=19%  Similarity=0.214  Sum_probs=44.2

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEe
Q 013489          384 RTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIY  440 (442)
Q Consensus       384 ~~~~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f  440 (442)
                      +...+...++|+|-|||..++.++|+.+|+.||.|+.|+     .|...+|..||+|
T Consensus        68 p~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir-----~t~~~~~~~~v~F  119 (549)
T KOG4660|consen   68 PSEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIR-----ETPNKRGIVFVEF  119 (549)
T ss_pred             CCcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhh-----cccccCceEEEEE
Confidence            333456678999999999999999999999999999975     4555689999998

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.84  E-value=0.0064  Score=43.78  Aligned_cols=60  Identities=20%  Similarity=0.145  Sum_probs=51.1

Q ss_pred             HhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHH
Q 013489           34 QSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGEL   94 (442)
Q Consensus        34 ~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~l   94 (442)
                      ...++++.+..+++++|..+|.++.+|..++..+... +....+...|++++..+|.....
T Consensus         6 ~~~~~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~-g~~~~A~~~l~~~l~~~p~~~~~   65 (73)
T PF13371_consen    6 LQQEDYEEALEVLERALELDPDDPELWLQRARCLFQL-GRYEEALEDLERALELSPDDPDA   65 (73)
T ss_pred             HhCCCHHHHHHHHHHHHHhCcccchhhHHHHHHHHHh-ccHHHHHHHHHHHHHHCCCcHHH
Confidence            4578899999999999999999999999999887754 45677999999999999976554

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=96.81  E-value=0.15  Score=49.81  Aligned_cols=87  Identities=14%  Similarity=0.039  Sum_probs=61.8

Q ss_pred             HHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHH
Q 013489           33 EQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEI  112 (442)
Q Consensus        33 e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~  112 (442)
                      ....|.++.+...+.-.+...|.|+-+|..-...+...++. ..+.+-|++|+...|.+.-+|..|...+-. .+...++
T Consensus       316 ~~~~~~~d~A~~~l~~L~~~~P~N~~~~~~~~~i~~~~nk~-~~A~e~~~kal~l~P~~~~l~~~~a~all~-~g~~~ea  393 (484)
T COG4783         316 TYLAGQYDEALKLLQPLIAAQPDNPYYLELAGDILLEANKA-KEAIERLKKALALDPNSPLLQLNLAQALLK-GGKPQEA  393 (484)
T ss_pred             HHHhcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCh-HHHHHHHHHHHhcCCCccHHHHHHHHHHHh-cCChHHH
Confidence            33456777788888888888888888888888777765544 447788888888888888888888876654 4444455


Q ss_pred             HHHHHHHHh
Q 013489          113 STVFEKSLL  121 (442)
Q Consensus       113 ~~i~~~al~  121 (442)
                      ..++++.+.
T Consensus       394 i~~L~~~~~  402 (484)
T COG4783         394 IRILNRYLF  402 (484)
T ss_pred             HHHHHHHhh
Confidence            555555443

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=96.77  E-value=0.045  Score=53.30  Aligned_cols=101  Identities=16%  Similarity=-0.039  Sum_probs=81.9

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      .++..+...|...|.    |.-.|..-.+.....+....+...|.+++...|...-+|+.|.+.+.+.+ .+..+..++.
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            455556666666664    66566666676778899999999999999999999999999999888554 4557889999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCC
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRAS  108 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~  108 (442)
                      +.+...|.....|...++..+.....
T Consensus       399 ~~~~~~p~dp~~w~~LAqay~~~g~~  424 (484)
T COG4783         399 RYLFNDPEDPNGWDLLAQAYAELGNR  424 (484)
T ss_pred             HHhhcCCCCchHHHHHHHHHHHhCch
Confidence            99999999999999999877764443

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=96.76  E-value=0.063  Score=46.11  Aligned_cols=81  Identities=12%  Similarity=-0.025  Sum_probs=61.9

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCC---HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVS---SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRS   98 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~---~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y   98 (442)
                      ....+...+......|+++.+..+|++++...|..   ..+|...+..+.. .+..+.+...|.+|+...|.....|..+
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~-~g~~~~A~~~~~~al~~~p~~~~~~~~l  112 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYAS-NGEHDKALEYYHQALELNPKQPSALNNI  112 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHhCcccHHHHHHH
Confidence            44467777777778899999999999999876653   3567766665553 4566789999999999999888888776


Q ss_pred             HHHHH
Q 013489           99 LLSLE  103 (442)
Q Consensus        99 ~~~le  103 (442)
                      ...+.
T Consensus       113 g~~~~  117 (172)
T PRK02603        113 AVIYH  117 (172)
T ss_pred             HHHHH
Confidence            65443

>PF13893 RRM_5: RNA recognition motif

Probab=96.73  E-value=0.0023  Score=43.56  Aligned_cols=29  Identities=31%  Similarity=0.480  Sum_probs=24.2

Q ss_pred             HHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          408 LRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       408 l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      |..+|++||.|.++.+..++     +|+|||+|.
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~   29 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFA   29 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEES
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEEC
Confidence            67899999999999987763     699999995

(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 ....

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=96.70  E-value=0.053  Score=42.83  Aligned_cols=99  Identities=10%  Similarity=0.070  Sum_probs=73.7

Q ss_pred             HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCC---HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCc---HHHHHHH
Q 013489           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVS---SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV---GELWVRS   98 (442)
Q Consensus        25 ~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~---~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s---~~lW~~y   98 (442)
                      .+..-+......|+.+.+..+|++++..+|.+   ...+..++..+... +..+.+...|++++...|..   ..+|...
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~   82 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQ-GKYADAAKAFLAVVKKYPKSPKAPDALLKL   82 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhh-ccHHHHHHHHHHHHHHCCCCCcccHHHHHH
Confidence            45555666677899999999999999988876   45666666655533 45677999999999988874   4567666


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHhCChh
Q 013489           99 LLSLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus        99 ~~~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                      ...+.. .+..+.+...|++++...+.
T Consensus        83 ~~~~~~-~~~~~~A~~~~~~~~~~~p~  108 (119)
T TIGR02795        83 GMSLQE-LGDKEKAKATLQQVIKRYPG  108 (119)
T ss_pred             HHHHHH-hCChHHHHHHHHHHHHHCcC
Confidence            665544 67778889999998876555

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.

>smart00777 Mad3_BUB1_I Mad3/BUB1 hoMad3/BUB1 homology region 1

Probab=96.69  E-value=0.029  Score=45.03  Aligned_cols=75  Identities=16%  Similarity=0.310  Sum_probs=55.0

Q ss_pred             HHHHHHHHHHHh--hhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh-chh-HHHHHHHHHHHHHhcccHHHH
Q 013489          161 RETFQRASDYLS--EQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI-SGA-MLEAWQSYISMEIELDHINEA  236 (442)
Q Consensus       161 r~~~~~a~~~l~--~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~-~~~-~~~~w~~~~~~e~~~g~~~~a  236 (442)
                      ...+++|+..+.  ..+.+.+..+++|+.|+++.   + +   .+.+|.-+... -+. .+.+|..|+.+....|++..|
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            345566665542  23345566789999998652   3 3   57788888877 444 456999999999999999999


Q ss_pred             HHHHHH
Q 013489          237 RSIYKR  242 (442)
Q Consensus       237 r~i~~r  242 (442)
                      ..||+.
T Consensus       119 ~~iy~~  124 (125)
T smart00777      119 DEVYQL  124 (125)
T ss_pred             HHHHHc
Confidence            999975

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.

>PRK11906 transcriptional regulator; Provisional

Probab=96.66  E-value=0.12  Score=50.59  Aligned_cols=174  Identities=12%  Similarity=-0.021  Sum_probs=103.7

Q ss_pred             HHHcCCCcH---HHH--HHHHHHHHH----ccCCHHHHHHHHHHHH---hCChhhHHHHHHHHHHHHHHHHHHhhccCcc
Q 013489           84 ATKNCPWVG---ELW--VRSLLSLER----SRASEEEISTVFEKSL---LCAFSTFEEYLDLFLTRIDGLRRRILFSGEV  151 (442)
Q Consensus        84 Al~~~p~s~---~lW--~~y~~~le~----~~~~~~~~~~i~~~al---~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~  151 (442)
                      +.+.-|.+.   .-|  -.|++-...    .......+..+|.+|+   ...|.....|-.  +++|... +....... 
T Consensus       240 ~~r~~~~~l~~~~a~~~d~ylrg~~~~~~~t~~~~~~Al~lf~ra~~~~~ldp~~a~a~~~--lA~~h~~-~~~~g~~~-  315 (458)
T PRK11906        240 SVRLAKQDQGYKNHYLSDEMLAGKKELYDFTPESIYRAMTIFDRLQNKSDIQTLKTECYCL--LAECHMS-LALHGKSE-  315 (458)
T ss_pred             hhcCCCCCcccccchhhHHHHHHHHHhhccCHHHHHHHHHHHHHHhhcccCCcccHHHHHH--HHHHHHH-HHHhcCCC-
Confidence            444446666   778  777764443    1223466888899999   444443333322  2222111 11111111 


Q ss_pred             chhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcc
Q 013489          152 EGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELD  231 (442)
Q Consensus       152 ~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g  231 (442)
                       ...+........++|.+       .++......-..+......+ +.+.|...|++++..+|+....|..+.....-.|
T Consensus       316 -~~~~~~~a~~~A~rAve-------ld~~Da~a~~~~g~~~~~~~-~~~~a~~~f~rA~~L~Pn~A~~~~~~~~~~~~~G  386 (458)
T PRK11906        316 -LELAAQKALELLDYVSD-------ITTVDGKILAIMGLITGLSG-QAKVSHILFEQAKIHSTDIASLYYYRALVHFHNE  386 (458)
T ss_pred             -chHHHHHHHHHHHHHHh-------cCCCCHHHHHHHHHHHHhhc-chhhHHHHHHHHhhcCCccHHHHHHHHHHHHHcC
Confidence             11223233333344433       22222223333444445556 6999999999999999999999999999988899


Q ss_pred             cHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHh
Q 013489          232 HINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLE  271 (442)
Q Consensus       232 ~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~  271 (442)
                      +.+.|+..+++|+.. .|......|...|+..--.+|-.+
T Consensus       387 ~~~~a~~~i~~alrL-sP~~~~~~~~~~~~~~~~~~~~~~  425 (458)
T PRK11906        387 KIEEARICIDKSLQL-EPRRRKAVVIKECVDMYVPNPLKN  425 (458)
T ss_pred             CHHHHHHHHHHHhcc-CchhhHHHHHHHHHHHHcCCchhh
Confidence            999999999999973 243444567788886654444333

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=96.65  E-value=0.042  Score=50.31  Aligned_cols=99  Identities=14%  Similarity=-0.036  Sum_probs=78.5

Q ss_pred             HHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHc
Q 013489           26 YMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERS  105 (442)
Q Consensus        26 w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~  105 (442)
                      .+.=.+-.++.+++..|+..|.+||..+|.+.-+..+-+.-+. .++..+.+.+-++.||+..|.....|...-+ ....
T Consensus        84 LK~eGN~~m~~~~Y~eAv~kY~~AI~l~P~nAVyycNRAAAy~-~Lg~~~~AVkDce~Al~iDp~yskay~RLG~-A~~~  161 (304)
T KOG0553|consen   84 LKNEGNKLMKNKDYQEAVDKYTEAIELDPTNAVYYCNRAAAYS-KLGEYEDAVKDCESALSIDPHYSKAYGRLGL-AYLA  161 (304)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHhcCCCcchHHHHHHHHHH-HhcchHHHHHHHHHHHhcChHHHHHHHHHHH-HHHc
Confidence            3333444456678999999999999999999999998887555 3455677889999999999998888888655 4445


Q ss_pred             cCCHHHHHHHHHHHHhCChhh
Q 013489          106 RASEEEISTVFEKSLLCAFST  126 (442)
Q Consensus       106 ~~~~~~~~~i~~~al~~~~~~  126 (442)
                      .+.++++..-|.+||...|.+
T Consensus       162 ~gk~~~A~~aykKaLeldP~N  182 (304)
T KOG0553|consen  162 LGKYEEAIEAYKKALELDPDN  182 (304)
T ss_pred             cCcHHHHHHHHHhhhccCCCc
Confidence            678888888899999988773

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=96.64  E-value=0.013  Score=43.57  Aligned_cols=78  Identities=13%  Similarity=0.108  Sum_probs=55.1

Q ss_pred             HHHHHHHHhhhhcCch--hhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHH
Q 013489          164 FQRASDYLSEQMKNTD--GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYK  241 (442)
Q Consensus       164 ~~~a~~~l~~~~~~~~--~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~  241 (442)
                      ++.|+.++++.+...+  +...+|...+......| +..+|-.++++ +...+.+..+..-++......|+++.|+.+|+
T Consensus         5 y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~-~y~~A~~~~~~-~~~~~~~~~~~~l~a~~~~~l~~y~eAi~~l~   82 (84)
T PF12895_consen    5 YENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQG-KYEEAIELLQK-LKLDPSNPDIHYLLARCLLKLGKYEEAIKALE   82 (84)
T ss_dssp             HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTT-HHHHHHHHHHC-HTHHHCHHHHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCC-CHHHHHHHHHH-hCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHh
Confidence            3444444444443222  13446666788888888 89999999998 66777777766666888888899999999988


Q ss_pred             HH
Q 013489          242 RC  243 (442)
Q Consensus       242 ra  243 (442)
                      +|
T Consensus        83 ~~   84 (84)
T PF12895_consen   83 KA   84 (84)
T ss_dssp             HH
T ss_pred             cC
Confidence            75

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=96.57  E-value=0.77  Score=44.14  Aligned_cols=243  Identities=10%  Similarity=-0.007  Sum_probs=129.3

Q ss_pred             HHHHHHHHHHHHhcC-ChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 013489           23 FQQYMIYLKYEQSSG-DPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        23 ~~~w~~y~~~e~~~g-~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~  101 (442)
                      ...|+.-..+.-... .......++-.-....|.|+.+-...++.+...+ +...+...|+++....|....---.|...
T Consensus       197 ls~wika~Aq~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~G-dn~~a~~~Fe~~~~~dpy~i~~MD~Ya~L  275 (564)
T KOG1174|consen  197 LSKWIKALAQMFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNG-DYFQAEDIFSSTLCANPDNVEAMDLYAVL  275 (564)
T ss_pred             HHHHHHHHHHHHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhc-CchHHHHHHHHHhhCChhhhhhHHHHHHH
Confidence            346776555554332 2334455667777789999999999998777554 44558899999999888765544455543


Q ss_pred             HHHccCCHHHHHHHHHHHHhCChhhHHHH---H-HHH-----HHHHHHHHHHhhc-cCccchhhhHHHH---HHHHHHHH
Q 013489          102 LERSRASEEEISTVFEKSLLCAFSTFEEY---L-DLF-----LTRIDGLRRRILF-SGEVEGVLDYSLI---RETFQRAS  168 (442)
Q Consensus       102 le~~~~~~~~~~~i~~~al~~~~~~~~~~---~-~~~-----~~~~~~l~rr~~~-~~~~~~~~~~~~~---r~~~~~a~  168 (442)
                      |.+ .+..+....+-.+.+.....+....   . -+|     ...+.+...-+.. ....+.++--..+   ...-+.|.
T Consensus       276 L~~-eg~~e~~~~L~~~Lf~~~~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~~r~~~alilKG~lL~~~~R~~~A~  354 (564)
T KOG1174|consen  276 LGQ-EGGCEQDSALMDYLFAKVKYTASHWFVHAQLLYDEKKFERALNFVEKCIDSEPRNHEALILKGRLLIALERHTQAV  354 (564)
T ss_pred             HHh-ccCHhhHHHHHHHHHhhhhcchhhhhhhhhhhhhhhhHHHHHHHHHHHhccCcccchHHHhccHHHHhccchHHHH
Confidence            443 4667777777777665432211111   0 111     1111111111110 0111111100000   00012222


Q ss_pred             HHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHH-HHHHhc-ccHHHHHHHHHHHHhc
Q 013489          169 DYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYI-SMEIEL-DHINEARSIYKRCYSK  246 (442)
Q Consensus       169 ~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~-~~e~~~-g~~~~ar~i~~ral~~  246 (442)
                      -.+..+..-.|..+++|.-...-+...+ .+..|--+-+.+++.+|.+.....-+. ...... .-.++|.++|++++. 
T Consensus       355 IaFR~Aq~Lap~rL~~Y~GL~hsYLA~~-~~kEA~~~An~~~~~~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~-  432 (564)
T KOG1174|consen  355 IAFRTAQMLAPYRLEIYRGLFHSYLAQK-RFKEANALANWTIRLFQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLK-  432 (564)
T ss_pred             HHHHHHHhcchhhHHHHHHHHHHHHhhc-hHHHHHHHHHHHHHHhhcchhhhhhhcceeeccCchhHHHHHHHHHhhhc-
Confidence            2222221123444555555555555667 788888888888888888776333221 211111 246899999999997 


Q ss_pred             ccCCCChHHHH--HHHHHHHHHhCCH
Q 013489          247 RFTGTGSEDIC--HAWLRFEREYGTL  270 (442)
Q Consensus       247 ~~~~~~~~~i~--~~~~~fE~~~G~~  270 (442)
                       +.++....+.  -.....|..+|+.
T Consensus       433 -~~P~Y~~AV~~~AEL~~~Eg~~~D~  457 (564)
T KOG1174|consen  433 -INPIYTPAVNLIAELCQVEGPTKDI  457 (564)
T ss_pred             -cCCccHHHHHHHHHHHHhhCccchH
Confidence             3445444332  3445566666654

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=96.56  E-value=0.003  Score=62.17  Aligned_cols=54  Identities=19%  Similarity=0.314  Sum_probs=50.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....+.+|||+||...++..+.++...||.+...+++.|..+|-++||||.+|.
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~  339 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYC  339 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeee
Confidence            345669999999999999999999999999999999999999999999999985

>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=96.45  E-value=0.09  Score=51.25  Aligned_cols=104  Identities=16%  Similarity=0.184  Sum_probs=66.5

Q ss_pred             HHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHH
Q 013489          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRC  243 (442)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ra  243 (442)
                      ++.|+.+++......+.   ++...|++....+ +..+|-.+++++++..|.++.++...++|....++++-|..+.++|
T Consensus       185 ~~~ai~lle~L~~~~pe---v~~~LA~v~l~~~-~E~~AI~ll~~aL~~~p~d~~LL~~Qa~fLl~k~~~~lAL~iAk~a  260 (395)
T PF09295_consen  185 YDEAIELLEKLRERDPE---VAVLLARVYLLMN-EEVEAIRLLNEALKENPQDSELLNLQAEFLLSKKKYELALEIAKKA  260 (395)
T ss_pred             HHHHHHHHHHHHhcCCc---HHHHHHHHHHhcC-cHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            45555555554433332   4455666665555 6677888888888888877888888888888888888888888888


Q ss_pred             HhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHH
Q 013489          244 YSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSV  277 (442)
Q Consensus       244 l~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~  277 (442)
                      +..  .+    .-+..|..+-+.|=..++++.|+
T Consensus       261 v~l--sP----~~f~~W~~La~~Yi~~~d~e~AL  288 (395)
T PF09295_consen  261 VEL--SP----SEFETWYQLAECYIQLGDFENAL  288 (395)
T ss_pred             HHh--Cc----hhHHHHHHHHHHHHhcCCHHHHH
Confidence            862  22    23345555555554444444443

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=96.41  E-value=0.0025  Score=58.41  Aligned_cols=53  Identities=13%  Similarity=0.240  Sum_probs=45.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCC--CeeEEEEeeCCCCCCCcceEEEEe
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVG--GVSSIRILHDKFTGKSRVVQSDIY  440 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G--~i~~~~~~~~~~~g~~~g~~fv~f  440 (442)
                      ......+|||||-+.+|++||.+.....|  .+.++++..++.+|+++|||.|..
T Consensus        77 ~Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~  131 (498)
T KOG4849|consen   77 EGRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVL  131 (498)
T ss_pred             cCceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEe
Confidence            34556899999999999999998887777  667888888888999999999864

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=96.41  E-value=0.68  Score=41.68  Aligned_cols=93  Identities=8%  Similarity=0.080  Sum_probs=68.7

Q ss_pred             chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHH
Q 013489          178 TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDIC  257 (442)
Q Consensus       178 ~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~  257 (442)
                      .++..+.|...+-.+.+.| +.+.||.-|.++++..|+...+.....-.....|+.+.|+.++.++...  + .....|-
T Consensus       130 ~p~d~~~~~~lgaaldq~G-r~~~Ar~ay~qAl~L~~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~--~-~ad~~v~  205 (257)
T COG5010         130 APTDWEAWNLLGAALDQLG-RFDEARRAYRQALELAPNEPSIANNLGMSLLLRGDLEDAETLLLPAYLS--P-AADSRVR  205 (257)
T ss_pred             CCCChhhhhHHHHHHHHcc-ChhHHHHHHHHHHHhccCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhC--C-CCchHHH
Confidence            3444456666666667888 9999999999999999999988888888888899999999999999863  3 3233555


Q ss_pred             HHHHHHHHHhCCHhhHH
Q 013489          258 HAWLRFEREYGTLEDFD  274 (442)
Q Consensus       258 ~~~~~fE~~~G~~~~~~  274 (442)
                      +...-.-...|+.+.-+
T Consensus       206 ~NLAl~~~~~g~~~~A~  222 (257)
T COG5010         206 QNLALVVGLQGDFREAE  222 (257)
T ss_pred             HHHHHHHhhcCChHHHH
Confidence            55444444456654433

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=96.38  E-value=0.89  Score=42.66  Aligned_cols=235  Identities=12%  Similarity=0.034  Sum_probs=134.5

Q ss_pred             HhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHH
Q 013489           21 EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (442)
Q Consensus        21 ~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~  100 (442)
                      .+.+-......-..-.|.+..+..-|..||..+|++......-+.-...-++. ..+..-+.|.+..-|.-...-+....
T Consensus        36 advekhlElGk~lla~~Q~sDALt~yHaAve~dp~~Y~aifrRaT~yLAmGks-k~al~Dl~rVlelKpDF~~ARiQRg~  114 (504)
T KOG0624|consen   36 ADVEKHLELGKELLARGQLSDALTHYHAAVEGDPNNYQAIFRRATVYLAMGKS-KAALQDLSRVLELKPDFMAARIQRGV  114 (504)
T ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhcCC-ccchhhHHHHHhcCccHHHHHHHhch
Confidence            34444444444334456677778888888888887665443333222212222 23566778888888865444444333


Q ss_pred             HHHHccCCHHHHHHHHHHHHhCChhh--HHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHH-----HHHHHHHHhh
Q 013489          101 SLERSRASEEEISTVFEKSLLCAFST--FEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRET-----FQRASDYLSE  173 (442)
Q Consensus       101 ~le~~~~~~~~~~~i~~~al~~~~~~--~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~-----~~~a~~~l~~  173 (442)
                      .+. ..+..+.+..-|...|+..++.  ..+..+-. ..++-.+            .-+..+...     ...++.++..
T Consensus       115 vll-K~Gele~A~~DF~~vl~~~~s~~~~~eaqskl-~~~~e~~------------~l~~ql~s~~~~GD~~~ai~~i~~  180 (504)
T KOG0624|consen  115 VLL-KQGELEQAEADFDQVLQHEPSNGLVLEAQSKL-ALIQEHW------------VLVQQLKSASGSGDCQNAIEMITH  180 (504)
T ss_pred             hhh-hcccHHHHHHHHHHHHhcCCCcchhHHHHHHH-HhHHHHH------------HHHHHHHHHhcCCchhhHHHHHHH
Confidence            333 3678899999999999776641  11111100 0000000            000111111     2345555555


Q ss_pred             hhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCCh
Q 013489          174 QMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGS  253 (442)
Q Consensus       174 ~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~  253 (442)
                      .+...+=...++.+-++.+...| .+..|..=+..+-+...++.+.......++...|+.+........||.  +.++ .
T Consensus       181 llEi~~Wda~l~~~Rakc~i~~~-e~k~AI~Dlk~askLs~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLK--ldpd-H  256 (504)
T KOG0624|consen  181 LLEIQPWDASLRQARAKCYIAEG-EPKKAIHDLKQASKLSQDNTEGHYKISQLLYTVGDAENSLKEIRECLK--LDPD-H  256 (504)
T ss_pred             HHhcCcchhHHHHHHHHHHHhcC-cHHHHHHHHHHHHhccccchHHHHHHHHHHHhhhhHHHHHHHHHHHHc--cCcc-h
Confidence            44433334457777777777778 788888778777777788888888888888888888888888888885  4433 2


Q ss_pred             HHHHHHHHHHHHHhCCHhhHH
Q 013489          254 EDICHAWLRFEREYGTLEDFD  274 (442)
Q Consensus       254 ~~i~~~~~~fE~~~G~~~~~~  274 (442)
                      ...|-.|..+-...-++++.+
T Consensus       257 K~Cf~~YKklkKv~K~les~e  277 (504)
T KOG0624|consen  257 KLCFPFYKKLKKVVKSLESAE  277 (504)
T ss_pred             hhHHHHHHHHHHHHHHHHHHH
Confidence            344444444444433444433

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=96.33  E-value=0.06  Score=49.29  Aligned_cols=89  Identities=19%  Similarity=0.185  Sum_probs=74.3

Q ss_pred             HHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHH
Q 013489          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYK  241 (442)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~  241 (442)
                      ..|+.|+..+..++.-.|...-+|..-|..+.++| .++.|.+=.+.+|..+|.+...|..........|+++.|..-|+
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            44666666666666656666668888888889999 89999999999999999999999999999999999999999999


Q ss_pred             HHHhcccCCCCh
Q 013489          242 RCYSKRFTGTGS  253 (442)
Q Consensus       242 ral~~~~~~~~~  253 (442)
                      +||.  +.+++.
T Consensus       174 KaLe--ldP~Ne  183 (304)
T KOG0553|consen  174 KALE--LDPDNE  183 (304)
T ss_pred             hhhc--cCCCcH
Confidence            9997  555544

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=96.21  E-value=0.92  Score=48.30  Aligned_cols=184  Identities=10%  Similarity=0.017  Sum_probs=107.5

Q ss_pred             CHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHH--HH-HH
Q 013489           56 SSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFE--EY-LD  132 (442)
Q Consensus        56 ~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~--~~-~~  132 (442)
                      ....|..|+....+    ...+...|-||++..|.-...|...-. +.+...+...++..|.+|+..+...+.  .+ .+
T Consensus       460 ~~~~w~a~~~~rK~----~~~al~ali~alrld~~~apaf~~LG~-iYrd~~Dm~RA~kCf~KAFeLDatdaeaaaa~ad  534 (1238)
T KOG1127|consen  460 NSEFWVALGCMRKN----SALALHALIRALRLDVSLAPAFAFLGQ-IYRDSDDMKRAKKCFDKAFELDATDAEAAAASAD  534 (1238)
T ss_pred             HHHHHHHHHHhhhh----HHHHHHHHHHHHhcccchhHHHHHHHH-HHHHHHHHHHHHHHHHHHhcCCchhhhhHHHHHH
Confidence            44677777764432    345778888888888877777776444 444334566788888888876554211  11 11


Q ss_pred             H------HHHHHHHHHHHhhccCccchhhhHHH------HHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHH
Q 013489          133 L------FLTRIDGLRRRILFSGEVEGVLDYSL------IRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMV  200 (442)
Q Consensus       133 ~------~~~~~~~l~rr~~~~~~~~~~~~~~~------~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~  200 (442)
                      .      |......+-+.............|-.      -...+..++..+..++...|..+..|.-..+.+...| .++
T Consensus       535 tyae~~~we~a~~I~l~~~qka~a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR~dPkD~n~W~gLGeAY~~sG-ry~  613 (1238)
T KOG1127|consen  535 TYAEESTWEEAFEICLRAAQKAPAFACKENWVQRGPYYLEAHNLHGAVCEFQSALRTDPKDYNLWLGLGEAYPESG-RYS  613 (1238)
T ss_pred             HhhccccHHHHHHHHHHHhhhchHHHHHhhhhhccccccCccchhhHHHHHHHHhcCCchhHHHHHHHHHHHHhcC-cee
Confidence            1      11111111110000000000000100      0012234455555555556777889999988888888 789


Q ss_pred             HHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          201 SARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       201 ~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      .|.++|.++....|.+.-.-..-+-++...|.+..+..++...+.
T Consensus       614 ~AlKvF~kAs~LrP~s~y~~fk~A~~ecd~GkYkeald~l~~ii~  658 (1238)
T KOG1127|consen  614 HALKVFTKASLLRPLSKYGRFKEAVMECDNGKYKEALDALGLIIY  658 (1238)
T ss_pred             hHHHhhhhhHhcCcHhHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            999999999988887765545555677778888888887777664

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=96.19  E-value=2  Score=44.95  Aligned_cols=85  Identities=8%  Similarity=0.061  Sum_probs=52.7

Q ss_pred             HHHHHHHcCCCHHHHHHHHHHH------HHh-----------------c-hhHHHHHHHHHHHHHhcccHHHHHHH----
Q 013489          188 WAHLEQSMGKDMVSARGVWERL------LKI-----------------S-GAMLEAWQSYISMEIELDHINEARSI----  239 (442)
Q Consensus       188 ~a~~e~~~~~~~~~ar~i~~~~------l~~-----------------~-~~~~~~w~~~~~~e~~~g~~~~ar~i----  239 (442)
                      .|+++...|++..+|-.+|.++      |..                 + .+.+.+...-++|-..+.++++|..+    
T Consensus      1027 aArYyEe~g~~~~~AVmLYHkAGm~~kALelAF~tqQf~aL~lIa~DLd~~sDp~ll~RcadFF~~~~qyekAV~lL~~a 1106 (1416)
T KOG3617|consen 1027 AARYYEELGGYAHKAVMLYHKAGMIGKALELAFRTQQFSALDLIAKDLDAGSDPKLLRRCADFFENNQQYEKAVNLLCLA 1106 (1416)
T ss_pred             HHHHHHHcchhhhHHHHHHHhhcchHHHHHHHHhhcccHHHHHHHHhcCCCCCHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence            3555566666777777776654      211                 1 23467888888888888888888776    


Q ss_pred             --HHHHHhcccC----------------C-CC-----hHHHHHHHHHHHHHhCCHhh
Q 013489          240 --YKRCYSKRFT----------------G-TG-----SEDICHAWLRFEREYGTLED  272 (442)
Q Consensus       240 --~~ral~~~~~----------------~-~~-----~~~i~~~~~~fE~~~G~~~~  272 (442)
                        |.+|++-...                . +.     ...|+....+|....|+...
T Consensus      1107 r~~~~AlqlC~~~nv~vtee~aE~mTp~Kd~~~~e~~R~~vLeqvae~c~qQG~Yh~ 1163 (1416)
T KOG3617|consen 1107 REFSGALQLCKNRNVRVTEEFAELMTPTKDDMPNEQERKQVLEQVAELCLQQGAYHA 1163 (1416)
T ss_pred             HHHHHHHHHHhcCCCchhHHHHHhcCcCcCCCccHHHHHHHHHHHHHHHHhccchHH
Confidence              4555532100                0 11     12577778888888887543

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=96.16  E-value=0.0054  Score=58.05  Aligned_cols=52  Identities=23%  Similarity=0.357  Sum_probs=43.6

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          385 TKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       385 ~~~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....+..|+|||.|||++.|+..|++-|..||.|..+.|+   ..|+++|  .|-|.
T Consensus       530 ~gaarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadim---e~GkskG--VVrF~  581 (608)
T KOG4212|consen  530 VGAARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM---ENGKSKG--VVRFF  581 (608)
T ss_pred             ccccccccEEEEecCCccccHHHHHHHHHhccceehhhhh---ccCCccc--eEEec
Confidence            3345678999999999999999999999999999999883   3688888  56663

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=96.09  E-value=0.2  Score=39.44  Aligned_cols=56  Identities=16%  Similarity=0.049  Sum_probs=32.8

Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHhchhH---HHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          189 AHLEQSMGKDMVSARGVWERLLKISGAM---LEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       189 a~~e~~~~~~~~~ar~i~~~~l~~~~~~---~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      +......+ +.+.|...|+.++..+|++   ...+..++......|+++.|..+|++++.
T Consensus         9 ~~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~   67 (119)
T TIGR02795         9 ALLVLKAG-DYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVK   67 (119)
T ss_pred             HHHHHHcC-CHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHH
Confidence            33334445 6666666666666665543   34555556666666666666666666664

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.

>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=96.00  E-value=0.084  Score=38.42  Aligned_cols=63  Identities=19%  Similarity=0.255  Sum_probs=51.2

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh---ch-h---HHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKI---SG-A---MLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~---~~-~---~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ..++...+.+....| ++++|...|+++++.   .+ +   ...++...+.+....|+++.|...|++|+.
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            456777888888888 999999999999976   22 2   244778888888899999999999999985

...

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=95.94  E-value=0.48  Score=37.89  Aligned_cols=92  Identities=17%  Similarity=0.076  Sum_probs=68.2

Q ss_pred             HHHHHHHHhcCChhhHHHHHHHHHhcCCCC---HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCC---cHHHHHHHHH
Q 013489           27 MIYLKYEQSSGDPGRVQLLYERAITDFPVS---SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPW---VGELWVRSLL  100 (442)
Q Consensus        27 ~~y~~~e~~~g~~~~~~~lyERal~~~p~~---~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~---s~~lW~~y~~  100 (442)
                      ...+......|+.+++..+|++++..-+..   ...++.+..-+. ..+..+.+..+++.++..+|.   +..++..++.
T Consensus         5 ~~~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr-~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al   83 (120)
T PF12688_consen    5 YELAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLR-NLGRYDEALALLEEALEEFPDDELNAALRVFLAL   83 (120)
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHH-HcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHH
Confidence            344444567899999999999999964433   467888887666 456678899999999999888   7888888887


Q ss_pred             HHHHccCCHHHHHHHHHHHH
Q 013489          101 SLERSRASEEEISTVFEKSL  120 (442)
Q Consensus       101 ~le~~~~~~~~~~~i~~~al  120 (442)
                      .+.. .+..+++...+-.++
T Consensus        84 ~L~~-~gr~~eAl~~~l~~l  102 (120)
T PF12688_consen   84 ALYN-LGRPKEALEWLLEAL  102 (120)
T ss_pred             HHHH-CCCHHHHHHHHHHHH
Confidence            7766 455555555555545

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=95.94  E-value=1.1  Score=39.62  Aligned_cols=63  Identities=24%  Similarity=0.241  Sum_probs=45.1

Q ss_pred             HHHHHHHhcCChhhHHHHHHHHHhcCCCCH-----HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHH
Q 013489           28 IYLKYEQSSGDPGRVQLLYERAITDFPVSS-----DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGE   93 (442)
Q Consensus        28 ~y~~~e~~~g~~~~~~~lyERal~~~p~~~-----~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~   93 (442)
                      .-+.-....|+...+...|+..+..+|.++     .+|+.++.|..   ++...+...|++.++..|.+..
T Consensus        10 ~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~---~~y~~A~~~~~~fi~~yP~~~~   77 (203)
T PF13525_consen   10 QKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQ---GDYEEAIAAYERFIKLYPNSPK   77 (203)
T ss_dssp             HHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHT---T-HHHHHHHHHHHHHH-TT-TT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHCCCCcc
Confidence            334445678999999999999999998765     57777776633   4567799999999999998763

>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=95.94  E-value=0.17  Score=49.42  Aligned_cols=76  Identities=14%  Similarity=0.073  Sum_probs=40.7

Q ss_pred             cCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHH
Q 013489           36 SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEIS  113 (442)
Q Consensus        36 ~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~  113 (442)
                      .++...+..+..++|..+|.+..++...+.|+.... ..+.|..+..+|+...|.....|...+. .+...++++.+.
T Consensus       213 ~~~E~~AI~ll~~aL~~~p~d~~LL~~Qa~fLl~k~-~~~lAL~iAk~av~lsP~~f~~W~~La~-~Yi~~~d~e~AL  288 (395)
T PF09295_consen  213 MNEEVEAIRLLNEALKENPQDSELLNLQAEFLLSKK-KYELALEIAKKAVELSPSEFETWYQLAE-CYIQLGDFENAL  288 (395)
T ss_pred             cCcHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHHhCchhHHHHHHHHH-HHHhcCCHHHHH
Confidence            344445555566666666666666666666555433 2345556666666666666666665554 222244444443

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=95.80  E-value=0.35  Score=41.18  Aligned_cols=78  Identities=12%  Similarity=-0.014  Sum_probs=61.1

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCH---HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS---DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRS   98 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~---~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y   98 (442)
                      ....|...+......|+++.+...|++++...|.+.   ..|......+. ..+..+.+...|++|+...|.....|...
T Consensus        34 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~-~~g~~~eA~~~~~~Al~~~~~~~~~~~~l  112 (168)
T CHL00033         34 EAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHT-SNGEHTKALEYYFQALERNPFLPQALNNM  112 (168)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHH-HcCCHHHHHHHHHHHHHhCcCcHHHHHHH
Confidence            456788888888889999999999999998766543   46777666555 44566789999999999989887777665


Q ss_pred             HH
Q 013489           99 LL  100 (442)
Q Consensus        99 ~~  100 (442)
                      ..
T Consensus       113 a~  114 (168)
T CHL00033        113 AV  114 (168)
T ss_pred             HH
Confidence            54

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=95.73  E-value=0.044  Score=40.73  Aligned_cols=81  Identities=16%  Similarity=0.095  Sum_probs=55.3

Q ss_pred             cCChhhHHHHHHHHHhcCCC--CHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHH
Q 013489           36 SGDPGRVQLLYERAITDFPV--SSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEIS  113 (442)
Q Consensus        36 ~g~~~~~~~lyERal~~~p~--~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~  113 (442)
                      +|+++.|..+|++++...|.  +...|...+.-+.. .+..+.+..++++ ...-|....++..+++.+.. .+..+++.
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~-~~~y~~A~~~~~~-~~~~~~~~~~~~l~a~~~~~-l~~y~eAi   78 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQ-QGKYEEAIELLQK-LKLDPSNPDIHYLLARCLLK-LGKYEEAI   78 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHH-TTHHHHHHHHHHC-HTHHHCHHHHHHHHHHHHHH-TT-HHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHH-CCCHHHHHHHHHH-hCCCCCCHHHHHHHHHHHHH-hCCHHHHH
Confidence            57888999999999999885  45677765555543 3456778888888 55555554555555664443 67788888


Q ss_pred             HHHHHH
Q 013489          114 TVFEKS  119 (442)
Q Consensus       114 ~i~~~a  119 (442)
                      .+|+++
T Consensus        79 ~~l~~~   84 (84)
T PF12895_consen   79 KALEKA   84 (84)
T ss_dssp             HHHHHH
T ss_pred             HHHhcC
Confidence            888774

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=95.71  E-value=0.43  Score=48.57  Aligned_cols=172  Identities=13%  Similarity=0.029  Sum_probs=98.2

Q ss_pred             HHHHhcCCCCHHHHHHHHHHHHHhc----chhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHH--ccCC-----HHHHHHH
Q 013489           47 ERAITDFPVSSDLWLDYTQYLDKTL----KVGNVVRDVYSRATKNCPWVGELWVRSLLSLER--SRAS-----EEEISTV  115 (442)
Q Consensus        47 ERal~~~p~~~~lW~~Y~~~l~~~~----~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~--~~~~-----~~~~~~i  115 (442)
                      +|+...-|.+.+.|-.|+.-.....    .....+..+|++|+..-|.....|...+.....  ...+     ...+...
T Consensus       327 ~~~~~~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ldP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~  406 (517)
T PRK10153        327 ERLQQGLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSEPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTE  406 (517)
T ss_pred             HHHhccCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHH
Confidence            4445567788888888876543211    224568899999999999988777764332211  1111     2334444


Q ss_pred             HHHHHhCChh--hHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHH
Q 013489          116 FEKSLLCAFS--TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQ  193 (442)
Q Consensus       116 ~~~al~~~~~--~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~  193 (442)
                      ..+++..+..  ....+..+-...  ..            ..++......+++|+.       ..+ ....|...+.+..
T Consensus       407 ~~~a~al~~~~~~~~~~~ala~~~--~~------------~g~~~~A~~~l~rAl~-------L~p-s~~a~~~lG~~~~  464 (517)
T PRK10153        407 LDNIVALPELNVLPRIYEILAVQA--LV------------KGKTDEAYQAINKAID-------LEM-SWLNYVLLGKVYE  464 (517)
T ss_pred             HHHhhhcccCcCChHHHHHHHHHH--Hh------------cCCHHHHHHHHHHHHH-------cCC-CHHHHHHHHHHHH
Confidence            5555443211  111111110000  00            0233344444555544       344 3457888899988


Q ss_pred             HcCCCHHHHHHHHHHHHHhchhHHH-HHHHHHHHHHhcccHHHHHHHHHHHH
Q 013489          194 SMGKDMVSARGVWERLLKISGAMLE-AWQSYISMEIELDHINEARSIYKRCY  244 (442)
Q Consensus       194 ~~~~~~~~ar~i~~~~l~~~~~~~~-~w~~~~~~e~~~g~~~~ar~i~~ral  244 (442)
                      ..| +.+.|...|++++..+|.... +|.+=.-|.   -+++...-.+.+++
T Consensus       465 ~~G-~~~eA~~~~~~A~~L~P~~pt~~~~~~~~f~---~~~~~~~~~~~~~~  512 (517)
T PRK10153        465 LKG-DNRLAADAYSTAFNLRPGENTLYWIENLVFQ---TSVETVVPYLYRFL  512 (517)
T ss_pred             HcC-CHHHHHHHHHHHHhcCCCCchHHHHHhcccc---ccHHHHHHHHHhcc
Confidence            889 999999999999999887653 555544443   35555555555554

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=95.69  E-value=2  Score=45.92  Aligned_cols=90  Identities=11%  Similarity=-0.019  Sum_probs=72.8

Q ss_pred             HHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcc--CCHH
Q 013489           33 EQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSR--ASEE  110 (442)
Q Consensus        33 e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~--~~~~  110 (442)
                      +....+++.++..-+.+|..+|+|...|+-....+.....+.+++...|-.|....|...-.|......+++.+  ...+
T Consensus        12 al~nk~YeealEqskkvLk~dpdNYnA~vFLGvAl~sl~q~le~A~ehYv~AaKldpdnlLAWkGL~nLye~~~dIl~ld   91 (1238)
T KOG1127|consen   12 ALRNKEYEEALEQSKKVLKEDPDNYNAQVFLGVALWSLGQDLEKAAEHYVLAAKLDPDNLLAWKGLGNLYERYNDILDLD   91 (1238)
T ss_pred             HHhhccHHHHHHHHHHHHhcCCCcchhhhHHHHHHHhccCCHHHHHHHHHHHHhcChhhhHHHHHHHHHHHccchhhhhh
Confidence            34456788888999999999999999999999988877777889999999999999999999998777666522  2346


Q ss_pred             HHHHHHHHHHhC
Q 013489          111 EISTVFEKSLLC  122 (442)
Q Consensus       111 ~~~~i~~~al~~  122 (442)
                      ++-.+|++++..
T Consensus        92 ~~~~~yq~~~l~  103 (1238)
T KOG1127|consen   92 RAAKCYQRAVLI  103 (1238)
T ss_pred             HhHHHHHHHHHh
Confidence            677788887743

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=95.65  E-value=0.047  Score=47.28  Aligned_cols=53  Identities=15%  Similarity=0.127  Sum_probs=38.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEee-CCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILH-DKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~-~~~~g~~~g~~fv~f~  441 (442)
                      ..-+|+||++||.++...+|..+|..|-.-..+.|-. ++...-.+.+|||+|.
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~   85 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFT   85 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEec
Confidence            4467999999999999999999999886554444322 2222224589999995

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=95.64  E-value=0.68  Score=38.36  Aligned_cols=59  Identities=14%  Similarity=0.081  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHH
Q 013489          184 LYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCY  244 (442)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral  244 (442)
                      ..+.++.+....+ +++.|..+++.+ ...+-...++.-..+.....|+.+.|+..|++||
T Consensus        87 a~l~LA~~~~~~~-~~d~Al~~L~~~-~~~~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~Al  145 (145)
T PF09976_consen   87 ARLRLARILLQQG-QYDEALATLQQI-PDEAFKALAAELLGDIYLAQGDYDEARAAYQKAL  145 (145)
T ss_pred             HHHHHHHHHHHcC-CHHHHHHHHHhc-cCcchHHHHHHHHHHHHHHCCCHHHHHHHHHHhC
Confidence            3444566666666 777777777552 2223334466666677777777777777777764

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=95.63  E-value=0.19  Score=46.34  Aligned_cols=61  Identities=11%  Similarity=0.103  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH---HHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          184 LYAYWAHLEQSMGKDMVSARGVWERLLKISGAM---LEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~---~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      .+...+.++...| +++.|...|.+++..+|++   .+.|...+......|+.+.|+.+|++++.
T Consensus       182 A~y~LG~~y~~~g-~~~~A~~~f~~vv~~yP~s~~~~dAl~klg~~~~~~g~~~~A~~~~~~vi~  245 (263)
T PRK10803        182 ANYWLGQLNYNKG-KKDDAAYYFASVVKNYPKSPKAADAMFKVGVIMQDKGDTAKAKAVYQQVIK  245 (263)
T ss_pred             HHHHHHHHHHHcC-CHHHHHHHHHHHHHHCCCCcchhHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3444445555555 6666666666666665543   34555555555555666666666666665

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=95.55  E-value=0.045  Score=52.99  Aligned_cols=52  Identities=19%  Similarity=0.250  Sum_probs=43.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeE-EEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSS-IRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~-~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .....|-+.+||+.++++||.+||+..-.|.. +.++.+ ..|++-|=|||.|+
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d-~rgR~tGEAfVqF~  153 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMD-QRGRPTGEAFVQFE  153 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeecc-CCCCcccceEEEec
Confidence            34458999999999999999999997755554 567777 68889999999996

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=95.55  E-value=0.012  Score=35.31  Aligned_cols=33  Identities=12%  Similarity=0.279  Sum_probs=30.4

Q ss_pred             HHHHHHHhchhHHHHHHHHHHHHHhcccHHHHH
Q 013489          205 VWERLLKISGAMLEAWQSYISMEIELDHINEAR  237 (442)
Q Consensus       205 i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar  237 (442)
                      +|+++|+.+|+++..|..++.+....|+++.|+
T Consensus         1 ~y~kAie~~P~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen    1 CYKKAIELNPNNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             ChHHHHHHCCCCHHHHHHHHHHHHHCcCHHhhc
Confidence            378999999999999999999999999999886

>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=95.53  E-value=0.55  Score=44.04  Aligned_cols=94  Identities=16%  Similarity=0.249  Sum_probs=59.0

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHH
Q 013489          181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAW  260 (442)
Q Consensus       181 ~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~  260 (442)
                      ...+...|+.+...- +++..|--+|+.+...++..+.+....+...+..|+++.|..++..|+..  ....+..+.. -
T Consensus       166 l~qLa~awv~l~~g~-e~~~~A~y~f~El~~~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~--~~~~~d~LaN-l  241 (290)
T PF04733_consen  166 LTQLAEAWVNLATGG-EKYQDAFYIFEELSDKFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEK--DPNDPDTLAN-L  241 (290)
T ss_dssp             HHHHHHHHHHHHHTT-TCCCHHHHHHHHHHCCS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC---CCHHHHHHH-H
T ss_pred             HHHHHHHHHHHHhCc-hhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh--ccCCHHHHHH-H
Confidence            345555565554333 26788888888877777777777777888888888888888888888863  3344554443 4


Q ss_pred             HHHHHHhCCH-hhHHHHHH
Q 013489          261 LRFEREYGTL-EDFDHSVQ  278 (442)
Q Consensus       261 ~~fE~~~G~~-~~~~~~~~  278 (442)
                      +-.....|.. +.+.+.+.
T Consensus       242 iv~~~~~gk~~~~~~~~l~  260 (290)
T PF04733_consen  242 IVCSLHLGKPTEAAERYLS  260 (290)
T ss_dssp             HHHHHHTT-TCHHHHHHHH
T ss_pred             HHHHHHhCCChhHHHHHHH
Confidence            6666666765 44444443

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.

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=95.30  E-value=0.27  Score=42.14  Aligned_cols=50  Identities=10%  Similarity=0.019  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhccc
Q 013489          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDH  232 (442)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~  232 (442)
                      ..++..++.+....| +.+.|...|.+++...|+....|..+..+....|+
T Consensus        72 ~~~~~~la~~~~~~g-~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~  121 (172)
T PRK02603         72 SYILYNMGIIYASNG-EHDKALEYYHQALELNPKQPSALNNIAVIYHKRGE  121 (172)
T ss_pred             HHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCC
Confidence            457777888888888 99999999999999999888877777776666554

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=95.27  E-value=2.3  Score=38.77  Aligned_cols=67  Identities=15%  Similarity=0.114  Sum_probs=51.2

Q ss_pred             HHHHHhcCChhhHHHHHHHHHhcCCCCH-----HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHH-HHHHHH
Q 013489           30 LKYEQSSGDPGRVQLLYERAITDFPVSS-----DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGE-LWVRSL   99 (442)
Q Consensus        30 ~~~e~~~g~~~~~~~lyERal~~~p~~~-----~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~-lW~~y~   99 (442)
                      +.-....|+.+.+...|+..+...|.++     .+|+.|+.|-.   ++.+.+...|+++++..|.+.. -|..|+
T Consensus        39 A~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a~~a~l~la~ayy~~---~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~  111 (243)
T PRK10866         39 AQQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKN---ADLPLAQAAIDRFIRLNPTHPNIDYVLYM  111 (243)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhc---CCHHHHHHHHHHHHHhCcCCCchHHHHHH
Confidence            3333567999999999999999999875     37888877643   4567799999999999998754 344444

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=95.17  E-value=0.042  Score=53.53  Aligned_cols=53  Identities=11%  Similarity=0.127  Sum_probs=40.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCC-CC--CCcc---eEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKF-TG--KSRV---VQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~-~g--~~~g---~~fv~f~  441 (442)
                      ..-.+.||||+||++++++.|...|..||.+ .|.++.... .+  -++|   |.|+.|.
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe  314 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFE  314 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEec
Confidence            3446799999999999999999999999985 566764211 12  2556   9999985

>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=95.15  E-value=0.43  Score=39.51  Aligned_cols=45  Identities=18%  Similarity=0.170  Sum_probs=20.7

Q ss_pred             hhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHH
Q 013489           74 GNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKS  119 (442)
Q Consensus        74 ~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~a  119 (442)
                      .+.+..++.+++...|.+..+|...|..+.. .++...+..+|+++
T Consensus        78 ~~~a~~~~~~~l~~dP~~E~~~~~lm~~~~~-~g~~~~A~~~Y~~~  122 (146)
T PF03704_consen   78 YEEALRLLQRALALDPYDEEAYRLLMRALAA-QGRRAEALRVYERY  122 (146)
T ss_dssp             HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHH-TT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCCCHHHHHHHHHHHHH-CcCHHHHHHHHHHH
Confidence            3445555555555555555555555543333 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=95.10  E-value=2.5  Score=39.52  Aligned_cols=121  Identities=12%  Similarity=0.109  Sum_probs=72.8

Q ss_pred             HHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHhch-----h-HHHHHHHHHHHHHhcc
Q 013489          159 LIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSM-GKDMVSARGVWERLLKISG-----A-MLEAWQSYISMEIELD  231 (442)
Q Consensus       159 ~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~-~~~~~~ar~i~~~~l~~~~-----~-~~~~w~~~~~~e~~~g  231 (442)
                      .....+++|+.++... ........++...+.++... + +++.|.+.|++++..+.     . ...+....+.+....|
T Consensus        92 ~Ai~~~~~A~~~y~~~-G~~~~aA~~~~~lA~~ye~~~~-d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~  169 (282)
T PF14938_consen   92 EAIECYEKAIEIYREA-GRFSQAAKCLKELAEIYEEQLG-DYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLG  169 (282)
T ss_dssp             HHHHHHHHHHHHHHHC-T-HHHHHHHHHHHHHHHCCTT---HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHhc-CcHHHHHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhC
Confidence            4445666666655322 11223346777788887777 6 89999999999998731     1 1358889999999999


Q ss_pred             cHHHHHHHHHHHHhcccCCCCh----HHHHHHHHHHHHHhCCHhhHHHHHHhhc
Q 013489          232 HINEARSIYKRCYSKRFTGTGS----EDICHAWLRFEREYGTLEDFDHSVQKVT  281 (442)
Q Consensus       232 ~~~~ar~i~~ral~~~~~~~~~----~~i~~~~~~fE~~~G~~~~~~~~~~~~~  281 (442)
                      +++.|..+|++.....+..+..    ...+..-+-.--..|++...+.+++++.
T Consensus       170 ~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~  223 (282)
T PF14938_consen  170 RYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYC  223 (282)
T ss_dssp             -HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHG
T ss_pred             CHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            9999999999988643222211    1122111222233477766666666653

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=95.08  E-value=2.9  Score=39.00  Aligned_cols=123  Identities=20%  Similarity=0.215  Sum_probs=79.0

Q ss_pred             hhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchh------HH-HHHHHHHHHH
Q 013489          155 LDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA------ML-EAWQSYISME  227 (442)
Q Consensus       155 ~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~------~~-~~w~~~~~~e  227 (442)
                      .++......|++|.+++...- .......+....+.+....+ +++.|.++|+++.....+      ++ ..++..+-+.
T Consensus       129 ~d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l~~~l~-~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~  206 (282)
T PF14938_consen  129 GDYEKAIEYYQKAAELYEQEG-SPHSAAECLLKAADLYARLG-RYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCH  206 (282)
T ss_dssp             --HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHHHHHhC-CHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHH
Confidence            366677788889988875432 11223568888999999999 999999999999976311      12 3667777777


Q ss_pred             HhcccHHHHHHHHHHHHhcc--cCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          228 IELDHINEARSIYKRCYSKR--FTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       228 ~~~g~~~~ar~i~~ral~~~--~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                      ...||+..|+..|++.....  +....--.+....++=- +.|+.+.+..++...
T Consensus       207 L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~-~~~D~e~f~~av~~~  260 (282)
T PF14938_consen  207 LAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAY-EEGDVEAFTEAVAEY  260 (282)
T ss_dssp             HHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHH-HTT-CCCHHHHCHHH
T ss_pred             HHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHH-HhCCHHHHHHHHHHH
Confidence            77899999999999987531  22111112333323221 247888888777654

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=95.05  E-value=0.94  Score=37.51  Aligned_cols=25  Identities=20%  Similarity=0.247  Sum_probs=11.5

Q ss_pred             HHHHHHhcCChhhHHHHHHHHHhcC
Q 013489           29 YLKYEQSSGDPGRVQLLYERAITDF   53 (442)
Q Consensus        29 y~~~e~~~g~~~~~~~lyERal~~~   53 (442)
                      .+......|+++.+...|+.++...
T Consensus        54 lA~~~~~~g~~~~A~~~l~~~~~~~   78 (145)
T PF09976_consen   54 LAKAAYEQGDYDEAKAALEKALANA   78 (145)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhC
Confidence            3333334445555555555555443

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=94.99  E-value=0.05  Score=53.02  Aligned_cols=54  Identities=19%  Similarity=0.177  Sum_probs=48.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhc-cCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFS-DVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~-~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      -+..+|||||+||.-++..+|-.+|. -||.|.-+-|=.|+.-+-++|-|=|+|.
T Consensus       367 lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFs  421 (520)
T KOG0129|consen  367 IDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFS  421 (520)
T ss_pred             cCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeec
Confidence            45567999999999999999999999 7999999999999878889999999985

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=94.83  E-value=0.35  Score=41.23  Aligned_cols=60  Identities=12%  Similarity=0.077  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHH-------hcccHHHHHHHHHHH
Q 013489          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEI-------ELDHINEARSIYKRC  243 (442)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~-------~~g~~~~ar~i~~ra  243 (442)
                      .+|...+.+....| +.+.|...|++++...|.....|...+.+..       ..|+++.|...|++|
T Consensus        73 ~~~~~lg~~~~~~g-~~~eA~~~~~~Al~~~~~~~~~~~~la~i~~~~~~~~~~~g~~~~A~~~~~~a  139 (168)
T CHL00033         73 YILYNIGLIHTSNG-EHTKALEYYFQALERNPFLPQALNNMAVICHYRGEQAIEQGDSEIAEAWFDQA  139 (168)
T ss_pred             HHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHhhHHHHHcccHHHHHHHHHHH
Confidence            35666666766777 7777777777777777666666655555555       445555444444433

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=94.82  E-value=0.55  Score=43.29  Aligned_cols=98  Identities=10%  Similarity=0.163  Sum_probs=70.4

Q ss_pred             HHHHHHHHH-HHhcCChhhHHHHHHHHHhcCCCC-----HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCc---HHH
Q 013489           24 QQYMIYLKY-EQSSGDPGRVQLLYERAITDFPVS-----SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV---GEL   94 (442)
Q Consensus        24 ~~w~~y~~~-e~~~g~~~~~~~lyERal~~~p~~-----~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s---~~l   94 (442)
                      ..|-.++.. ....|+++.+...|+..|..+|.+     ..+|+..+.|.   .++.+.+...|.+++..+|.+   ...
T Consensus       143 ~~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~---~g~~~~A~~~f~~vv~~yP~s~~~~dA  219 (263)
T PRK10803        143 NTDYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYN---KGKKDDAAYYFASVVKNYPKSPKAADA  219 (263)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHH---cCCHHHHHHHHHHHHHHCCCCcchhHH
Confidence            344444443 355789999999999999999987     34565555543   356677999999999988875   456


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCChh
Q 013489           95 WVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus        95 W~~y~~~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                      |......+. ..++.+.+..+|++.+...|.
T Consensus       220 l~klg~~~~-~~g~~~~A~~~~~~vi~~yP~  249 (263)
T PRK10803        220 MFKVGVIMQ-DKGDTAKAKAVYQQVIKKYPG  249 (263)
T ss_pred             HHHHHHHHH-HcCCHHHHHHHHHHHHHHCcC
Confidence            655444333 468889999999998865444

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=94.80  E-value=0.037  Score=48.97  Aligned_cols=39  Identities=23%  Similarity=0.266  Sum_probs=34.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCC
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFT  429 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~  429 (442)
                      ...||+++||+.+....|+++|+.||.|-.|.+.....+
T Consensus        74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s  112 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDS  112 (278)
T ss_pred             ceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhH
Confidence            348999999999999999999999999999988766444

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=94.77  E-value=0.087  Score=45.96  Aligned_cols=49  Identities=20%  Similarity=0.285  Sum_probs=43.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...+..+|+.|||.+++.+.+..+|.+|+.-..++++...     +|.|||+|.
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~  191 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFL  191 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecc
Confidence            3456699999999999999999999999999999998863     589999985

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=94.76  E-value=0.35  Score=39.62  Aligned_cols=61  Identities=18%  Similarity=0.123  Sum_probs=43.9

Q ss_pred             HHHHHHhcCChhhHHHHHHHHHhcCCCC-----HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcH
Q 013489           29 YLKYEQSSGDPGRVQLLYERAITDFPVS-----SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVG   92 (442)
Q Consensus        29 y~~~e~~~g~~~~~~~lyERal~~~p~~-----~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~   92 (442)
                      =+.-....|+...+...||......|..     ..||+.|+.|..   ++.+.+...++|.++..|.+.
T Consensus        16 ~a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~---~~y~~A~a~~~rFirLhP~hp   81 (142)
T PF13512_consen   16 EAQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQ---GDYEEAIAAYDRFIRLHPTHP   81 (142)
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHc---cCHHHHHHHHHHHHHhCCCCC
Confidence            3343456778888888888888887764     368888887754   345667888888888887654

>PRK11906 transcriptional regulator; Provisional

Probab=94.75  E-value=1.7  Score=42.81  Aligned_cols=172  Identities=9%  Similarity=0.055  Sum_probs=94.6

Q ss_pred             HHhcCCCCH---HHH--HHHHHHHHHh----cchhhHHHHHHHHHH---HcCCCcHH-----HHHHHHHHHHHc---cCC
Q 013489           49 AITDFPVSS---DLW--LDYTQYLDKT----LKVGNVVRDVYSRAT---KNCPWVGE-----LWVRSLLSLERS---RAS  108 (442)
Q Consensus        49 al~~~p~~~---~lW--~~Y~~~l~~~----~~~~~~~~~v~erAl---~~~p~s~~-----lW~~y~~~le~~---~~~  108 (442)
                      +...-|.+.   +-|  -.|+.-...-    ......+..+|.||+   ..-|....     -|+...+.+...   ...
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            333346666   777  5555433321    123345778899999   56665443     233322222111   122


Q ss_pred             HHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHH
Q 013489          109 EEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYW  188 (442)
Q Consensus       109 ~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~  188 (442)
                      ..++..+-++|+..++.+.....  .+..+..+.                   ..++.|...++.+..-+|.....|.+.
T Consensus       320 ~~~a~~~A~rAveld~~Da~a~~--~~g~~~~~~-------------------~~~~~a~~~f~rA~~L~Pn~A~~~~~~  378 (458)
T PRK11906        320 AQKALELLDYVSDITTVDGKILA--IMGLITGLS-------------------GQAKVSHILFEQAKIHSTDIASLYYYR  378 (458)
T ss_pred             HHHHHHHHHHHHhcCCCCHHHHH--HHHHHHHhh-------------------cchhhHHHHHHHHhhcCCccHHHHHHH
Confidence            34567778888877665332211  111110110                   113333344444443467777788888


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHhchhHHH--HHHHHHHHHHhcccHHHHHHHHHHH
Q 013489          189 AHLEQSMGKDMVSARGVWERLLKISGAMLE--AWQSYISMEIELDHINEARSIYKRC  243 (442)
Q Consensus       189 a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~--~w~~~~~~e~~~g~~~~ar~i~~ra  243 (442)
                      +-+..-.| +.+.|++..+++++..|....  +...++++... .-++++..+|-+-
T Consensus       379 ~~~~~~~G-~~~~a~~~i~~alrLsP~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~  433 (458)
T PRK11906        379 ALVHFHNE-KIEEARICIDKSLQLEPRRRKAVVIKECVDMYVP-NPLKNNIKLYYKE  433 (458)
T ss_pred             HHHHHHcC-CHHHHHHHHHHHhccCchhhHHHHHHHHHHHHcC-CchhhhHHHHhhc
Confidence            88877778 999999999999999887653  44445544433 3355566665543

>KOG3824 consensus Huntingtin interacting protein HYPE [General function prediction only]

Probab=94.48  E-value=3.8  Score=38.02  Aligned_cols=61  Identities=16%  Similarity=0.250  Sum_probs=52.2

Q ss_pred             HHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHH
Q 013489           33 EQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGEL   94 (442)
Q Consensus        33 e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~l   94 (442)
                      ..+.|+.++++.+||.||...|.++++-+.|..|.+.+ +++-.+-..|-+|+..-|...+.
T Consensus       126 ~~~~Gk~ekA~~lfeHAlalaP~~p~~L~e~G~f~E~~-~~iv~ADq~Y~~ALtisP~nseA  186 (472)
T KOG3824|consen  126 SRKDGKLEKAMTLFEHALALAPTNPQILIEMGQFREMH-NEIVEADQCYVKALTISPGNSEA  186 (472)
T ss_pred             HHhccchHHHHHHHHHHHhcCCCCHHHHHHHhHHHHhh-hhhHhhhhhhheeeeeCCCchHH
Confidence            35678999999999999999999999999999999876 44455788999999999976554

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=94.10  E-value=0.045  Score=47.39  Aligned_cols=45  Identities=22%  Similarity=0.364  Sum_probs=35.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      |+||.||..++++++|+.+|+.|.....++|-..  .|  -..||++|.
T Consensus       212 tlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~g--~~vaf~~~~  256 (284)
T KOG1457|consen  212 TLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--GG--MPVAFADFE  256 (284)
T ss_pred             hHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--CC--cceEeecHH
Confidence            8999999999999999999999886666665432  23  358888874

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=93.91  E-value=0.066  Score=32.11  Aligned_cols=26  Identities=15%  Similarity=0.254  Sum_probs=20.3

Q ss_pred             HHHHHHhcCCCCHHHHHHHHHHHHHh
Q 013489           45 LYERAITDFPVSSDLWLDYTQYLDKT   70 (442)
Q Consensus        45 lyERal~~~p~~~~lW~~Y~~~l~~~   70 (442)
                      +|++||..+|.++..|..++.++...
T Consensus         1 ~y~kAie~~P~n~~a~~nla~~~~~~   26 (34)
T PF13431_consen    1 CYKKAIELNPNNAEAYNNLANLYLNQ   26 (34)
T ss_pred             ChHHHHHHCCCCHHHHHHHHHHHHHC
Confidence            37888888888888888888876644

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=93.74  E-value=2.6  Score=40.63  Aligned_cols=97  Identities=18%  Similarity=0.156  Sum_probs=66.1

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHH----HHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHH
Q 013489          181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAML----EAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDI  256 (442)
Q Consensus       181 ~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~----~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i  256 (442)
                      .+..|..-+.-..+.| ++..|-++|..+|..+|++.    .++..-+..-.++|....|..-.+.|+.  +.   + ..
T Consensus       248 ~le~~k~~gN~~fk~G-~y~~A~E~Yteal~idP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al~--iD---~-sy  320 (486)
T KOG0550|consen  248 KLEVKKERGNDAFKNG-NYRKAYECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEALK--ID---S-SY  320 (486)
T ss_pred             HHHHHHhhhhhHhhcc-chhHHHHHHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhhhhh--cC---H-HH
Confidence            3456666666667777 89999999999999988764    3566666666778888888888888885  22   3 34


Q ss_pred             HHHHHHHHHHhCCHhhHHHHHHhhchhH
Q 013489          257 CHAWLRFEREYGTLEDFDHSVQKVTPRL  284 (442)
Q Consensus       257 ~~~~~~fE~~~G~~~~~~~~~~~~~~~~  284 (442)
                      ..+++.=-+.|-.+++++.+++-+.+.+
T Consensus       321 ikall~ra~c~l~le~~e~AV~d~~~a~  348 (486)
T KOG0550|consen  321 IKALLRRANCHLALEKWEEAVEDYEKAM  348 (486)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4466666666666666666665544433

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=93.67  E-value=0.35  Score=47.35  Aligned_cols=67  Identities=12%  Similarity=-0.023  Sum_probs=59.3

Q ss_pred             chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHH---HHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          178 TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLE---AWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       178 ~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~---~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      .+.....|..++..+...| +++.|...|+++|..+|++.+   .|...+-.....|+++.|...|++|+.
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            3456678888888888888 999999999999999999875   488888899999999999999999997

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=93.66  E-value=0.33  Score=47.52  Aligned_cols=68  Identities=13%  Similarity=0.070  Sum_probs=58.5

Q ss_pred             ChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHH---HHHHHHHHHHhcchhhHHHHHHHHHHHc
Q 013489           19 DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDL---WLDYTQYLDKTLKVGNVVRDVYSRATKN   87 (442)
Q Consensus        19 ~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~l---W~~Y~~~l~~~~~~~~~~~~v~erAl~~   87 (442)
                      +|.....|.++.......|+++.++..|++||..+|++...   |.+-+..+.. .+..+.+...|++|+..
T Consensus        71 dP~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~aeA~~A~yNLAcaya~-LGr~dEAla~LrrALel  141 (453)
T PLN03098         71 DVKTAEDAVNLGLSLFSKGRVKDALAQFETALELNPNPDEAQAAYYNKACCHAY-REEGKKAADCLRTALRD  141 (453)
T ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHh
Confidence            56788899999999999999999999999999999999865   8777776654 45668899999999995

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=93.32  E-value=0.082  Score=49.28  Aligned_cols=54  Identities=26%  Similarity=0.282  Sum_probs=46.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeE--------EEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSS--------IRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~--------~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....-+|||.+||..++.+++..+|.+||.|..        |.|-+|+.|++++|=|-|+|.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~  124 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYE  124 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeec
Confidence            345569999999999999999999999997753        557788899999999998874

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=93.30  E-value=3.5  Score=32.95  Aligned_cols=62  Identities=15%  Similarity=-0.010  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchh---HHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGA---MLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~---~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      +.++.++.....+| .++.|..+++.++..+|+   +..++..++......|..+.|...+-.++.
T Consensus        39 ~a~i~lastlr~LG-~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L~~~gr~~eAl~~~l~~la  103 (120)
T PF12688_consen   39 RALIQLASTLRNLG-RYDEALALLEEALEEFPDDELNAALRVFLALALYNLGRPKEALEWLLEALA  103 (120)
T ss_pred             HHHHHHHHHHHHcC-CHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            34455555566677 788888888888877776   555666666666667777777777766664

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=93.26  E-value=5.9  Score=38.33  Aligned_cols=159  Identities=13%  Similarity=0.039  Sum_probs=97.0

Q ss_pred             chhhHHHHHHHHHHHcCCCcHHHHHHHHH-HHHHccCCHHHHHHHHHHHHhCChhhHHHHH--------HHHHHHHHHHH
Q 013489           72 KVGNVVRDVYSRATKNCPWVGELWVRSLL-SLERSRASEEEISTVFEKSLLCAFSTFEEYL--------DLFLTRIDGLR  142 (442)
Q Consensus        72 ~~~~~~~~v~erAl~~~p~s~~lW~~y~~-~le~~~~~~~~~~~i~~~al~~~~~~~~~~~--------~~~~~~~~~l~  142 (442)
                      ++...+.++--+-++.-+.+  ....|++ .+...+.+.+.+..-|+++|..++.....-.        ..|...-+.+-
T Consensus       183 ~~~~~a~~ea~~ilkld~~n--~~al~vrg~~~yy~~~~~ka~~hf~qal~ldpdh~~sk~~~~~~k~le~~k~~gN~~f  260 (486)
T KOG0550|consen  183 GDYDEAQSEAIDILKLDATN--AEALYVRGLCLYYNDNADKAINHFQQALRLDPDHQKSKSASMMPKKLEVKKERGNDAF  260 (486)
T ss_pred             ccchhHHHHHHHHHhcccch--hHHHHhcccccccccchHHHHHHHhhhhccChhhhhHHhHhhhHHHHHHHHhhhhhHh
Confidence            33344555555555555543  2223332 1222356677788888888888776332211        22211110000


Q ss_pred             HHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHH
Q 013489          143 RRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQS  222 (442)
Q Consensus       143 rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~  222 (442)
                                +.+.+......|..|+.+   ...+..+...++..-+.....+| .+..|..-.+.++..++......+.
T Consensus       261 ----------k~G~y~~A~E~Yteal~i---dP~n~~~naklY~nra~v~~rLg-rl~eaisdc~~Al~iD~syikall~  326 (486)
T KOG0550|consen  261 ----------KNGNYRKAYECYTEALNI---DPSNKKTNAKLYGNRALVNIRLG-RLREAISDCNEALKIDSSYIKALLR  326 (486)
T ss_pred             ----------hccchhHHHHHHHHhhcC---CccccchhHHHHHHhHhhhcccC-CchhhhhhhhhhhhcCHHHHHHHHH
Confidence                      001122222333333332   22233445567777777888889 8999999999999999998888888


Q ss_pred             HHHHHHhcccHHHHHHHHHHHHhc
Q 013489          223 YISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       223 ~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      -+......++.+.|+.-|+.|++.
T Consensus       327 ra~c~l~le~~e~AV~d~~~a~q~  350 (486)
T KOG0550|consen  327 RANCHLALEKWEEAVEDYEKAMQL  350 (486)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhh
Confidence            888888889999999999999974

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=92.85  E-value=0.24  Score=41.73  Aligned_cols=47  Identities=19%  Similarity=0.281  Sum_probs=40.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ......|.|++||++.+.+||+++...-|.|.-..+.+|       |+|.|+|.
T Consensus       112 rrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~  158 (241)
T KOG0105|consen  112 RRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYL  158 (241)
T ss_pred             cccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeee
Confidence            355679999999999999999999999999988888777       57778774

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=92.54  E-value=0.35  Score=28.45  Aligned_cols=31  Identities=16%  Similarity=0.294  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHhchh
Q 013489          184 LYAYWAHLEQSMGKDMVSARGVWERLLKISGA  215 (442)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~  215 (442)
                      +|...+.+....| +++.|+..|++++..+|+
T Consensus         3 ~~~~lg~~~~~~~-~~~~A~~~~~~al~l~p~   33 (34)
T PF07719_consen    3 AWYYLGQAYYQLG-NYEEAIEYFEKALELDPN   33 (34)
T ss_dssp             HHHHHHHHHHHTT--HHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHHHHhC-CHHHHHHHHHHHHHHCcC
Confidence            4555566666666 677777777777766664

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 ....

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=92.41  E-value=3.3  Score=34.05  Aligned_cols=23  Identities=26%  Similarity=0.384  Sum_probs=11.2

Q ss_pred             cCChhhHHHHHHHHHhcCCCCHH
Q 013489           36 SGDPGRVQLLYERAITDFPVSSD   58 (442)
Q Consensus        36 ~g~~~~~~~lyERal~~~p~~~~   58 (442)
                      .+++..+...|+|.|..+|.++.
T Consensus        60 ~~~y~~A~a~~~rFirLhP~hp~   82 (142)
T PF13512_consen   60 QGDYEEAIAAYDRFIRLHPTHPN   82 (142)
T ss_pred             ccCHHHHHHHHHHHHHhCCCCCC
Confidence            44444455555555555554443

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=92.35  E-value=0.28  Score=32.86  Aligned_cols=43  Identities=12%  Similarity=0.074  Sum_probs=31.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +.|-|.+.|++..+ .+..+|.+||.|.++.+...      ..+.||.|.
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~------~~~~~l~y~   44 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPES------TNWMYLKYK   44 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCCC------CcEEEEEEC
Confidence            47888898877554 45568889999999887622      347888875

>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=92.33  E-value=1.2  Score=36.70  Aligned_cols=61  Identities=20%  Similarity=0.150  Sum_probs=51.0

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          184 LYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      +....+......| +++.|..++.+++..+|.+-.+|...+......|+...|..+|+++..
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            4445666667788 999999999999999999999999999999999999999999998764

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=92.32  E-value=13  Score=37.13  Aligned_cols=67  Identities=13%  Similarity=0.150  Sum_probs=38.8

Q ss_pred             chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          178 TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       178 ~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      .|....++..-|-.+..++ ++..|.+-.+.+++.+|+....|+.=........+++.|-..|..++.
T Consensus       388 ~P~Da~lYsNRAac~~kL~-~~~~aL~Da~~~ieL~p~~~kgy~RKg~al~~mk~ydkAleay~eale  454 (539)
T KOG0548|consen  388 DPEDARLYSNRAACYLKLG-EYPEALKDAKKCIELDPNFIKAYLRKGAALRAMKEYDKALEAYQEALE  454 (539)
T ss_pred             CCchhHHHHHHHHHHHHHh-hHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3444455555555555555 566666666666666666665555555555555556666666666664

>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=92.31  E-value=0.26  Score=38.37  Aligned_cols=44  Identities=18%  Similarity=0.301  Sum_probs=27.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +.|.|.+++..++.++|+..|+.+|.|.-|.+....      .-|||-|.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~   45 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFK   45 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEES
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEEC
Confidence            578899999999999999999999999888876642      36778775

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]

Probab=92.24  E-value=11  Score=36.18  Aligned_cols=215  Identities=14%  Similarity=0.051  Sum_probs=121.3

Q ss_pred             HHHHHHHHHHhcCChhhHHHHHHHHHhcCCC-CHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHH
Q 013489           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPV-SSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLE  103 (442)
Q Consensus        25 ~w~~y~~~e~~~g~~~~~~~lyERal~~~p~-~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le  103 (442)
                      .++.-+..-...||.+++-.+..++-..-++ .-.+-+.-...+... ++...++.-...++..-|....+-..-.+ ..
T Consensus       120 ~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~-~d~~aA~~~v~~ll~~~pr~~~vlrLa~r-~y  197 (400)
T COG3071         120 AYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNR-RDYPAARENVDQLLEMTPRHPEVLRLALR-AY  197 (400)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhC-CCchhHHHHHHHHHHhCcCChHHHHHHHH-HH
Confidence            4444445555678888888888888876332 223344444444433 34455778888888888877665444444 22


Q ss_pred             HccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhh------------HHHH---------HH
Q 013489          104 RSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLD------------YSLI---------RE  162 (442)
Q Consensus       104 ~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~------------~~~~---------r~  162 (442)
                      ...+....+-.+..+.-+.+.-+-.++..+....+..+-+..-.....+...+            ...+         ..
T Consensus       198 ~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~lr~~p~l~~~~a~~li~l~  277 (400)
T COG3071         198 IRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPRKLRNDPELVVAYAERLIRLG  277 (400)
T ss_pred             HHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhccHHhhcChhHHHHHHHHHHHcC
Confidence            23566666666666554444433444444443322222221111111110000            0000         01


Q ss_pred             HHHHHHHHHhhhhcC-chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHH
Q 013489          163 TFQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYK  241 (442)
Q Consensus       163 ~~~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~  241 (442)
                      ..+.|..++...++. .|+.  +...+.   .-..++...-.+..++.++.+|+++.+|.....+..+++...+|...|+
T Consensus       278 ~~~~A~~~i~~~Lk~~~D~~--L~~~~~---~l~~~d~~~l~k~~e~~l~~h~~~p~L~~tLG~L~~k~~~w~kA~~~le  352 (400)
T COG3071         278 DHDEAQEIIEDALKRQWDPR--LCRLIP---RLRPGDPEPLIKAAEKWLKQHPEDPLLLSTLGRLALKNKLWGKASEALE  352 (400)
T ss_pred             ChHHHHHHHHHHHHhccChh--HHHHHh---hcCCCCchHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhHHHHHHHHHH
Confidence            123444444444432 2222  222222   2233477778888888888899999999999999999999999999999


Q ss_pred             HHHhc
Q 013489          242 RCYSK  246 (442)
Q Consensus       242 ral~~  246 (442)
                      .|+..
T Consensus       353 aAl~~  357 (400)
T COG3071         353 AALKL  357 (400)
T ss_pred             HHHhc
Confidence            99974

>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=92.07  E-value=3.3  Score=35.37  Aligned_cols=55  Identities=18%  Similarity=0.153  Sum_probs=31.6

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCC-------hhhHHHHHHHHHhcCCCCHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGD-------PGRVQLLYERAITDFPVSSD   58 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~-------~~~~~~lyERal~~~p~~~~   58 (442)
                      .+|+.||.....+|. |.+++..|-..+...-+...       ++.++.-||.||..+|...+
T Consensus         9 ~ark~aea~y~~nP~-DadnL~~WG~ALLELAqfk~g~es~~miedAisK~eeAL~I~P~~hd   70 (186)
T PF06552_consen    9 HARKKAEAAYAKNPL-DADNLTNWGGALLELAQFKQGPESKKMIEDAISKFEEALKINPNKHD   70 (186)
T ss_dssp             HHHHHHHHHHHH-TT--HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH-TT-HH
T ss_pred             HHHHHHHHHHHhCcH-hHHHHHHHHHHHHHHHhccCcchHHHHHHHHHHHHHHHHhcCCchHH
Confidence            367788888877773 56666666665554422221       34556667778888887654

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.

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=91.69  E-value=0.46  Score=27.90  Aligned_cols=32  Identities=13%  Similarity=0.071  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCC
Q 013489           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVS   56 (442)
Q Consensus        25 ~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~   56 (442)
                      .|..........|+++.++..|+++|..+|.+
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            56666677777888888888888888887764

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 ....

>PRK15331 chaperone protein SicA; Provisional

Probab=91.51  E-value=7.7  Score=32.73  Aligned_cols=86  Identities=7%  Similarity=-0.004  Sum_probs=66.9

Q ss_pred             HHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhh
Q 013489          193 QSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLED  272 (442)
Q Consensus       193 ~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~  272 (442)
                      ...| +++.|..+|.-+...++.+...|+.++-.....++++.|..+|..|..  +..++|.-.+.. -+.-...|+.+.
T Consensus        48 y~~G-k~~eA~~~F~~L~~~d~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~--l~~~dp~p~f~a-gqC~l~l~~~~~  123 (165)
T PRK15331         48 YNQG-RLDEAETFFRFLCIYDFYNPDYTMGLAAVCQLKKQFQKACDLYAVAFT--LLKNDYRPVFFT-GQCQLLMRKAAK  123 (165)
T ss_pred             HHCC-CHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--cccCCCCccchH-HHHHHHhCCHHH
Confidence            4566 999999999999999998899999999999999999999999999997  344555444433 333344577777


Q ss_pred             HHHHHHhhch
Q 013489          273 FDHSVQKVTP  282 (442)
Q Consensus       273 ~~~~~~~~~~  282 (442)
                      -..|+..+..
T Consensus       124 A~~~f~~a~~  133 (165)
T PRK15331        124 ARQCFELVNE  133 (165)
T ss_pred             HHHHHHHHHh
Confidence            7777666544

>PRK15331 chaperone protein SicA; Provisional

Probab=91.29  E-value=5.1  Score=33.78  Aligned_cols=102  Identities=8%  Similarity=-0.142  Sum_probs=75.8

Q ss_pred             ChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHH
Q 013489           19 DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRS   98 (442)
Q Consensus        19 ~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y   98 (442)
                      ..+.++.--.|+--....|+.+.|..+|.-....+|.+++.|+..+.-.. ..+..+.+...|..|...-+.++.... |
T Consensus        33 s~~~le~iY~~Ay~~y~~Gk~~eA~~~F~~L~~~d~~n~~Y~~GLaa~~Q-~~k~y~~Ai~~Y~~A~~l~~~dp~p~f-~  110 (165)
T PRK15331         33 PQDMMDGLYAHAYEFYNQGRLDEAETFFRFLCIYDFYNPDYTMGLAAVCQ-LKKQFQKACDLYAVAFTLLKNDYRPVF-F  110 (165)
T ss_pred             CHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHcccCCCCccc-h
Confidence            34566666666766678899999999999999999999999998887544 345667899999999986655443222 2


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHhC
Q 013489           99 LLSLERSRASEEEISTVFEKSLLC  122 (442)
Q Consensus        99 ~~~le~~~~~~~~~~~i~~~al~~  122 (442)
                      +..+....++.+.++..|+.++..
T Consensus       111 agqC~l~l~~~~~A~~~f~~a~~~  134 (165)
T PRK15331        111 TGQCQLLMRKAAKARQCFELVNER  134 (165)
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHhC
Confidence            333444468889999999998864

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=91.08  E-value=8.9  Score=37.02  Aligned_cols=65  Identities=12%  Similarity=0.230  Sum_probs=35.3

Q ss_pred             hhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhccc-HHHHHHHHHHHHh
Q 013489          180 GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDH-INEARSIYKRCYS  245 (442)
Q Consensus       180 ~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~-~~~ar~i~~ral~  245 (442)
                      +.+...-.-++....++ +++.||..|+++++..|++-.+-.+++.+-..... .++.+++|.+++.
T Consensus       289 ~N~KALyRrG~A~l~~~-e~~~A~~df~ka~k~~P~Nka~~~el~~l~~k~~~~~~kekk~y~~mF~  354 (397)
T KOG0543|consen  289 NNVKALYRRGQALLALG-EYDLARDDFQKALKLEPSNKAARAELIKLKQKIREYEEKEKKMYANMFA  354 (397)
T ss_pred             CchhHHHHHHHHHHhhc-cHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            33333333444445555 66666666666666666665555566655554442 3344666666554

>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=90.90  E-value=0.69  Score=27.19  Aligned_cols=32  Identities=19%  Similarity=0.335  Sum_probs=22.4

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchh
Q 013489          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGA  215 (442)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~  215 (442)
                      ++|...+.++...| +.+.|.+.|+++++..|+
T Consensus         2 ~~~~~lg~~y~~~~-~~~~A~~~~~~a~~~~~~   33 (34)
T PF13181_consen    2 EAYYNLGKIYEQLG-DYEEALEYFEKALELNPD   33 (34)
T ss_dssp             HHHHHHHHHHHHTT-SHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHcC-CHHHHHHHHHHHHhhCCC
Confidence            35666677777777 777777777777777664

...

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=90.73  E-value=4.6  Score=32.61  Aligned_cols=82  Identities=15%  Similarity=0.208  Sum_probs=63.1

Q ss_pred             HcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHH---HHHHhCCH
Q 013489          194 SMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLR---FEREYGTL  270 (442)
Q Consensus       194 ~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~---fE~~~G~~  270 (442)
                      .-| +++.|.+.|.++|...|.....+..-++-.+..|+.+.|..-+++|+.  +..+....-+++|.+   +-+..|+.
T Consensus        55 E~g-~Ld~AlE~F~qal~l~P~raSayNNRAQa~RLq~~~e~ALdDLn~Ale--Lag~~trtacqa~vQRg~lyRl~g~d  131 (175)
T KOG4555|consen   55 EAG-DLDGALELFGQALCLAPERASAYNNRAQALRLQGDDEEALDDLNKALE--LAGDQTRTACQAFVQRGLLYRLLGND  131 (175)
T ss_pred             hcc-chHHHHHHHHHHHHhcccchHhhccHHHHHHHcCChHHHHHHHHHHHH--hcCccchHHHHHHHHHHHHHHHhCch
Confidence            345 899999999999999998888888888888888999999999999987  455556666666665   45666777


Q ss_pred             hhHHHHHH
Q 013489          271 EDFDHSVQ  278 (442)
Q Consensus       271 ~~~~~~~~  278 (442)
                      +..+.-++
T Consensus       132 d~AR~DFe  139 (175)
T KOG4555|consen  132 DAARADFE  139 (175)
T ss_pred             HHHHHhHH
Confidence            65554333

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=90.68  E-value=13  Score=33.92  Aligned_cols=181  Identities=13%  Similarity=0.134  Sum_probs=96.3

Q ss_pred             HHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHH
Q 013489           59 LWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRI  138 (442)
Q Consensus        59 lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~  138 (442)
                      --..+..|+.....-.+.+..+++.-....-.+..+|...........++++++..+.++..........-++-+-+.+ 
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            3445555554333223445567777666555566688777666666678888888777762211100011111111111 


Q ss_pred             HHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhc-Cch-hhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH
Q 013489          139 DGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMK-NTD-GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM  216 (442)
Q Consensus       139 ~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~-~~~-~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~  216 (442)
                                               ++-|...+..... +.+ ...++-..|+.+-..-. .+..|-=||+.+-.++|..
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                                     1222222222211 111 12234444555533333 5777888888888765555


Q ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCC
Q 013489          217 LEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGT  269 (442)
Q Consensus       217 ~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~  269 (442)
                      +.+-.-.+-+.+..|+++.|-.+++.||.+  ....|+.+... +-.-...|-
T Consensus       207 ~~llnG~Av~~l~~~~~eeAe~lL~eaL~k--d~~dpetL~Nl-iv~a~~~Gk  256 (299)
T KOG3081|consen  207 PLLLNGQAVCHLQLGRYEEAESLLEEALDK--DAKDPETLANL-IVLALHLGK  256 (299)
T ss_pred             hHHHccHHHHHHHhcCHHHHHHHHHHHHhc--cCCCHHHHHHH-HHHHHHhCC
Confidence            666666667777778888888888888874  33456544433 444555563

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=90.58  E-value=0.15  Score=44.11  Aligned_cols=37  Identities=22%  Similarity=0.274  Sum_probs=34.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCC
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDK  427 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~  427 (442)
                      .+||||+|+...++++-|.++|-+.|+|..|.|+.++
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~   45 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ   45 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc
Confidence            4699999999999999999999999999999999984

>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=90.36  E-value=8.6  Score=36.05  Aligned_cols=80  Identities=15%  Similarity=0.102  Sum_probs=52.6

Q ss_pred             HHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccH-HHHHHHHHH
Q 013489          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHI-NEARSIYKR  242 (442)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~-~~ar~i~~r  242 (442)
                      ++.|.-+++......+..+.+..-.+-.....| +++.|.++++.++..+|+++++....+-+....|+. +.+...+..
T Consensus       183 ~~~A~y~f~El~~~~~~t~~~lng~A~~~l~~~-~~~eAe~~L~~al~~~~~~~d~LaNliv~~~~~gk~~~~~~~~l~q  261 (290)
T PF04733_consen  183 YQDAFYIFEELSDKFGSTPKLLNGLAVCHLQLG-HYEEAEELLEEALEKDPNDPDTLANLIVCSLHLGKPTEAAERYLSQ  261 (290)
T ss_dssp             CCHHHHHHHHHHCCS--SHHHHHHHHHHHHHCT--HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHTT-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhC-CHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCChhHHHHHHHH
Confidence            455555555544444445556666677777777 888888888888888888888888888887777754 566666665


Q ss_pred             HH
Q 013489          243 CY  244 (442)
Q Consensus       243 al  244 (442)
                      ..
T Consensus       262 L~  263 (290)
T PF04733_consen  262 LK  263 (290)
T ss_dssp             CH
T ss_pred             HH
Confidence            44

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.

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=90.10  E-value=7.8  Score=37.41  Aligned_cols=89  Identities=13%  Similarity=0.143  Sum_probs=69.0

Q ss_pred             hHHHHHHHHHHHHHHHhhhhcCc--------hhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHH
Q 013489          156 DYSLIRETFQRASDYLSEQMKNT--------DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISME  227 (442)
Q Consensus       156 ~~~~~r~~~~~a~~~l~~~~~~~--------~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e  227 (442)
                      .+......|++|+.+|.......        ...+.+++..|-...+++ .+..|....+++|...|+++.....-.+..
T Consensus       223 k~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~-~~~~Ai~~c~kvLe~~~~N~KALyRrG~A~  301 (397)
T KOG0543|consen  223 KFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLACHLNLAACYLKLK-EYKEAIESCNKVLELDPNNVKALYRRGQAL  301 (397)
T ss_pred             hHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHHHhhHHHHHHHhhh-hHHHHHHHHHHHHhcCCCchhHHHHHHHHH
Confidence            45566677788877775332211        112246666777777888 899999999999999999999888888888


Q ss_pred             HhcccHHHHHHHHHHHHh
Q 013489          228 IELDHINEARSIYKRCYS  245 (442)
Q Consensus       228 ~~~g~~~~ar~i~~ral~  245 (442)
                      ...|+++.||..|++|+.
T Consensus       302 l~~~e~~~A~~df~ka~k  319 (397)
T KOG0543|consen  302 LALGEYDLARDDFQKALK  319 (397)
T ss_pred             HhhccHHHHHHHHHHHHH
Confidence            889999999999999997

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=89.68  E-value=26  Score=35.72  Aligned_cols=114  Identities=14%  Similarity=0.080  Sum_probs=64.5

Q ss_pred             HHHHHHHHhhhhcCchhh-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhch------hHHHHHHHHHHHH-HhcccHHH
Q 013489          164 FQRASDYLSEQMKNTDGL-LRLYAYWAHLEQSMGKDMVSARGVWERLLKISG------AMLEAWQSYISME-IELDHINE  235 (442)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~-~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~------~~~~~w~~~~~~e-~~~g~~~~  235 (442)
                      ...+..+|.......+.. ..+.+..+++-...| ++..|.+++...+....      .+.+--..+|.++ ...++...
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            344555554444433332 446666788888888 89999999884442211      1112233444433 34456667


Q ss_pred             HHHHHHHHHhcc---cCC-CChHHHHHHHHHHHHHhCCHhhHHHHHH
Q 013489          236 ARSIYKRCYSKR---FTG-TGSEDICHAWLRFEREYGTLEDFDHSVQ  278 (442)
Q Consensus       236 ar~i~~ral~~~---~~~-~~~~~i~~~~~~fE~~~G~~~~~~~~~~  278 (442)
                      |-.++..|+.-.   .+. ..--.+|..-..|+..+|+.++-...++
T Consensus       436 a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~lr~G~~~ea~s~le  482 (652)
T KOG2376|consen  436 ASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKLRHGNEEEASSLLE  482 (652)
T ss_pred             HHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHHhcCchHHHHHHHH
Confidence            777888777431   111 1112456677899999998775444443

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=89.67  E-value=0.23  Score=44.22  Aligned_cols=49  Identities=16%  Similarity=0.152  Sum_probs=43.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..|||.||+.-++.+.+..-|+.||+|....+..| ..|++-|=++|.|+
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~   80 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFA   80 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhh
Confidence            48999999999999999999999999988777777 68888888888886

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=89.59  E-value=19  Score=34.15  Aligned_cols=48  Identities=10%  Similarity=0.076  Sum_probs=40.6

Q ss_pred             CHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          198 DMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       198 ~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ++..|......+|...|+++++...-++-......++.|..-|+.|..
T Consensus       322 ~~~eAiqqC~evL~~d~~dv~~l~dRAeA~l~dE~YD~AI~dye~A~e  369 (504)
T KOG0624|consen  322 QFGEAIQQCKEVLDIDPDDVQVLCDRAEAYLGDEMYDDAIHDYEKALE  369 (504)
T ss_pred             CHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh
Confidence            788899999999999999999888887777666678888888888886

>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=89.47  E-value=2.4  Score=30.55  Aligned_cols=70  Identities=16%  Similarity=0.236  Sum_probs=43.7

Q ss_pred             chhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcc-cCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhhch
Q 013489          213 SGAMLEAWQSYISMEIELDHINEARSIYKRCYSKR-FTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTP  282 (442)
Q Consensus       213 ~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~-~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~~~  282 (442)
                      +|+-..++...+.+....|+++.|...|++|+... ...+....+...+.++=..+....+++.|++-...
T Consensus         1 H~~~a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~   71 (78)
T PF13424_consen    1 HPDTANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQK   71 (78)
T ss_dssp             -HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            46667788889999999999999999999999641 11222233455555555555444445555544433

...

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=89.34  E-value=5.8  Score=32.05  Aligned_cols=88  Identities=16%  Similarity=0.113  Sum_probs=68.9

Q ss_pred             cCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcC-CCcH---HHHHHHHHHHHHccCCHHH
Q 013489           36 SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNC-PWVG---ELWVRSLLSLERSRASEEE  111 (442)
Q Consensus        36 ~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~-p~s~---~lW~~y~~~le~~~~~~~~  111 (442)
                      .|+.+.+...|..+|..+|...+.+.+-+.-+.-. ++.+.+.+-+++|+..- |..-   ..+.... .+.+..++.+.
T Consensus        56 ~g~Ld~AlE~F~qal~l~P~raSayNNRAQa~RLq-~~~e~ALdDLn~AleLag~~trtacqa~vQRg-~lyRl~g~dd~  133 (175)
T KOG4555|consen   56 AGDLDGALELFGQALCLAPERASAYNNRAQALRLQ-GDDEEALDDLNKALELAGDQTRTACQAFVQRG-LLYRLLGNDDA  133 (175)
T ss_pred             ccchHHHHHHHHHHHHhcccchHhhccHHHHHHHc-CChHHHHHHHHHHHHhcCccchHHHHHHHHHH-HHHHHhCchHH
Confidence            58999999999999999999999999998876644 45677899999999865 3322   3344433 36677889999


Q ss_pred             HHHHHHHHHhCChh
Q 013489          112 ISTVFEKSLLCAFS  125 (442)
Q Consensus       112 ~~~i~~~al~~~~~  125 (442)
                      +|.-|+.|-+.+.+
T Consensus       134 AR~DFe~AA~LGS~  147 (175)
T KOG4555|consen  134 ARADFEAAAQLGSK  147 (175)
T ss_pred             HHHhHHHHHHhCCH
Confidence            99999999877654

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=89.19  E-value=0.75  Score=26.67  Aligned_cols=28  Identities=25%  Similarity=0.218  Sum_probs=20.1

Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhchhH
Q 013489          188 WAHLEQSMGKDMVSARGVWERLLKISGAM  216 (442)
Q Consensus       188 ~a~~e~~~~~~~~~ar~i~~~~l~~~~~~  216 (442)
                      .+.+....| +.+.|..+|++++..+|++
T Consensus         6 ~a~~~~~~g-~~~~A~~~~~~~~~~~P~s   33 (33)
T PF13174_consen    6 LARCYYKLG-DYDEAIEYFQRLIKRYPDS   33 (33)
T ss_dssp             HHHHHHHHC-HHHHHHHHHHHHHHHSTTS
T ss_pred             HHHHHHHcc-CHHHHHHHHHHHHHHCcCC
Confidence            444555566 7888888888888887763

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=89.16  E-value=1.5  Score=25.80  Aligned_cols=31  Identities=19%  Similarity=0.261  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHhchh
Q 013489          184 LYAYWAHLEQSMGKDMVSARGVWERLLKISGA  215 (442)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~  215 (442)
                      +|...+......+ +++.|...|+++++.+|+
T Consensus         3 ~~~~~g~~~~~~~-~~~~A~~~~~~al~~~p~   33 (34)
T PF00515_consen    3 AYYNLGNAYFQLG-DYEEALEYYQRALELDPD   33 (34)
T ss_dssp             HHHHHHHHHHHTT--HHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHHHHhC-CchHHHHHHHHHHHHCcC
Confidence            4555566666666 777777777777777665

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 ....

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=89.01  E-value=18  Score=32.96  Aligned_cols=55  Identities=24%  Similarity=0.228  Sum_probs=41.4

Q ss_pred             hhhHHHHHHhhcCCCCC-hHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHH
Q 013489            3 NARAHLEEQISRQDLSD-SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDL   59 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~-~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~l   59 (442)
                      +|...|+..+...|.+. ..+...|+.|+-  .+.++...+...|++.|..+|.++.+
T Consensus        50 ~Ai~~f~~l~~~yP~s~~a~~a~l~la~ay--y~~~~y~~A~~~~e~fi~~~P~~~~~  105 (243)
T PRK10866         50 QAITQLEALDNRYPFGPYSQQVQLDLIYAY--YKNADLPLAQAAIDRFIRLNPTHPNI  105 (243)
T ss_pred             HHHHHHHHHHHhCCCChHHHHHHHHHHHHH--HhcCCHHHHHHHHHHHHHhCcCCCch
Confidence            56788999998888642 112235666666  55789999999999999999998865

>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=88.99  E-value=5.4  Score=34.10  Aligned_cols=81  Identities=20%  Similarity=0.158  Sum_probs=47.0

Q ss_pred             hhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc---------chhhHHHHHHHHHHHcCCCcHH-HHHHHHHH--HHHccC
Q 013489           40 GRVQLLYERAITDFPVSSDLWLDYTQYLDKTL---------KVGNVVRDVYSRATKNCPWVGE-LWVRSLLS--LERSRA  107 (442)
Q Consensus        40 ~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~---------~~~~~~~~v~erAl~~~p~s~~-lW~~y~~~--le~~~~  107 (442)
                      +.++..||.....+|++.+.+.++...|....         .-.+.+..-|+.||+..|.... +|..=.-+  +-....
T Consensus         8 E~ark~aea~y~~nP~DadnL~~WG~ALLELAqfk~g~es~~miedAisK~eeAL~I~P~~hdAlw~lGnA~ts~A~l~~   87 (186)
T PF06552_consen    8 EHARKKAEAAYAKNPLDADNLTNWGGALLELAQFKQGPESKKMIEDAISKFEEALKINPNKHDALWCLGNAYTSLAFLTP   87 (186)
T ss_dssp             HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH--
T ss_pred             HHHHHHHHHHHHhCcHhHHHHHHHHHHHHHHHhccCcchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHhhcC
Confidence            45778889999999999999998876665321         1234577889999999998754 55432111  111123


Q ss_pred             CHHHHHHHHHHHH
Q 013489          108 SEEEISTVFEKSL  120 (442)
Q Consensus       108 ~~~~~~~i~~~al  120 (442)
                      +..++...|++|.
T Consensus        88 d~~~A~~~F~kA~  100 (186)
T PF06552_consen   88 DTAEAEEYFEKAT  100 (186)
T ss_dssp             -HHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHH
Confidence            3345555555555

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.

>KOG3824 consensus Huntingtin interacting protein HYPE [General function prediction only]

Probab=88.94  E-value=1.1  Score=41.48  Aligned_cols=51  Identities=16%  Similarity=0.163  Sum_probs=47.9

Q ss_pred             HcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          194 SMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       194 ~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ..| +.++|..+|+-++...|+++++.++|..|...++++-.|..+|-+|+.
T Consensus       128 ~~G-k~ekA~~lfeHAlalaP~~p~~L~e~G~f~E~~~~iv~ADq~Y~~ALt  178 (472)
T KOG3824|consen  128 KDG-KLEKAMTLFEHALALAPTNPQILIEMGQFREMHNEIVEADQCYVKALT  178 (472)
T ss_pred             hcc-chHHHHHHHHHHHhcCCCCHHHHHHHhHHHHhhhhhHhhhhhhheeee
Confidence            445 899999999999999999999999999999999999999999999996

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=88.82  E-value=1.4  Score=32.27  Aligned_cols=40  Identities=15%  Similarity=0.203  Sum_probs=27.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEe
Q 013489          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIY  440 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f  440 (442)
                      .||--..|.+....||.++|++||.| .|.++.|.       -|||..
T Consensus        10 HVFhltFPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l   49 (87)
T PF08675_consen   10 HVFHLTFPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVAL   49 (87)
T ss_dssp             CEEEEE--TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEE
T ss_pred             eEEEEeCchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEe
Confidence            45544599999999999999999987 67788773       567654

; 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.

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=88.18  E-value=1  Score=26.46  Aligned_cols=31  Identities=23%  Similarity=0.116  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHhcCChhhHHHHHHHHHhcCCC
Q 013489           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPV   55 (442)
Q Consensus        25 ~w~~y~~~e~~~g~~~~~~~lyERal~~~p~   55 (442)
                      .|..-+......|+++.+...|++||..+|.
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            4666666666777888888888888887775

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 ....

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=88.03  E-value=0.73  Score=43.82  Aligned_cols=45  Identities=20%  Similarity=0.138  Sum_probs=36.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..-|.++|||++++|.++-.++.+||.|+.+.+...+      .-||++|+
T Consensus        28 SkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGk------nQAflem~   72 (492)
T KOG1190|consen   28 SKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGK------NQAFLEMA   72 (492)
T ss_pred             cceeEeccCCccccHHHHHHhcccccceeeeeeeccc------hhhhhhhc
Confidence            4589999999999999999999999999988765542      25666654

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=87.46  E-value=0.21  Score=52.11  Aligned_cols=53  Identities=23%  Similarity=0.273  Sum_probs=43.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .....|||+|||+..+++.+++..|..+|.|.+|+|-+. .-+..--||||.|.
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP-~~~~esa~~f~~~~  421 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTP-HIKTESAYAFVSLL  421 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccC-CCCcccchhhhhhh
Confidence            455679999999999999999999999999999988665 24444457777763

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=86.91  E-value=11  Score=37.56  Aligned_cols=91  Identities=14%  Similarity=0.055  Sum_probs=58.1

Q ss_pred             HHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHH
Q 013489           33 EQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEI  112 (442)
Q Consensus        33 e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~  112 (442)
                      ..+.|++..++..|..||..+|.+..+..+-+.-+.+. .....+..-.+.++..-|.-...|..-...+.. ....+.+
T Consensus       368 ~Fk~gdy~~Av~~YteAIkr~P~Da~lYsNRAac~~kL-~~~~~aL~Da~~~ieL~p~~~kgy~RKg~al~~-mk~ydkA  445 (539)
T KOG0548|consen  368 AFKKGDYPEAVKHYTEAIKRDPEDARLYSNRAACYLKL-GEYPEALKDAKKCIELDPNFIKAYLRKGAALRA-MKEYDKA  445 (539)
T ss_pred             HHhccCHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHH-hhHHHHHHHHHHHHhcCchHHHHHHHHHHHHHH-HHHHHHH
Confidence            34567888888888888888888877776655443322 233445555777777777666666555443332 3456677


Q ss_pred             HHHHHHHHhCChh
Q 013489          113 STVFEKSLLCAFS  125 (442)
Q Consensus       113 ~~i~~~al~~~~~  125 (442)
                      ...|+.++...+.
T Consensus       446 leay~eale~dp~  458 (539)
T KOG0548|consen  446 LEAYQEALELDPS  458 (539)
T ss_pred             HHHHHHHHhcCch
Confidence            7778887776655

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=86.84  E-value=39  Score=34.47  Aligned_cols=67  Identities=18%  Similarity=0.113  Sum_probs=45.3

Q ss_pred             hhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc------hh----HH----H-HHHHHHHHHHhcccHHHHHHHHHHH
Q 013489          179 DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS------GA----ML----E-AWQSYISMEIELDHINEARSIYKRC  243 (442)
Q Consensus       179 ~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~------~~----~~----~-~w~~~~~~e~~~g~~~~ar~i~~ra  243 (442)
                      ...+++.-.-|-++...| ++..|.+++++++..+      .+    ..    . +-...+=.....|+.+.|.+||...
T Consensus       172 e~syel~yN~Ac~~i~~g-ky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~ea~~iy~~~  250 (652)
T KOG2376|consen  172 EDSYELLYNTACILIENG-KYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTAEASSIYVDI  250 (652)
T ss_pred             cchHHHHHHHHHHHHhcc-cHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHH
Confidence            345666666677778888 8999999999995442      11    11    1 3333333444579999999999998


Q ss_pred             Hhc
Q 013489          244 YSK  246 (442)
Q Consensus       244 l~~  246 (442)
                      +..
T Consensus       251 i~~  253 (652)
T KOG2376|consen  251 IKR  253 (652)
T ss_pred             HHh
Confidence            875

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=86.41  E-value=0.76  Score=40.50  Aligned_cols=47  Identities=17%  Similarity=0.329  Sum_probs=38.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       387 ~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +....+.++|-|++..+.+.+|.++|+++|.+....+        .++++||+|.
T Consensus        95 p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs  141 (216)
T KOG0106|consen   95 PSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFS  141 (216)
T ss_pred             cccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeeh
Confidence            3456789999999999999999999999999854433        3579999995

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=86.33  E-value=5.8  Score=34.93  Aligned_cols=55  Identities=25%  Similarity=0.182  Sum_probs=36.5

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSD   58 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~   58 (442)
                      .|...|+..+...|.+. -..+++...+......|+...+...|++.+..+|.++.
T Consensus        23 ~Ai~~f~~l~~~~P~s~-~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~   77 (203)
T PF13525_consen   23 EAIKLFEKLIDRYPNSP-YAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPK   77 (203)
T ss_dssp             HHHHHHHHHHHH-TTST-THHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TT
T ss_pred             HHHHHHHHHHHHCCCCh-HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcc
Confidence            46778888888877532 22234444444446789999999999999999999884

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=86.19  E-value=1.4  Score=43.78  Aligned_cols=52  Identities=13%  Similarity=0.163  Sum_probs=40.0

Q ss_pred             CCCceEEEcCCCCCCCH------HHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATY------EDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~------~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .....|+|.|+|---..      .-|..+|+.+|+|+.+.++.+. .|..+||.|++|+
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e-~ggtkG~lf~E~~  113 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDE-EGGTKGYLFVEYA  113 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCc-cCCeeeEEEEEec
Confidence            33457899999865332      1355789999999999999985 4559999999996

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=85.89  E-value=2.8  Score=39.72  Aligned_cols=49  Identities=18%  Similarity=0.305  Sum_probs=39.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhcc---C-CCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSD---V-GGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~---~-G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      -.|-..+||+++++.++..||.+   . |....|-++.. ..|+.-|=|||.|+
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa  214 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFA  214 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEec
Confidence            47888999999999999999963   2 24456666665 58999999999996

>KOG0530 consensus Protein farnesyltransferase, alpha subunit/protein geranylgeranyltransferase type I, alpha subunit [Posttranslational modification, protein turnover, chaperones]

Probab=85.83  E-value=28  Score=31.83  Aligned_cols=75  Identities=11%  Similarity=0.125  Sum_probs=39.7

Q ss_pred             HHHhhhhcCchhhHHHHHHHHHHHHHcCCCHH-HHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHH
Q 013489          169 DYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMV-SARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCY  244 (442)
Q Consensus       169 ~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~-~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral  244 (442)
                      +++.....+++..+++|..---+-..+| ++. +-.++...++..+..++-+|..---..+.+++++.-...-...|
T Consensus        99 ~~l~eI~e~npKNYQvWHHRr~ive~l~-d~s~rELef~~~~l~~DaKNYHaWshRqW~~r~F~~~~~EL~y~~~Ll  174 (318)
T KOG0530|consen   99 EYLDEIIEDNPKNYQVWHHRRVIVELLG-DPSFRELEFTKLMLDDDAKNYHAWSHRQWVLRFFKDYEDELAYADELL  174 (318)
T ss_pred             HHHHHHHHhCccchhHHHHHHHHHHHhc-CcccchHHHHHHHHhccccchhhhHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            3444444445555666665544445555 555 55555666666666666666555545555555544443333333

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=85.65  E-value=1.4  Score=25.40  Aligned_cols=22  Identities=27%  Similarity=0.428  Sum_probs=13.4

Q ss_pred             hcCChhhHHHHHHHHHhcCCCC
Q 013489           35 SSGDPGRVQLLYERAITDFPVS   56 (442)
Q Consensus        35 ~~g~~~~~~~lyERal~~~p~~   56 (442)
                      ..|+.+.+..+|++.+..+|.+
T Consensus        12 ~~g~~~~A~~~~~~~~~~~P~s   33 (33)
T PF13174_consen   12 KLGDYDEAIEYFQRLIKRYPDS   33 (33)
T ss_dssp             HHCHHHHHHHHHHHHHHHSTTS
T ss_pred             HccCHHHHHHHHHHHHHHCcCC
Confidence            3456666666666666666653

>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=85.00  E-value=1.8  Score=25.35  Aligned_cols=32  Identities=22%  Similarity=0.201  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHhcCChhhHHHHHHHHHhcCCC
Q 013489           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPV   55 (442)
Q Consensus        24 ~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~   55 (442)
                      ++|..........|+++.+...|++++..+|.
T Consensus         2 ~~~~~lg~~y~~~~~~~~A~~~~~~a~~~~~~   33 (34)
T PF13181_consen    2 EAYYNLGKIYEQLGDYEEALEYFEKALELNPD   33 (34)
T ss_dssp             HHHHHHHHHHHHTTSHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            35677777777788888888888888887773

...

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=84.96  E-value=2.3  Score=36.91  Aligned_cols=68  Identities=21%  Similarity=0.219  Sum_probs=42.7

Q ss_pred             HhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHH
Q 013489           34 QSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER  104 (442)
Q Consensus        34 ~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~  104 (442)
                      ...|++..+..-|.+||..||..+. =..-|.|....  ..-.-+.-.+-||..|...-.||-.|...|++
T Consensus       106 F~ngdyeeA~skY~~Ale~cp~~~~-e~rsIly~Nra--aa~iKl~k~e~aI~dcsKaiel~pty~kAl~R  173 (271)
T KOG4234|consen  106 FKNGDYEEANSKYQEALESCPSTST-EERSILYSNRA--AALIKLRKWESAIEDCSKAIELNPTYEKALER  173 (271)
T ss_pred             hhcccHHHHHHHHHHHHHhCccccH-HHHHHHHhhhH--HHHHHhhhHHHHHHHHHhhHhcCchhHHHHHH
Confidence            3468889999999999999987665 11222222110  00112345566777777777788888887776

>PF15297 CKAP2_C: Cytoskeleton-associated protein 2 C-terminus

Probab=84.91  E-value=14  Score=35.02  Aligned_cols=52  Identities=15%  Similarity=0.167  Sum_probs=44.5

Q ss_pred             cCCCHHHHHHHHHHHHHhchhH---HHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          195 MGKDMVSARGVWERLLKISGAM---LEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       195 ~~~~~~~ar~i~~~~l~~~~~~---~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      -|.-.+.++.+++.+++..|+-   +.+|+..+.++...|.++.+..||+.|+..
T Consensus       115 eGcp~eei~~~L~~li~~IP~A~K~aKYWIC~Arl~~~~~~~e~vi~iyEeAi~a  169 (353)
T PF15297_consen  115 EGCPKEEILATLSDLIKNIPDAKKLAKYWICLARLEPRTGPIEDVIAIYEEAILA  169 (353)
T ss_pred             cCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHc
Confidence            3446778889999999887754   569999999999999999999999999973

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=84.88  E-value=23  Score=30.46  Aligned_cols=62  Identities=15%  Similarity=0.142  Sum_probs=53.1

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc---hhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKIS---GAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~---~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ..+...+.++...| +.+.|.+.|.++...+   ....++|+..+.+-..+|+...+...+.+|-.
T Consensus        37 ~~~~~l~~~~~~~G-d~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~  101 (177)
T PF10602_consen   37 MALEDLADHYCKIG-DLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAES  101 (177)
T ss_pred             HHHHHHHHHHHHhh-hHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            56777888999999 9999999999988873   23467999999999999999999999888875

This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.

>TIGR02996 rpt_mate_G_obs repeat-companion domain TIGR02996

Probab=84.51  E-value=2  Score=26.91  Aligned_cols=26  Identities=31%  Similarity=0.362  Sum_probs=16.6

Q ss_pred             HHHHHhcCCCCHHHHHHHHHHHHHhc
Q 013489           46 YERAITDFPVSSDLWLDYTQYLDKTL   71 (442)
Q Consensus        46 yERal~~~p~~~~lW~~Y~~~l~~~~   71 (442)
                      |.+||..+|.+...|+-|+.||..++
T Consensus         5 ll~AI~~~P~ddt~RLvYADWL~e~g   30 (42)
T TIGR02996         5 LLRAILAHPDDDTPRLVYADWLDEHG   30 (42)
T ss_pred             HHHHHHhCCCCcchHHHHHHHHHHcC
Confidence            55666666666666666666666544

This model describes an abundant paralogous domain of Gemmata obscuriglobus UQM 2246, a member of the Planctomycetes. The domain also occurs, although rarely, in Myxococcus xanthus DK 1622 and related species. Most member proteins have extensive repeats similar to the leucine-rich repeat, or another repeat class or region of low-complexity sequence. This domain is not repeated, and in Gemmata is usually found at the protein N-terminus.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=83.29  E-value=78  Score=34.89  Aligned_cols=61  Identities=11%  Similarity=0.060  Sum_probs=46.6

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHhc---h---hHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          185 YAYWAHLEQSMGKDMVSARGVWERLLKIS---G---AMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       185 ~~~~a~~e~~~~~~~~~ar~i~~~~l~~~---~---~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      +...+......| +.+.|..++++++...   +   ....+...++......|+.+.|+..+.+|+..
T Consensus       694 ~~~~a~~~~~~g-~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~l  760 (903)
T PRK04841        694 WRNIARAQILLG-QFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKL  760 (903)
T ss_pred             HHHHHHHHHHcC-CHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            455677777778 8899999999998762   1   22345667777778889999999999999974

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=83.19  E-value=12  Score=34.12  Aligned_cols=46  Identities=15%  Similarity=0.192  Sum_probs=22.4

Q ss_pred             CHHHHHHHHHHHHHhchhHH-----HHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          198 DMVSARGVWERLLKISGAML-----EAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       198 ~~~~ar~i~~~~l~~~~~~~-----~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ++..|...|...++.+|++.     .+|+-=..|  ..|+++.|-.+|.+++.
T Consensus       156 dy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y--~qg~y~~Aa~~f~~~~k  206 (262)
T COG1729         156 DYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLY--AQGDYEDAAYIFARVVK  206 (262)
T ss_pred             CHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHH--hcccchHHHHHHHHHHH
Confidence            45555555555555554432     244332222  24555555555555554

>KOG1166 consensus Mitotic checkpoint serine/threonine protein kinase [Cell cycle control, cell division, chromosome partitioning]

Probab=82.99  E-value=17  Score=39.80  Aligned_cols=71  Identities=10%  Similarity=0.191  Sum_probs=55.7

Q ss_pred             CHHHHHHHHHHHHHh--chhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCH
Q 013489          198 DMVSARGVWERLLKI--SGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTL  270 (442)
Q Consensus       198 ~~~~ar~i~~~~l~~--~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~  270 (442)
                      ....++.+|..+...  -+....++..|+.+....+...+|..+|..++++.  ....+.+-+.+..|.+..|--
T Consensus        93 ~~~d~~d~f~~m~~kgIg~~lalfYe~~a~~lE~k~~~keA~~v~q~Giq~~--aeP~~rL~~~~~~F~~r~~r~  165 (974)
T KOG1166|consen   93 ELQDAEDFFSYLENKGIGTTLALFYEAYAKHLERKEYFKEAKEVFQLGIQNK--AEPLERLLRQYSNFQQRLMRQ  165 (974)
T ss_pred             HHhhHHHHHHHHHhccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--cCCHHHHHHHHHHHHHHHhhh
Confidence            467888888888876  44556678888888888888999999999999853  334678889999998887753

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=82.85  E-value=2.4  Score=40.77  Aligned_cols=37  Identities=35%  Similarity=0.581  Sum_probs=34.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeC
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHD  426 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~  426 (442)
                      ..++|.+-|||.+-.-+-|.++|+.||.|..|+|...
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckP  266 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKP  266 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCC
Confidence            4579999999999989999999999999999999876

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=82.83  E-value=34  Score=30.41  Aligned_cols=50  Identities=10%  Similarity=0.071  Sum_probs=25.1

Q ss_pred             hhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCC
Q 013489           40 GRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPW   90 (442)
Q Consensus        40 ~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~   90 (442)
                      ..++.=|..+|...|.-+++..-..-|+. ..++.+.+.++|+-.+...|.
T Consensus        82 ~LAR~DftQaLai~P~m~~vfNyLG~Yl~-~a~~fdaa~eaFds~~ELDp~  131 (297)
T COG4785          82 ALARNDFSQALAIRPDMPEVFNYLGIYLT-QAGNFDAAYEAFDSVLELDPT  131 (297)
T ss_pred             HHHhhhhhhhhhcCCCcHHHHHHHHHHHH-hcccchHHHHHhhhHhccCCc
Confidence            44444556666666666665543333333 223444455555555555554

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=81.82  E-value=1.2  Score=45.15  Aligned_cols=44  Identities=18%  Similarity=0.124  Sum_probs=36.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....+|||||+...+...-++.+...||.|.++....         |||+.|.
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~   81 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFL   81 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchh
Confidence            3445999999999999999999999999987764332         8888774

>PF15297 CKAP2_C: Cytoskeleton-associated protein 2 C-terminus

Probab=81.77  E-value=15  Score=34.91  Aligned_cols=60  Identities=20%  Similarity=0.259  Sum_probs=45.7

Q ss_pred             cchhhHHHHHHHHHHHcCCCcH---HHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHH
Q 013489           71 LKVGNVVRDVYSRATKNCPWVG---ELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYL  131 (442)
Q Consensus        71 ~~~~~~~~~v~erAl~~~p~s~---~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~  131 (442)
                      +=..+.++.+++..+.++|...   ..|+=.++ |+...++++.+-.||+.|+..+-..++++.
T Consensus       116 Gcp~eei~~~L~~li~~IP~A~K~aKYWIC~Ar-l~~~~~~~e~vi~iyEeAi~agAqPieElR  178 (353)
T PF15297_consen  116 GCPKEEILATLSDLIKNIPDAKKLAKYWICLAR-LEPRTGPIEDVIAIYEEAILAGAQPIEELR  178 (353)
T ss_pred             CCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHH-HHhhcCCHHHHHHHHHHHHHcCCChHHHHH
Confidence            3345678999999999999754   57888888 455578889999999999987765444433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	442
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	2e-30
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	2e-07
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	6e-28
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	1e-09
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	2e-07
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	5e-04
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	4e-26
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	7e-25
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	6e-14
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	9e-05
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	5e-12
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	5e-11
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	7e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	8e-09
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-08
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	3e-07
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-07
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	6e-07
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	8e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-06
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-06
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-06
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-06
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-06
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-06
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-06
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-06
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	3e-06
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	5e-06
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-06
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	5e-06
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	5e-06
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	5e-06
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	7e-06
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	7e-06
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	9e-06
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-05
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-05
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-04
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-05
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-05
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-05
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-05
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	3e-05
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-05
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-05
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-05
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	5e-05
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	6e-05
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	6e-05
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	6e-05
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	6e-05
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	7e-04
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-04
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-04
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-04
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-04
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-04
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-04
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-04
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-04
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-04
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-04
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-04
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	8e-04
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-04
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-04
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-04
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-04
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-04
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-04
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-04
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	3e-04
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-04
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-04
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-04
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-04
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	9e-04
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	4e-04
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-04
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	5e-04
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	5e-04
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	5e-04
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	5e-04
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	6e-04
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	6e-04
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	6e-04
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	7e-04
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	8e-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 =  123 bits (308), Expect = 2e-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 = 52.4 bits (124), Expect = 2e-07
 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 =  114 bits (287), Expect = 6e-28
 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 = 59.1 bits (142), Expect = 1e-09
 Identities = 43/288 (14%), Positives = 92/288 (31%), 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 R Y  +           ++     + +   S   + A +     E  +  ++  R+ 
Sbjct: 166 QLWRDYNKYEE--------GINIHLAKKMIEDRSRDYMNARRVAKEYETVMKGLD--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 = 52.2 bits (124), Expect = 2e-07
 Identities = 29/204 (14%), Positives = 67/204 (32%), Gaps = 20/204 (9%)

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 -WQSYISMEIELDHINEARSIYKR 242
            W+ Y   E  ++     + I  R
Sbjct: 167 LWRDYNKYEEGINIHLAKKMIEDR 190

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7 Length = 530

 Score = 41.4 bits (96), Expect = 5e-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 =  106 bits (266), Expect = 4e-26
 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 =  105 bits (263), Expect = 7e-25
 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 = 72.6 bits (177), Expect = 6e-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 = 43.7 bits (102), Expect = 9e-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 = 61.6 bits (150), Expect = 5e-12
 Identities = 18/60 (30%), Positives = 30/60 (50%)

Query: 374 KQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           K P+++ V   +    D  T F   +  +    DL  FFS VG V  +RI+ D+ + +S+
Sbjct: 8   KSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 67

>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 = 59.0 bits (143), Expect = 5e-11
 Identities = 18/78 (23%), Positives = 34/78 (43%)

Query: 356 AEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDV 415
           A     + T   +      +     +    K   D+ + ++ N++  +T +DL   FS  
Sbjct: 1   AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC 60

Query: 416 GGVSSIRILHDKFTGKSR 433
           G ++ I IL DKF+G  +
Sbjct: 61  GSINRITILCDKFSGHPK 78

>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 = 54.4 bits (132), Expect = 7e-10
 Identities = 15/44 (34%), Positives = 25/44 (56%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           D  + ++ N++  AT E+L   F   G V+ + IL DKF+G  +
Sbjct: 5   DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPK 48

>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 = 57.6 bits (138), Expect = 6e-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 = 44.1 bits (103), Expect = 1e-04
 Identities = 48/433 (11%), Positives = 118/433 (27%), Gaps = 112/433 (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 415
             ++ L  F    
Sbjct: 373 KMFDRLSVFPPSA 385

>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 = 53.7 bits (129), Expect = 8e-09
 Identities = 17/95 (17%), Positives = 36/95 (37%), Gaps = 2/95 (2%)

Query: 341 PKKVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKG--FTDECTAFLSN 398
            + V      +V      + G + + T ++  K   + +               +  + N
Sbjct: 18  TEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDN 77

Query: 399 INLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           +  + + + LRR F   G V  + I  D++T +SR
Sbjct: 78  LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESR 112

>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 = 49.5 bits (119), Expect = 5e-08
 Identities = 17/44 (38%), Positives = 24/44 (54%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
            + T ++SN+    T  DL R FS  G V  + I+ DK T KS+
Sbjct: 15  SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSK 58

>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 = 47.7 bits (114), Expect = 3e-07
 Identities = 11/51 (21%), Positives = 21/51 (41%)

Query: 383 GRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           G     T+  T F+ N++  +  E L       G +  +R++    T  S+
Sbjct: 7   GLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSK 57

>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 = 47.3 bits (113), Expect = 3e-07
 Identities = 18/39 (46%), Positives = 27/39 (69%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F+ NI  +AT E L+  FS+VG V S R+++D+ TGK +
Sbjct: 12  FVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPK 50

>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 = 46.8 bits (112), Expect = 6e-07
 Identities = 15/52 (28%), Positives = 25/52 (48%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
            G  +   D  T  ++N++      DL+  F   G +S I +  DK TG+S+
Sbjct: 6   SGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSK 57

>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 = 46.1 bits (110), Expect = 8e-07
 Identities = 12/39 (30%), Positives = 23/39 (58%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           +L +I    T E +    S+VG V +++++ D  TG+S+
Sbjct: 6   YLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSK 44

>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 = 48.6 bits (115), Expect = 1e-06
 Identities = 19/92 (20%), Positives = 35/92 (38%), Gaps = 3/92 (3%)

Query: 345 HDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTA-FLSNINLKA 403
           +D       N  +  E R+   T+         K A P     +T +  A ++ N+    
Sbjct: 21  YDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWT 80

Query: 404 TYEDLRRFFSDVGG--VSSIRILHDKFTGKSR 433
           T EDL      +G   +  I+   ++  G+S+
Sbjct: 81  TDEDLTEAVHSLGVNDILEIKFFENRANGQSK 112

>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 = 46.1 bits (110), Expect = 1e-06
 Identities = 11/44 (25%), Positives = 18/44 (40%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
              T  + N+  + + + LRR F   G V  + I  +  T   R
Sbjct: 12  GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPR 55

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 1/41 (2%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           TA++ N+       D+   F D   + S+R++ DK T K +
Sbjct: 17  TAYVGNLPFNTVQGDIDAIFKD-LSIRSVRLVRDKDTDKFK 56

>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 = 45.8 bits (109), Expect = 1e-06
 Identities = 13/64 (20%), Positives = 25/64 (39%)

Query: 370 EQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFT 429
                           KG       ++ +++   T + LR  F   G + SI+++ D  T
Sbjct: 5   HHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSET 64

Query: 430 GKSR 433
           G+S+
Sbjct: 65  GRSK 68

>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 = 44.9 bits (107), Expect = 2e-06
 Identities = 11/39 (28%), Positives = 24/39 (61%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           ++ N+   AT E ++  FS  G V ++++++D+ T K +
Sbjct: 5   YVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPK 43

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 46.7 bits (111), Expect = 2e-06
 Identities = 17/98 (17%), Positives = 42/98 (42%), Gaps = 1/98 (1%)

Query: 336 HAPQKPKKVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAF 395
              Q   ++ +K K +       +          E+ + +   +  PG  +   +    F
Sbjct: 18  DGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRS-VEGWILF 76

Query: 396 LSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           +++I+ +A  ++++  F D G + +I +  D+ TG S+
Sbjct: 77  VTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 114

>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 = 44.9 bits (107), Expect = 2e-06
 Identities = 13/48 (27%), Positives = 23/48 (47%)

Query: 386 KGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
            G +     F+ N++  ++ EDL + FS  G +S +    D  T K +
Sbjct: 3   SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPK 50

>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 = 44.5 bits (106), Expect = 3e-06
 Identities = 11/47 (23%), Positives = 24/47 (51%)

Query: 387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           G +     ++ +++   T + LR  F   G + +I ++ D  TG+S+
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSK 47

>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 = 44.6 bits (106), Expect = 3e-06
 Identities = 12/45 (26%), Positives = 21/45 (46%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
            D    F+  I      +DL+  F + G +  + +L D+FTG  +
Sbjct: 11  HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHK 55

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 44.2 bits (105), Expect = 5e-06
 Identities = 11/44 (25%), Positives = 25/44 (56%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           +    F++ ++ +AT ED+   F++ G + +I +  D+ TG  +
Sbjct: 22  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 65

>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 = 43.7 bits (104), Expect = 5e-06
 Identities = 12/39 (30%), Positives = 23/39 (58%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
            +  ++L  T  DLR  FS  G ++ + I++D+ + +SR
Sbjct: 19  GVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR 57

>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 = 44.7 bits (106), Expect = 5e-06
 Identities = 12/67 (17%), Positives = 26/67 (38%)

Query: 367 TVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHD 426
            +++  ++Q                    ++ I        LR+ F   G + S++I+ D
Sbjct: 18  QLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCD 77

Query: 427 KFTGKSR 433
           + T +SR
Sbjct: 78  RETRQSR 84

>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 = 43.8 bits (104), Expect = 5e-06
 Identities = 10/45 (22%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           T     F+ N+N   +  +L+   S++   + + ++ D  TG +R
Sbjct: 15  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNR 58

>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 = 43.8 bits (104), Expect = 5e-06
 Identities = 12/44 (27%), Positives = 23/44 (52%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           DE   F+  ++     + L + FS  G +S + ++ D+ T +SR
Sbjct: 11  DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSR 54

>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 = 43.8 bits (104), Expect = 7e-06
 Identities = 11/39 (28%), Positives = 25/39 (64%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F+++I+ +A  ++++  F D G + +I +  D+ TG S+
Sbjct: 30  FVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 68

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 43.9 bits (104), Expect = 7e-06
 Identities = 8/39 (20%), Positives = 12/39 (30%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
             + +N       L+      G V  + IL    T K  
Sbjct: 10  TFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHL 48

>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 = 43.9 bits (104), Expect = 9e-06
 Identities = 13/44 (29%), Positives = 24/44 (54%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
             C   +  ++L  T  DLR  FS  G ++ + I++D+ + +SR
Sbjct: 45  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR 88

>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 = 43.9 bits (104), Expect = 1e-05
 Identities = 11/39 (28%), Positives = 24/39 (61%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F++ ++ +AT ED+   F++ G + +I +  D+ TG  +
Sbjct: 26  FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 64

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 44.6 bits (106), Expect = 2e-05
 Identities = 11/60 (18%), Positives = 25/60 (41%)

Query: 374 KQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           +Q  + +   R          ++ +I  +   + +R+ F+  G + SI +  D  T K +
Sbjct: 11  QQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHK 70

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 13/62 (20%), Positives = 29/62 (46%), Gaps = 3/62 (4%)

Query: 372 PKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGK 431
            + QPI D +    + F      ++++++   + +D++  F   G + S  +  D  TGK
Sbjct: 109 GQAQPIIDQLAEEARAFN---RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGK 165

Query: 432 SR 433
            +
Sbjct: 166 HK 167

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 43.2 bits (102), Expect = 2e-05
 Identities = 12/51 (23%), Positives = 22/51 (43%)

Query: 383 GRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
                     +  + N+  + + + LRR F   G V  + I  D++T +SR
Sbjct: 39  RPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESR 89

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 2/43 (4%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVG--GVSSIRILHDKFTGKSR 433
           T  L NI      + +    S      V++IR++ DK T ++R
Sbjct: 11  TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNR 53

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 1/52 (1%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
             R     ++   F+S +    T E+L       G V  +R++ ++  GK +
Sbjct: 8   VFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPK 58

>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 = 41.9 bits (99), Expect = 2e-05
 Identities = 7/52 (13%), Positives = 15/52 (28%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
            G + G        + N+    + +++  FF     +     L     G   
Sbjct: 6   SGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPT 57

>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 = 42.3 bits (100), Expect = 3e-05
 Identities = 15/51 (29%), Positives = 30/51 (58%)

Query: 383 GRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           G+ K  ++    F+ +++ + T ED++  F+  G +S  R++ D  TGKS+
Sbjct: 7   GQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSK 57

>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 = 41.4 bits (98), Expect = 3e-05
 Identities = 10/47 (21%), Positives = 20/47 (42%)

Query: 387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           G +     ++  +    T +DL +     G + S + + DK T K +
Sbjct: 1   GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCK 47

>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 = 42.5 bits (100), Expect = 4e-05
 Identities = 14/63 (22%), Positives = 25/63 (39%)

Query: 371 QPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTG 430
           Q + Q  +     + K     CT ++ N++   T E +   FS  G +  I +  DK   
Sbjct: 19  QYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKK 78

Query: 431 KSR 433
            + 
Sbjct: 79  TAC 81

>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 = 41.0 bits (97), Expect = 4e-05
 Identities = 9/44 (20%), Positives = 18/44 (40%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
            +   ++  +  +   + L   F   G ++ I+I  D  T K R
Sbjct: 6   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR 49

>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 = 41.5 bits (98), Expect = 5e-05
 Identities = 10/42 (23%), Positives = 16/42 (38%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
              +L N++ + T  DL   F+         I     TG+ R
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMR 67

>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 = 41.1 bits (97), Expect = 6e-05
 Identities = 11/51 (21%), Positives = 21/51 (41%)

Query: 383 GRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           G +   T +   ++  +  +   + L   F   G ++ I+I  D  T K R
Sbjct: 4   GSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR 54

>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 = 40.7 bits (96), Expect = 6e-05
 Identities = 7/52 (13%), Positives = 15/52 (28%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
            G + G        + N+    + +++  FF     +     L     G   
Sbjct: 6   SGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPT 57

>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 = 41.1 bits (97), Expect = 6e-05
 Identities = 9/44 (20%), Positives = 20/44 (45%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
            + T ++  ++ K +   L   F   G V +  +  D+ TG+ +
Sbjct: 14  QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQ 57

>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 = 42.7 bits (101), Expect = 6e-05
 Identities = 16/61 (26%), Positives = 22/61 (36%), Gaps = 4/61 (6%)

Query: 377 IKDAVP----GRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKS 432
            K AV      R          F+  I        LR +F   G +  I I+ D+ +GK 
Sbjct: 86  PKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK 145

Query: 433 R 433
           R
Sbjct: 146 R 146

>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 = 39.6 bits (93), Expect = 7e-04
 Identities = 11/39 (28%), Positives = 20/39 (51%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F+  ++ + T E LR  F   G ++   ++ D  T +SR
Sbjct: 17  FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSR 55

>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 = 41.8 bits (99), Expect = 1e-04
 Identities = 12/39 (30%), Positives = 19/39 (48%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           +++N+    T + L   F   G +    IL DK TG+ R
Sbjct: 93  YVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPR 131

>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 = 40.4 bits (95), Expect = 1e-04
 Identities = 12/57 (21%), Positives = 21/57 (36%), Gaps = 1/57 (1%)

Query: 378 KDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDK-FTGKSR 433
                G+           + NI  +A   ++R  FS  G + ++R+      TG  R
Sbjct: 2   SSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHR 58

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 11/42 (26%), Positives = 22/42 (52%), Gaps = 2/42 (4%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKF-TGKSR 433
           TAFL N+    T E ++ FF  +  +S++R+  +     + +
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLK 57

>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 = 39.4 bits (93), Expect = 1e-04
 Identities = 13/39 (33%), Positives = 19/39 (48%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F+ ++N+    E LR  F D     S  ++ D  TG SR
Sbjct: 5   FVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSR 43

>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 = 41.4 bits (98), Expect = 1e-04
 Identities = 14/39 (35%), Positives = 23/39 (58%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           ++S +    T ++L + FS  G + + RIL D+ TG SR
Sbjct: 92  YVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSR 130

>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 = 39.9 bits (94), Expect = 4e-04
 Identities = 11/39 (28%), Positives = 21/39 (53%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
            ++ +    T E+ R  F  +G + S +++ DK TG+S 
Sbjct: 6   IVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSL 44

>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 = 40.1 bits (94), Expect = 2e-04
 Identities = 17/60 (28%), Positives = 23/60 (38%), Gaps = 8/60 (13%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSS--------IRILHDKFTGKSR 433
            G     +D    ++  +N   T +DL  FF   G V          I I  DK TGK +
Sbjct: 6   SGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPK 65

>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 = 41.6 bits (97), Expect = 2e-04
 Identities = 8/96 (8%), Positives = 25/96 (26%), Gaps = 6/96 (6%)

Query: 338 PQKPKKVHDKEKRQVQNLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLS 397
             K   +   +   +++ +   +     +       +Q  K+      +           
Sbjct: 76  VSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKN------RIQHPSNVLHFF 129

Query: 398 NINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           N  L+ T E+      ++G      +       +  
Sbjct: 130 NAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERS 165

>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 = 39.5 bits (93), Expect = 2e-04
 Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 2/42 (4%)

Query: 393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFT-GKSR 433
           TAFL N+    T E ++ FF     +S++R+  +     + +
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRG-LNISAVRLPREPSNPERLK 61

>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 = 39.5 bits (93), Expect = 2e-04
 Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 3/42 (7%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
            T F+  ++   T E L+  F    G    RI+ D+ TG S+
Sbjct: 16  KTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSK 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 Length = 167

 Score = 41.0 bits (97), Expect = 2e-04
 Identities = 12/39 (30%), Positives = 20/39 (51%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F+  I      ++   FFS  G +   +++ DK TG+SR
Sbjct: 91  FVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSR 129

>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 = 39.0 bits (92), Expect = 8e-04
 Identities = 15/44 (34%), Positives = 26/44 (59%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           + C  F+  +N   T ++LR +F   G V+ ++I+ D  TG+SR
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSR 45

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 11/52 (21%), Positives = 20/52 (38%)

Query: 382 PGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
            G     T +   ++  +  +   + L   F   G ++ I+I  D  T K R
Sbjct: 54  GGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR 105

>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 = 39.6 bits (93), Expect = 2e-04
 Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 8/53 (15%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSS--------IRILHDKFTGKSR 433
           +D  T F+  +    T E +  +F  +G + +        I +  D+ TGK +
Sbjct: 11  SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLK 63

>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 = 40.0 bits (94), Expect = 2e-04
 Identities = 11/76 (14%), Positives = 32/76 (42%), Gaps = 1/76 (1%)

Query: 358 ENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGG 417
            +     +   +    +  + D+  G  +G        +SN++   +  D++  F++ G 
Sbjct: 2   ASMTGGQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGT 61

Query: 418 VSSIRILHDKFTGKSR 433
           +    + +D+ +G+S 
Sbjct: 62  LKKAAVDYDR-SGRSL 76

>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 = 39.1 bits (92), Expect = 2e-04
 Identities = 9/41 (21%), Positives = 19/41 (46%), Gaps = 2/41 (4%)

Query: 395 FLSNINLKATYEDLRRFFSDVGG--VSSIRILHDKFTGKSR 433
           ++ N+    T EDL      +G   +  I+   ++  G+S+
Sbjct: 5   YIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSK 45

>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 = 39.1 bits (92), Expect = 2e-04
 Identities = 11/39 (28%), Positives = 22/39 (56%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F+ +++ + T   +   F+  G +S  R++ D  TGKS+
Sbjct: 10  FVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSK 48

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 39.7 bits (93), Expect = 3e-04
 Identities = 12/39 (30%), Positives = 19/39 (48%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F+ ++  + T  DL   F   G V S ++  DK T  S+
Sbjct: 44  FIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSK 82

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 40.3 bits (94), Expect = 3e-04
 Identities = 14/83 (16%), Positives = 31/83 (37%), Gaps = 3/83 (3%)

Query: 354 NLAEENEGRETKQTVEEQPKKQPIKDAVPGRTKGFTDECTA-FLSNINLKATYEDLRRFF 412
           NL  ++         E  PK      A+     G  +   A ++ + +   T + L +  
Sbjct: 17  NLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVI 76

Query: 413 SDVGG--VSSIRILHDKFTGKSR 433
             +G   V  ++   ++  G+S+
Sbjct: 77  RSIGVYDVVELKFAENRANGQSK 99

>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 = 38.8 bits (91), Expect = 3e-04
 Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
            + T F+ N+  +   E L   F   G ++ + I  D+  GK +
Sbjct: 15  ADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPK 57

>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 = 39.0 bits (91), Expect = 3e-04
 Identities = 10/44 (22%), Positives = 20/44 (45%), Gaps = 2/44 (4%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           D+    +  +   A   D+R FF  +  V ++ +L D   G++ 
Sbjct: 15  DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNN 56

>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 = 38.8 bits (91), Expect = 3e-04
 Identities = 12/39 (30%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F+  I+++    ++R FF+  G V  ++I+ D+ TG S+
Sbjct: 13  FVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSK 50

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 11/36 (30%), Positives = 17/36 (47%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDK 427
            TA++ NI   AT  DL   F + G +   +   +K
Sbjct: 28  TTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK 63

>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 = 40.3 bits (95), Expect = 4e-04
 Identities = 9/45 (20%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           T     F+ N+N   +  +L+   S++   + + ++  + TG +R
Sbjct: 11  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNR 54

>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 = 40.3 bits (95), Expect = 4e-04
 Identities = 15/39 (38%), Positives = 19/39 (48%), Gaps = 1/39 (2%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F+  I+ K T  D+R  FS  G +   RIL     G SR
Sbjct: 99  FIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSR 136

>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 = 39.1 bits (92), Expect = 9e-04
 Identities = 11/45 (24%), Positives = 19/45 (42%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           +D    F+  +    + +DLR  F   G V  I +L D+     +
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQ 45

>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 = 39.1 bits (91), Expect = 4e-04
 Identities = 9/60 (15%), Positives = 17/60 (28%)

Query: 374 KQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           K P                  +L  +  +A  + +  FF  +  V     +     GK+ 
Sbjct: 8   KSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKAT 67

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 41.1 bits (97), Expect = 4e-04
 Identities = 6/39 (15%), Positives = 17/39 (43%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
            ++N+    T +         G +    +++ + TG+S+
Sbjct: 99  CVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSK 137

>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 = 38.4 bits (90), Expect = 5e-04
 Identities = 14/47 (29%), Positives = 19/47 (40%)

Query: 387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           G +     F+ N+N   T E L+  FS VG + S  I   K      
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVL 47

>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 = 38.0 bits (89), Expect = 5e-04
 Identities = 8/36 (22%), Positives = 16/36 (44%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDK 427
            T ++  +    T  DLR  F   G + +I ++  +
Sbjct: 13  TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ 48

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 38.2 bits (89), Expect = 5e-04
 Identities = 8/41 (19%), Positives = 12/41 (29%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVV 435
            + NI     +E L       G V S   ++         V
Sbjct: 19  QIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNV 59

>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 = 38.3 bits (90), Expect = 5e-04
 Identities = 9/39 (23%), Positives = 18/39 (46%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F+  I       +LR +F   G V+ + +++D    + R
Sbjct: 14  FVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPR 52

>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 = 38.5 bits (90), Expect = 6e-04
 Identities = 11/39 (28%), Positives = 20/39 (51%)

Query: 395 FLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           F+ ++  +   +DL + F   G V S ++  DK T  S+
Sbjct: 29  FIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 67

>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 = 38.0 bits (89), Expect = 6e-04
 Identities = 6/35 (17%), Positives = 16/35 (45%)

Query: 398 NINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKS 432
           N++   T   + + FS +G   S +++ +  +   
Sbjct: 22  NLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP 56

>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 = 38.4 bits (90), Expect = 6e-04
 Identities = 15/56 (26%), Positives = 25/56 (44%)

Query: 378 KDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
              VP  +   +  C  F+  ++ + T E LR +F   G V    ++ D  T +SR
Sbjct: 12  SGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSR 67

>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 = 38.3 bits (89), Expect = 7e-04
 Identities = 10/45 (22%), Positives = 18/45 (40%)

Query: 389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
            ++    L  +    T E++ +FFS +  V +   L     GK  
Sbjct: 40  ANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKIT 84

>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 = 38.2 bits (89), Expect = 8e-04
 Identities = 10/52 (19%), Positives = 22/52 (42%), Gaps = 2/52 (3%)

Query: 383 GRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGV-SSIRILHDKFTGKSR 433
           G     + +  A ++NI    T  D+ +F   +    +++ +L D   G+  
Sbjct: 7   GEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGL 57

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	442
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.97
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.94
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.93
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	99.93
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.9
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.89
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	99.87
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.84
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.56
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.54
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.53
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.53
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.53
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.52
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	99.51
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.49
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.47
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.47
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.46
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.46
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.46
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.45
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.44
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.44
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.44
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.43
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.42
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.42
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.42
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.42
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.41
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.41
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.4
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.4
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.39
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.39
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.37
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.36
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.36
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.36
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.36
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.36
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.36
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.36
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.36
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.36
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.35
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.35
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.35
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.35
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.35
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	99.34
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.34
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.34
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.34
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.34
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.33
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.33
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.33
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.33
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.33
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.33
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.33
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.33
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.32
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.32
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.32
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.32
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.32
2div_A	99	TRNA selenocysteine associated protein; structural	99.32
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.31
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.31
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.31
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.31
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.31
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.31
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.31
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.31
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.31
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.3
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.3
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.3
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.3
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.3
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.3
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.3
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.3
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.29
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.29
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.29
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.29
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.29
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.28
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.28
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.28
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.28
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.28
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.28
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.27
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.27
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.27
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.27
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.27
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.27
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.26
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.26
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.26
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.25
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.25
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.25
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.25
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.25
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.25
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.25
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.24
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.24
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.24
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.24
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.24
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.24
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.24
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.24
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.24
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.24
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.23
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.23
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.23
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.22
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.22
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.22
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.22
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.22
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.22
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.22
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.21
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.21
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.21
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.2
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.2
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.2
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.2
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.2
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.19
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.19
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.19
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.18
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.18
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.18
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.17
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.17
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.17
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.17
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.16
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.16
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.15
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.15
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.15
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.14
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.14
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.14
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.13
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.13
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.13
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.1
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.09
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.09
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.09
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	98.67
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.08
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.07
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.07
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.07
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.06
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.06
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.05
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.04
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.03
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.03
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.03
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.03
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.02
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.02
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.02
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.01
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.01
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.01
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.01
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.01
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	98.99
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.99
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	98.99
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	98.98
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	98.97
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.97
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	98.97
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	98.97
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	98.97
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	98.96
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	98.96
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	98.95
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	98.95
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	98.94
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	98.93
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	98.93
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	98.93
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	98.93
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	98.93
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	98.91
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	98.91
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	98.91
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.91
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	98.9
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	98.9
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	98.9
4g1t_A	472	Interferon-induced protein with tetratricopeptide	98.89
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	98.89
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	98.88
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	98.88
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	98.88
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	98.87
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	98.86
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	98.86
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	98.85
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	98.85
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	98.84
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.84
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.84
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.82
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.82
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	98.81
1x5p_A	97	Negative elongation factor E; structure genomics,	98.81
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	98.81
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	98.79
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.79
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	98.77
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.76
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	98.75
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	98.74
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.73
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	98.73
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	98.73
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	98.72
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.72
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.71
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.71
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	98.71
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	98.69
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	98.68
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.68
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.67
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	98.66
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.65
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	98.65
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.65
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.65
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.64
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	98.64
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	98.64
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	98.62
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	98.61
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	98.61
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	98.6
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	98.59
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.57
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.57
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.56
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.54
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.52
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.51
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.51
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.5
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.49
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.49
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.47
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.47
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	98.46
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.45
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.45
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.45
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.43
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.42
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.41
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.39
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	98.36
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.36
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.33
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.32
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.32
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.3
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.3
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.28
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.27
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	98.27
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.27
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	98.26
3esl_A	202	Checkpoint serine/threonine-protein kinase BUB1; m	98.26
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.26
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	98.26
2wvi_A	164	Mitotic checkpoint serine/threonine-protein kinase	98.26
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.26
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.25
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.24
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.24
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	98.24
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.23
4a1g_A	152	Mitotic checkpoint serine/threonine-protein kinas;	98.21
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.19
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.18
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.18
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	98.18
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.17
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.17
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.17
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.15
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.15
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	98.15
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.14
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.14
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.13
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.12
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	98.1
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.08
3esl_A	202	Checkpoint serine/threonine-protein kinase BUB1; m	98.07
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	98.07
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.07
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	98.03
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.02
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.02
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.01
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.99
4aez_C	223	MAD3, mitotic spindle checkpoint component MAD3; c	97.98
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.97
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	97.97
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	97.97
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.95
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.93
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.93
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.93
4a1g_A	152	Mitotic checkpoint serine/threonine-protein kinas;	97.9
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.89
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	97.88
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.88
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	97.82
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	97.82
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	97.81
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.81
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	97.81
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	97.8
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	97.8
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.79
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.77
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.76
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.74
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.74
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.73
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.72
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	97.72
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	97.72
4aez_C	223	MAD3, mitotic spindle checkpoint component MAD3; c	97.71
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.7
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.67
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.67
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.65
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.65
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.64
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.63
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	97.63
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.62
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	97.61
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.6
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	97.59
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.58
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.56
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.54
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.54
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	97.54
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.53
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	97.49
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.41
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.4
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.37
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.35
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.32
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.28
2wvi_A	164	Mitotic checkpoint serine/threonine-protein kinase	97.27
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	97.26
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	97.22
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	97.2
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	97.19
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.15
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	97.15
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.15
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.06
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	97.01
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.01
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	96.99
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	96.94
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	96.93
2l6j_A	111	TPR repeat-containing protein associated with HSP;	96.91
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	96.89
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	96.87
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	96.82
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	96.8
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	96.75
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.71
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	96.61
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	96.59
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	96.57
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.42
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	96.4
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	96.39
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	96.34
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	96.2
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	96.18
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	96.17
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	95.64
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	95.17
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	94.96
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	94.78
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	94.11
1klx_A	138	Cysteine rich protein B; structural genomics, heli	93.84
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	93.77
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	93.2
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	92.54
1pc2_A	152	Mitochondria fission protein; unknown function; NM	92.53
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	91.81
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	91.67
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	90.93
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	90.59
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	90.42
1pc2_A	152	Mitochondria fission protein; unknown function; NM	88.87
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	88.25
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	86.42
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	85.67
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	81.3

>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=99.97  E-value=1e-28  Score=255.00  Aligned_cols=244  Identities=15%  Similarity=0.177  Sum_probs=200.2

Q ss_pred             hHhHHHHHHHHHHHHhcC-------ChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHH-HHHHHHHHcCCCc
Q 013489           20 SEKFQQYMIYLKYEQSSG-------DPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVR-DVYSRATKNCPWV   91 (442)
Q Consensus        20 ~~~~~~w~~y~~~e~~~g-------~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~-~v~erAl~~~p~s   91 (442)
                      ...+..|+.|++||+..+       ..+|++.+||+||..+|.++++|++|+.|+...++. +.++ .||+||+.+||.+
T Consensus       299 ~~ql~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~~p~~~~lW~~ya~~~~~~~~~-~~a~r~il~rAi~~~P~s  377 (679)
T 4e6h_A          299 VQQLLIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQHVCFAPEIWFNMANYQGEKNTD-STVITKYLKLGQQCIPNS  377 (679)
T ss_dssp             HHHHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHSCC-TTHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCcH-HHHHHHHHHHHHHhCCCC
Confidence            356789999999999865       246788999999999999999999999999877543 4565 9999999999999


Q ss_pred             HHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhH------------------HHHHHHHHHHHHHHHHHhhccCccch
Q 013489           92 GELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTF------------------EEYLDLFLTRIDGLRRRILFSGEVEG  153 (442)
Q Consensus        92 ~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~------------------~~~~~~~~~~~~~l~rr~~~~~~~~~  153 (442)
                      ..||..|+.+.+. .++.+.++.+|++++...+...                  ...-.+|..++...+|.         
T Consensus       378 ~~Lwl~~a~~ee~-~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~---------  447 (679)
T 4e6h_A          378 AVLAFSLSEQYEL-NTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRI---------  447 (679)
T ss_dssp             HHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHH---------
T ss_pred             HHHHHHHHHHHHH-hCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHc---------
Confidence            9999999997776 6789999999999997532110                  01334677776555443         


Q ss_pred             hhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccH
Q 013489          154 VLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHI  233 (442)
Q Consensus       154 ~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~  233 (442)
                       .++...|.+|.+|+..+      ......+|..+|.+|...+++++.||++|+++|+.+|+...+|+.|++|+...|+.
T Consensus       448 -~~l~~AR~vf~~A~~~~------~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~~fe~~~~~~  520 (679)
T 4e6h_A          448 -QGLAASRKIFGKCRRLK------KLVTPDIYLENAYIEYHISKDTKTACKVLELGLKYFATDGEYINKYLDFLIYVNEE  520 (679)
T ss_dssp             -HCHHHHHHHHHHHHHTG------GGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCH
T ss_pred             -CCHHHHHHHHHHHHHhc------CCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHhCCCH
Confidence             35667888888887752      12235689999999999886799999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhhc
Q 013489          234 NEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (442)
Q Consensus       234 ~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~~  281 (442)
                      ++||.+|++|+....+...+..||..|++||..+|+++++..+.+++.
T Consensus       521 ~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~  568 (679)
T 4e6h_A          521 SQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFF  568 (679)
T ss_dssp             HHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            999999999998532234577999999999999999999988777763

>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=6.2e-25  Score=226.87  Aligned_cols=268  Identities=12%  Similarity=0.103  Sum_probs=193.1

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCC---hhhHHHHHHHHHhcCC--CCHHHHHHHHHHHHHhcch----
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGD---PGRVQLLYERAITDFP--VSSDLWLDYTQYLDKTLKV----   73 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~---~~~~~~lyERal~~~p--~~~~lW~~Y~~~l~~~~~~----   73 (442)
                      .+|..||.+|...|.    ....|..|+++|.+.|+   ++.+..+|+|||..+|  .++++|..|+.|+......    
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            578999999999887    77889999999999888   9999999999999984  7889999999998765432    


Q ss_pred             ---hhHHHHHHHHHHHcC----CCcHHHHHHHHHHHHH--------ccCCHHHHHHHHHHHHhCChhhHH----HHHHHH
Q 013489           74 ---GNVVRDVYSRATKNC----PWVGELWVRSLLSLER--------SRASEEEISTVFEKSLLCAFSTFE----EYLDLF  134 (442)
Q Consensus        74 ---~~~~~~v~erAl~~~----p~s~~lW~~y~~~le~--------~~~~~~~~~~i~~~al~~~~~~~~----~~~~~~  134 (442)
                         .+.++.+|++|+..+    |.++.||..|+.++..        .++..+.++.||+++|..|...+.    .|..+.
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               245789999999865    4478899999987653        123357799999999987654322    222211


Q ss_pred             HHH--------H-----HHHH-HH-----------hh---cc---------------------CccchhhhH--------
Q 013489          135 LTR--------I-----DGLR-RR-----------IL---FS---------------------GEVEGVLDY--------  157 (442)
Q Consensus       135 ~~~--------~-----~~l~-rr-----------~~---~~---------------------~~~~~~~~~--------  157 (442)
                      ...        +     +|.. |.           +.   ..                     ..|..+.++        
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        0     0000 00           00   00                     001111222        


Q ss_pred             ------HHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHH-HHHHHHHHhchhHHHHHHHHHHHHHhc
Q 013489          158 ------SLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSAR-GVWERLLKISGAMLEAWQSYISMEIEL  230 (442)
Q Consensus       158 ------~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar-~i~~~~l~~~~~~~~~w~~~~~~e~~~  230 (442)
                            .+++.+|++|+..       .+...++|..|++++...| +.+.|+ ++|++++..+|.+..+|+.|+.+|...
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                  2344555666554       4566789999999999998 788886 999999999999999999999999999


Q ss_pred             ccHHHHHHHHHHHHhcc----------cCCC---------ChHHHHHHHHHHHHHhCCHhhHHHHHHhhch
Q 013489          231 DHINEARSIYKRCYSKR----------FTGT---------GSEDICHAWLRFEREYGTLEDFDHSVQKVTP  282 (442)
Q Consensus       231 g~~~~ar~i~~ral~~~----------~~~~---------~~~~i~~~~~~fE~~~G~~~~~~~~~~~~~~  282 (442)
                      |++++||.||++++...          .+..         ....+|..|++||+..|+++..+.++.++..
T Consensus       392 ~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~  462 (679)
T 4e6h_A          392 TKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRR  462 (679)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            99999999999999731          1110         1345899999999999999888887777643

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.93  E-value=1.5e-23  Score=198.22  Aligned_cols=241  Identities=21%  Similarity=0.275  Sum_probs=188.9

Q ss_pred             ChHhHHHHHHHHHHHHhc----CCh----hhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh------cchh-------hHH
Q 013489           19 DSEKFQQYMIYLKYEQSS----GDP----GRVQLLYERAITDFPVSSDLWLDYTQYLDKT------LKVG-------NVV   77 (442)
Q Consensus        19 ~~~~~~~w~~y~~~e~~~----g~~----~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~------~~~~-------~~~   77 (442)
                      ++.+...|+.|++||++.    +++    +++..+|+++|..+|.++++|..|+.++...      .++.       +.+
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            345788999999999986    243    6888999999999999999999999998643      2333       679


Q ss_pred             HHHHHHHHH-cCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhh
Q 013489           78 RDVYSRATK-NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLD  156 (442)
Q Consensus        78 ~~v~erAl~-~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~  156 (442)
                      +.+|+||+. ..|.+..+|..|+.+++. .++.+.++.+|++++...+.....   +|..+...+.+ .         .+
T Consensus        84 ~~~~~rAl~~~~p~~~~~~~~~~~~~~~-~~~~~~A~~~~~~al~~~p~~~~~---~~~~~~~~~~~-~---------~~  149 (308)
T 2ond_A           84 ANIYERAISTLLKKNMLLYFAYADYEES-RMKYEKVHSIYNRLLAIEDIDPTL---VYIQYMKFARR-A---------EG  149 (308)
T ss_dssp             HHHHHHHHTTTTTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTSSSSCTHH---HHHHHHHHHHH-H---------HC
T ss_pred             HHHHHHHHHHhCcccHHHHHHHHHHHHh-cCCHHHHHHHHHHHHhccccCccH---HHHHHHHHHHH-h---------cC
Confidence            999999999 579999999999986665 688999999999999987653321   33333322221 1         34


Q ss_pred             HHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHH
Q 013489          157 YSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEA  236 (442)
Q Consensus       157 ~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~a  236 (442)
                      +...+..|++|+..       .+....+|..++.++....++++.|+.+|++++..+|++..+|..|+.++...|++++|
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            44555566666543       34446788888888876433999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcc-cCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          237 RSIYKRCYSKR-FTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       237 r~i~~ral~~~-~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                      +.+|++|+... ++++....+|..|+.||..+|+.+....+..+.
T Consensus       223 ~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a  267 (308)
T 2ond_A          223 RVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRR  267 (308)
T ss_dssp             HHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHH
T ss_pred             HHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            99999999841 233346689999999999999998877655543

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=99.93  E-value=4e-24  Score=214.66  Aligned_cols=245  Identities=12%  Similarity=0.116  Sum_probs=186.5

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCC-------hhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhH
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGD-------PGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNV   76 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~-------~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~   76 (442)
                      +|..|+.++...+.   .+.+.|..|++||+.++.       ..++..+|+|||..+|.++.+|++|+.|+... ++.+.
T Consensus       156 ar~~y~~~~~~~~~---~s~~~W~~y~~~E~~~~~~~~~~~~~~Rv~~~ye~al~~~p~~~~lW~~ya~~~~~~-~~~~~  231 (493)
T 2uy1_A          156 SFQRYQQIQPLIRG---WSVKNAARLIDLEMENGMKLGGRPHESRMHFIHNYILDSFYYAEEVYFFYSEYLIGI-GQKEK  231 (493)
T ss_dssp             HHHHHHHHHHHHHT---CSHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHT-TCHHH
T ss_pred             HHHHHHHHHHHHhh---ccHHHHHHHHHHHhcCCccCcchhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHc-CCHHH
Confidence            46667766644332   145789999999986521       46789999999999999999999999999865 46688


Q ss_pred             HHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCh-----hhHHHHHHHHHHHHHHHHHHhhccCcc
Q 013489           77 VRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAF-----STFEEYLDLFLTRIDGLRRRILFSGEV  151 (442)
Q Consensus        77 ~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~-----~~~~~~~~~~~~~~~~l~rr~~~~~~~  151 (442)
                      ++.||+||+.. |++..||..|+.+++.  .  +..+.++++.+....     ........+|..|+.+++|.       
T Consensus       232 ar~i~erAi~~-P~~~~l~~~y~~~~e~--~--~~~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~y~~~~~r~-------  299 (493)
T 2uy1_A          232 AKKVVERGIEM-SDGMFLSLYYGLVMDE--E--AVYGDLKRKYSMGEAESAEKVFSKELDLLRINHLNYVLKK-------  299 (493)
T ss_dssp             HHHHHHHHHHH-CCSSHHHHHHHHHTTC--T--HHHHHHHHHTC----------CHHHHHHHHHHHHHHHHHH-------
T ss_pred             HHHHHHHHHhC-CCcHHHHHHHHhhcch--h--HHHHHHHHHHHhhccchhhhhcccccHHHHHHHHHHHHHc-------
Confidence            99999999999 9999999999875432  1  113333333211110     01122346777777666543       


Q ss_pred             chhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcc
Q 013489          152 EGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELD  231 (442)
Q Consensus       152 ~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g  231 (442)
                         .++...|.+|++| ..       ......+|..+|.+|...+++++.||.+|+.+++.+|+...+|+.|++||...|
T Consensus       300 ---~~~~~AR~i~~~A-~~-------~~~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~~~~~~~~~~~yid~e~~~~  368 (493)
T 2uy1_A          300 ---RGLELFRKLFIEL-GN-------EGVGPHVFIYCAFIEYYATGSRATPYNIFSSGLLKHPDSTLLKEEFFLFLLRIG  368 (493)
T ss_dssp             ---HCHHHHHHHHHHH-TT-------SCCCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHT
T ss_pred             ---CCHHHHHHHHHHh-hC-------CCCChHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcC
Confidence               3466778888888 21       112356899999999998867999999999999999998999999999999999


Q ss_pred             cHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhhch
Q 013489          232 HINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTP  282 (442)
Q Consensus       232 ~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~~~  282 (442)
                      +.++||.+|+++..       ...+|..|++||..+|++++++.++++...
T Consensus       369 ~~~~aR~l~er~~k-------~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          369 DEENARALFKRLEK-------TSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             CHHHHHHHHHHSCC-------BHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH-------HHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            99999999999832       468999999999999999999887776544

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.90  E-value=6e-22  Score=201.41  Aligned_cols=240  Identities=21%  Similarity=0.265  Sum_probs=185.1

Q ss_pred             hHHHHHHHHHHHHhcC----Ch----hhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh------cchhh-------HHHHH
Q 013489           22 KFQQYMIYLKYEQSSG----DP----GRVQLLYERAITDFPVSSDLWLDYTQYLDKT------LKVGN-------VVRDV   80 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g----~~----~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~------~~~~~-------~~~~v   80 (442)
                      ....|..|+.++...+    ++    .++..+|++||..+|.++.+|+.|+.++...      .++.+       .++.+
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            4679999999998643    33    4788999999999999999999999998852      34433       79999


Q ss_pred             HHHHHH-cCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHH
Q 013489           81 YSRATK-NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSL  159 (442)
Q Consensus        81 ~erAl~-~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~  159 (442)
                      |+||+. .+|.+..+|..|+.+++. .++.+.++.+|++++..++....   .+|..+...+++ .         .++..
T Consensus       309 ~~~Al~~~~p~~~~l~~~~~~~~~~-~g~~~~A~~~~~~al~~~p~~~~---~~~~~~~~~~~~-~---------~~~~~  374 (530)
T 2ooe_A          309 YERAISTLLKKNMLLYFAYADYEES-RMKYEKVHSIYNRLLAIEDIDPT---LVYIQYMKFARR-A---------EGIKS  374 (530)
T ss_dssp             HHHHTTTTCSSCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHSSSSCHH---HHHHHHHHHHHH-H---------HHHHH
T ss_pred             HHHHHHHhCcccHHHHHHHHHHHHh-cCCHHHHHHHHHHHhCccccCch---HHHHHHHHHHHH-h---------cCHHH
Confidence            999998 789999999999986655 68899999999999998765422   234433333322 1         23445


Q ss_pred             HHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHH
Q 013489          160 IRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSI  239 (442)
Q Consensus       160 ~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i  239 (442)
                      .+..|++|+..       .+....++...+.++....++++.|+.+|+++++.+|+++.+|+.|++++...|++++||.+
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            55566666542       33334566666666654334999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcc-cCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhhch
Q 013489          240 YKRCYSKR-FTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTP  282 (442)
Q Consensus       240 ~~ral~~~-~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~~~  282 (442)
                      |++|+... .++.....+|..|++||..+|+.+++..+..++..
T Consensus       448 ~~~al~~~~~~~~~~~~lw~~~~~~e~~~G~~~~~~~~~~r~~~  491 (530)
T 2ooe_A          448 FERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFT  491 (530)
T ss_dssp             HHHHHHSCCSCGGGCHHHHHHHHHHHHHSSCHHHHHHHHHHHHH
T ss_pred             HHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            99999842 11123457999999999999999998877766543

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.89  E-value=4.8e-21  Score=194.73  Aligned_cols=271  Identities=15%  Similarity=0.188  Sum_probs=192.5

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhh----HHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGN----VVR   78 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~----~~~   78 (442)
                      .+|..||.+|...|.    +...|..|+.++...|+++.++.+|+|||..+| ++++|+.|+.|+....++.+    .++
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            578999999999886    788999999999999999999999999999999 78899999998876544433    355


Q ss_pred             HHHHHHHHcC---CCcHHHHHHHHHHHHHc--------cCCHHHHHHHHHHHHhCChhhH---H-HHHHHHHHH------
Q 013489           79 DVYSRATKNC---PWVGELWVRSLLSLERS--------RASEEEISTVFEKSLLCAFSTF---E-EYLDLFLTR------  137 (442)
Q Consensus        79 ~v~erAl~~~---p~s~~lW~~y~~~le~~--------~~~~~~~~~i~~~al~~~~~~~---~-~~~~~~~~~------  137 (442)
                      .+|++|+..+   |.+..+|..|+.++...        .+..+.++.+|++++..+....   + .|..+....      
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            6999999876   46789999999866541        4567889999999998543321   1 121111000      


Q ss_pred             --H-----HHHHHH-----------hhcc-------C----------ccchhhhHHHHH--------HHHHHHHHHHhhh
Q 013489          138 --I-----DGLRRR-----------ILFS-------G----------EVEGVLDYSLIR--------ETFQRASDYLSEQ  174 (442)
Q Consensus       138 --~-----~~l~rr-----------~~~~-------~----------~~~~~~~~~~~r--------~~~~~a~~~l~~~  174 (442)
                        +     .+...+           ....       .          .+..+.++..-.        ....+++..+..+
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              0     000000           0000       0          000111111000        0012333344444


Q ss_pred             hcCchhhHHHHHHHHHHHHH-------cCCCHH-------HHHHHHHHHHH-hchhHHHHHHHHHHHHHhcccHHHHHHH
Q 013489          175 MKNTDGLLRLYAYWAHLEQS-------MGKDMV-------SARGVWERLLK-ISGAMLEAWQSYISMEIELDHINEARSI  239 (442)
Q Consensus       175 ~~~~~~~~~l~~~~a~~e~~-------~~~~~~-------~ar~i~~~~l~-~~~~~~~~w~~~~~~e~~~g~~~~ar~i  239 (442)
                      +...+....+|..|+.++..       .| +++       .|+.+|++++. .+|++..+|..|+.++...|++++|+.+
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            44445667899999999876       56 776       89999999998 6899999999999999999999999999


Q ss_pred             HHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhhc
Q 013489          240 YKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (442)
Q Consensus       240 ~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~~  281 (442)
                      |++++.  .++..+..+|..|..|++..|+.+....++.++.
T Consensus       344 ~~~al~--~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al  383 (530)
T 2ooe_A          344 YNRLLA--IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAR  383 (530)
T ss_dssp             HHHHHH--SSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhC--ccccCchHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            999997  3445555799999999999998877766666653

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=99.87  E-value=1.2e-20  Score=189.45  Aligned_cols=216  Identities=14%  Similarity=0.088  Sum_probs=150.9

Q ss_pred             chhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHH
Q 013489            2 CNARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVY   81 (442)
Q Consensus         2 ~~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~   81 (442)
                      ..+|..||.+|...|.                   |+++++..+|+|||..+| ++++|..|+.|........+.++.+|
T Consensus        12 ~~aR~vyer~l~~~P~-------------------~~~e~~~~iferal~~~p-s~~LW~~Y~~f~~~~~~~~~~i~~~f   71 (493)
T 2uy1_A           12 SSPSAIMEHARRLYMS-------------------KDYRSLESLFGRCLKKSY-NLDLWMLYIEYVRKVSQKKFKLYEVY   71 (493)
T ss_dssp             CCHHHHHHHHHHHHHT-------------------TCHHHHHHHHHHHSTTCC-CHHHHHHHHHHHHHHC----CTHHHH
T ss_pred             HHHHHHHHHHHHHCCC-------------------CCHHHHHHHHHHHhccCC-CHHHHHHHHHHHHHhCchHHHHHHHH
Confidence            4578888888877652                   678999999999999998 99999999999998765556789999


Q ss_pred             HHHHHcC---CCcHHHHHHHHHHHHH---ccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhh--ccCcc-c
Q 013489           82 SRATKNC---PWVGELWVRSLLSLER---SRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRIL--FSGEV-E  152 (442)
Q Consensus        82 erAl~~~---p~s~~lW~~y~~~le~---~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~--~~~~~-~  152 (442)
                      ++|+.++   |.++.||..|+.+++.   .++..+.++.+|++|+..+......+   |..|..+......  ....+ +
T Consensus        72 e~al~~vg~d~~s~~iW~~Yi~f~~~~~~~~~~~~~vR~iy~rAL~~P~~~~~~l---w~~Y~~fE~~~~~~~~~~~~~~  148 (493)
T 2uy1_A           72 EFTLGQFENYWDSYGLYKEYIEEEGKIEDEQTRIEKIRNGYMRALQTPMGSLSEL---WKDFENFELELNKITGKKIVGD  148 (493)
T ss_dssp             HHHHHHSTTCTTCHHHHHHHHHHTSSCSSHHHHHHHHHHHHHHHHTSCCTTHHHH---HHHHHHHHHHHCHHHHHHHHHH
T ss_pred             HHHHHHcCCCcccHHHHHHHHHHHHhchhhhHHHHHHHHHHHHHHhChhhhHHHH---HHHHHHHHHHhccccHHHHHHH
Confidence            9999975   6789999999997642   13456789999999999766544332   3222222111000  00000 0


Q ss_pred             hhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCC------HHHHHHHHHHHHHhchhHHHHHHHHHHH
Q 013489          153 GVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKD------MVSARGVWERLLKISGAMLEAWQSYISM  226 (442)
Q Consensus       153 ~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~------~~~ar~i~~~~l~~~~~~~~~w~~~~~~  226 (442)
                      ...++...+..+..+...+..      ....+|..|+.+|...+..      ..+++.+|++++..+|....+|+.|+.|
T Consensus       149 ~~~~y~~ar~~y~~~~~~~~~------~s~~~W~~y~~~E~~~~~~~~~~~~~~Rv~~~ye~al~~~p~~~~lW~~ya~~  222 (493)
T 2uy1_A          149 TLPIFQSSFQRYQQIQPLIRG------WSVKNAARLIDLEMENGMKLGGRPHESRMHFIHNYILDSFYYAEEVYFFYSEY  222 (493)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHT------CSHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HhHHHHHHHHHHHHHHHHHhh------ccHHHHHHHHHHHhcCCccCcchhhHHHHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            001222334444444443321      1346899999998754211      3567889999999999889999999999


Q ss_pred             HHhcccHHHHHHHHHHHHhc
Q 013489          227 EIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       227 e~~~g~~~~ar~i~~ral~~  246 (442)
                      +...|+++.||.+|++|+..
T Consensus       223 ~~~~~~~~~ar~i~erAi~~  242 (493)
T 2uy1_A          223 LIGIGQKEKAKKVVERGIEM  242 (493)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHhC
Confidence            99999999999999999973

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.84  E-value=6.4e-19  Score=166.29  Aligned_cols=217  Identities=15%  Similarity=0.178  Sum_probs=175.8

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHh-------cCCh-------hhHHHHHHHHHh-cCCCCHHHHHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQS-------SGDP-------GRVQLLYERAIT-DFPVSSDLWLDYTQYL   67 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~-------~g~~-------~~~~~lyERal~-~~p~~~~lW~~Y~~~l   67 (442)
                      .+...|+.+|...|.    +.++|..|+.++..       .|++       +.++.+|+|||. .+|.+..+|..|+.++
T Consensus        34 ~a~~~~~~al~~~p~----~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~  109 (308)
T 2ond_A           34 RVMFAYEQCLLVLGH----HPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYE  109 (308)
T ss_dssp             HHHHHHHHHHHHHTT----CHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCC----CHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHH
Confidence            355799999998886    88899999999864       4886       899999999999 6999999999999988


Q ss_pred             HHhcchhhHHHHHHHHHHHcCCCcHH-HHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhh
Q 013489           68 DKTLKVGNVVRDVYSRATKNCPWVGE-LWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRIL  146 (442)
Q Consensus        68 ~~~~~~~~~~~~v~erAl~~~p~s~~-lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~  146 (442)
                      ... +..+.++.+|++|+...|.... +|..|+.++.+ .+..+.++.+|++|+...+..+..++..-  .   +..+. 
T Consensus       110 ~~~-~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~-~~~~~~A~~~~~~a~~~~p~~~~~~~~~a--~---~~~~~-  181 (308)
T 2ond_A          110 ESR-MKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARR-AEGIKSGRMIFKKAREDARTRHHVYVTAA--L---MEYYC-  181 (308)
T ss_dssp             HHT-TCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHH-HHCHHHHHHHHHHHHTSTTCCTHHHHHHH--H---HHHHT-
T ss_pred             Hhc-CCHHHHHHHHHHHHhccccCccHHHHHHHHHHHH-hcCHHHHHHHHHHHHhcCCCCHHHHHHHH--H---HHHHH-
Confidence            755 4667899999999999998876 99999986654 67889999999999988766543333111  0   00000 


Q ss_pred             ccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh---ch-hHHHHHHH
Q 013489          147 FSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI---SG-AMLEAWQS  222 (442)
Q Consensus       147 ~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~---~~-~~~~~w~~  222 (442)
                             ..++...+..|++|+..       .+....+|..++.++...| +++.|+.+|++++..   .| +...+|..
T Consensus       182 -------~~~~~~A~~~~~~al~~-------~p~~~~~~~~~~~~~~~~g-~~~~A~~~~~~al~~~~l~p~~~~~l~~~  246 (308)
T 2ond_A          182 -------SKDKSVAFKIFELGLKK-------YGDIPEYVLAYIDYLSHLN-EDNNTRVLFERVLTSGSLPPEKSGEIWAR  246 (308)
T ss_dssp             -------SCCHHHHHHHHHHHHHH-------HTTCHHHHHHHHHHHHTTC-CHHHHHHHHHHHHHSSSSCGGGCHHHHHH
T ss_pred             -------cCCHHHHHHHHHHHHHh-------CCCcHHHHHHHHHHHHHCC-CHHHHHHHHHHHHhccCCCHHHHHHHHHH
Confidence                   13455666777777765       3445679999999999999 999999999999995   45 36789999


Q ss_pred             HHHHHHhcccHHHHHHHHHHHHhc
Q 013489          223 YISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       223 ~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      |+.|+...|+.+.|+.++++++..
T Consensus       247 ~~~~~~~~g~~~~a~~~~~~a~~~  270 (308)
T 2ond_A          247 FLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             HHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHH
Confidence            999999999999999999999973

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.56  E-value=2.4e-13  Score=130.56  Aligned_cols=237  Identities=11%  Similarity=-0.012  Sum_probs=134.3

Q ss_pred             HHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHH
Q 013489            6 AHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRAT   85 (442)
Q Consensus         6 ~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl   85 (442)
                      ..++..+...+.....+...|...+......|+++.+..+|++++..+|.+...|...+..+... ++.+.+...|++++
T Consensus        48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~-g~~~~A~~~~~~al  126 (365)
T 4eqf_A           48 SASEKGYYFHTENPFKDWPGAFEEGLKRLKEGDLPVTILFMEAAILQDPGDAEAWQFLGITQAEN-ENEQAAIVALQRCL  126 (365)
T ss_dssp             -----CCCCCSSCTTTTCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHH
T ss_pred             HHHHHhhhcccCCcccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHC-CCHHHHHHHHHHHH
Confidence            34444444333211123446778888788889999999999999999999999999888877644 45677899999999


Q ss_pred             HcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHH-------------------HHHHHHHHHHHhh
Q 013489           86 KNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDL-------------------FLTRIDGLRRRIL  146 (442)
Q Consensus        86 ~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~-------------------~~~~~~~l~rr~~  146 (442)
                      ...|.....|...+..+. ..++.+.+...|++++...+.....+..+                   +......+.+-+.
T Consensus       127 ~~~p~~~~~~~~l~~~~~-~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  205 (365)
T 4eqf_A          127 ELQPNNLKALMALAVSYT-NTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAH  205 (365)
T ss_dssp             HHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCHHHHCC-------------------CCHHHHHHHHHHHHHHH
T ss_pred             hcCCCCHHHHHHHHHHHH-ccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHH
Confidence            999988888888776444 46888899999999987655421111000                   0000111110000


Q ss_pred             -ccC--ccchh---hhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHH
Q 013489          147 -FSG--EVEGV---LDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAW  220 (442)
Q Consensus       147 -~~~--~~~~~---~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w  220 (442)
                       .+.  ....+   ..+......+++|+.++...+...+....+|...+.++...| +++.|...|++++..+|+...+|
T Consensus       206 ~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g-~~~~A~~~~~~al~~~p~~~~~~  284 (365)
T 4eqf_A          206 QNGDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTVRPEDYSLWNRLGATLANGD-RSEEAVEAYTRALEIQPGFIRSR  284 (365)
T ss_dssp             HSCSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             hCcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcC-CHHHHHHHHHHHHhcCCCchHHH
Confidence             000  00000   000011122334444444443333334445555555555555 56666666666666555555555


Q ss_pred             HHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          221 QSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       221 ~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ...+.+....|+++.|...|++++.
T Consensus       285 ~~l~~~~~~~g~~~~A~~~~~~al~  309 (365)
T 4eqf_A          285 YNLGISCINLGAYREAVSNFLTALS  309 (365)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            5555555555666666666666554

>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=99.54  E-value=3e-12  Score=123.97  Aligned_cols=266  Identities=14%  Similarity=0.066  Sum_probs=156.8

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ++...++.++...|.    +...|...+......|+++.+..+|++++...|.+...|...+..+... +..+.+...|+
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            455667777777665    5667777777777788888888888888888888888887777666543 34566778888


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHH---------HHHHHHHh-hccCccc
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTR---------IDGLRRRI-LFSGEVE  152 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~---------~~~l~rr~-~~~~~~~  152 (442)
                      +++...|....+|...... ....+..+++..+|++++...+.....+..+-..+         +..+.+-+ ..+...+
T Consensus       126 ~al~~~p~~~~~~~~l~~~-~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~  204 (388)
T 1w3b_A          126 SALQYNPDLYCVRSDLGNL-LKALGRLEEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLD  204 (388)
T ss_dssp             HHHHHCTTCTHHHHHHHHH-HHTTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHH
T ss_pred             HHHHhCCCcHHHHHHHHHH-HHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHH
Confidence            8888778777777776653 33467777778888887765554332222211111         00010000 0000000


Q ss_pred             hhhhH---HHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHh
Q 013489          153 GVLDY---SLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE  229 (442)
Q Consensus       153 ~~~~~---~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~  229 (442)
                      .+...   ......+++|+..+...+...+....+|...+.+....| +++.|...|++++...|+...+|...+.....
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            00000   000011233444443333333444556666677777777 77777777777777777777777777777777


Q ss_pred             cccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHH
Q 013489          230 LDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQ  278 (442)
Q Consensus       230 ~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~  278 (442)
                      .|+++.|..+|++++..  .++.+ .++..........|+.+.-....+
T Consensus       284 ~g~~~~A~~~~~~al~~--~p~~~-~~~~~l~~~~~~~g~~~~A~~~~~  329 (388)
T 1w3b_A          284 KGSVAEAEDCYNTALRL--CPTHA-DSLNNLANIKREQGNIEEAVRLYR  329 (388)
T ss_dssp             HSCHHHHHHHHHHHHHH--CTTCH-HHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhh--CcccH-HHHHHHHHHHHHcCCHHHHHHHHH
Confidence            77777777777777762  22333 344444555555566554443333

>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=99.53  E-value=5.8e-12  Score=118.34  Aligned_cols=264  Identities=9%  Similarity=0.039  Sum_probs=164.9

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ++...|+.++...|.    +...+..++......|+++.+..+|++++..+|.++..|...+..+...+...+.+...|+
T Consensus        40 ~A~~~~~~~l~~~p~----~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~  115 (330)
T 3hym_B           40 MCYKLTSVVMEKDPF----HASCLPVHIGTLVELNKANELFYLSHKLVDLYPSNPVSWFAVGCYYLMVGHKNEHARRYLS  115 (330)
T ss_dssp             HHHHHHHHHHHHCTT----CTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTHHHHHHHHHHHHSCSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCC----ChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence            456677777777664    4455666666666677777777778888777777777777777666544425566777777


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHH---------HHHHHHHHhh-ccCccc
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLT---------RIDGLRRRIL-FSGEVE  152 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~---------~~~~l~rr~~-~~~~~~  152 (442)
                      +++...|.....|......+. ..++.+.+...|++++...+.....+..+-..         ....+.+-+. .+....
T Consensus       116 ~a~~~~~~~~~~~~~l~~~~~-~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~  194 (330)
T 3hym_B          116 KATTLEKTYGPAWIAYGHSFA-VESEHDQAMAAYFTAAQLMKGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIAPEDPF  194 (330)
T ss_dssp             HHHTTCTTCTHHHHHHHHHHH-HHTCHHHHHHHHHHHHHHTTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHH
T ss_pred             HHHHhCCccHHHHHHHHHHHH-HccCHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCCCChH
Confidence            777777777777777665433 35677777777777776544321111111100         1111111100 001000


Q ss_pred             ----------hhhhHHHHHHHHHHHHHHHhhhhcC--chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHH
Q 013489          153 ----------GVLDYSLIRETFQRASDYLSEQMKN--TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAW  220 (442)
Q Consensus       153 ----------~~~~~~~~r~~~~~a~~~l~~~~~~--~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w  220 (442)
                                ...++......|++++.........  .+....+|...+.+....| +++.|...|++++...|++..+|
T Consensus       195 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~a~~~~~~~~~~~  273 (330)
T 3hym_B          195 VMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLK-KYAEALDYHRQALVLIPQNASTY  273 (330)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHSTTCSHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhc-CHHHHHHHHHHHHhhCccchHHH
Confidence                      0122333334444444433221111  1334568888999998899 99999999999999999999999


Q ss_pred             HHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHH
Q 013489          221 QSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFD  274 (442)
Q Consensus       221 ~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~  274 (442)
                      ...+.+....|+++.|...|++++.  +.++.+......-..++...|+.+.+.
T Consensus       274 ~~la~~~~~~g~~~~A~~~~~~al~--~~p~~~~~~~~l~~~~~~~~g~~~a~~  325 (330)
T 3hym_B          274 SAIGYIHSLMGNFENAVDYFHTALG--LRRDDTFSVTMLGHCIEMYIGDSEAYI  325 (330)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHTTTT--TCSCCHHHHHHHHHHHHTTTTC-----
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHc--cCCCchHHHHHHHHHHHHHhCchhccC
Confidence            9999999999999999999999997  344555444444444677788876544

>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=99.53  E-value=4.5e-12  Score=119.13  Aligned_cols=222  Identities=9%  Similarity=-0.065  Sum_probs=136.8

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~  101 (442)
                      +.+.+...+......|+++.+..+|++++...|.+...|..++..+... +..+.+..+|++++...|.+..+|......
T Consensus        21 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~-~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~   99 (330)
T 3hym_B           21 NLDVVVSLAERHYYNCDFKMCYKLTSVVMEKDPFHASCLPVHIGTLVEL-NKANELFYLSHKLVDLYPSNPVSWFAVGCY   99 (330)
T ss_dssp             CCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTTHHHHHHHHHHH-TCHHHHHHHHHHHHHHCTTSTHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCChhhHHHHHHHHHHh-hhHHHHHHHHHHHHHhCcCCHHHHHHHHHH
Confidence            4556777777778889999999999999999999999999888877644 466789999999999999999999998876


Q ss_pred             HHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHH---------HHHHHHHhh-ccCccchhh---hHHHHHHHHHHHH
Q 013489          102 LERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTR---------IDGLRRRIL-FSGEVEGVL---DYSLIRETFQRAS  168 (442)
Q Consensus       102 le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~---------~~~l~rr~~-~~~~~~~~~---~~~~~r~~~~~a~  168 (442)
                      +.......+.+...|++++...+.....+..+-..+         +..+.+-+. .......+.   ........++.|.
T Consensus       100 ~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~  179 (330)
T 3hym_B          100 YLMVGHKNEHARRYLSKATTLEKTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKGCHLPMLYIGLEYGLTNNSKLAE  179 (330)
T ss_dssp             HHHSCSCHHHHHHHHHHHHTTCTTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCSHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHhhhhHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhhHHHHH
Confidence            655333889999999999987665333222211111         011110000 000000000   0000112234455


Q ss_pred             HHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc---------hhHHHHHHHHHHHHHhcccHHHHHHH
Q 013489          169 DYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS---------GAMLEAWQSYISMEIELDHINEARSI  239 (442)
Q Consensus       169 ~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~---------~~~~~~w~~~~~~e~~~g~~~~ar~i  239 (442)
                      .++...+...+....+|...+.+....| +++.|..+|++++...         |....+|...+.+....|+++.|..+
T Consensus       180 ~~~~~al~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  258 (330)
T 3hym_B          180 RFFSQALSIAPEDPFVMHEVGVVAFQNG-EWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDY  258 (330)
T ss_dssp             HHHHHHHTTCTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHhCCCChHHHHHHHHHHHHcc-cHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHH
Confidence            5554444444444455555555555555 5666666666666553         33345555555555555666666666


Q ss_pred             HHHHHh
Q 013489          240 YKRCYS  245 (442)
Q Consensus       240 ~~ral~  245 (442)
                      |++++.
T Consensus       259 ~~~a~~  264 (330)
T 3hym_B          259 HRQALV  264 (330)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            666654

>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=99.53  E-value=7.6e-12  Score=121.15  Aligned_cols=266  Identities=13%  Similarity=0.106  Sum_probs=193.0

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      +|...|+.++...|.    +...|...+......|+++.+...|++++..+|.+...|......+.. .+..+.+..+|+
T Consensus        85 ~A~~~~~~al~~~p~----~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~-~g~~~~A~~~~~  159 (388)
T 1w3b_A           85 EAIEHYRHALRLKPD----FIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKA-LGRLEEAKACYL  159 (388)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHT-TSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcc----hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHH-ccCHHHHHHHHH
Confidence            577889999988775    677899898888889999999999999999999999999998887764 356677999999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHH---------HHHHHHHhh-ccCccc
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTR---------IDGLRRRIL-FSGEVE  152 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~---------~~~l~rr~~-~~~~~~  152 (442)
                      +++...|.....|......+ ...+..+.+...|++++...+.....+..+-..+         +..+.+-+. .+....
T Consensus       160 ~al~~~p~~~~~~~~l~~~~-~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~  238 (388)
T 1w3b_A          160 KAIETQPNFAVAWSNLGCVF-NAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAV  238 (388)
T ss_dssp             HHHHHCTTCHHHHHHHHHHH-HTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHH
T ss_pred             HHHHhCCCCHHHHHHHHHHH-HHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcCCHH
Confidence            99999999999998877644 4578889999999999987776544433322211         111111110 111110


Q ss_pred             hhhh---HHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHh
Q 013489          153 GVLD---YSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE  229 (442)
Q Consensus       153 ~~~~---~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~  229 (442)
                      .+..   .-.....++.|+.++...+...+.....|...+.+....| +++.|..+|++++..+|++..+|...+.+...
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            0000   0011123466777776666655666678888999999999 99999999999999999999999999999999


Q ss_pred             cccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHH
Q 013489          230 LDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQ  278 (442)
Q Consensus       230 ~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~  278 (442)
                      .|+++.|..+|++++..  .++.+ .++......-...|+.+.-...++
T Consensus       318 ~g~~~~A~~~~~~al~~--~p~~~-~~~~~l~~~~~~~g~~~~A~~~~~  363 (388)
T 1w3b_A          318 QGNIEEAVRLYRKALEV--FPEFA-AAHSNLASVLQQQGKLQEALMHYK  363 (388)
T ss_dssp             TTCHHHHHHHHHHHTTS--CTTCH-HHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhc--CCCcH-HHHHHHHHHHHHcCCHHHHHHHHH
Confidence            99999999999999973  33333 345555555555676554443333

>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=99.52  E-value=3.4e-12  Score=122.25  Aligned_cols=269  Identities=12%  Similarity=0.076  Sum_probs=166.8

Q ss_pred             HHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHH
Q 013489            7 HLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATK   86 (442)
Q Consensus         7 ~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~   86 (442)
                      .|+.++...+.....+...|...+......|+++.+..+|++++...|.+...|...+..+... +..+.+...|++++.
T Consensus        48 ~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~-g~~~~A~~~~~~al~  126 (368)
T 1fch_A           48 TYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAEN-EQELLAISALRRCLE  126 (368)
T ss_dssp             HHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHH
T ss_pred             hhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHC-cCHHHHHHHHHHHHh
Confidence            5676765554311112345777777777888999999999999999999999988888766643 456778899999999


Q ss_pred             cCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHH------------------HH------HHHHHHHHHH
Q 013489           87 NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEY------------------LD------LFLTRIDGLR  142 (442)
Q Consensus        87 ~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~------------------~~------~~~~~~~~l~  142 (442)
                      ..|....+|...+..+. ..+..+.+...|++++...+.....+                  +.      -+...+..+.
T Consensus       127 ~~~~~~~~~~~l~~~~~-~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~  205 (368)
T 1fch_A          127 LKPDNQTALMALAVSFT-NESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFL  205 (368)
T ss_dssp             HCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHH-HcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHH
Confidence            88988888888776444 46788888889998887654321110                  00      0001111111


Q ss_pred             HHhh-ccC--ccchhh---hHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH
Q 013489          143 RRIL-FSG--EVEGVL---DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM  216 (442)
Q Consensus       143 rr~~-~~~--~~~~~~---~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~  216 (442)
                      +-+. .+.  ....+.   .+......++.|+.++..++...+....+|...+.+....| +++.|..+|++++...|+.
T Consensus       206 ~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~al~~~~~~  284 (368)
T 1fch_A          206 AAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGN-QSEEAVAAYRRALELQPGY  284 (368)
T ss_dssp             HHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCc
Confidence            1000 011  000000   00111122455555555554434445567777777777777 7888888888888877777


Q ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCC-C--------hHHHHHHHHHHHHHhCCHhhHHHHHHh
Q 013489          217 LEAWQSYISMEIELDHINEARSIYKRCYSKRFTGT-G--------SEDICHAWLRFEREYGTLEDFDHSVQK  279 (442)
Q Consensus       217 ~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~-~--------~~~i~~~~~~fE~~~G~~~~~~~~~~~  279 (442)
                      ..+|...+.+....|+++.|...|++++... +.. .        ...+|......-...|..+....+..+
T Consensus       285 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  355 (368)
T 1fch_A          285 IRSRYNLGISCINLGAHREAVEHFLEALNMQ-RKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAADAR  355 (368)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-HTC------CCCCCHHHHHHHHHHHHHHTCGGGHHHHHTT
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCCCccccccchhhHHHHHHHHHHHHhCChHhHHHhHHH
Confidence            7777777777777788888888888877632 211 0        134566666666666776666555443

>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=99.51  E-value=1.3e-13  Score=110.64  Aligned_cols=60  Identities=10%  Similarity=0.202  Sum_probs=52.9

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          184 LYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ||+.||.++. .+ |+++||.+|+.+++.+..-..+|+.|++||.++|++.+||+|+.+|+.
T Consensus        63 LWIrYA~~~e-i~-D~d~aR~vy~~a~~~hKkFAKiwi~~AqFEiRqgnl~kARkILg~AiG  122 (161)
T 4h7y_A           63 IQVRFAELKA-IQ-EPDDARDYFQMARANCKKFAFVHISFAQFELSQGNVKKSKQLLQKAVE  122 (161)
T ss_dssp             HHHHHHHHHH-HH-CGGGCHHHHHHHHHHCTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHH-hc-CHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcccHHHHHHHHHHHhc
Confidence            7778887754 35 899999999999988666688999999999999999999999999997

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.49  E-value=2e-11  Score=115.93  Aligned_cols=214  Identities=14%  Similarity=0.010  Sum_probs=115.5

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (442)
                      |...|+.++...|.    +...|...+......|+++.+...|++++...|.+...|...+..+... ++.+.+...|++
T Consensus        22 A~~~~~~~l~~~p~----~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~A~~~~~~   96 (359)
T 3ieg_A           22 ALSQFHAAVDGDPD----NYIAYYRRATVFLAMGKSKAALPDLTKVIALKMDFTAARLQRGHLLLKQ-GKLDEAEDDFKK   96 (359)
T ss_dssp             HHHHHHHHHHHCTT----CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHhhCcc----cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHc-CChHHHHHHHHH
Confidence            44556666655553    4556666666666666666666666666666666666666666555433 344556666666


Q ss_pred             HHHcCC---CcHHHHHHH------------HHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhcc
Q 013489           84 ATKNCP---WVGELWVRS------------LLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFS  148 (442)
Q Consensus        84 Al~~~p---~s~~lW~~y------------~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~  148 (442)
                      ++...|   .....|..+            +. +....+..+.+..+|++++...+.....+..+-..+.          
T Consensus        97 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~-~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~----------  165 (359)
T 3ieg_A           97 VLKSNPSEQEEKEAESQLVKADEMQRLRSQAL-DAFDGADYTAAITFLDKILEVCVWDAELRELRAECFI----------  165 (359)
T ss_dssp             HHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH----------
T ss_pred             HHhcCCcccChHHHHHHHHHHHHHHHHHHHHH-HHHHccCHHHHHHHHHHHHHhCCCchHHHHHHHHHHH----------
Confidence            666666   555555444            12 2223455666666666666544433222211111110          


Q ss_pred             CccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHH-----
Q 013489          149 GEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSY-----  223 (442)
Q Consensus       149 ~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~-----  223 (442)
                                 ....++.|+.++...+...+.....|...+.+....| +++.|...|++++...|+....|..+     
T Consensus       166 -----------~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~  233 (359)
T 3ieg_A          166 -----------KEGEPRKAISDLKAASKLKSDNTEAFYKISTLYYQLG-DHELSLSEVRECLKLDQDHKRCFAHYKQVKK  233 (359)
T ss_dssp             -----------HTTCHHHHHHHHHHHHTTCSCCHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             -----------HCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcC-CHHHHHHHHHHHHhhCccchHHHHHHHHHHH
Confidence                       0112333444444444333444456666666666666 66666666666666666655544433     


Q ss_pred             -------HHHHHhcccHHHHHHHHHHHHh
Q 013489          224 -------ISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       224 -------~~~e~~~g~~~~ar~i~~ral~  245 (442)
                             +......|+++.|..+|++++.
T Consensus       234 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~  262 (359)
T 3ieg_A          234 LNKLIESAEELIRDGRYTDATSKYESVMK  262 (359)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence                   3334455666666666666665

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.47  E-value=9.6e-12  Score=119.26  Aligned_cols=244  Identities=11%  Similarity=-0.014  Sum_probs=151.1

Q ss_pred             HHHHHHHHHhcCChhhHHHHHHHHHhcCCC----CHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 013489           26 YMIYLKYEQSSGDPGRVQLLYERAITDFPV----SSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        26 w~~y~~~e~~~g~~~~~~~lyERal~~~p~----~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~  101 (442)
                      |+.........+..    ..++.++...+.    +...|...+..+... ++.+.+..+|++++...|....+|......
T Consensus        34 wl~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-g~~~~A~~~~~~al~~~p~~~~~~~~lg~~  108 (365)
T 4eqf_A           34 WISENQEAQNQVTV----SASEKGYYFHTENPFKDWPGAFEEGLKRLKE-GDLPVTILFMEAAILQDPGDAEAWQFLGIT  108 (365)
T ss_dssp             -----------------------CCCCCSSCTTTTCTTHHHHHHHHHHH-TCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHhhhhhhhhhh----HHHHHhhhcccCCcccchhHHHHHHHHHHHC-CCHHHHHHHHHHHHHhCcCCHHHHHHHHHH
Confidence            66555533323333    334454444443    345588888777654 456789999999999999999999998875


Q ss_pred             HHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHH---------HHHHHHHhh-ccC---ccchh----------hhHH
Q 013489          102 LERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTR---------IDGLRRRIL-FSG---EVEGV----------LDYS  158 (442)
Q Consensus       102 le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~---------~~~l~rr~~-~~~---~~~~~----------~~~~  158 (442)
                      +. ..++.+.+...|++++...+.....+..+-..+         +..+.+-+. .+.   .....          ....
T Consensus       109 ~~-~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~  187 (365)
T 4eqf_A          109 QA-ENENEQAAIVALQRCLELQPNNLKALMALAVSYTNTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSP  187 (365)
T ss_dssp             HH-HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCHHHHCC------------------
T ss_pred             HH-HCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHH
Confidence            55 478899999999999987665433332221111         111111110 000   00000          0011


Q ss_pred             HHHHHHHHHHHHHhhhhcCchh--hHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHH
Q 013489          159 LIRETFQRASDYLSEQMKNTDG--LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEA  236 (442)
Q Consensus       159 ~~r~~~~~a~~~l~~~~~~~~~--~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~a  236 (442)
                      .....+++|+.++...+...+.  ...+|...+.++...| +++.|..+|++++...|++..+|..++......|+++.|
T Consensus       188 ~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A  266 (365)
T 4eqf_A          188 VDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGVLFHLSG-EFNRAIDAFNAALTVRPEDYSLWNRLGATLANGDRSEEA  266 (365)
T ss_dssp             -CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             hhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHH
Confidence            1123455666666555544444  5678888999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHh
Q 013489          237 RSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQK  279 (442)
Q Consensus       237 r~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~  279 (442)
                      ..+|++++..  .++.+ .++..........|+.+.-...+++
T Consensus       267 ~~~~~~al~~--~p~~~-~~~~~l~~~~~~~g~~~~A~~~~~~  306 (365)
T 4eqf_A          267 VEAYTRALEI--QPGFI-RSRYNLGISCINLGAYREAVSNFLT  306 (365)
T ss_dssp             HHHHHHHHHH--CTTCH-HHHHHHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHhc--CCCch-HHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            9999999973  33333 4555566666667776554444444

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.47  E-value=3.1e-12  Score=113.86  Aligned_cols=198  Identities=14%  Similarity=-0.013  Sum_probs=127.2

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~  101 (442)
                      +...|..........|+++.+...|+++|..+|.++..|......+... +..+.+...|++++...|.....|..+...
T Consensus         4 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~-g~~~~A~~~~~~al~~~P~~~~a~~~lg~~   82 (217)
T 2pl2_A            4 AEQNPLRLGVQLYALGRYDAALTLFERALKENPQDPEALYWLARTQLKL-GLVNPALENGKTLVARTPRYLGGYMVLSEA   82 (217)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHhCCCcHHHHHHHHHH
Confidence            5567888888888999999999999999999999999999998877654 556779999999999999999999887765


Q ss_pred             HHHcc-----------CCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHH
Q 013489          102 LERSR-----------ASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDY  170 (442)
Q Consensus       102 le~~~-----------~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~  170 (442)
                      +.. .           +..+++...|++++...|.....+..+-..+.     ..         .++......|++++..
T Consensus        83 ~~~-~~~~~~~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~lg~~~~-----~~---------g~~~~A~~~~~~al~~  147 (217)
T 2pl2_A           83 YVA-LYRQAEDRERGKGYLEQALSVLKDAERVNPRYAPLHLQRGLVYA-----LL---------GERDKAEASLKQALAL  147 (217)
T ss_dssp             HHH-HHHTCSSHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-----HT---------TCHHHHHHHHHHHHHH
T ss_pred             HHH-hhhhhhhhcccccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHH-----Hc---------CChHHHHHHHHHHHhc
Confidence            544 4           55666777777777665553332222211110     00         2233333344444332


Q ss_pred             HhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHH
Q 013489          171 LSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCY  244 (442)
Q Consensus       171 l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral  244 (442)
                             . ....+|...+.+....| +++.|...|++++..+|++..+|..++.+....|+++.|...|+++-
T Consensus       148 -------~-~~~~~~~~la~~~~~~g-~~~~A~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~~  212 (217)
T 2pl2_A          148 -------E-DTPEIRSALAELYLSMG-RLDEALAQYAKALEQAPKDLDLRVRYASALLLKGKAEEAARAAALEH  212 (217)
T ss_dssp             -------C-CCHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTC---------------
T ss_pred             -------c-cchHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHHh
Confidence                   2 33446666666666666 67777777777777777777777777777777777777777776654

>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=99.46  E-value=2e-11  Score=120.22  Aligned_cols=232  Identities=13%  Similarity=0.017  Sum_probs=134.0

Q ss_pred             HHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHH
Q 013489            7 HLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATK   86 (442)
Q Consensus         7 ~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~   86 (442)
                      .+...+...|    .+...|...+......|+++.+..+|++++..+|.+...|...+..+... +..+.+...|++++.
T Consensus        14 ~~~~~~~~~p----~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~-g~~~~A~~~~~~al~   88 (450)
T 2y4t_A           14 GTENLYFQSM----ADVEKHLELGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAM-GKSKAALPDLTKVIQ   88 (450)
T ss_dssp             ---------C----HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHH
T ss_pred             cccccccccH----HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHC-CCHHHHHHHHHHHHh
Confidence            3445555544    37778888888777888888888888888888888888888887766543 455678888888888


Q ss_pred             cCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhH---HHHHHHHHH---------------------HHHHHH
Q 013489           87 NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTF---EEYLDLFLT---------------------RIDGLR  142 (442)
Q Consensus        87 ~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~---~~~~~~~~~---------------------~~~~l~  142 (442)
                      ..|.....|...+..+.. .+..+.+..+|++++...+...   ..+..+...                     .+..+.
T Consensus        89 ~~p~~~~~~~~l~~~~~~-~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~  167 (450)
T 2y4t_A           89 LKMDFTAARLQRGHLLLK-QGKLDEAEDDFKKVLKSNPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLD  167 (450)
T ss_dssp             HCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             cCCCcHHHHHHHHHHHHH-cCCHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            888888888777764443 6778888888888887655432   221111000                     000000


Q ss_pred             HHhh-ccCccchhh---hHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHH
Q 013489          143 RRIL-FSGEVEGVL---DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLE  218 (442)
Q Consensus       143 rr~~-~~~~~~~~~---~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~  218 (442)
                      +-+. .+.....+.   .+-.....++.|+.++...+...+.....|...+.+....| +++.|..+|++++...|+...
T Consensus       168 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~p~~~~  246 (450)
T 2y4t_A          168 KILEVCVWDAELRELRAECFIKEGEPRKAISDLKAASKLKNDNTEAFYKISTLYYQLG-DHELSLSEVRECLKLDQDHKR  246 (450)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHCSCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHH
T ss_pred             HHHHhCCCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCChHH
Confidence            0000 000000000   00000011233444444333323334456666777777777 777777777777777777666


Q ss_pred             HHHHH------------HHHHHhcccHHHHHHHHHHHHh
Q 013489          219 AWQSY------------ISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       219 ~w~~~------------~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      +|..+            +......|+++.|..+|++++.
T Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~  285 (450)
T 2y4t_A          247 CFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMK  285 (450)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            66555            5566666777777777777775

>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=99.46  E-value=7.2e-14  Score=107.83  Aligned_cols=53  Identities=25%  Similarity=0.368  Sum_probs=50.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||||||+++|+++|+.+|++||.|.+|+|+.|+.+|+++|||||+|.
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~   69 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYV   69 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEEC
Confidence            44569999999999999999999999999999999999999999999999995

>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=99.46  E-value=1e-11  Score=116.49  Aligned_cols=219  Identities=10%  Similarity=-0.026  Sum_probs=122.0

Q ss_pred             HHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHH
Q 013489           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLE  103 (442)
Q Consensus        24 ~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le  103 (442)
                      ..|...+......|+++.+..+|++++..+|.+...|...+..+... ++.+.+...|++++...|.....|...+..+.
T Consensus        22 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~  100 (327)
T 3cv0_A           22 ENPMEEGLSMLKLANLAEAALAFEAVCQAAPEREEAWRSLGLTQAEN-EKDGLAIIALNHARMLDPKDIAVHAALAVSHT  100 (327)
T ss_dssp             SCHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHHhcCcCCHHHHHHHHHHHH
Confidence            34555566566677777777777777777777777777766655533 44566777777777777777777776665443


Q ss_pred             HccCCHHHHHHHHHHHHhCChhhHHHHHHH------------------H------HHHHHHHHHHhh-ccCccchh---h
Q 013489          104 RSRASEEEISTVFEKSLLCAFSTFEEYLDL------------------F------LTRIDGLRRRIL-FSGEVEGV---L  155 (442)
Q Consensus       104 ~~~~~~~~~~~i~~~al~~~~~~~~~~~~~------------------~------~~~~~~l~rr~~-~~~~~~~~---~  155 (442)
                       ..+..+.+...|++++...+.....+..+                  +      ......+.+-+. .......+   .
T Consensus       101 -~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la  179 (327)
T 3cv0_A          101 -NEHNANAALASLRAWLLSQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPNDAQLHASLG  179 (327)
T ss_dssp             -HTTCHHHHHHHHHHHHHTSTTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHHSTTCHHHHHHHH
T ss_pred             -HcCCHHHHHHHHHHHHHhCCccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhCCCCHHHHHHHH
Confidence             35667777777777775543311110000                  0      000000100000 00000000   0


Q ss_pred             hHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHH
Q 013489          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINE  235 (442)
Q Consensus       156 ~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~  235 (442)
                      .+-.....++.|+.++...+...+....+|...+.+....| +++.|..+|++++...|+...+|...+.+....|+++.
T Consensus       180 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~g~~~~  258 (327)
T 3cv0_A          180 VLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGN-RPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDL  258 (327)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhccHHH
Confidence            00000112344444444443333444556666666666666 77777777777777777767777777777777777777


Q ss_pred             HHHHHHHHHh
Q 013489          236 ARSIYKRCYS  245 (442)
Q Consensus       236 ar~i~~ral~  245 (442)
                      |...|++++.
T Consensus       259 A~~~~~~a~~  268 (327)
T 3cv0_A          259 AAKQLVRAIY  268 (327)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            7777777775

>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=99.45  E-value=7.3e-11  Score=116.26  Aligned_cols=201  Identities=13%  Similarity=0.018  Sum_probs=137.8

Q ss_pred             hHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHH
Q 013489           41 RVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSL  120 (442)
Q Consensus        41 ~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al  120 (442)
                      .....+.+++..+|.+...|...+..+... ++.+.+..+|++++...|....+|...+..+. ..+..+.+...|++++
T Consensus        10 ~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~-g~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~-~~g~~~~A~~~~~~al   87 (450)
T 2y4t_A           10 GVDLGTENLYFQSMADVEKHLELGKKLLAA-GQLADALSQFHAAVDGDPDNYIAYYRRATVFL-AMGKSKAALPDLTKVI   87 (450)
T ss_dssp             -------------CHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHH
T ss_pred             cccccccccccccHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHhCCccHHHHHHHHHHHH-HCCCHHHHHHHHHHHH
Confidence            345568888889999999999999877754 46678999999999999999999999887554 4788999999999999


Q ss_pred             hCChhhHHHHHHHHHHH---------HHHHHHHhhc--cCcc---chhhhH---------------HHHHHHHHHHHHHH
Q 013489          121 LCAFSTFEEYLDLFLTR---------IDGLRRRILF--SGEV---EGVLDY---------------SLIRETFQRASDYL  171 (442)
Q Consensus       121 ~~~~~~~~~~~~~~~~~---------~~~l~rr~~~--~~~~---~~~~~~---------------~~~r~~~~~a~~~l  171 (442)
                      ...+.....+..+-..+         ...+. +...  +...   ..+..+               ......++.|+.++
T Consensus        88 ~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~  166 (450)
T 2y4t_A           88 QLKMDFTAARLQRGHLLLKQGKLDEAEDDFK-KVLKSNPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFL  166 (450)
T ss_dssp             HHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH-HHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             hcCCCcHHHHHHHHHHHHHcCCHHHHHHHHH-HHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            87665433332222111         11111 1111  1110   000000               01122346677777


Q ss_pred             hhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          172 SEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       172 ~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ...+...+....++...+.+....| +++.|..+|++++..+|++..+|...+.+....|+++.|..+|++++.
T Consensus       167 ~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  239 (450)
T 2y4t_A          167 DKILEVCVWDAELRELRAECFIKEG-EPRKAISDLKAASKLKNDNTEAFYKISTLYYQLGDHELSLSEVRECLK  239 (450)
T ss_dssp             HHHHHHCTTCHHHHHHHHHHHHHTT-CGGGGHHHHHHHHHHHCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCChHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            6666555566678888999999999 999999999999999999999999999999999999999999999997

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.44  E-value=5.2e-11  Score=121.89  Aligned_cols=264  Identities=11%  Similarity=-0.021  Sum_probs=158.7

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      +++..|+..+.. +    .+...|...+......|+++.+..+|++++...|.+...|..++..+... +..+.+..+|+
T Consensus       290 ~A~~~~~~~~~~-~----~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~-g~~~~A~~~~~  363 (597)
T 2xpi_A          290 RAEDYLSSINGL-E----KSSDLLLCKADTLFVRSRFIDVLAITTKILEIDPYNLDVYPLHLASLHES-GEKNKLYLISN  363 (597)
T ss_dssp             HHHHHHHTSTTG-G----GCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCCTTHHHHHHHHHHH-TCHHHHHHHHH
T ss_pred             HHHHHHHHhhcC-C----chHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHh-CCHHHHHHHHH
Confidence            345556655544 2    36778999999888899999999999999998899888998888877644 45567888999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHH---------HHHHHHHhh-ccCccc
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTR---------IDGLRRRIL-FSGEVE  152 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~---------~~~l~rr~~-~~~~~~  152 (442)
                      +++...|....+|...+..+. ..+..+++..+|++++...+.....+..+-..+         +..+.+-+. ......
T Consensus       364 ~~~~~~~~~~~~~~~l~~~~~-~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  442 (597)
T 2xpi_A          364 DLVDRHPEKAVTWLAVGIYYL-CVNKISEARRYFSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQGTHL  442 (597)
T ss_dssp             HHHHHCTTSHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTTTCSH
T ss_pred             HHHhhCcccHHHHHHHHHHHH-HhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchH
Confidence            999888888888888766444 468888899999998876554332222111111         011110000 000000


Q ss_pred             hh---hhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh------chhH-HHHHHH
Q 013489          153 GV---LDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI------SGAM-LEAWQS  222 (442)
Q Consensus       153 ~~---~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~------~~~~-~~~w~~  222 (442)
                      .+   ...-...+.+++|..++...+...+.....|...+.+....| +++.|..+|++++..      .|+. ..+|..
T Consensus       443 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~  521 (597)
T 2xpi_A          443 PYLFLGMQHMQLGNILLANEYLQSSYALFQYDPLLLNELGVVAFNKS-DMQTAINHFQNALLLVKKTQSNEKPWAATWAN  521 (597)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhC-CHHHHHHHHHHHHHhhhccccchhhHHHHHHH
Confidence            00   000011122344444444443323333455666666666666 677777777777666      3333 556777


Q ss_pred             HHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHH
Q 013489          223 YISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSV  277 (442)
Q Consensus       223 ~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~  277 (442)
                      .+......|+++.|..+|++++..  .++.+ .+|..........|+.+.....+
T Consensus       522 l~~~~~~~g~~~~A~~~~~~~~~~--~p~~~-~~~~~l~~~~~~~g~~~~A~~~~  573 (597)
T 2xpi_A          522 LGHAYRKLKMYDAAIDALNQGLLL--STNDA-NVHTAIALVYLHKKIPGLAITHL  573 (597)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--SSCCH-HHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHh--CCCCh-HHHHHHHHHHHHhCCHHHHHHHH
Confidence            777766777777777777777652  22222 45555555555666655444333

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.44  E-value=3.7e-11  Score=122.94  Aligned_cols=251  Identities=10%  Similarity=-0.018  Sum_probs=170.3

Q ss_pred             HHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHc
Q 013489           26 YMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERS  105 (442)
Q Consensus        26 w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~  105 (442)
                      |...+......|+++.+..+|++++.. |.+...|...+..+... +..+.+..+|++++...|.....|..++..+. .
T Consensus       275 ~~~~~~~~~~~g~~~~A~~~~~~~~~~-~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~-~  351 (597)
T 2xpi_A          275 YMLKLNKTSHEDELRRAEDYLSSINGL-EKSSDLLLCKADTLFVR-SRFIDVLAITTKILEIDPYNLDVYPLHLASLH-E  351 (597)
T ss_dssp             HHTTSCTTTTHHHHHHHHHHHHTSTTG-GGCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHCTTCCTTHHHHHHHHH-H
T ss_pred             HHHHHHHHcCcchHHHHHHHHHHhhcC-CchHHHHHHHHHHHHHh-cCHHHHHHHHHHHHHcCcccHHHHHHHHHHHH-H
Confidence            333344444567889999999999987 78999999999877754 46678999999999999988889988887555 4


Q ss_pred             cCCHHHHHHHHHHHHhCChhhHHHHHHHHHHH---------HHHHHHHh-hccCccchh---hhHHHHHHHHHHHHHHHh
Q 013489          106 RASEEEISTVFEKSLLCAFSTFEEYLDLFLTR---------IDGLRRRI-LFSGEVEGV---LDYSLIRETFQRASDYLS  172 (442)
Q Consensus       106 ~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~---------~~~l~rr~-~~~~~~~~~---~~~~~~r~~~~~a~~~l~  172 (442)
                      .+..+++..+|++++...+.....+..+-..+         ...+.+-+ ........+   ...-...+.+++|+.++.
T Consensus       352 ~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  431 (597)
T 2xpi_A          352 SGEKNKLYLISNDLVDRHPEKAVTWLAVGIYYLCVNKISEARRYFSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYT  431 (597)
T ss_dssp             HTCHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            78889999999999876554333222211111         11111100 011111100   111111233466777666


Q ss_pred             hhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcc----c
Q 013489          173 EQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKR----F  248 (442)
Q Consensus       173 ~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~----~  248 (442)
                      ......+.....|...+..+...| +++.|..+|++++...|++..+|...+......|+++.|..+|++++...    .
T Consensus       432 ~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  510 (597)
T 2xpi_A          432 TAARLFQGTHLPYLFLGMQHMQLG-NILLANEYLQSSYALFQYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQS  510 (597)
T ss_dssp             HHHHTTTTCSHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHhCccchHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhcccc
Confidence            665545555667888888888888 89999999999999888888889999999888999999999999988631    0


Q ss_pred             CCCChHHHHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          249 TGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       249 ~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                      .++....+|..........|+.+.-...+++.
T Consensus       511 ~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  542 (597)
T 2xpi_A          511 NEKPWAATWANLGHAYRKLKMYDAAIDALNQG  542 (597)
T ss_dssp             CSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             chhhHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            11111357777777777788876655555443

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.44  E-value=1.2e-13  Score=105.30  Aligned_cols=51  Identities=24%  Similarity=0.238  Sum_probs=47.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCC--eeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGG--VSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~--i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      -.||||+|||+++|+++|+++|++||.  |.+|++++|+.||++||||||+|.
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~   61 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLS   61 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECS
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEEC
Confidence            349999999999999999999999995  679999999999999999999995

>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=99.43  E-value=2.4e-13  Score=102.38  Aligned_cols=53  Identities=25%  Similarity=0.419  Sum_probs=50.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+.+|++||.|.+|+++.++.+|+++|||||+|.
T Consensus         9 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~   61 (87)
T 3s7r_A            9 EDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFK   61 (87)
T ss_dssp             SCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEEC
Confidence            45679999999999999999999999999999999999889999999999995

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.42  E-value=8.9e-13  Score=105.44  Aligned_cols=56  Identities=23%  Similarity=0.275  Sum_probs=51.9

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          386 KGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       386 ~~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....+.++|||+|||+++++++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~   90 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFD   90 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEEC
Confidence            34456789999999999999999999999999999999999889999999999996

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.42  E-value=2.9e-10  Score=107.76  Aligned_cols=213  Identities=11%  Similarity=-0.012  Sum_probs=162.9

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~  101 (442)
                      +.+.|...+......|+++.+..+|++++..+|.++..|...+..+... ++.+.+...|++++...|.....|......
T Consensus         2 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~-~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~   80 (359)
T 3ieg_A            2 DVEKHLELGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAM-GKSKAALPDLTKVIALKMDFTAARLQRGHL   80 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHc-cCHHHHHHHHHHHHHhCCCcchHHHHHHHH
Confidence            4667888888888999999999999999999999999999999877654 466789999999999999999999888775


Q ss_pred             HHHccCCHHHHHHHHHHHHhCCh---hhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCc
Q 013489          102 LERSRASEEEISTVFEKSLLCAF---STFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNT  178 (442)
Q Consensus       102 le~~~~~~~~~~~i~~~al~~~~---~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~  178 (442)
                      +. ..+..+.+...|++++...+   .....+..+....  ........       .........++.|+.++...+...
T Consensus        81 ~~-~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~~~~~~-------a~~~~~~~~~~~A~~~~~~~~~~~  150 (359)
T 3ieg_A           81 LL-KQGKLDEAEDDFKKVLKSNPSEQEEKEAESQLVKAD--EMQRLRSQ-------ALDAFDGADYTAAITFLDKILEVC  150 (359)
T ss_dssp             HH-HHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHH--HHHHHHHH-------HHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HH-HcCChHHHHHHHHHHHhcCCcccChHHHHHHHHHHH--HHHHHHHH-------HHHHHHccCHHHHHHHHHHHHHhC
Confidence            54 46889999999999998877   5333222211100  00000000       000011123345555555544445


Q ss_pred             hhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          179 DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       179 ~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      +....++...+.+....| +++.|..+|++++...|+...+|...+.+....|+++.|..+|++++..
T Consensus       151 ~~~~~~~~~~~~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~  217 (359)
T 3ieg_A          151 VWDAELRELRAECFIKEG-EPRKAISDLKAASKLKSDNTEAFYKISTLYYQLGDHELSLSEVRECLKL  217 (359)
T ss_dssp             TTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHTTCSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            556678888999999999 9999999999999999999999999999999999999999999999973

>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=99.42  E-value=4.8e-11  Score=114.13  Aligned_cols=238  Identities=10%  Similarity=-0.025  Sum_probs=161.4

Q ss_pred             cCChhhHHH-HHHHHHhcCCCCH----HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHH
Q 013489           36 SGDPGRVQL-LYERAITDFPVSS----DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEE  110 (442)
Q Consensus        36 ~g~~~~~~~-lyERal~~~p~~~----~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~  110 (442)
                      .|+++.+.. .|++++...|.++    ..|...+..+... ++.+.+...|++++...|....+|......+. ..++.+
T Consensus        38 ~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~-g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~-~~g~~~  115 (368)
T 1fch_A           38 LSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQE-GDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQA-ENEQEL  115 (368)
T ss_dssp             --------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHT-TCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHH-HTTCHH
T ss_pred             HHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHC-CCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH-HCcCHH
Confidence            367788888 9999999888764    5577777666644 46678999999999999999999998777444 478899


Q ss_pred             HHHHHHHHHHhCChhhHHHHHHHHHHH---------HHHHHHHhh-ccCccch------------------hhhHHHHHH
Q 013489          111 EISTVFEKSLLCAFSTFEEYLDLFLTR---------IDGLRRRIL-FSGEVEG------------------VLDYSLIRE  162 (442)
Q Consensus       111 ~~~~i~~~al~~~~~~~~~~~~~~~~~---------~~~l~rr~~-~~~~~~~------------------~~~~~~~r~  162 (442)
                      .+...|++++...+.....+..+-..+         +..+.+-+. .+.....                  ....-....
T Consensus       116 ~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  195 (368)
T 1fch_A          116 LAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDS  195 (368)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHhhhhcccHHHHHHHHHhhcc
Confidence            999999999987665433332222111         111111110 0110000                  011111345


Q ss_pred             HHHHHHHHHhhhhcCchh--hHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHH
Q 013489          163 TFQRASDYLSEQMKNTDG--LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIY  240 (442)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~--~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~  240 (442)
                      .+++|+.++...+...+.  ...+|...+.+....| +++.|..+|++++...|+...+|...+.+....|+++.|..+|
T Consensus       196 ~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  274 (368)
T 1fch_A          196 LFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSG-EYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAY  274 (368)
T ss_dssp             HHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            567777777766654555  5678888999998889 9999999999999999999999999999999999999999999


Q ss_pred             HHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHh
Q 013489          241 KRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQK  279 (442)
Q Consensus       241 ~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~  279 (442)
                      ++++..  .++.+ .++..........|+.+.-...+++
T Consensus       275 ~~al~~--~~~~~-~~~~~l~~~~~~~g~~~~A~~~~~~  310 (368)
T 1fch_A          275 RRALEL--QPGYI-RSRYNLGISCINLGAHREAVEHFLE  310 (368)
T ss_dssp             HHHHHH--CTTCH-HHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHh--CCCcH-HHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            999973  33434 4555556666666776554444443

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.42  E-value=2.6e-13  Score=105.34  Aligned_cols=52  Identities=13%  Similarity=0.272  Sum_probs=48.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||||||+++|+++|+.+|++||.|.+|+|+.++. |+++|||||+|.
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~   60 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFD   60 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEEC
Confidence            3457999999999999999999999999999999999975 999999999995

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.41  E-value=6.8e-14  Score=106.25  Aligned_cols=50  Identities=22%  Similarity=0.325  Sum_probs=48.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVG-GVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+|||+|||+++|+++|+.+|++|| .|.+|+|++|+.||++||||||+|.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~   52 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFS   52 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEec
Confidence            4899999999999999999999999 8999999999999999999999995

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.41  E-value=3.5e-13  Score=106.04  Aligned_cols=51  Identities=18%  Similarity=0.144  Sum_probs=49.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||+++++++|+++|++||.|.+|+|+.|+.||+++|||||+|.
T Consensus         6 ~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~   56 (110)
T 3s8s_A            6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFT   56 (110)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEEC
Confidence            469999999999999999999999999999999999999999999999996

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.40  E-value=3.4e-13  Score=106.16  Aligned_cols=54  Identities=24%  Similarity=0.455  Sum_probs=48.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..+.++|||+|||+++++++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~   75 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM   75 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEEC
Confidence            355679999999999999999999999999999999999889999999999995

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.40  E-value=4e-13  Score=109.52  Aligned_cols=54  Identities=22%  Similarity=0.199  Sum_probs=50.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeE--EEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSS--IRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~--~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....++|||||||+++++++|+.+|++||.|..  |+|+.|+.||++||||||+|.
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~   75 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLS   75 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEEC
Confidence            345679999999999999999999999999976  999999889999999999995

>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=99.39  E-value=5.3e-13  Score=106.07  Aligned_cols=54  Identities=28%  Similarity=0.414  Sum_probs=50.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..+.++|||+|||+++++++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~   75 (114)
T 2cq4_A           22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC   75 (114)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEES
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeC
Confidence            345679999999999999999999999999999999999989999999999995

>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=99.39  E-value=1.7e-10  Score=104.28  Aligned_cols=203  Identities=12%  Similarity=0.029  Sum_probs=156.7

Q ss_pred             ChHh-HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHH
Q 013489           19 DSEK-FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVR   97 (442)
Q Consensus        19 ~~~~-~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~   97 (442)
                      ++.. ...|...+......|+++.+..+|++++..+|.+...|...+..+.. .++.+.+...|++++...|....+|..
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            4555 67899999988899999999999999999999999999999887664 456678999999999999999999998


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHh--CChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhh
Q 013489           98 SLLSLERSRASEEEISTVFEKSLL--CAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQM  175 (442)
Q Consensus        98 y~~~le~~~~~~~~~~~i~~~al~--~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~  175 (442)
                      ++..+.. .+..+++..+|++++.  ..+.....+..+-..+.     ..         .++......|++++.      
T Consensus       111 la~~~~~-~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~-----~~---------g~~~~A~~~~~~~~~------  169 (252)
T 2ho1_A          111 YGGFLYE-QKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSL-----QM---------KKPAQAKEYFEKSLR------  169 (252)
T ss_dssp             HHHHHHH-TTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHH-----HT---------TCHHHHHHHHHHHHH------
T ss_pred             HHHHHHH-HhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHH-----Hc---------CCHHHHHHHHHHHHh------
Confidence            8875544 7889999999999998  43333222222111110     10         233333344444433      


Q ss_pred             cCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          176 KNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       176 ~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                       ..+....++...+.+....| +++.|..+|++++...|+....|...+.+....|+++.|..+|++++.
T Consensus       170 -~~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~  237 (252)
T 2ho1_A          170 -LNRNQPSVALEMADLLYKER-EYVPARQYYDLFAQGGGQNARSLLLGIRLAKVFEDRDTAASYGLQLKR  237 (252)
T ss_dssp             -HCSCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -cCcccHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence             23444567888888888888 899999999999999988888899999998899999999999999987

>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=99.37  E-value=1.1e-12  Score=103.08  Aligned_cols=57  Identities=23%  Similarity=0.389  Sum_probs=52.1

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          385 TKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       385 ~~~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +....+.++|||+|||+.+++++|+.+|++||.|.+|+++.++.+|+++|||||+|.
T Consensus        20 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~   76 (108)
T 2jrs_A           20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS   76 (108)
T ss_dssp             CCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEES
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEEC
Confidence            333456689999999999999999999999999999999999889999999999995

>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=99.36  E-value=1.3e-12  Score=101.79  Aligned_cols=53  Identities=25%  Similarity=0.342  Sum_probs=50.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+.+++++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~   65 (103)
T 2cqg_A           13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFT   65 (103)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEES
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEEC
Confidence            44579999999999999999999999999999999999889999999999995

>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=99.36  E-value=1.5e-10  Score=111.98  Aligned_cols=203  Identities=9%  Similarity=0.015  Sum_probs=159.4

Q ss_pred             ChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHH
Q 013489           19 DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRS   98 (442)
Q Consensus        19 ~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y   98 (442)
                      +++...+|..........|+++++..+|+++|..+|.+..+|......+...+.+.+.+...|++|+...|.+..+|...
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            56778899999998889999999999999999999999999999998887655447889999999999999999999998


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCc
Q 013489           99 LLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNT  178 (442)
Q Consensus        99 ~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~  178 (442)
                      ...+.. .+..+++...|++|+...+.....+..+-..+     .+.                ..++.|+.++..++...
T Consensus       173 g~~~~~-~g~~~eAl~~~~kal~ldP~~~~a~~~lg~~~-----~~~----------------g~~~eAl~~~~~al~l~  230 (382)
T 2h6f_A          173 RVLVEW-LRDPSQELEFIADILNQDAKNYHAWQHRQWVI-----QEF----------------KLWDNELQYVDQLLKED  230 (382)
T ss_dssp             HHHHHH-HTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHH-----HHH----------------TCCTTHHHHHHHHHHHC
T ss_pred             HHHHHH-ccCHHHHHHHHHHHHHhCccCHHHHHHHHHHH-----HHc----------------CChHHHHHHHHHHHHhC
Confidence            775554 68888999999999998877554443322111     111                12233444444444445


Q ss_pred             hhhHHHHHHHHHHHHHcCCCHHHH-----HHHHHHHHHhchhHHHHHHHHHHHHHhcc--cHHHHHHHHHHH
Q 013489          179 DGLLRLYAYWAHLEQSMGKDMVSA-----RGVWERLLKISGAMLEAWQSYISMEIELD--HINEARSIYKRC  243 (442)
Q Consensus       179 ~~~~~l~~~~a~~e~~~~~~~~~a-----r~i~~~~l~~~~~~~~~w~~~~~~e~~~g--~~~~ar~i~~ra  243 (442)
                      +.....|...+.+...+++..+.|     ...|.+++..+|++...|.....+....|  +++.|...+.++
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            666778999888888855354666     58999999999999999999998888777  688999888886

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.36  E-value=1.2e-12  Score=98.10  Aligned_cols=52  Identities=17%  Similarity=0.220  Sum_probs=49.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +.++|||+|||+++++++|+.+|++||.|.+|+++.++.+|+++|||||+|.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~   55 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFD   55 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEES
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEEC
Confidence            4569999999999999999999999999999999999889999999999996

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.36  E-value=8.2e-10  Score=99.58  Aligned_cols=224  Identities=6%  Similarity=-0.098  Sum_probs=172.1

Q ss_pred             HhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCc-------HH
Q 013489           21 EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV-------GE   93 (442)
Q Consensus        21 ~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s-------~~   93 (442)
                      ...+.|...+......|+++.+..+|++++... .++..|...+..+.. .++.+.+...|++++...|..       ..
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            456788888888889999999999999999999 889999988887664 456678999999999987765       57


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhh
Q 013489           94 LWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSE  173 (442)
Q Consensus        94 lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~  173 (442)
                      +|......+. ..++.+.+...|++++...+.. .    ++                        .....+++|+..+..
T Consensus        81 ~~~~l~~~~~-~~~~~~~A~~~~~~a~~~~~~~-~----~~------------------------~~~~~~~~a~~~~~~  130 (258)
T 3uq3_A           81 SFARIGNAYH-KLGDLKKTIEYYQKSLTEHRTA-D----IL------------------------TKLRNAEKELKKAEA  130 (258)
T ss_dssp             HHHHHHHHHH-HTTCHHHHHHHHHHHHHHCCCH-H----HH------------------------HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHH-HcccHHHHHHHHHHHHhcCchh-H----HH------------------------HHHhHHHHHHHHHHH
Confidence            7777666444 4688899999999999755441 1    01                        011334555555555


Q ss_pred             hhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCCh
Q 013489          174 QMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGS  253 (442)
Q Consensus       174 ~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~  253 (442)
                      .+...+....+|...+.+....| +++.|...|++++...|++..+|...+......|+++.|..+|++++..  .++.+
T Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~~~~~  207 (258)
T 3uq3_A          131 EAYVNPEKAEEARLEGKEYFTKS-DWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEK--DPNFV  207 (258)
T ss_dssp             HHHCCHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCH
T ss_pred             HHHcCcchHHHHHHHHHHHHHhc-CHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CHHHH
Confidence            55556666778889999998888 9999999999999999999999999999999999999999999999973  33444


Q ss_pred             HHHHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          254 EDICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       254 ~~i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                       .++..........|+.+.-...++++
T Consensus       208 -~~~~~l~~~~~~~g~~~~A~~~~~~a  233 (258)
T 3uq3_A          208 -RAYIRKATAQIAVKEYASALETLDAA  233 (258)
T ss_dssp             -HHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             -HHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence             45555566666677766555445444

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.36  E-value=4.4e-10  Score=99.10  Aligned_cols=202  Identities=13%  Similarity=0.058  Sum_probs=151.7

Q ss_pred             hHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHH
Q 013489           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSL   99 (442)
Q Consensus        20 ~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~   99 (442)
                      +.+...|...+......|+++.+..+|++++..+|.+..+|...+..+.. .++.+.+...|++++...|....+|...+
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            45778899999988999999999999999999999999999998887664 45667899999999999999999998887


Q ss_pred             HHHHHcc-CCHHHHHHHHHHHHh--CChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhc
Q 013489          100 LSLERSR-ASEEEISTVFEKSLL--CAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMK  176 (442)
Q Consensus       100 ~~le~~~-~~~~~~~~i~~~al~--~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~  176 (442)
                      ..+. .. ++.+.+...|++++.  ..+.....+..+-..+.     ..         .++......|++++.       
T Consensus        84 ~~~~-~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~-----~~---------~~~~~A~~~~~~~~~-------  141 (225)
T 2vq2_A           84 WFLC-GRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSA-----KQ---------GQFGLAEAYLKRSLA-------  141 (225)
T ss_dssp             HHHH-TTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHH-----HT---------TCHHHHHHHHHHHHH-------
T ss_pred             HHHH-HhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHH-----Hc---------CCHHHHHHHHHHHHH-------
Confidence            7444 47 889999999999998  22222222221111110     00         233333344444433       


Q ss_pred             CchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhch-hHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          177 NTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG-AMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       177 ~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~-~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ..+.....+...+.+....| +++.|..+|++++...| +....|...+.+....|+.+.+..+++.++.
T Consensus       142 ~~~~~~~~~~~la~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  210 (225)
T 2vq2_A          142 AQPQFPPAFKELARTKMLAG-QLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQA  210 (225)
T ss_dssp             HSTTCHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hCCCCchHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence            23444567778888888888 89999999999999888 7788887778888888899999888888875

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.36  E-value=6e-13  Score=104.46  Aligned_cols=50  Identities=14%  Similarity=0.231  Sum_probs=48.7

Q ss_pred             ceEEEcCC----CCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNI----NLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl----~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..||||||    |+.+++.+|+.+|+.||.|.+|.++.|+.||+|+|||||+|.
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~   56 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYA   56 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEEC
Confidence            48999999    999999999999999999999999999999999999999996

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.36  E-value=1.6e-12  Score=100.44  Aligned_cols=53  Identities=23%  Similarity=0.424  Sum_probs=49.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeE--------EEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSS--------IRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~--------~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||||||+++++++|+.+|+.||.|.+        ++++.++.+|+++|||||+|.
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~   71 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD   71 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEEC
Confidence            34579999999999999999999999999999        999999899999999999995

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.36  E-value=8.8e-13  Score=105.11  Aligned_cols=53  Identities=17%  Similarity=0.340  Sum_probs=50.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++++++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~   77 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFS   77 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeC
Confidence            44579999999999999999999999999999999999889999999999995

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.36  E-value=2e-12  Score=99.86  Aligned_cols=53  Identities=17%  Similarity=0.291  Sum_probs=49.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~   60 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE   60 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEEC
Confidence            34569999999999999999999999999999999999889999999999995

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.35  E-value=5e-10  Score=102.22  Aligned_cols=218  Identities=11%  Similarity=0.004  Sum_probs=159.5

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ++...|+.++...+..++.+...|...+......|+++.+..+|++++..+|.+..+|...+..+.. .+..+.+...|+
T Consensus        23 ~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~-~~~~~~A~~~~~  101 (275)
T 1xnf_A           23 VILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQ-AGNFDAAYEAFD  101 (275)
T ss_dssp             HHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHH-ccCHHHHHHHHH
Confidence            3566788888765433456778999999999999999999999999999999999999999887764 456678999999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRE  162 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~  162 (442)
                      +++...|....+|......+.. .++.+.+...|++++...+.......  +...+  .  ..         .++.....
T Consensus       102 ~al~~~~~~~~~~~~la~~~~~-~g~~~~A~~~~~~a~~~~~~~~~~~~--~~~~~--~--~~---------~~~~~A~~  165 (275)
T 1xnf_A          102 SVLELDPTYNYAHLNRGIALYY-GGRDKLAQDDLLAFYQDDPNDPFRSL--WLYLA--E--QK---------LDEKQAKE  165 (275)
T ss_dssp             HHHHHCTTCTHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHH--HHHHH--H--HH---------HCHHHHHH
T ss_pred             HHHhcCccccHHHHHHHHHHHH-hccHHHHHHHHHHHHHhCCCChHHHH--HHHHH--H--Hh---------cCHHHHHH
Confidence            9999999999999988775544 78899999999999987665432221  11111  0  00         22223333


Q ss_pred             HHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchh----HHHHHHHHHHHHHhcccHHHHHH
Q 013489          163 TFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA----MLEAWQSYISMEIELDHINEARS  238 (442)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~----~~~~w~~~~~~e~~~g~~~~ar~  238 (442)
                      .+.+++..       .+.....|. .+.+....+ +.+.|...+.+++...|.    ...+|...+.+....|+++.|..
T Consensus       166 ~~~~~~~~-------~~~~~~~~~-~~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  236 (275)
T 1xnf_A          166 VLKQHFEK-------SDKEQWGWN-IVEFYLGNI-SEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATA  236 (275)
T ss_dssp             HHHHHHHH-------SCCCSTHHH-HHHHHTTSS-CHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHhc-------CCcchHHHH-HHHHHHHhc-CHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHH
Confidence            33333332       222222232 444445556 678999999999987654    36799999999999999999999


Q ss_pred             HHHHHHhc
Q 013489          239 IYKRCYSK  246 (442)
Q Consensus       239 i~~ral~~  246 (442)
                      .|++++..
T Consensus       237 ~~~~al~~  244 (275)
T 1xnf_A          237 LFKLAVAN  244 (275)
T ss_dssp             HHHHHHTT
T ss_pred             HHHHHHhC
Confidence            99999973

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.35  E-value=3.1e-13  Score=104.62  Aligned_cols=52  Identities=17%  Similarity=0.177  Sum_probs=49.5

Q ss_pred             CCceEEEcCCCC------CCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINL------KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~------~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+      ++++++|+.+|++||.|.+|+|+.++.||+++|||||+|.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~   62 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECG   62 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEES
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEEC
Confidence            356999999999      9999999999999999999999999999999999999995

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.35  E-value=2.2e-10  Score=98.43  Aligned_cols=167  Identities=14%  Similarity=0.079  Sum_probs=133.1

Q ss_pred             HhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHH
Q 013489           21 EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (442)
Q Consensus        21 ~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~  100 (442)
                      ++..+|..........|+++.|...|+++|..+|.++..|...+..+.. .+..+.+...+.+++...|.....|.....
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            4567899999988999999999999999999999999999999887664 456677999999999999999888888765


Q ss_pred             HHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchh
Q 013489          101 SLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG  180 (442)
Q Consensus       101 ~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~  180 (442)
                      .+.. .+..+.+...+.+++...+                                                       .
T Consensus        82 ~~~~-~~~~~~a~~~~~~a~~~~~-------------------------------------------------------~  105 (184)
T 3vtx_A           82 ANFM-IDEKQAAIDALQRAIALNT-------------------------------------------------------V  105 (184)
T ss_dssp             HHHH-TTCHHHHHHHHHHHHHHCT-------------------------------------------------------T
T ss_pred             HHHH-cCCHHHHHHHHHHHHHhCc-------------------------------------------------------c
Confidence            4433 4556666666666554322                                                       2


Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       181 ~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ....|...+.+....| +++.|.+.|+++++.+|++..+|...+......|+++.|...|++|+.
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            2234555666667777 899999999999999998889999999988888999999999999986

>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=99.35  E-value=1.1e-12  Score=102.80  Aligned_cols=53  Identities=25%  Similarity=0.459  Sum_probs=50.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.
T Consensus        11 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~   63 (106)
T 2dgp_A           11 HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYC   63 (106)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEEC
Confidence            45679999999999999999999999999999999999889999999999995

>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=99.35  E-value=2.2e-12  Score=100.84  Aligned_cols=53  Identities=17%  Similarity=0.278  Sum_probs=50.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|++||.|.+|+|+.++.+|+++|||||+|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~   65 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFL   65 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEEC
Confidence            45679999999999999999999999999999999999889999999999996

>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=99.34  E-value=6.4e-12  Score=100.84  Aligned_cols=103  Identities=14%  Similarity=0.229  Sum_probs=89.4

Q ss_pred             hHhHHHHHHHHHHHHhcCCh------hhHHHHHHHHHhcCCCC--------HHHHHHHHHHHHHhcchhhHHHHHHHHHH
Q 013489           20 SEKFQQYMIYLKYEQSSGDP------GRVQLLYERAITDFPVS--------SDLWLDYTQYLDKTLKVGNVVRDVYSRAT   85 (442)
Q Consensus        20 ~~~~~~w~~y~~~e~~~g~~------~~~~~lyERal~~~p~~--------~~lW~~Y~~~l~~~~~~~~~~~~v~erAl   85 (442)
                      +.+++.|..|+..+++.|++      ++++.+|+||+...|..        .-+|+.|+.|..  .++++.++++|..|+
T Consensus        10 p~~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~~Pp~k~~~wrrYI~LWIrYA~~~e--i~D~d~aR~vy~~a~   87 (161)
T 4h7y_A           10 ANNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEALPPDKYGQNESFARIQVRFAELKA--IQEPDDARDYFQMAR   87 (161)
T ss_dssp             CCSHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHHSCGGGGTTCHHHHHHHHHHHHHHH--HHCGGGCHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHcCCccccccHHHHHHHHHHHHHHHH--hcCHHHHHHHHHHHH
Confidence            34899999999999999999      99999999999988753        359999998854  367889999999999


Q ss_pred             HcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh
Q 013489           86 KNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus        86 ~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                      .+|..-..+|+.|+. +|.++++...++.|+.+|+.+++.
T Consensus        88 ~~hKkFAKiwi~~Aq-FEiRqgnl~kARkILg~AiG~~~k  126 (161)
T 4h7y_A           88 ANCKKFAFVHISFAQ-FELSQGNVKKSKQLLQKAVERGAV  126 (161)
T ss_dssp             HHCTTBHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHTTCB
T ss_pred             HHhHHHHHHHHHHHH-HHHHcccHHHHHHHHHHHhccCCC
Confidence            988767899999999 555589999999999999987654

>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=99.34  E-value=2.3e-12  Score=101.82  Aligned_cols=53  Identities=19%  Similarity=0.304  Sum_probs=50.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++++++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~   65 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFM   65 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEEC
Confidence            44579999999999999999999999999999999999999999999999995

>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=99.34  E-value=5.6e-13  Score=101.01  Aligned_cols=50  Identities=18%  Similarity=0.276  Sum_probs=46.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCC--CeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVG--GVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G--~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+|||||||+++++++|+++|++||  .|.+++++.++.+|+++|||||+|.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~   53 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVG   53 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEEC
Confidence            4899999999999999999999999  9999999999999999999999995

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.34  E-value=1.5e-12  Score=102.02  Aligned_cols=53  Identities=23%  Similarity=0.330  Sum_probs=50.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+.+++++|+.+|+.||.|.+|.|+.++.+|+++|||||+|.
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~   73 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE   73 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEEC
Confidence            45679999999999999999999999999999999999999999999999996

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.34  E-value=4.8e-11  Score=106.97  Aligned_cols=216  Identities=11%  Similarity=0.029  Sum_probs=146.9

Q ss_pred             HHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHH
Q 013489           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLE  103 (442)
Q Consensus        24 ~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le  103 (442)
                      ..|...+......|+++.+..+|++++..+|.+..+|...+..+.. .++.+.+...|++++...|....+|...+..+.
T Consensus        24 ~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~-~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~  102 (243)
T 2q7f_A           24 MTGGQQMGRGSEFGDYEKAAEAFTKAIEENKEDAIPYINFANLLSS-VNELERALAFYDKALELDSSAATAYYGAGNVYV  102 (243)
T ss_dssp             ------------------CCTTHHHHHTTCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHcCCcchHHHHHHHHHHH
Confidence            3566666666778999999999999999999999999999887764 456678999999999999999999988877554


Q ss_pred             HccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHH
Q 013489          104 RSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLR  183 (442)
Q Consensus       104 ~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~  183 (442)
                       ..++.+.+...|++++...+.....+..+-..+.     ..         .++......+++++.       ..+....
T Consensus       103 -~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~-----~~---------~~~~~A~~~~~~~~~-------~~~~~~~  160 (243)
T 2q7f_A          103 -VKEMYKEAKDMFEKALRAGMENGDLFYMLGTVLV-----KL---------EQPKLALPYLQRAVE-------LNENDTE  160 (243)
T ss_dssp             -HTTCHHHHHHHHHHHHHHTCCSHHHHHHHHHHHH-----HT---------SCHHHHHHHHHHHHH-------HCTTCHH
T ss_pred             -HhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH-----Hh---------ccHHHHHHHHHHHHH-------hCCccHH
Confidence             4688999999999999766554332222111110     10         233333344444443       2344556


Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHH
Q 013489          184 LYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRF  263 (442)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~f  263 (442)
                      ++...+.+....| +++.|..+|++++...|+...+|..++.+....|+++.|..+|++++..  .++.+ .++.....+
T Consensus       161 ~~~~l~~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--~p~~~-~~~~~~~~l  236 (243)
T 2q7f_A          161 ARFQFGMCLANEG-MLDEALSQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKAIDI--QPDHM-LALHAKKLL  236 (243)
T ss_dssp             HHHHHHHHHHHHT-CCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHH--CTTCH-HHHHHHTC-
T ss_pred             HHHHHHHHHHHcC-CHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHcc--CcchH-HHHHHHHHH
Confidence            8888899989999 9999999999999999999999999999999999999999999999973  33444 344444444


Q ss_pred             HHH
Q 013489          264 ERE  266 (442)
Q Consensus       264 E~~  266 (442)
                      ...
T Consensus       237 ~~~  239 (243)
T 2q7f_A          237 GHH  239 (243)
T ss_dssp             ---
T ss_pred             Hhh
Confidence            433

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.33  E-value=2.7e-12  Score=99.89  Aligned_cols=53  Identities=21%  Similarity=0.280  Sum_probs=50.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+.+++++|+.+|+.||.|.+|.|+.++.+|+++|||||+|.
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~   63 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFH   63 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEES
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEEC
Confidence            44679999999999999999999999999999999999889999999999995

>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=99.33  E-value=6e-10  Score=104.28  Aligned_cols=218  Identities=10%  Similarity=0.017  Sum_probs=146.9

Q ss_pred             HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHH
Q 013489           57 SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLT  136 (442)
Q Consensus        57 ~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~  136 (442)
                      ...|...+..+... ++.+.+..+|++++...|....+|...+..+. ..+..+.+...|++++...+.....+..+-..
T Consensus        21 ~~~~~~~a~~~~~~-~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~   98 (327)
T 3cv0_A           21 HENPMEEGLSMLKL-ANLAEAALAFEAVCQAAPEREEAWRSLGLTQA-ENEKDGLAIIALNHARMLDPKDIAVHAALAVS   98 (327)
T ss_dssp             SSCHHHHHHHHHHT-TCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHh-ccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH-HcCCHHHHHHHHHHHHhcCcCCHHHHHHHHHH
Confidence            34556665555533 45677999999999999999999998776444 46889999999999998766543333222111


Q ss_pred             H---------HHHHHHHhh-ccCccchhhh------------------HHHHHHHHHHHHHHHhhhhcCchhhHHHHHHH
Q 013489          137 R---------IDGLRRRIL-FSGEVEGVLD------------------YSLIRETFQRASDYLSEQMKNTDGLLRLYAYW  188 (442)
Q Consensus       137 ~---------~~~l~rr~~-~~~~~~~~~~------------------~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~  188 (442)
                      +         ...+.+-+. .+........                  +......+++|+.++...+...+....++...
T Consensus        99 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l  178 (327)
T 3cv0_A           99 HTNEHNANAALASLRAWLLSQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPNDAQLHASL  178 (327)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTSTTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHHSTTCHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhCCCCHHHHHHH
Confidence            1         111111110 0110000000                  01112445666666666655455566788889


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhC
Q 013489          189 AHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYG  268 (442)
Q Consensus       189 a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G  268 (442)
                      +.+....| +++.|..+|++++...|+...+|...+.+....|+++.|..+|++++..  .++.+ .++..........|
T Consensus       179 a~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--~~~~~-~~~~~l~~~~~~~g  254 (327)
T 3cv0_A          179 GVLYNLSN-NYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDI--NPGYV-RVMYNMAVSYSNMS  254 (327)
T ss_dssp             HHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCH-HHHHHHHHHHHHTT
T ss_pred             HHHHHHhc-cHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCH-HHHHHHHHHHHHhc
Confidence            99988889 9999999999999999999999999999999999999999999999973  33334 45556666666778


Q ss_pred             CHhhHHHHHHhh
Q 013489          269 TLEDFDHSVQKV  280 (442)
Q Consensus       269 ~~~~~~~~~~~~  280 (442)
                      +.+.-...++++
T Consensus       255 ~~~~A~~~~~~a  266 (327)
T 3cv0_A          255 QYDLAAKQLVRA  266 (327)
T ss_dssp             CHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHH
Confidence            766554444443

>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=99.33  E-value=8.6e-13  Score=102.13  Aligned_cols=52  Identities=21%  Similarity=0.393  Sum_probs=47.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCC-CCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDK-FTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~-~~g~~~g~~fv~f~  441 (442)
                      ...++|||||||+++++++|+.+|+.|| |.+|+|+.++ .+|+++|||||+|.
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~   69 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFE   69 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEEC
Confidence            4567999999999999999999999999 9999999997 59999999999996

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.33  E-value=2.2e-12  Score=100.78  Aligned_cols=53  Identities=28%  Similarity=0.389  Sum_probs=50.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+.+++++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~   66 (105)
T 2dh8_A           14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK   66 (105)
T ss_dssp             SSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEEC
Confidence            45679999999999999999999999999999999999899999999999995

>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=99.33  E-value=1.8e-12  Score=102.22  Aligned_cols=53  Identities=23%  Similarity=0.340  Sum_probs=50.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+.+++++|+.+|+.||.|.+|.++.++.+|+++|||||+|.
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~   76 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE   76 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEEC
Confidence            45679999999999999999999999999999999999889999999999995

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.33  E-value=2.4e-12  Score=100.18  Aligned_cols=54  Identities=26%  Similarity=0.359  Sum_probs=50.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..+.++|||+|||+.+++++|+.+|+.||.|.+|.|+.++.+|+++|||||+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~   65 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFH   65 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEEC
Confidence            345679999999999999999999999999999999999889999999999995

>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=99.33  E-value=3.2e-12  Score=99.64  Aligned_cols=52  Identities=19%  Similarity=0.307  Sum_probs=48.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeE-EEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSS-IRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~-~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++++++|+++|++||.|.+ |+|+.+ .+|+++|||||+|.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~   65 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFA   65 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEEC
Confidence            34579999999999999999999999999987 899999 79999999999995

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.33  E-value=9.8e-13  Score=96.48  Aligned_cols=50  Identities=26%  Similarity=0.517  Sum_probs=48.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ++|||+|||+++++++|+.+|++||.|.+++++.++.+|+++|||||+|.
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~   50 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM   50 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEc
Confidence            48999999999999999999999999999999999889999999999995

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.32  E-value=1.4e-12  Score=109.27  Aligned_cols=53  Identities=11%  Similarity=0.282  Sum_probs=48.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCC--CeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVG--GVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G--~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||||||+++++++|+.+|+.||  .|.+|+|+.|+.+|+++|||||+|.
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~  107 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVA  107 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEEC
Confidence            3567999999999999999999999999  9999999999999999999999995

>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=99.32  E-value=1.9e-12  Score=97.43  Aligned_cols=53  Identities=21%  Similarity=0.304  Sum_probs=49.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||.++++++|+.+|++||.|.+|+++.++.+|+++|||||+|.
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~   56 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFF   56 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEEC
Confidence            34579999999999999999999999999999999999889999999999995

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.32  E-value=5.2e-12  Score=100.58  Aligned_cols=53  Identities=25%  Similarity=0.378  Sum_probs=50.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~   67 (116)
T 2cqd_A           15 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMA   67 (116)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEEC
Confidence            45679999999999999999999999999999999999899999999999995

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.32  E-value=5.2e-12  Score=96.47  Aligned_cols=52  Identities=35%  Similarity=0.478  Sum_probs=49.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+.+++++|+.+|++||.|.+|+++.++.+|+++|||||+|.
T Consensus        15 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~   66 (94)
T 2e5h_A           15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFL   66 (94)
T ss_dssp             CTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEEC
Confidence            4569999999999999999999999999999999999889999999999995

>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=99.32  E-value=3.7e-12  Score=101.31  Aligned_cols=53  Identities=23%  Similarity=0.312  Sum_probs=50.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~   75 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYD   75 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEEC
Confidence            45679999999999999999999999999999999999889999999999995

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.32  E-value=2.6e-12  Score=99.25  Aligned_cols=53  Identities=13%  Similarity=0.235  Sum_probs=49.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCee-EEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVS-SIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~-~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++++++|+.+|++||.|. +|+|+.++.+|+++|||||+|.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~   60 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFA   60 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECS
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeC
Confidence            3457999999999999999999999999999 9999999889999999999995

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.31  E-value=4e-12  Score=99.65  Aligned_cols=53  Identities=21%  Similarity=0.343  Sum_probs=49.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeC-CCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHD-KFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~-~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|+.||.|.+|+|+.+ +.+|+++|||||+|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~   66 (107)
T 2cph_A           13 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFI   66 (107)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEES
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEEC
Confidence            44579999999999999999999999999999999998 789999999999995

>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=99.31  E-value=3.4e-12  Score=98.54  Aligned_cols=53  Identities=23%  Similarity=0.356  Sum_probs=50.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+.+++++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~   58 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFM   58 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEEC
Confidence            34579999999999999999999999999999999999889999999999996

>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=99.31  E-value=2.3e-12  Score=96.47  Aligned_cols=53  Identities=19%  Similarity=0.186  Sum_probs=50.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+.+|++||.|.+|.++.++.+|+++|||||+|.
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~   57 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE   57 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEEC
Confidence            34579999999999999999999999999999999999889999999999995

>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=99.31  E-value=3.5e-10  Score=109.43  Aligned_cols=221  Identities=9%  Similarity=0.000  Sum_probs=164.4

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCC-hhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGD-PGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVY   81 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~-~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~   81 (442)
                      +|...|+.+|..+|.    +..+|..........|. ++.++..|+++|..+|.+..+|......+... +..+.+...|
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----NYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVEWL-RDPSQELEFI  189 (382)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-TCCTTHHHHH
T ss_pred             HHHHHHHHHHHhCcc----CHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHc-cCHHHHHHHH
Confidence            466788889988876    88899999998889996 99999999999999999999999998877654 4567799999


Q ss_pred             HHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHH
Q 013489           82 SRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIR  161 (442)
Q Consensus        82 erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r  161 (442)
                      ++|+...|.....|......+.. .+..+++...|++++...+.....+..+...+.     ++..  ..+      .  
T Consensus       190 ~kal~ldP~~~~a~~~lg~~~~~-~g~~~eAl~~~~~al~l~P~~~~a~~~lg~~l~-----~l~~--~~~------e--  253 (382)
T 2h6f_A          190 ADILNQDAKNYHAWQHRQWVIQE-FKLWDNELQYVDQLLKEDVRNNSVWNQRYFVIS-----NTTG--YND------R--  253 (382)
T ss_dssp             HHHHHHCTTCHHHHHHHHHHHHH-HTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHH-----HTTC--SCS------H--
T ss_pred             HHHHHhCccCHHHHHHHHHHHHH-cCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHH-----HhcC--cch------H--
Confidence            99999999999999987765554 677888999999999887775544433332221     1100  000      0  


Q ss_pred             HHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCC-CHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcc--------c
Q 013489          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGK-DMVSARGVWERLLKISGAMLEAWQSYISMEIELD--------H  232 (442)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~-~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g--------~  232 (442)
                      ..++.++.++..++...+.....|.+.+.+....|. +.+.|.+.+.++ ...|++..++..++++....|        +
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            112223333333333355566788888877766552 478899999887 778888888888888777653        3


Q ss_pred             -HHHHHHHHHHH-Hh
Q 013489          233 -INEARSIYKRC-YS  245 (442)
Q Consensus       233 -~~~ar~i~~ra-l~  245 (442)
                       ++.|..+|+++ +.
T Consensus       333 ~~~~A~~~~~~l~~~  347 (382)
T 2h6f_A          333 ILNKALELCEILAKE  347 (382)
T ss_dssp             HHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHH
Confidence             58999999998 65

>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=99.31  E-value=5.1e-12  Score=98.70  Aligned_cols=52  Identities=19%  Similarity=0.326  Sum_probs=48.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|+.||.|.+|+|+.++ +|+++|||||+|.
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~   64 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFS   64 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeC
Confidence            346799999999999999999999999999999999996 8999999999995

>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=99.31  E-value=2.9e-12  Score=95.42  Aligned_cols=50  Identities=28%  Similarity=0.329  Sum_probs=48.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ++|||+|||+++++++|+.+|++||.|.++.++.++.+|+++|||||+|.
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~   51 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFT   51 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEEC
Confidence            58999999999999999999999999999999999899999999999995

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.31  E-value=4.7e-12  Score=96.95  Aligned_cols=52  Identities=19%  Similarity=0.362  Sum_probs=49.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+.+++++|+.+|+.||.|.+|.++.++.+|+++|||||+|.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~   55 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFS   55 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEES
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEEC
Confidence            4569999999999999999999999999999999999889999999999995

>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=99.31  E-value=3.3e-12  Score=101.38  Aligned_cols=52  Identities=17%  Similarity=0.270  Sum_probs=48.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCe-eEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGV-SSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i-~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+.+|+.||.| .+|+|+.|+ +|+++|||||+|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~   65 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFK   65 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECS
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEEC
Confidence            445799999999999999999999999999 899999997 9999999999995

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.31  E-value=1.7e-12  Score=94.61  Aligned_cols=49  Identities=22%  Similarity=0.457  Sum_probs=47.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +|||+|||+++++++|+.+|++||.|.+|+++.++.+|+++|||||+|.
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~   49 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFE   49 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECS
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEEC
Confidence            5899999999999999999999999999999999889999999999995

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.30  E-value=1.7e-12  Score=100.89  Aligned_cols=52  Identities=25%  Similarity=0.451  Sum_probs=49.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++++++|+.+|+.||.|.+|+|+.++ +|+++|||||+|.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~   58 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFY   58 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEEC
Confidence            345799999999999999999999999999999999997 9999999999995

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.30  E-value=4e-12  Score=97.31  Aligned_cols=53  Identities=25%  Similarity=0.367  Sum_probs=49.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|+.||.|.+|.++.++.+|+++|||||+|.
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~   65 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE   65 (95)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEEC
Confidence            34579999999999999999999999999999999999889999999999995

>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=99.30  E-value=3.1e-12  Score=99.20  Aligned_cols=51  Identities=18%  Similarity=0.241  Sum_probs=46.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++++++|+++|++||. .+|+|+.++ +|+++|||||+|.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~   63 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFA   63 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEEC
Confidence            34579999999999999999999999994 599999996 9999999999996

>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=99.30  E-value=4.3e-12  Score=102.89  Aligned_cols=53  Identities=25%  Similarity=0.367  Sum_probs=50.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~   96 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE   96 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEEC
Confidence            44679999999999999999999999999999999999999999999999996

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.30  E-value=6.1e-12  Score=97.30  Aligned_cols=52  Identities=21%  Similarity=0.417  Sum_probs=49.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+.+++++|+.+|+.||.|.+|+|+.++ +|+++|||||+|.
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~   66 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYE   66 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEEC
Confidence            445799999999999999999999999999999999996 9999999999995

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.30  E-value=5.1e-12  Score=98.32  Aligned_cols=52  Identities=23%  Similarity=0.372  Sum_probs=48.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++++++|+.+|+.|| |.+|+|+.++.+|+++|||||+|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~   64 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFD   64 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEES
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEEC
Confidence            3457999999999999999999999997 999999999889999999999995

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.30  E-value=5.1e-12  Score=100.45  Aligned_cols=53  Identities=25%  Similarity=0.406  Sum_probs=50.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+.+++++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~   65 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFF   65 (115)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEEC
Confidence            45679999999999999999999999999999999999889999999999995

>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=99.30  E-value=6.2e-10  Score=112.11  Aligned_cols=267  Identities=10%  Similarity=-0.039  Sum_probs=164.8

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      +|...|+.+|...|.    +...|...+......|+++.+...|++++..+|.+...|...+..+... +..+.+...|+
T Consensus        43 ~A~~~~~~al~~~p~----~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~-g~~~~A~~~~~  117 (537)
T 3fp2_A           43 EAIKYYQYAIELDPN----EPVFYSNISACYISTGDLEKVIEFTTKALEIKPDHSKALLRRASANESL-GNFTDAMFDLS  117 (537)
T ss_dssp             -CHHHHHHHHHHCTT----CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHhhCCC----CcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHc-CCHHHHHHHHH
Confidence            567788999988775    6778888888888899999999999999999999999999888776644 34455666664


Q ss_pred             HHHHcCCCcHHHH-------------------------------------------------------------------
Q 013489           83 RATKNCPWVGELW-------------------------------------------------------------------   95 (442)
Q Consensus        83 rAl~~~p~s~~lW-------------------------------------------------------------------   95 (442)
                       ++...|.....|                                                                   
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             554444322211                                                                   


Q ss_pred             -HHHHHHHH--------HccCCHHHHHHHHHHHHhCChhhHHHH---HHHHHH-------------HHHHHHHHhhccCc
Q 013489           96 -VRSLLSLE--------RSRASEEEISTVFEKSLLCAFSTFEEY---LDLFLT-------------RIDGLRRRILFSGE  150 (442)
Q Consensus        96 -~~y~~~le--------~~~~~~~~~~~i~~~al~~~~~~~~~~---~~~~~~-------------~~~~l~rr~~~~~~  150 (442)
                       ..... +.        ...+..+.+..+|++++...+......   ...+..             ....+.+-+.....
T Consensus       197 ~~~l~~-~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~~~  275 (537)
T 3fp2_A          197 SDALQR-LYSATDEGYLVANDLLTKSTDMYHSLLSANTVDDPLRENAALALCYTGIFHFLKNNLLDAQVLLQESINLHPT  275 (537)
T ss_dssp             HHHHHH-HHTCSHHHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHH-HHHhhhhhhHHHHHHHHHHHHHHHHHHHHCCCcchhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCC
Confidence             11110 10        001245678888888887655532211   111100             00011100000000


Q ss_pred             cchhhhHHH---HHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHH
Q 013489          151 VEGVLDYSL---IRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISME  227 (442)
Q Consensus       151 ~~~~~~~~~---~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e  227 (442)
                      ...+.....   ....++.|+.++...+...+....+|...+.+....| +++.|...|++++...|+...+|...+.+.
T Consensus       276 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~la~~~  354 (537)
T 3fp2_A          276 PNSYIFLALTLADKENSQEFFKFFQKAVDLNPEYPPTYYHRGQMYFILQ-DYKNAKEDFQKAQSLNPENVYPYIQLACLL  354 (537)
T ss_dssp             HHHHHHHHHHTCCSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCSHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHhcCHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            000000000   0011255566655555445555678888898888888 899999999999999999889999999999


Q ss_pred             HhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          228 IELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       228 ~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                      ...|+++.|..+|++++..  .++.+ .++..........|+.+.-...++++
T Consensus       355 ~~~g~~~~A~~~~~~~~~~--~~~~~-~~~~~l~~~~~~~g~~~~A~~~~~~a  404 (537)
T 3fp2_A          355 YKQGKFTESEAFFNETKLK--FPTLP-EVPTFFAEILTDRGDFDTAIKQYDIA  404 (537)
T ss_dssp             HHTTCHHHHHHHHHHHHHH--CTTCT-HHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHh--CCCCh-HHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            9999999999999999973  33334 46666667777778876655555443

>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=99.29  E-value=5.3e-12  Score=98.42  Aligned_cols=51  Identities=22%  Similarity=0.395  Sum_probs=48.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCC-CCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFT-GKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~-g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+.+++++|+.+|+.|| |.+|+|+.++.+ |+++|||||+|.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~   65 (104)
T 1wi8_A           14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFE   65 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEES
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEEC
Confidence            457999999999999999999999999 999999999887 999999999995

>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=99.29  E-value=4.2e-12  Score=97.43  Aligned_cols=51  Identities=24%  Similarity=0.347  Sum_probs=48.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||..+++++|+.+|+.||.|.+|+++.++.+|+++|||||+|.
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~   52 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFR   52 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEES
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEEC
Confidence            469999999999999999999999999999999999889999999999995

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.29  E-value=2.4e-10  Score=102.35  Aligned_cols=201  Identities=9%  Similarity=0.035  Sum_probs=148.9

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ++...|+.++...|.    +...|...+......|+++.+..+|++++...|.+..+|...+..+.. .++.+.+...|+
T Consensus        41 ~A~~~~~~~l~~~~~----~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~-~~~~~~A~~~~~  115 (243)
T 2q7f_A           41 KAAEAFTKAIEENKE----DAIPYINFANLLSSVNELERALAFYDKALELDSSAATAYYGAGNVYVV-KEMYKEAKDMFE  115 (243)
T ss_dssp             -CCTTHHHHHTTCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCcc----cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcchHHHHHHHHHHHH-hccHHHHHHHHH
Confidence            355678888887665    677898889888899999999999999999999999999999887764 456678999999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRE  162 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~  162 (442)
                      +++...|....+|..++..+. ..+..+.+...|++++...+.....+..+-..+.     ..         .++.....
T Consensus       116 ~~~~~~~~~~~~~~~~a~~~~-~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~-----~~---------~~~~~A~~  180 (243)
T 2q7f_A          116 KALRAGMENGDLFYMLGTVLV-KLEQPKLALPYLQRAVELNENDTEARFQFGMCLA-----NE---------GMLDEALS  180 (243)
T ss_dssp             HHHHHTCCSHHHHHHHHHHHH-HTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-----HH---------TCCHHHHH
T ss_pred             HHHHhCCCCHHHHHHHHHHHH-HhccHHHHHHHHHHHHHhCCccHHHHHHHHHHHH-----Hc---------CCHHHHHH
Confidence            999999999999998887554 4788999999999999776554332222111110     00         22223333


Q ss_pred             HHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcc
Q 013489          163 TFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELD  231 (442)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g  231 (442)
                      .|++++.       ..+....+|...+.++...| +++.|..+|++++...|++..+|..+..+....|
T Consensus       181 ~~~~~~~-------~~~~~~~~~~~la~~~~~~~-~~~~A~~~~~~~~~~~p~~~~~~~~~~~l~~~~~  241 (243)
T 2q7f_A          181 QFAAVTE-------QDPGHADAFYNAGVTYAYKE-NREKALEMLDKAIDIQPDHMLALHAKKLLGHHHH  241 (243)
T ss_dssp             HHHHHHH-------HCTTCHHHHHHHHHHHHHTT-CTTHHHHHHHHHHHHCTTCHHHHHHHTC------
T ss_pred             HHHHHHH-------hCcccHHHHHHHHHHHHHcc-CHHHHHHHHHHHHccCcchHHHHHHHHHHHhhcc
Confidence            4444433       23445568888999999999 9999999999999999999998888777765544

>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=99.29  E-value=1.4e-12  Score=95.08  Aligned_cols=49  Identities=24%  Similarity=0.368  Sum_probs=47.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +|||+|||+++++++|+.+|++||.|.+|.++.++.+|+++|||||+|.
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~   49 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFK   49 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECS
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEEC
Confidence            6999999999999999999999999999999999899999999999995

>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=99.29  E-value=4.8e-12  Score=95.62  Aligned_cols=51  Identities=27%  Similarity=0.495  Sum_probs=49.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||+++++++|+.+|++||.|.+++++.++.+|+++|||||+|.
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~   56 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFS   56 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEES
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEEC
Confidence            469999999999999999999999999999999999889999999999995

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.28  E-value=4.1e-12  Score=98.70  Aligned_cols=52  Identities=17%  Similarity=0.173  Sum_probs=49.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+.+++++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.
T Consensus        11 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~   62 (102)
T 2cqb_A           11 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE   62 (102)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEEC
Confidence            4569999999999999999999999999999999999899999999999995

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.28  E-value=5.6e-12  Score=98.30  Aligned_cols=52  Identities=19%  Similarity=0.233  Sum_probs=48.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhcc-CCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSD-VGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~-~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++++++|+.+|+. ||.|.+|+|+.++ +|+++|||||+|.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~   59 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFT   59 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEEC
Confidence            34579999999999999999999999 9999999999997 9999999999996

>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=99.28  E-value=4.5e-12  Score=95.64  Aligned_cols=47  Identities=21%  Similarity=0.319  Sum_probs=43.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||||||+++++++|+.+|++||.|.+|+|+.+     +||||||+|.
T Consensus        10 ~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~   56 (89)
T 3d2w_A           10 HGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFA   56 (89)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEEC
Confidence            3469999999999999999999999999999999885     7899999996

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.28  E-value=5.2e-12  Score=98.59  Aligned_cols=51  Identities=14%  Similarity=0.127  Sum_probs=46.4

Q ss_pred             CCCceEEEcCCCCCC------CHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKA------TYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~------~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||||||+.+      ++++|+.+|++||.|.+|+|+  +.+|+++|||||+|.
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~   69 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYA   69 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEEC
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEEC
Confidence            446799999999999      789999999999999999998  368999999999996

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.28  E-value=5.5e-12  Score=97.93  Aligned_cols=53  Identities=23%  Similarity=0.407  Sum_probs=49.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.
T Consensus        10 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~   62 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFE   62 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEEC
Confidence            34579999999999999999999999999999999999889999999999995

>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=99.28  E-value=3.9e-12  Score=99.68  Aligned_cols=52  Identities=25%  Similarity=0.196  Sum_probs=48.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCC---eeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGG---VSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~---i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+.+|+.||.   |.+|+|+.++. |+++|||||+|.
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~   63 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEME   63 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBS
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEEC
Confidence            45679999999999999999999999998   89999999975 999999999995

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.27  E-value=4.3e-12  Score=99.31  Aligned_cols=51  Identities=20%  Similarity=0.359  Sum_probs=47.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+++|++| .|.+|+|+.|+ +|+++|||||+|.
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~-~g~~~G~afV~F~   64 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFL   64 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEEC
Confidence            445799999999999999999999999 89999999996 5999999999996

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.27  E-value=4.5e-12  Score=97.26  Aligned_cols=52  Identities=21%  Similarity=0.251  Sum_probs=49.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEE-EEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSI-RILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~-~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+.+++++|+.+|+.||.|.++ +|+.++.+|+++|||||+|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~   56 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFA   56 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEEC
Confidence            45799999999999999999999999999999 99999889999999999995

>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=99.27  E-value=5.2e-12  Score=101.85  Aligned_cols=53  Identities=13%  Similarity=0.134  Sum_probs=47.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+.+|+.||.|.++.++.+..+|+++|||||+|.
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~   75 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFR   75 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEEC
Confidence            45679999999999999999999999999998666666689999999999996

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.27  E-value=5.7e-12  Score=100.55  Aligned_cols=52  Identities=15%  Similarity=0.197  Sum_probs=48.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCC---eeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGG---VSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~---i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+.+|+.||.   |.+|+|+.++. |+++|||||+|.
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~   69 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELE   69 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEEC
Confidence            45679999999999999999999999999   89999999965 999999999996

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.27  E-value=1.4e-11  Score=101.63  Aligned_cols=53  Identities=19%  Similarity=0.186  Sum_probs=50.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|++||.|.+++++.++.+|+++|||||+|.
T Consensus        61 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~  113 (140)
T 2ku7_A           61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE  113 (140)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEES
T ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEEC
Confidence            45679999999999999999999999999999999999899999999999995

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.27  E-value=8.3e-12  Score=98.88  Aligned_cols=53  Identities=32%  Similarity=0.472  Sum_probs=49.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCee--------EEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVS--------SIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~--------~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+.+++++|+.+|+.||.|.        .|+|+.++.+|+++|||||+|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~   73 (113)
T 2cpe_A           13 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE   73 (113)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBS
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEEC
Confidence            4567999999999999999999999999999        6999999899999999999995

>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=99.26  E-value=7.1e-12  Score=101.38  Aligned_cols=53  Identities=23%  Similarity=0.330  Sum_probs=50.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+.+++++|+.+|+.||.|.+|.|+.++.+|+++|||||+|.
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~   72 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE   72 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEEC
Confidence            45679999999999999999999999999999999999889999999999996

>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=99.26  E-value=1.9e-11  Score=96.90  Aligned_cols=52  Identities=31%  Similarity=0.431  Sum_probs=49.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+.+++++|+.+|+.||.|.+|+|+.++ +|+++|||||+|.
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~   74 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARME   74 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEEC
Confidence            456799999999999999999999999999999999997 9999999999995

>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=99.26  E-value=6.6e-12  Score=96.12  Aligned_cols=52  Identities=21%  Similarity=0.383  Sum_probs=48.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|++||.|.+|+|+.++ +|+++|||||+|.
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~   65 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFK   65 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCceEEEEEEC
Confidence            345799999999999999999999999999999999996 5999999999995

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.25  E-value=8.4e-12  Score=98.10  Aligned_cols=52  Identities=19%  Similarity=0.302  Sum_probs=47.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....++|||+|||.++++++|+.+|+.||.|.+|+++.++  ++++|||||+|.
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~   77 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFE   77 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECC
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEEC
Confidence            4566799999999999999999999999999999999984  458999999996

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.25  E-value=5e-10  Score=102.24  Aligned_cols=114  Identities=10%  Similarity=-0.086  Sum_probs=52.1

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHH----HHHHHHHHHHhcchhhHHHH
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDL----WLDYTQYLDKTLKVGNVVRD   79 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~l----W~~Y~~~l~~~~~~~~~~~~   79 (442)
                      |...|+.+|...|.    +...|...+......|+++.+...|++++. .|.++.+    |...+..+.. .+..+.+..
T Consensus        22 A~~~~~~~l~~~p~----~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~-~~~~~~~~~~~~~~lg~~~~~-~~~~~~A~~   95 (272)
T 3u4t_A           22 AIEVFNKLEAKKYN----SPYIYNRRAVCYYELAKYDLAQKDIETYFS-KVNATKAKSADFEYYGKILMK-KGQDSLAIQ   95 (272)
T ss_dssp             HHHHHHHHHHTTCC----CSTTHHHHHHHHHHTTCHHHHHHHHHHHHT-TSCTTTCCHHHHHHHHHHHHH-TTCHHHHHH
T ss_pred             HHHHHHHHHHhCCC----cHHHHHHHHHHHHHHhhHHHHHHHHHHHHh-ccCchhHHHHHHHHHHHHHHH-cccHHHHHH
Confidence            34445555544443    233444444444445555555555555555 2322222    4444443332 223344555


Q ss_pred             HHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCh
Q 013489           80 VYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAF  124 (442)
Q Consensus        80 v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~  124 (442)
                      .|++++...|....+|......+. ..++.+.+...|++++...+
T Consensus        96 ~~~~a~~~~~~~~~~~~~l~~~~~-~~~~~~~A~~~~~~al~~~~  139 (272)
T 3u4t_A           96 QYQAAVDRDTTRLDMYGQIGSYFY-NKGNFPLAIQYMEKQIRPTT  139 (272)
T ss_dssp             HHHHHHHHSTTCTHHHHHHHHHHH-HTTCHHHHHHHHGGGCCSSC
T ss_pred             HHHHHHhcCcccHHHHHHHHHHHH-HccCHHHHHHHHHHHhhcCC
Confidence            555555555555555555444222 24445555555555554433

>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=99.25  E-value=1.1e-11  Score=99.34  Aligned_cols=51  Identities=20%  Similarity=0.247  Sum_probs=46.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCee--EEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVS--SIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~--~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++++++|+++|++| .|.  +|+|+.|+. |+++|||||+|.
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~   92 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFA   92 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEEC
Confidence            345699999999999999999999999 566  999999965 999999999995

>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=99.25  E-value=5.9e-12  Score=102.58  Aligned_cols=52  Identities=13%  Similarity=0.165  Sum_probs=48.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCC---eeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGG---VSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~---i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++|+++|+++|++||.   |.+|+|+.|+. |+++|||||+|.
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~   96 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELG   96 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEEC
Confidence            45679999999999999999999999999   89999999975 999999999995

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.25  E-value=1.3e-11  Score=95.90  Aligned_cols=51  Identities=20%  Similarity=0.359  Sum_probs=48.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+.+++++|+.+|+.||.|.+|+|+.+  +|+++|||||+|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~   63 (103)
T 2d9p_A           13 YQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFS   63 (103)
T ss_dssp             SSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEEC
Confidence            45679999999999999999999999999999999998  8999999999995

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.25  E-value=6.3e-12  Score=99.72  Aligned_cols=52  Identities=8%  Similarity=0.125  Sum_probs=47.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCC---CCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFT---GKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~---g~~~g~~fv~f~  441 (442)
                      ...++|||||||+++++++|+.+|++||.|. +.++.++.+   |+++|||||+|.
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~   60 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQ   60 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCS
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEEC
Confidence            3457999999999999999999999999999 888888777   899999999995

>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=99.25  E-value=6.6e-12  Score=112.31  Aligned_cols=52  Identities=17%  Similarity=0.272  Sum_probs=48.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCC--CeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVG--GVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G--~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+++++++|+.+|+.||  .|.+|+|+.|+.||+++|||||+|.
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~  120 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVG  120 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEEC
Confidence            567999999999999999999999999  9999999999999999999999995

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.24  E-value=6.6e-12  Score=92.99  Aligned_cols=48  Identities=15%  Similarity=0.150  Sum_probs=44.5

Q ss_pred             ceEEEcCCCCCC------CHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKA------TYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~------~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ++|||||||+.+      ++++|+.+|++||.|.+|+++  +.+|+++|||||+|.
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~   55 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYA   55 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEES
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEEC
Confidence            599999999999      779999999999999999988  369999999999995

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.24  E-value=8.4e-12  Score=102.82  Aligned_cols=54  Identities=20%  Similarity=0.205  Sum_probs=50.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....++|||+|||.++++++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~   92 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQ   92 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEEC
Confidence            345679999999999999999999999999999999999889999999999995

>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=99.24  E-value=1.1e-11  Score=98.62  Aligned_cols=52  Identities=21%  Similarity=0.348  Sum_probs=48.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+.+|+.||.|.+|.|+.++ +|+++|||||+|.
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~   56 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFE   56 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEEC
Confidence            345699999999999999999999999999999999996 9999999999995

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.24  E-value=8.9e-10  Score=109.99  Aligned_cols=103  Identities=14%  Similarity=0.040  Sum_probs=77.9

Q ss_pred             hHHHHHHHHHHHHhcCCh-hhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDP-GRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~-~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~  100 (442)
                      +...|...+......|++ +.+...|+++|..+|.+...|...+..+... ++.+.+...|++|+...|. ...|..+..
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            667788888877788888 8888888888888888888888888766644 4567788888888888887 577777665


Q ss_pred             HHHHcc---------CCHHHHHHHHHHHHhCChhhH
Q 013489          101 SLERSR---------ASEEEISTVFEKSLLCAFSTF  127 (442)
Q Consensus       101 ~le~~~---------~~~~~~~~i~~~al~~~~~~~  127 (442)
                      .+ ...         +..+++...|++++...+...
T Consensus       179 ~~-~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~  213 (474)
T 4abn_A          179 VL-RQLQTDSGDEHSRHVMDSVRQAKLAVQMDVLDG  213 (474)
T ss_dssp             HH-TTCCCSCHHHHHHHHHHHHHHHHHHHHHCTTCH
T ss_pred             HH-HHhccCChhhhhhhHHHHHHHHHHHHHhCCCCH
Confidence            33 334         566778888888887665543

>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=99.24  E-value=2.5e-12  Score=100.30  Aligned_cols=52  Identities=37%  Similarity=0.476  Sum_probs=49.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+.+++++|+.+|+.||.|.+|+++.++.+|+++|||||+|.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~   58 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQ   58 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECS
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEEC
Confidence            4569999999999999999999999999999999999889999999999995

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.24  E-value=7.2e-12  Score=111.21  Aligned_cols=51  Identities=22%  Similarity=0.236  Sum_probs=49.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||||||+++++++|+++|++||.|.+|+|++|+.||+++|||||+|.
T Consensus        15 ~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~   65 (213)
T 4f02_A           15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQ   65 (213)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeC
Confidence            469999999999999999999999999999999999999999999999995

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.24  E-value=8.6e-12  Score=96.09  Aligned_cols=47  Identities=9%  Similarity=0.066  Sum_probs=43.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||||||+++++++|+.+|++||.|.+|+|+.+      ||||||+|.
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~   60 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMN   60 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEEC
Confidence            34569999999999999999999999999999999875      699999995

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.24  E-value=1.1e-09  Score=109.36  Aligned_cols=249  Identities=8%  Similarity=0.041  Sum_probs=179.3

Q ss_pred             hhhHHHHHHhh-----c--CCCC---ChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcc
Q 013489            3 NARAHLEEQIS-----R--QDLS---DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLK   72 (442)
Q Consensus         3 ~~r~~yE~~l~-----~--~~~~---~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~   72 (442)
                      ++...|+.++.     .  .|..   ++.....|...+......|+++.+..+|++++...|. ...|...+..+.. .+
T Consensus       207 ~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~~~-~~~~~~l~~~~~~-~~  284 (514)
T 2gw1_A          207 KADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLKNDPLGAHEDIKKAIELFPR-VNSYIYMALIMAD-RN  284 (514)
T ss_dssp             HHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHT-SS
T ss_pred             HHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcc-HHHHHHHHHHHHH-CC
Confidence            35566777776     3  3321   1456778988899888999999999999999999999 9999888887664 44


Q ss_pred             hhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccc
Q 013489           73 VGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVE  152 (442)
Q Consensus        73 ~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~  152 (442)
                      ..+.+...|++++...|....+|...+..+.. .++.+.+...|++++...+.....+..+-..+.     .        
T Consensus       285 ~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~-----~--------  350 (514)
T 2gw1_A          285 DSTEYYNYFDKALKLDSNNSSVYYHRGQMNFI-LQNYDQAGKDFDKAKELDPENIFPYIQLACLAY-----R--------  350 (514)
T ss_dssp             CCTTGGGHHHHHHTTCTTCTHHHHHHHHHHHH-TTCTTHHHHHHHHHHHTCSSCSHHHHHHHHHTT-----T--------
T ss_pred             CHHHHHHHHHHHhhcCcCCHHHHHHHHHHHHH-hCCHHHHHHHHHHHHHhChhhHHHHHHHHHHHH-----H--------
Confidence            56778999999999999999999887775544 688899999999999876654332222211110     0        


Q ss_pred             hhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHH------HHHHHHHH
Q 013489          153 GVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLE------AWQSYISM  226 (442)
Q Consensus       153 ~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~------~w~~~~~~  226 (442)
                       ..++......|++++..       .+....+|...+.+....| +++.|..+|++++...|+...      +|...+..
T Consensus       351 -~~~~~~A~~~~~~~~~~-------~~~~~~~~~~la~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~  421 (514)
T 2gw1_A          351 -ENKFDDCETLFSEAKRK-------FPEAPEVPNFFAEILTDKN-DFDKALKQYDLAIELENKLDGIYVGIAPLVGKATL  421 (514)
T ss_dssp             -TTCHHHHHHHHHHHHHH-------STTCSHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHTSSSCSSCSHHHHHHHHH
T ss_pred             -cCCHHHHHHHHHHHHHH-------cccCHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHH
Confidence             12333344444444432       3344567888888888888 899999999999998877644      88888888


Q ss_pred             HHh---cccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHh
Q 013489          227 EIE---LDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQK  279 (442)
Q Consensus       227 e~~---~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~  279 (442)
                      ...   .|+++.|...|++++..  .++.+ .++..........|+.+.-...+++
T Consensus       422 ~~~~~~~~~~~~A~~~~~~a~~~--~~~~~-~~~~~la~~~~~~g~~~~A~~~~~~  474 (514)
T 2gw1_A          422 LTRNPTVENFIEATNLLEKASKL--DPRSE-QAKIGLAQMKLQQEDIDEAITLFEE  474 (514)
T ss_dssp             HHTSCCTTHHHHHHHHHHHHHHH--CTTCH-HHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HhhhhhcCCHHHHHHHHHHHHHh--CcccH-HHHHHHHHHHHHhcCHHHHHHHHHH
Confidence            888   89999999999999873  33333 4555666666677876654444443

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.24  E-value=6.4e-12  Score=96.81  Aligned_cols=53  Identities=28%  Similarity=0.307  Sum_probs=48.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCC---CCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKF---TGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~---~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+.+|+.||.|.+|+|+.++.   ||+++|||||+|.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~   58 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYK   58 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEEC
Confidence            3457999999999999999999999999999999999876   6699999999995

>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=99.24  E-value=6.6e-12  Score=99.74  Aligned_cols=49  Identities=18%  Similarity=0.268  Sum_probs=45.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..+|||||||+++++++|+++|+.||.|.+|+|+.++  +.++|||||+|.
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~   53 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFE   53 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEES
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEEC
Confidence            3489999999999999999999999999999999984  458999999996

>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=99.23  E-value=2.7e-12  Score=97.26  Aligned_cols=50  Identities=22%  Similarity=0.325  Sum_probs=48.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ++|||||||+++++++|+++|++||.|.+|+++.++.+|+++|||||+|.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~   51 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ   51 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEEC
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEEC
Confidence            58999999999999999999999999999999999889999999999996

>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=99.23  E-value=1.5e-11  Score=96.43  Aligned_cols=52  Identities=15%  Similarity=0.341  Sum_probs=49.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|+.||.|.+|.|+.++ +|+++|||||+|.
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~   78 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFE   78 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEEC
Confidence            456799999999999999999999999999999999996 9999999999995

>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=99.23  E-value=1.1e-11  Score=97.48  Aligned_cols=53  Identities=17%  Similarity=0.189  Sum_probs=49.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCC-eeEEEEe-eCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGG-VSSIRIL-HDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~-i~~~~~~-~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+.+|+.||. |.+|.++ .++.+|+++|||||+|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~   60 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYE   60 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEES
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEec
Confidence            34679999999999999999999999998 9999998 88889999999999995

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.22  E-value=2.5e-09  Score=94.85  Aligned_cols=201  Identities=11%  Similarity=0.011  Sum_probs=144.3

Q ss_pred             CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHH
Q 013489           53 FPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLD  132 (442)
Q Consensus        53 ~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~  132 (442)
                      .|.++..|......+... +..+.+...|++++...|.....|......+.. .+..+++...|++++...|.....+..
T Consensus         1 ~p~~~~~~~~lg~~~~~~-g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~-~g~~~~A~~~~~~al~~~P~~~~a~~~   78 (217)
T 2pl2_A            1 MQTAEQNPLRLGVQLYAL-GRYDAALTLFERALKENPQDPEALYWLARTQLK-LGLVNPALENGKTLVARTPRYLGGYMV   78 (217)
T ss_dssp             ---CCHHHHHHHHHHHHT-TCHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHhCCCcHHHHHH
Confidence            377888999998877654 456779999999999999999999988775554 788999999999999887775544433


Q ss_pred             HHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh
Q 013489          133 LFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI  212 (442)
Q Consensus       133 ~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~  212 (442)
                      +-..+...-    ...      .+.....+.+++|+..+..++...|.....|...+.+....| +++.|...|++++..
T Consensus        79 lg~~~~~~~----~~~------~~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~lg~~~~~~g-~~~~A~~~~~~al~~  147 (217)
T 2pl2_A           79 LSEAYVALY----RQA------EDRERGKGYLEQALSVLKDAERVNPRYAPLHLQRGLVYALLG-ERDKAEASLKQALAL  147 (217)
T ss_dssp             HHHHHHHHH----HTC------SSHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhh----hhh------hhhcccccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcC-ChHHHHHHHHHHHhc
Confidence            332221110    000      011122355677777776666656667788999999999999 999999999999999


Q ss_pred             chhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCH
Q 013489          213 SGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTL  270 (442)
Q Consensus       213 ~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~  270 (442)
                      . ++..+|...+......|+++.|...|++++..  .++.+ .++......-...|+.
T Consensus       148 ~-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~P~~~-~~~~~la~~~~~~g~~  201 (217)
T 2pl2_A          148 E-DTPEIRSALAELYLSMGRLDEALAQYAKALEQ--APKDL-DLRVRYASALLLKGKA  201 (217)
T ss_dssp             C-CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCH-HHHHHHHHHHTC----
T ss_pred             c-cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCh-HHHHHHHHHHHHccCH
Confidence            9 88999999999999999999999999999973  44444 3444444443444443

>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=99.22  E-value=8.4e-12  Score=96.13  Aligned_cols=52  Identities=10%  Similarity=0.098  Sum_probs=48.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+.+++++|+.+|+.||.|..+.++.++.+|+++|||||+|.
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~   65 (98)
T 2cqp_A           14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFE   65 (98)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEEC
Confidence            4579999999999999999999999999999988888899999999999995

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.22  E-value=7.6e-12  Score=100.03  Aligned_cols=52  Identities=13%  Similarity=0.209  Sum_probs=47.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCe----eEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGV----SSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i----~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+++|++||.|    .+|+|+.+ .+|+++|||||+|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~   76 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFA   76 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEEC
Confidence            345699999999999999999999999975    69999999 59999999999995

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.22  E-value=2e-11  Score=92.83  Aligned_cols=51  Identities=24%  Similarity=0.406  Sum_probs=47.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+.+++++|+.+|++||.|.+|+++.+  +|+++|||||+|.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~   56 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFE   56 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEEC
Confidence            34579999999999999999999999999999999984  8999999999995

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.22  E-value=1.6e-09  Score=98.91  Aligned_cols=199  Identities=8%  Similarity=0.017  Sum_probs=151.0

Q ss_pred             HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCc----HHHHHHH
Q 013489           23 FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV----GELWVRS   98 (442)
Q Consensus        23 ~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s----~~lW~~y   98 (442)
                      .+.+..++......|+++.+..+|++++..+|.+...|...+..... .++.+.+...|++++. .|..    ...|...
T Consensus         3 ~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~-~~~~~~A~~~~~~a~~-~~~~~~~~~~~~~~l   80 (272)
T 3u4t_A            3 DDVEFRYADFLFKNNNYAEAIEVFNKLEAKKYNSPYIYNRRAVCYYE-LAKYDLAQKDIETYFS-KVNATKAKSADFEYY   80 (272)
T ss_dssp             --CHHHHHHHHHTTTCHHHHHHHHHHHHHTTCCCSTTHHHHHHHHHH-TTCHHHHHHHHHHHHT-TSCTTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHH-HhhHHHHHHHHHHHHh-ccCchhHHHHHHHHH
Confidence            34678888888899999999999999999999999999998886654 4566789999999999 4433    3447776


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCc
Q 013489           99 LLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNT  178 (442)
Q Consensus        99 ~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~  178 (442)
                      ...+. ..+..+.+...|++++...+.....+..+-..+                     .....+++|+.++..++...
T Consensus        81 g~~~~-~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~---------------------~~~~~~~~A~~~~~~al~~~  138 (272)
T 3u4t_A           81 GKILM-KKGQDSLAIQQYQAAVDRDTTRLDMYGQIGSYF---------------------YNKGNFPLAIQYMEKQIRPT  138 (272)
T ss_dssp             HHHHH-HTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHH---------------------HHTTCHHHHHHHHGGGCCSS
T ss_pred             HHHHH-HcccHHHHHHHHHHHHhcCcccHHHHHHHHHHH---------------------HHccCHHHHHHHHHHHhhcC
Confidence            65444 478899999999999987665433332222111                     11134677777777777666


Q ss_pred             hhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhccc---HHHHHHHHHHHHhc
Q 013489          179 DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDH---INEARSIYKRCYSK  246 (442)
Q Consensus       179 ~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~---~~~ar~i~~ral~~  246 (442)
                      +....+|...+......+ +++.|..+|++++..+|++...|...+......|+   ++.|...|++++..
T Consensus       139 ~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~  208 (272)
T 3u4t_A          139 TTDPKVFYELGQAYYYNK-EYVKADSSFVKVLELKPNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEV  208 (272)
T ss_dssp             CCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHH
Confidence            666778888884444555 89999999999999999988888888887777777   88899999999974

>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=99.22  E-value=1.5e-11  Score=104.48  Aligned_cols=53  Identities=23%  Similarity=0.340  Sum_probs=49.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|+++|||||+|.
T Consensus        70 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~  122 (165)
T 1rk8_A           70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE  122 (165)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEEC
Confidence            45679999999999999999999999999999999999899999999999995

>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=99.22  E-value=2.9e-11  Score=93.16  Aligned_cols=46  Identities=11%  Similarity=0.029  Sum_probs=42.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+.+++++|+.+|++||.|.+|.++.+      ||||||+|.
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~   59 (101)
T 2cq1_A           14 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELA   59 (101)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEEC
Confidence            4569999999999999999999999999999988865      799999995

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.21  E-value=1.5e-09  Score=97.74  Aligned_cols=207  Identities=11%  Similarity=0.002  Sum_probs=155.6

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCC-------HHHHHHHHHHHHHhcchhh
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVS-------SDLWLDYTQYLDKTLKVGN   75 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~-------~~lW~~Y~~~l~~~~~~~~   75 (442)
                      +|...|+.++... .    +...|...+......|+++.+..+|++++...|.+       ..+|...+..+.. .++.+
T Consensus        23 ~A~~~~~~a~~~~-~----~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~   96 (258)
T 3uq3_A           23 EAIEHYNKAWELH-K----DITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFARIGNAYHK-LGDLK   96 (258)
T ss_dssp             HHHHHHHHHHHHS-C----CTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH-TTCHH
T ss_pred             HHHHHHHHHHHhh-c----cHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHHHHHH-cccHH
Confidence            4667788888776 3    56688888888889999999999999999988776       6788887776664 45667


Q ss_pred             HHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhh
Q 013489           76 VVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVL  155 (442)
Q Consensus        76 ~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~  155 (442)
                      .+...|++++...|.. .++..        .+..+.+...|++++...+.....+..+-..+.     ..         .
T Consensus        97 ~A~~~~~~a~~~~~~~-~~~~~--------~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~---------~  153 (258)
T 3uq3_A           97 KTIEYYQKSLTEHRTA-DILTK--------LRNAEKELKKAEAEAYVNPEKAEEARLEGKEYF-----TK---------S  153 (258)
T ss_dssp             HHHHHHHHHHHHCCCH-HHHHH--------HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH-----HT---------T
T ss_pred             HHHHHHHHHHhcCchh-HHHHH--------HhHHHHHHHHHHHHHHcCcchHHHHHHHHHHHH-----Hh---------c
Confidence            8999999999988863 22221        244677888999999876654433332221111     10         2


Q ss_pred             hHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHH
Q 013489          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINE  235 (442)
Q Consensus       156 ~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~  235 (442)
                      ++......|++++.       ..+....+|...+.+....| +++.|...|++++...|+...+|...+......|+++.
T Consensus       154 ~~~~A~~~~~~a~~-------~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~  225 (258)
T 3uq3_A          154 DWPNAVKAYTEMIK-------RAPEDARGYSNRAAALAKLM-SFPEAIADCNKAIEKDPNFVRAYIRKATAQIAVKEYAS  225 (258)
T ss_dssp             CHHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             CHHHHHHHHHHHHh-------cCcccHHHHHHHHHHHHHhC-CHHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHhhHHH
Confidence            33333344444443       34455678888999988889 99999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhc
Q 013489          236 ARSIYKRCYSK  246 (442)
Q Consensus       236 ar~i~~ral~~  246 (442)
                      |...|++++..
T Consensus       226 A~~~~~~a~~~  236 (258)
T 3uq3_A          226 ALETLDAARTK  236 (258)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            99999999973

>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=1.2e-09  Score=110.11  Aligned_cols=249  Identities=8%  Similarity=0.044  Sum_probs=172.0

Q ss_pred             hhhHHHHHHhhcCCCCChHh----HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHH
Q 013489            3 NARAHLEEQISRQDLSDSEK----FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVR   78 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~----~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~   78 (442)
                      ++...|+.++...|. ++.-    ...|..........|+++.+..+|++++...|. ...|...+..+. ..++.+.+.
T Consensus       220 ~A~~~~~~~l~~~p~-~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~l~~~~~-~~~~~~~A~  296 (537)
T 3fp2_A          220 KSTDMYHSLLSANTV-DDPLRENAALALCYTGIFHFLKNNLLDAQVLLQESINLHPT-PNSYIFLALTLA-DKENSQEFF  296 (537)
T ss_dssp             HHHHHHHHHHC--CC-CHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC-HHHHHHHHHHTC-CSSCCHHHH
T ss_pred             HHHHHHHHHHHHCCC-cchhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCC-chHHHHHHHHHH-HhcCHHHHH
Confidence            355677777777765 1111    224555556667789999999999999999999 888888777655 345667899


Q ss_pred             HHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHH
Q 013489           79 DVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYS  158 (442)
Q Consensus        79 ~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~  158 (442)
                      ..|++++...|....+|......+. ..+..+.+...|++++...+.....+..+-..+.     ..         .++.
T Consensus       297 ~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~-----~~---------g~~~  361 (537)
T 3fp2_A          297 KFFQKAVDLNPEYPPTYYHRGQMYF-ILQDYKNAKEDFQKAQSLNPENVYPYIQLACLLY-----KQ---------GKFT  361 (537)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCSHHHHHHHHHHH-----HT---------TCHH
T ss_pred             HHHHHHhccCCCCHHHHHHHHHHHH-hcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH-----Hc---------CCHH
Confidence            9999999999999999999887554 4788999999999999876653332222221111     10         2333


Q ss_pred             HHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHH------HHHHHHHHHhc--
Q 013489          159 LIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEA------WQSYISMEIEL--  230 (442)
Q Consensus       159 ~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~------w~~~~~~e~~~--  230 (442)
                      .....|++++.       ..+....+|..++.+....| +++.|...|++++...|+....      +...+.+....  
T Consensus       362 ~A~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~  433 (537)
T 3fp2_A          362 ESEAFFNETKL-------KFPTLPEVPTFFAEILTDRG-DFDTAIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQSS  433 (537)
T ss_dssp             HHHHHHHHHHH-------HCTTCTHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHCSSCSSTTHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHH-------hCCCChHHHHHHHHHHHHhC-CHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHHhh
Confidence            33344444443       34445568888899988888 9999999999999987765432      34445555566  


Q ss_pred             --------ccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          231 --------DHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       231 --------g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                              |+++.|..+|++++..  .++.+ .++..........|+.+.-...++++
T Consensus       434 ~~~~~~~~~~~~~A~~~~~~a~~~--~p~~~-~~~~~l~~~~~~~g~~~~A~~~~~~a  488 (537)
T 3fp2_A          434 QDPTQLDEEKFNAAIKLLTKACEL--DPRSE-QAKIGLAQLKLQMEKIDEAIELFEDS  488 (537)
T ss_dssp             C----CCHHHHHHHHHHHHHHHHH--CTTCH-HHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             ccchhhhHhHHHHHHHHHHHHHHh--CCCCH-HHHHHHHHHHHHhccHHHHHHHHHHH
Confidence                    9999999999999973  33444 56666667777778876555444443

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.21  E-value=2.7e-11  Score=97.59  Aligned_cols=53  Identities=15%  Similarity=0.338  Sum_probs=49.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....++|||+|||+.+++++|+.+|+.||.|.+|+|+.++ +|+++|||||+|.
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~   84 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFE   84 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEEC
Confidence            3456799999999999999999999999999999999997 9999999999995

>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=99.20  E-value=1.2e-11  Score=93.09  Aligned_cols=52  Identities=12%  Similarity=0.206  Sum_probs=48.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCC-CcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGK-SRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~-~~g~~fv~f~  441 (442)
                      ..++|||+|||+++++++|+.+|++||.|.+++++.++.++. ++|||||+|.
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~   55 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFE   55 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEe
Confidence            356999999999999999999999999999999999977766 9999999995

>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=99.20  E-value=2.2e-11  Score=102.38  Aligned_cols=53  Identities=23%  Similarity=0.332  Sum_probs=50.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|+.||.|.+|.|+.++.+|+++|||||+|.
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~   89 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYY   89 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEEC
Confidence            45679999999999999999999999999999999999999999999999995

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.20  E-value=3.1e-11  Score=91.48  Aligned_cols=51  Identities=18%  Similarity=0.184  Sum_probs=47.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++++++|+.+|+.| .|.+|+|+.+ .+|+++|||||+|.
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~   58 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFS   58 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECS
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEEC
Confidence            445799999999999999999999999 8999999999 79999999999995

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.20  E-value=3.5e-11  Score=95.42  Aligned_cols=52  Identities=33%  Similarity=0.495  Sum_probs=48.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|+.||.|.+|+|+.++ +|+++|||||+|.
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~   64 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFE   64 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEEC
Confidence            345799999999999999999999999999999999996 7999999999995

>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=99.20  E-value=2.5e-11  Score=102.34  Aligned_cols=53  Identities=23%  Similarity=0.361  Sum_probs=50.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++++++|+.+|+.||.|.+|+|+.|+.+|+++|||||+|.
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~  120 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFH  120 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEEC
Confidence            34579999999999999999999999999999999999889999999999995

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.19  E-value=1.5e-11  Score=99.16  Aligned_cols=52  Identities=29%  Similarity=0.530  Sum_probs=49.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +.++|||+|||+++++++|+.+|+.||.|.+|+++.++.+|+++|||||+|.
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~   86 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFA   86 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEEC
Confidence            3569999999999999999999999999999999999889999999999995

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.19  E-value=1.1e-11  Score=101.39  Aligned_cols=53  Identities=23%  Similarity=0.361  Sum_probs=49.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.
T Consensus        45 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~   97 (135)
T 2lea_A           45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFH   97 (135)
T ss_dssp             GGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEEC
Confidence            44579999999999999999999999999999999999889999999999995

>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=99.19  E-value=9.7e-12  Score=95.15  Aligned_cols=51  Identities=10%  Similarity=0.103  Sum_probs=48.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||+.+++++|+.+|++||.|..+.++.++.+|+++|||||+|.
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~   65 (95)
T 2ek1_A           15 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFE   65 (95)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEES
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEEC
Confidence            469999999999999999999999999999999998899999999999995

>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=99.18  E-value=7.4e-11  Score=91.67  Aligned_cols=51  Identities=20%  Similarity=0.309  Sum_probs=46.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|+.||.|.+|+|+.++.  .++|||||+|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~   63 (103)
T 2cq3_A           13 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFE   63 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEEC
Confidence            4457999999999999999999999999999999999843  38999999995

>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=99.18  E-value=1.5e-11  Score=100.48  Aligned_cols=51  Identities=20%  Similarity=0.246  Sum_probs=46.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++++++|+++|++|| |.+|+|+.|+ +|+++|||||+|.
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~-~g~srGfaFV~F~   94 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTGEADVEFA   94 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSS-SSCSSCCCEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECC-CCCCceEEEEEeC
Confidence            3456999999999999999999999999 7799999996 5999999999995

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.18  E-value=3.1e-09  Score=106.10  Aligned_cols=220  Identities=11%  Similarity=0.025  Sum_probs=168.1

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ++...|+.++...|.     ...|...+......|+++.+..+|++++..+|.+..+|...+..+... ++.+.+...|+
T Consensus       255 ~A~~~~~~~l~~~~~-----~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~A~~~~~  328 (514)
T 2gw1_A          255 GAHEDIKKAIELFPR-----VNSYIYMALIMADRNDSTEYYNYFDKALKLDSNNSSVYYHRGQMNFIL-QNYDQAGKDFD  328 (514)
T ss_dssp             HHHHHHHHHHHHCCC-----HHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCTTCTHHHHHHHHHHHHT-TCTTHHHHHHH
T ss_pred             HHHHHHHHHHhhCcc-----HHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCcCCHHHHHHHHHHHHHh-CCHHHHHHHHH
Confidence            456778888877653     567888888888999999999999999999999999999998877644 46678999999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRE  162 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~  162 (442)
                      +++...|....+|...+..+ ...++.+.+..+|++++...+.....+..+-..+.     +.         .++.....
T Consensus       329 ~~~~~~~~~~~~~~~l~~~~-~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~-----~~---------~~~~~A~~  393 (514)
T 2gw1_A          329 KAKELDPENIFPYIQLACLA-YRENKFDDCETLFSEAKRKFPEAPEVPNFFAEILT-----DK---------NDFDKALK  393 (514)
T ss_dssp             HHHHTCSSCSHHHHHHHHHT-TTTTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHH-----HT---------TCHHHHHH
T ss_pred             HHHHhChhhHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHHcccCHHHHHHHHHHHH-----HC---------CCHHHHHH
Confidence            99999999989998877644 45788999999999999765543332222111110     11         34444455


Q ss_pred             HHHHHHHHHhhhhcCchhhHHHHHHHHHHHHH---cCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHH
Q 013489          163 TFQRASDYLSEQMKNTDGLLRLYAYWAHLEQS---MGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSI  239 (442)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~---~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i  239 (442)
                      .|++++....... ........|...+.+...   .| +++.|...|++++...|+...+|...+.+....|+++.|...
T Consensus       394 ~~~~a~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  471 (514)
T 2gw1_A          394 QYDLAIELENKLD-GIYVGIAPLVGKATLLTRNPTVE-NFIEATNLLEKASKLDPRSEQAKIGLAQMKLQQEDIDEAITL  471 (514)
T ss_dssp             HHHHHHHHHHTSS-SCSSCSHHHHHHHHHHHTSCCTT-HHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHhhhccc-hHHHHHHHHHHHHHHHhhhhhcC-CHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhcCHHHHHHH
Confidence            5666655432110 000113477788888888   78 999999999999999999999999999999999999999999


Q ss_pred             HHHHHh
Q 013489          240 YKRCYS  245 (442)
Q Consensus       240 ~~ral~  245 (442)
                      |++++.
T Consensus       472 ~~~a~~  477 (514)
T 2gw1_A          472 FEESAD  477 (514)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            999997

>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=99.17  E-value=1.3e-09  Score=113.92  Aligned_cols=170  Identities=12%  Similarity=0.109  Sum_probs=141.8

Q ss_pred             CChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHH
Q 013489           18 SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVR   97 (442)
Q Consensus        18 ~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~   97 (442)
                      +.|++.+.|.+........|+++.|...|++||..+|.+...|......+... +..+.+...|++|++..|.....|..
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 SCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQ-GKLQEALMHYKEAIRISPTFADAYSN   82 (723)
T ss_dssp             --CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHhCCCCHHHHHH
Confidence            45678999999999999999999999999999999999999999999877754 55678999999999999999999999


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcC
Q 013489           98 SLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKN  177 (442)
Q Consensus        98 y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~  177 (442)
                      ....+.. .++.+++...|++|+...+.                                                    
T Consensus        83 Lg~~l~~-~g~~~~A~~~~~kAl~l~P~----------------------------------------------------  109 (723)
T 4gyw_A           83 MGNTLKE-MQDVQGALQCYTRAIQINPA----------------------------------------------------  109 (723)
T ss_dssp             HHHHHHH-TTCHHHHHHHHHHHHHHCTT----------------------------------------------------
T ss_pred             HHHHHHH-cCCHHHHHHHHHHHHHhCCC----------------------------------------------------
Confidence            7765544 67788888888887754333                                                    


Q ss_pred             chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          178 TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       178 ~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                         ....|...+.++...| +++.|...|+++++..|++...|..++......|+++.|...|++++.
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               2234555566667778 899999999999999999999999999999889998888888888875

>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=99.17  E-value=4.5e-11  Score=94.50  Aligned_cols=46  Identities=9%  Similarity=0.068  Sum_probs=42.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+++++++|+.+|++||.|.+|+|+.+      ||||||+|.
T Consensus        30 ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~   75 (119)
T 2ad9_A           30 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMN   75 (119)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEEC
Confidence            3569999999999999999999999999999999876      699999995

>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=99.17  E-value=2.6e-11  Score=105.97  Aligned_cols=53  Identities=23%  Similarity=0.335  Sum_probs=50.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+.+|+.||.|.+|.++.++.+|+++|||||+|.
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~   63 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA   63 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeC
Confidence            45679999999999999999999999999999999999889999999999996

>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=99.17  E-value=6.3e-11  Score=92.07  Aligned_cols=51  Identities=14%  Similarity=0.185  Sum_probs=46.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|++||.|.+|+|+.++.  .++|||||+|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~   63 (103)
T 2cqi_A           13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFY   63 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEES
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEEC
Confidence            4567999999999999999999999999999999999843  36899999995

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.16  E-value=5.7e-11  Score=90.54  Aligned_cols=45  Identities=9%  Similarity=0.098  Sum_probs=41.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +++|||+|||+++++++|+.+|++||.|.+|++++      +||||||+|.
T Consensus        21 s~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~   65 (100)
T 3r27_A           21 SPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFE   65 (100)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEES
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEEC
Confidence            45999999999999999999999999999999875      3699999995

>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=99.16  E-value=7.6e-09  Score=93.20  Aligned_cols=190  Identities=14%  Similarity=0.053  Sum_probs=144.5

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ++...|+.++...|.    +...|..++......|+++.+..+|++++...|.+..+|..++..+... ++.+.+...|+
T Consensus        55 ~A~~~~~~al~~~~~----~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~-g~~~~A~~~~~  129 (252)
T 2ho1_A           55 QAKVPLRKALEIDPS----SADAHAALAVVFQTEMEPKLADEEYRKALASDSRNARVLNNYGGFLYEQ-KRYEEAYQRLL  129 (252)
T ss_dssp             GGHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCC----hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHH-hHHHHHHHHHH
Confidence            577889999988765    6778888888888999999999999999999999999999998877644 56678999999


Q ss_pred             HHHH--cCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHH
Q 013489           83 RATK--NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLI  160 (442)
Q Consensus        83 rAl~--~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~  160 (442)
                      +++.  ..|....+|..++..+. ..+..+.+...|++++...+.....+..+-..+.     ..         .+    
T Consensus       130 ~~~~~~~~~~~~~~~~~la~~~~-~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~-----~~---------g~----  190 (252)
T 2ho1_A          130 EASQDTLYPERSRVFENLGLVSL-QMKKPAQAKEYFEKSLRLNRNQPSVALEMADLLY-----KE---------RE----  190 (252)
T ss_dssp             HHTTCTTCTTHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHH-----HT---------TC----
T ss_pred             HHHhCccCcccHHHHHHHHHHHH-HcCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHH-----Hc---------CC----
Confidence            9999  77888888888776444 4688999999999999766554332222211110     00         22    


Q ss_pred             HHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHH
Q 013489          161 RETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAW  220 (442)
Q Consensus       161 r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w  220 (442)
                         ++.|..++...+...+.....+...+.++...| +.+.|..++++++..+|++..++
T Consensus       191 ---~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g-~~~~A~~~~~~~~~~~p~~~~~~  246 (252)
T 2ho1_A          191 ---YVPARQYYDLFAQGGGQNARSLLLGIRLAKVFE-DRDTAASYGLQLKRLYPGSLEYQ  246 (252)
T ss_dssp             ---HHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTSHHHH
T ss_pred             ---HHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHcc-CHHHHHHHHHHHHHHCCCCHHHH
Confidence               344444454444444455567888888888888 99999999999999999877654

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.15  E-value=1.3e-08  Score=94.59  Aligned_cols=218  Identities=11%  Similarity=0.010  Sum_probs=153.1

Q ss_pred             HHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhc--CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHH
Q 013489            7 HLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITD--FPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRA   84 (442)
Q Consensus         7 ~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~--~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erA   84 (442)
                      .|+.++......++.....+..++.+....|+.+.+...|++.+..  +|.++.+|...+..+... +..+.+..+|++ 
T Consensus        49 ~~~~al~~~~~~~~~~~~a~~~la~~~~~~~~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~-g~~~~Al~~l~~-  126 (291)
T 3mkr_A           49 KYGVVLDEIKPSSAPELQAVRMFAEYLASHSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYD-QNPDAALRTLHQ-  126 (291)
T ss_dssp             CHHHHHHHSCTTSCHHHHHHHHHHHHHHCSTTHHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHT-TCHHHHHHHHTT-
T ss_pred             CHHHHHHHhcccCChhHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHC-CCHHHHHHHHhC-
Confidence            4555554433234456778888888888888899999999999876  599999988887766644 456778888887 


Q ss_pred             HHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHH
Q 013489           85 TKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETF  164 (442)
Q Consensus        85 l~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~  164 (442)
                          |.+..+|...+..+.. .+..+.+...|++++...+.....  .+...++..+. .                .+.+
T Consensus       127 ----~~~~~~~~~l~~~~~~-~g~~~~A~~~l~~~~~~~p~~~~~--~l~~a~~~l~~-~----------------~~~~  182 (291)
T 3mkr_A          127 ----GDSLECMAMTVQILLK-LDRLDLARKELKKMQDQDEDATLT--QLATAWVSLAA-G----------------GEKL  182 (291)
T ss_dssp             ----CCSHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHH--HHHHHHHHHHH-C----------------TTHH
T ss_pred             ----CCCHHHHHHHHHHHHH-CCCHHHHHHHHHHHHhhCcCcHHH--HHHHHHHHHHh-C----------------chHH
Confidence                7888888887765444 688889999999998776553211  11112221110 0                0223


Q ss_pred             HHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHH-HHHHHHHHH
Q 013489          165 QRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHIN-EARSIYKRC  243 (442)
Q Consensus       165 ~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~-~ar~i~~ra  243 (442)
                      ++|..++...+...+....+|...+.+....| +++.|...|++++..+|+++.+|..++.+....|+.. .+..+++++
T Consensus       183 ~eA~~~~~~~l~~~p~~~~~~~~la~~~~~~g-~~~eA~~~l~~al~~~p~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~  261 (291)
T 3mkr_A          183 QDAYYIFQEMADKCSPTLLLLNGQAACHMAQG-RWEAAEGVLQEALDKDSGHPETLINLVVLSQHLGKPPEVTNRYLSQL  261 (291)
T ss_dssp             HHHHHHHHHHHHHSCCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            44444444444334556678888888888888 8999999999999999999999999998888888765 578899998


Q ss_pred             HhcccCCCCh
Q 013489          244 YSKRFTGTGS  253 (442)
Q Consensus       244 l~~~~~~~~~  253 (442)
                      +.  +.++.|
T Consensus       262 ~~--~~P~~~  269 (291)
T 3mkr_A          262 KD--AHRSHP  269 (291)
T ss_dssp             HH--HCTTCH
T ss_pred             HH--hCCCCh
Confidence            86  344544

>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=99.15  E-value=3.4e-11  Score=90.69  Aligned_cols=47  Identities=23%  Similarity=0.328  Sum_probs=43.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+++++++|+.+|++||.|.+|+|+.+     ++|||||+|.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~   50 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFA   50 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEEC
Confidence            4579999999999999999999999999999999875     7899999995

>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=99.15  E-value=5e-11  Score=91.33  Aligned_cols=50  Identities=16%  Similarity=0.205  Sum_probs=45.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHH----HHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLR----RFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~----~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+.+++++|+    .+|++||.|.+|+|+.++.+   +|||||+|.
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~   60 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQME   60 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEEC
Confidence            455799999999999999999    99999999999999998655   899999995

>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=99.14  E-value=1.2e-10  Score=90.27  Aligned_cols=45  Identities=7%  Similarity=0.051  Sum_probs=41.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||+.+++++|+.+|++||.|.+|.++.+      ||||||+|.
T Consensus        15 ~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~   59 (104)
T 1wex_A           15 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFE   59 (104)
T ss_dssp             CSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEES
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEEC
Confidence            469999999999999999999999999999998764      699999995

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.14  E-value=1.8e-08  Score=99.86  Aligned_cols=235  Identities=11%  Similarity=0.026  Sum_probs=159.2

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHH---HhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh---cchhhH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYE---QSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKT---LKVGNV   76 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e---~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~---~~~~~~   76 (442)
                      +|...|+.+|...|.    +.+.|..++...   ...+..+.+...|+++|..+|.+..+|..+...+...   .+..+.
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            467788888887765    666676666543   3456778888999999999999998887776443322   234456


Q ss_pred             HHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhh
Q 013489           77 VRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLD  156 (442)
Q Consensus        77 ~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~  156 (442)
                      +...|++|+...|....+|......+ ...+..+.+...|++++...|.....+..+-..+...........  ......
T Consensus       232 a~~~~~~al~~~~~~~~~~~~lg~~~-~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~y~~~~~~~~~~~--~~~~~~  308 (472)
T 4g1t_A          232 GEKLVEEALEKAPGVTDVLRSAAKFY-RRKDEPDKAIELLKKALEYIPNNAYLHCQIGCCYRAKVFQVMNLR--ENGMYG  308 (472)
T ss_dssp             HHHHHHHHHHHCSSCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHC--------C
T ss_pred             HHHHHHHHHHhCccHHHHHHHHHHHH-HHcCchHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHhhhHH--HHHHHH
Confidence            88999999999999988888876644 447888999999999998777655544433333221111000000  000012


Q ss_pred             HHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHH---HHHHHHHHHHH-hccc
Q 013489          157 YSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAML---EAWQSYISMEI-ELDH  232 (442)
Q Consensus       157 ~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~---~~w~~~~~~e~-~~g~  232 (442)
                      .......++.|+.++..+....+.....+...+.+....| +++.|..+|++++...++..   .++..|..+.. ..|+
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            2233455667777776665545555557778888888888 99999999999999865543   35677776543 5689


Q ss_pred             HHHHHHHHHHHHh
Q 013489          233 INEARSIYKRCYS  245 (442)
Q Consensus       233 ~~~ar~i~~ral~  245 (442)
                      .+.|...|.+|+.
T Consensus       388 ~~~Ai~~y~kal~  400 (472)
T 4g1t_A          388 EDKAIHHFIEGVK  400 (472)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999999997

>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=99.14  E-value=6e-11  Score=91.29  Aligned_cols=46  Identities=13%  Similarity=0.028  Sum_probs=42.3

Q ss_pred             CCceEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINL-KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +.++|||+|||+ .+++++|+.+|++||.|.+|+|+.+      +|||||+|.
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~   60 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMA   60 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEES
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEEC
Confidence            356999999999 9999999999999999999999875      489999995

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.13  E-value=7.5e-12  Score=96.99  Aligned_cols=52  Identities=19%  Similarity=0.211  Sum_probs=47.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++++++|+.+|+.||.|.. .++.++.+|+++|||||+|.
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~   66 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFE   66 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEEC
Confidence            34679999999999999999999999999988 77777789999999999995

>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=99.13  E-value=2.1e-10  Score=90.06  Aligned_cols=50  Identities=12%  Similarity=0.305  Sum_probs=44.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|++||.|.+|.|+.   +++++|||||+|.
T Consensus        20 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~---~~~~~g~afV~f~   69 (109)
T 1x4a_A           20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFE   69 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEEC
Confidence            4567999999999999999999999999999999855   4568999999995

>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=99.13  E-value=1.1e-10  Score=91.12  Aligned_cols=46  Identities=9%  Similarity=0.008  Sum_probs=41.9

Q ss_pred             CCceEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLK-ATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||++ +++++|+.+|++||.|.+|+|++      +||||||+|.
T Consensus        24 p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~   70 (112)
T 1x4f_A           24 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEME   70 (112)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECS
T ss_pred             CCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEEC
Confidence            3579999999998 99999999999999999999874      4799999995

>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=99.10  E-value=1e-10  Score=92.22  Aligned_cols=53  Identities=9%  Similarity=0.203  Sum_probs=47.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHH---HHhccCCCeeEEEEeeCCCCC---CCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLR---RFFSDVGGVSSIRILHDKFTG---KSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~---~~f~~~G~i~~~~~~~~~~~g---~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+   .+|++||.|.+|.|+.++.+|   +++|||||+|.
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~   71 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYI   71 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEES
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEEC
Confidence            345699999999999999999   999999999999999987654   56699999995

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.09  E-value=1.2e-10  Score=93.71  Aligned_cols=48  Identities=17%  Similarity=0.243  Sum_probs=42.6

Q ss_pred             CceEEEcCCCCCCCHHHHH----HHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLR----RFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~----~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||||||+.+++++|+    .+|++||.|.+|.+.   .+|+++|||||+|.
T Consensus        29 ~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~---~~~~~rG~aFV~F~   80 (127)
T 2a3j_A           29 SQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDDNSGKAYIVFA   80 (127)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC---CCCSSCCCEEEEES
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec---cCCCcCCEEEEEEC
Confidence            5699999999999999876    699999999998774   37889999999995

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.09  E-value=2.6e-08  Score=87.55  Aligned_cols=202  Identities=10%  Similarity=-0.011  Sum_probs=146.3

Q ss_pred             cCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHH
Q 013489           52 DFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYL  131 (442)
Q Consensus        52 ~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~  131 (442)
                      ..|.++.+|...+..+... ++.+.+...|++++...|....+|...+..+. ..++.+.+..+|++++...+.....+.
T Consensus         3 ~~~~~~~~~~~~~~~~~~~-~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~A~~~~~~a~~~~~~~~~~~~   80 (225)
T 2vq2_A            3 KANQVSNIKTQLAMEYMRG-QDYRQATASIEDALKSDPKNELAWLVRAEIYQ-YLKVNDKAQESFRQALSIKPDSAEINN   80 (225)
T ss_dssp             -CCHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             CCcccHHHHHHHHHHHHHH-hhHHHHHHHHHHHHHhCccchHHHHHHHHHHH-HcCChHHHHHHHHHHHHhCCCChHHHH
Confidence            3567788888888776644 45678999999999999999999988777444 468899999999999987665433322


Q ss_pred             HHHHHHHHHHHHHhhccCccchh-hhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 013489          132 DLFLTRIDGLRRRILFSGEVEGV-LDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLL  210 (442)
Q Consensus       132 ~~~~~~~~~l~rr~~~~~~~~~~-~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l  210 (442)
                      .+-..+.              .. .++......|++++.     ....+....+|...+.+....| +++.|..+|++++
T Consensus        81 ~l~~~~~--------------~~~~~~~~A~~~~~~~~~-----~~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~~~  140 (225)
T 2vq2_A           81 NYGWFLC--------------GRLNRPAESMAYFDKALA-----DPTYPTPYIANLNKGICSAKQG-QFGLAEAYLKRSL  140 (225)
T ss_dssp             HHHHHHH--------------TTTCCHHHHHHHHHHHHT-----STTCSCHHHHHHHHHHHHHHTT-CHHHHHHHHHHHH
T ss_pred             HHHHHHH--------------HhcCcHHHHHHHHHHHHc-----CcCCcchHHHHHHHHHHHHHcC-CHHHHHHHHHHHH
Confidence            2211111              01 123333344444433     0033445678888899988888 9999999999999


Q ss_pred             HhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCC-CChHHHHHHHHHHHHHhCCHhhHHHHHH
Q 013489          211 KISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTG-TGSEDICHAWLRFEREYGTLEDFDHSVQ  278 (442)
Q Consensus       211 ~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~-~~~~~i~~~~~~fE~~~G~~~~~~~~~~  278 (442)
                      ...|++..+|...+.+....|+++.|..+|++++..  .+ +.+ ..+.....+....|+.+.......
T Consensus       141 ~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--~~~~~~-~~~~~~~~~~~~~~~~~~a~~~~~  206 (225)
T 2vq2_A          141 AAQPQFPPAFKELARTKMLAGQLGDADYYFKKYQSR--VEVLQA-DDLLLGWKIAKALGNAQAAYEYEA  206 (225)
T ss_dssp             HHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--HCSCCH-HHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCCH-HHHHHHHHHHHhcCcHHHHHHHHH
Confidence            999999999999999999999999999999999973  33 444 455666777778888776554433

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.09  E-value=1.4e-08  Score=101.17  Aligned_cols=219  Identities=10%  Similarity=-0.047  Sum_probs=156.4

Q ss_pred             hhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchh-hHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHH
Q 013489           39 PGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVG-NVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFE  117 (442)
Q Consensus        39 ~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~-~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~  117 (442)
                      .+.+...++.++...|.+..+|......+.. .++. +.+...|++|+...|.....|......+. ..++.+++...|+
T Consensus        84 ~~~al~~l~~~~~~~~~~a~~~~~lg~~~~~-~g~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~-~~g~~~~A~~~~~  161 (474)
T 4abn_A           84 MEKTLQQMEEVLGSAQVEAQALMLKGKALNV-TPDYSPEAEVLLSKAVKLEPELVEAWNQLGEVYW-KKGDVTSAHTCFS  161 (474)
T ss_dssp             HHHHHHHHHHHHTTCCCCHHHHHHHHHHHTS-SSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCchhHHHHHHHHHHHHh-ccccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHH-HcCCHHHHHHHHH
Confidence            3455667777788889999999999987764 4566 88999999999999999999999877444 4789999999999


Q ss_pred             HHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHc--
Q 013489          118 KSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSM--  195 (442)
Q Consensus       118 ~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~--  195 (442)
                      +++...+. ...+..+-..+.     ....       .+.......+++|+.++..++...+.....|..++.++...  
T Consensus       162 ~al~~~p~-~~~~~~lg~~~~-----~~~~-------~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~  228 (474)
T 4abn_A          162 GALTHCKN-KVSLQNLSMVLR-----QLQT-------DSGDEHSRHVMDSVRQAKLAVQMDVLDGRSWYILGNAYLSLYF  228 (474)
T ss_dssp             HHHTTCCC-HHHHHHHHHHHT-----TCCC-------SCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHhhCCC-HHHHHHHHHHHH-----Hhcc-------CChhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHH
Confidence            99988766 222222221111     1000       01112224455566666555554556667888888888777  


Q ss_pred             ------CCCHHHHHHHHHHHHHhch---hHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHH
Q 013489          196 ------GKDMVSARGVWERLLKISG---AMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFERE  266 (442)
Q Consensus       196 ------~~~~~~ar~i~~~~l~~~~---~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~  266 (442)
                            + +++.|...|++++...|   +...+|..++.+....|+++.|...|++|+.  +.++.+. .+.........
T Consensus       229 ~~~~~~g-~~~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~--l~p~~~~-a~~~l~~~~~~  304 (474)
T 4abn_A          229 NTGQNPK-ISQQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAA--LDPAWPE-PQQREQQLLEF  304 (474)
T ss_dssp             HTTCCHH-HHHHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTTCHH-HHHHHHHHHHH
T ss_pred             hhccccc-hHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--hCCCCHH-HHHHHHHHHHH
Confidence                  7 89999999999999999   8999999999999999999999999999997  3445442 33333333333


Q ss_pred             hCCHhhHHHHHHh
Q 013489          267 YGTLEDFDHSVQK  279 (442)
Q Consensus       267 ~G~~~~~~~~~~~  279 (442)
                         +..+..++..
T Consensus       305 ---lg~~~eAi~~  314 (474)
T 4abn_A          305 ---LSRLTSLLES  314 (474)
T ss_dssp             ---HHHHHHHHHH
T ss_pred             ---HHHHHHHHHH
Confidence               3344555543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=98.67  E-value=1.1e-11  Score=98.60  Aligned_cols=53  Identities=23%  Similarity=0.424  Sum_probs=49.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeE--------EEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSS--------IRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~--------~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+.+++++|+.+|+.||.|.+        |+|+.++.+|+++|||||+|.
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~   65 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD   65 (116)
Confidence            34569999999999999999999999999998        999999889999999999995

>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=99.08  E-value=4.8e-11  Score=94.75  Aligned_cols=53  Identities=19%  Similarity=0.214  Sum_probs=44.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|+.||.|..+.+..+..+|+++|||||+|.
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~   75 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFP   75 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEEC
Confidence            34679999999999999999999999999954433333338999999999995

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.07  E-value=2.4e-10  Score=88.37  Aligned_cols=49  Identities=24%  Similarity=0.287  Sum_probs=44.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+.+|++||.|   +++.+ .+|+++|||||+|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~   61 (101)
T 2fc9_A           13 GESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFA   61 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEEC
Confidence            446799999999999999999999999976   67777 79999999999995

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.07  E-value=1.7e-10  Score=98.71  Aligned_cols=53  Identities=15%  Similarity=0.338  Sum_probs=49.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....++|||+|||+.+++++|+.+|+.||.|.+|.|+.++ +|+++|||||+|.
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~  137 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFE  137 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeC
Confidence            3456799999999999999999999999999999999997 9999999999995

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.07  E-value=1.8e-10  Score=90.25  Aligned_cols=46  Identities=15%  Similarity=0.245  Sum_probs=42.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....++|||||||+++++++|+.+|++||.|.+|.++        +|||||+|.
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~   73 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFE   73 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEEC
Confidence            3556799999999999999999999999999999988        699999995

>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=99.06  E-value=2.4e-08  Score=84.75  Aligned_cols=167  Identities=10%  Similarity=-0.022  Sum_probs=132.9

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~  101 (442)
                      ....|...+......|+++.+..+|++++...|.+..+|...+..+.. .++.+.+...|++++...|....+|...+..
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            455677777777888999999999999999999999999888876664 4566779999999999999988888887764


Q ss_pred             HHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhh
Q 013489          102 LERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGL  181 (442)
Q Consensus       102 le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~  181 (442)
                      +.. .+..+.+...|++++...+.                                                       .
T Consensus        86 ~~~-~~~~~~A~~~~~~~~~~~~~-------------------------------------------------------~  109 (186)
T 3as5_A           86 YVQ-VQKYDLAVPLLIKVAEANPI-------------------------------------------------------N  109 (186)
T ss_dssp             HHH-HTCHHHHHHHHHHHHHHCTT-------------------------------------------------------C
T ss_pred             HHH-hcCHHHHHHHHHHHHhcCcH-------------------------------------------------------h
Confidence            443 56667777777766543221                                                       2


Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      ..+|...+.+....| +++.|..+|++++...|+...+|...+.+....|+++.|..+|++++..
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            234555666667777 8999999999999999988889999999998999999999999999863

>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=99.06  E-value=3.4e-10  Score=84.47  Aligned_cols=47  Identities=17%  Similarity=0.290  Sum_probs=42.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||..+++++|+.+|++||.|.+|+++.+      +|||||+|.
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~   56 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFA   56 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEES
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEEC
Confidence            34569999999999999999999999999999999874      699999995

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.05  E-value=1.3e-10  Score=85.27  Aligned_cols=45  Identities=18%  Similarity=0.158  Sum_probs=41.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...||||||++.+++++|+.+|.+||+|.+++++.      +||||||+|.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~   51 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYT   51 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEES
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEEC
Confidence            44899999999999999999999999999999865      6899999995

>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=99.05  E-value=2.2e-10  Score=99.64  Aligned_cols=50  Identities=14%  Similarity=0.305  Sum_probs=47.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||+++++++|+.+|++||.|.+|+|+++ .+|+++|||||+|.
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~-~~~~~kG~aFVeF~  158 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFD  158 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEEC-TTCCEEEEEEEEES
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEEC-CCCCcccEEEEEEC
Confidence            469999999999999999999999999999999998 47999999999995

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.04  E-value=8.4e-11  Score=91.00  Aligned_cols=46  Identities=24%  Similarity=0.229  Sum_probs=42.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||||||.++++++|+.+|+.||.|.+|+++      +++|||||+|.
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~   71 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYD   71 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECS
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEEC
Confidence            45799999999999999999999999999999987      45799999995

>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=99.03  E-value=3.5e-10  Score=86.66  Aligned_cols=45  Identities=27%  Similarity=0.360  Sum_probs=41.2

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINL-KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||||||+ ++++++|+.+|+.||.|.+|++.        +|||||+|.
T Consensus        20 ~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~   65 (97)
T 2xnq_A           20 HMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFD   65 (97)
T ss_dssp             CTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEES
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEEC
Confidence            4567999999998 99999999999999999999883        799999995

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.03  E-value=3.9e-10  Score=87.37  Aligned_cols=50  Identities=24%  Similarity=0.262  Sum_probs=44.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|+.|+   .|.++.++.+|+++|||||+|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~   62 (102)
T 2fc8_A           13 QPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFN   62 (102)
T ss_dssp             CCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECS
T ss_pred             CCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEEC
Confidence            4457999999999999999999999774   7888888889999999999995

>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=99.03  E-value=6.8e-08  Score=85.81  Aligned_cols=197  Identities=8%  Similarity=-0.046  Sum_probs=124.6

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCC-CCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFP-VSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p-~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~  100 (442)
                      +.+.|...+......|+++.+...|+++|...| .+...|...+.... ..++.+.+...|++|+...|....+|.....
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~-~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~   84 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCAD-NIKKYKEAADYFDIAIKKNYNLANAYIGKSA   84 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHTTCSHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHH-HhhcHHHHHHHHHHHHHhCcchHHHHHHHHH
Confidence            346788888888889999999999999999998 88888888665544 4566788999999999999999999999877


Q ss_pred             HHHHccCCHHHHHHHHHHHHhCChhhHHHHH---HHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcC
Q 013489          101 SLERSRASEEEISTVFEKSLLCAFSTFEEYL---DLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKN  177 (442)
Q Consensus       101 ~le~~~~~~~~~~~i~~~al~~~~~~~~~~~---~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~  177 (442)
                      .+. ..++.+.+...|++++...+.......   ..+....                 .+......+++|+.++..++..
T Consensus        85 ~~~-~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g-----------------~~~~~~~~~~~A~~~~~~al~~  146 (228)
T 4i17_A           85 AYR-DMKNNQEYIATLTEGIKAVPGNATIEKLYAIYYLKEG-----------------QKFQQAGNIEKAEENYKHATDV  146 (228)
T ss_dssp             HHH-HTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHH-----------------HHHHHTTCHHHHHHHHHHHTTS
T ss_pred             HHH-HcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHh-----------------HHHHHhccHHHHHHHHHHHHhc
Confidence            554 478899999999999987665332111   1111100                 0001112234444544444444


Q ss_pred             chh--hHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          178 TDG--LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       178 ~~~--~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      .+.  ....|...+.+....      +..+++++....+.....+.  .......+.++.|...|++++.
T Consensus       147 ~p~~~~~~~~~~l~~~~~~~------~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~~~~A~~~~~~a~~  208 (228)
T 4i17_A          147 TSKKWKTDALYSLGVLFYNN------GADVLRKATPLASSNKEKYA--SEKAKADAAFKKAVDYLGEAVT  208 (228)
T ss_dssp             SCHHHHHHHHHHHHHHHHHH------HHHHHHHHGGGTTTCHHHHH--HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcccHHHHHHHHHHHHHH------HHHHHHHHHhcccCCHHHHH--HHHHHHHHHHHHHHHHHHHHhh
Confidence            444  445555555544332      23344444444332222111  1122334556788888888886

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.03  E-value=2.7e-08  Score=85.12  Aligned_cols=156  Identities=11%  Similarity=0.030  Sum_probs=126.6

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      +|...|+.+|..+|.    +...|...+......|+++.+...|++++...|.+...|.......... ++.+.+...+.
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            467889999988876    7889999999999999999999999999999999999999998877644 45677999999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRE  162 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~  162 (442)
                      +++...|....+|......+.. .+..+++...|++++...+                                      
T Consensus        98 ~a~~~~~~~~~~~~~lg~~~~~-~g~~~~A~~~~~~~l~~~p--------------------------------------  138 (184)
T 3vtx_A           98 RAIALNTVYADAYYKLGLVYDS-MGEHDKAIEAYEKTISIKP--------------------------------------  138 (184)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCT--------------------------------------
T ss_pred             HHHHhCccchHHHHHHHHHHHH-hCCchhHHHHHHHHHHhcc--------------------------------------
Confidence            9999999999999887764443 6777777777777665332                                      


Q ss_pred             HHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHH
Q 013489          163 TFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAW  220 (442)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w  220 (442)
                                       ....+|...+.+....| +++.|...|+++++.+|+++..+
T Consensus       139 -----------------~~~~~~~~lg~~~~~~g-~~~~A~~~~~~al~~~p~~a~~~  178 (184)
T 3vtx_A          139 -----------------GFIRAYQSIGLAYEGKG-LRDEAVKYFKKALEKEEKKAKYE  178 (184)
T ss_dssp             -----------------TCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHTTHHHHHHC
T ss_pred             -----------------hhhhHHHHHHHHHHHCC-CHHHHHHHHHHHHhCCccCHHHH
Confidence                             22335666677777788 89999999999999999876543

>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=99.02  E-value=3e-10  Score=111.28  Aligned_cols=52  Identities=29%  Similarity=0.329  Sum_probs=49.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+.+|+++|..+|+.||.|..|.|+.++.+|+++|||||+|.
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~  152 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYE  152 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeec
Confidence            3569999999999999999999999999999999999889999999999996

>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=99.02  E-value=5.8e-10  Score=87.34  Aligned_cols=46  Identities=15%  Similarity=0.284  Sum_probs=42.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++++++|+.+|++||.|..|.|+.+       |||||+|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~   58 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFV   58 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEEC
Confidence            44679999999999999999999999999999999886       89999996

>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=99.02  E-value=4.9e-10  Score=88.85  Aligned_cols=48  Identities=21%  Similarity=0.368  Sum_probs=43.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||+.+++++|+.+|+.||.|.+|.++.+   ++++|||||+|.
T Consensus         8 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~   55 (115)
T 3lqv_A            8 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYE   55 (115)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEES
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEEC
Confidence            469999999999999999999999999999999875   456999999995

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.01  E-value=5.4e-10  Score=85.68  Aligned_cols=47  Identities=21%  Similarity=0.328  Sum_probs=41.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+.+++++|+.+|+.||.|. ++++.    ++++|||||+|.
T Consensus        18 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~   64 (97)
T 2e5j_A           18 LAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYP   64 (97)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECS
T ss_pred             CCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEEC
Confidence            356999999999999999999999999996 66665    368899999995

>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=99.01  E-value=6.8e-10  Score=85.44  Aligned_cols=47  Identities=21%  Similarity=0.304  Sum_probs=42.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+.+++++|+.+|++||.|.+|+++.+      +|||||+|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~   59 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLE   59 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEEC
Confidence            34579999999999999999999999999999998854      699999995

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.01  E-value=5.7e-08  Score=90.59  Aligned_cols=122  Identities=11%  Similarity=0.038  Sum_probs=75.9

Q ss_pred             HHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH------HHHHHHHHHHHHhc
Q 013489          157 YSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM------LEAWQSYISMEIEL  230 (442)
Q Consensus       157 ~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~------~~~w~~~~~~e~~~  230 (442)
                      +......+++++...... ........++...+.+....| +++.|..++++++...+..      ..++...+.+....
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            334444455555443321 112223457777888888888 8999999999999875443      55778888888889


Q ss_pred             ccHHHHHHHHHHHHhcccCCCChHH---HHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          231 DHINEARSIYKRCYSKRFTGTGSED---ICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       231 g~~~~ar~i~~ral~~~~~~~~~~~---i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                      |+++.|...|++++...-....+..   ++..........|+.+.-....+++
T Consensus       277 g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  329 (338)
T 3ro2_A          277 QDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKH  329 (338)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHH
Confidence            9999999999999864211122222   3334444455556655544444443

>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=99.01  E-value=1.4e-10  Score=89.04  Aligned_cols=49  Identities=24%  Similarity=0.352  Sum_probs=44.5

Q ss_pred             CCceEEEcCCCCCCCHHHHH----HHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLR----RFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~----~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+++++++|+    .+|++||.|.+|.++.   +|+++|||||+|.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~   59 (97)
T 1nu4_A            7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFK   59 (97)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeC
Confidence            35699999999999999999    9999999999998873   6888999999995

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.01  E-value=4.4e-08  Score=94.99  Aligned_cols=258  Identities=12%  Similarity=-0.000  Sum_probs=139.7

Q ss_pred             HhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHH----HHHHHHHHHHHhcchhhHHHHHHHHHHHcC------CC
Q 013489           21 EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSD----LWLDYTQYLDKTLKVGNVVRDVYSRATKNC------PW   90 (442)
Q Consensus        21 ~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~----lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~------p~   90 (442)
                      .....+...+......|+++.+..+|++++...|.+..    +|...+..+.. .++.+.+...|++|+..+      |.
T Consensus        46 ~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~lg~~~~~-~g~~~~A~~~~~~al~~~~~~~~~~~  124 (411)
T 4a1s_A           46 SMCLELALEGERLCNAGDCRAGVAFFQAAIQAGTEDLRTLSAIYSQLGNAYFY-LGDYNKAMQYHKHDLTLAKSMNDRLG  124 (411)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHH-HTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHccCchH
Confidence            34455556666666677777777777777777777663    45444444432 234556777777777652      33


Q ss_pred             cHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCC------hhhHHHHHH---H-----------------------HHHHH
Q 013489           91 VGELWVRSLLSLERSRASEEEISTVFEKSLLCA------FSTFEEYLD---L-----------------------FLTRI  138 (442)
Q Consensus        91 s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~------~~~~~~~~~---~-----------------------~~~~~  138 (442)
                      ...+|......+ ...+..+.+...|++++...      +.....+..   +                       +...+
T Consensus       125 ~~~~~~~l~~~~-~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~  203 (411)
T 4a1s_A          125 EAKSSGNLGNTL-KVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAV  203 (411)
T ss_dssp             HHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH-HHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHH
Confidence            344555544433 33566677777777766431      111111110   0                       10001


Q ss_pred             HHHHHHhhcc---Cc--------------cchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHH
Q 013489          139 DGLRRRILFS---GE--------------VEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVS  201 (442)
Q Consensus       139 ~~l~rr~~~~---~~--------------~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~  201 (442)
                      .++.+-+...   ..              .....++......|++++...... ........++...+.++...| +++.
T Consensus       204 ~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~-~~~~~~~~~~~~la~~~~~~g-~~~~  281 (411)
T 4a1s_A          204 EFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREF-GDRAAERRANSNLGNSHIFLG-QFED  281 (411)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHHHTTT-CHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhc-CCcHHHHHHHHHHHHHHHHCc-CHHH
Confidence            1110000000   00              000122333333444444433221 111222346777888888888 9999


Q ss_pred             HHHHHHHHHHhchhH------HHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChH---HHHHHHHHHHHHhCCHhh
Q 013489          202 ARGVWERLLKISGAM------LEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSE---DICHAWLRFEREYGTLED  272 (442)
Q Consensus       202 ar~i~~~~l~~~~~~------~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~---~i~~~~~~fE~~~G~~~~  272 (442)
                      |...|++++...+..      ..+|...+.+....|+++.|..+|++++...-....+.   .++..........|+.+.
T Consensus       282 A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~  361 (411)
T 4a1s_A          282 AAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHER  361 (411)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHH
Confidence            999999999885532      56788888888889999999999999986421111222   234444455556677655


Q ss_pred             HHHHHHhhch
Q 013489          273 FDHSVQKVTP  282 (442)
Q Consensus       273 ~~~~~~~~~~  282 (442)
                      -.....++..
T Consensus       362 A~~~~~~al~  371 (411)
T 4a1s_A          362 ALKYAEQHLQ  371 (411)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            5545544433

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.00  E-value=2.9e-08  Score=90.35  Aligned_cols=205  Identities=12%  Similarity=0.028  Sum_probs=140.7

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      +|...|+.++...|.    +...|...+......|+++.+..+|++++..+|.+..+|...+..+.. .++.+.+...|+
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            467789999988775    677899999999999999999999999999999999999999987764 456678999999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRE  162 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~  162 (442)
                      +++...|.....+..... .. ..++.+.+...|.+++...+.....+. +..    ..    ...      .+.     
T Consensus       136 ~a~~~~~~~~~~~~~~~~-~~-~~~~~~~A~~~~~~~~~~~~~~~~~~~-~~~----~~----~~~------~~~-----  193 (275)
T 1xnf_A          136 AFYQDDPNDPFRSLWLYL-AE-QKLDEKQAKEVLKQHFEKSDKEQWGWN-IVE----FY----LGN------ISE-----  193 (275)
T ss_dssp             HHHHHCTTCHHHHHHHHH-HH-HHHCHHHHHHHHHHHHHHSCCCSTHHH-HHH----HH----TTS------SCH-----
T ss_pred             HHHHhCCCChHHHHHHHH-HH-HhcCHHHHHHHHHHHHhcCCcchHHHH-HHH----HH----HHh------cCH-----
Confidence            999999988754443332 22 247788999999988865444211111 000    00    000      111     


Q ss_pred             HHHHHHHHHhhhhcCch----hhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHH
Q 013489          163 TFQRASDYLSEQMKNTD----GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARS  238 (442)
Q Consensus       163 ~~~~a~~~l~~~~~~~~----~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~  238 (442)
                        +.|+..+...+...+    ....+|...+.++...| +++.|...|++++..+|++..   .+.......|+++.|..
T Consensus       194 --~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~al~~~p~~~~---~~~~~~~~l~~~~~a~~  267 (275)
T 1xnf_A          194 --QTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLG-DLDSATALFKLAVANNVHNFV---EHRYALLELSLLGQDQD  267 (275)
T ss_dssp             --HHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHTTCCTTCH---HHHHHHHHHHHHHHC--
T ss_pred             --HHHHHHHHHHhcccccccccccHHHHHHHHHHHHcC-CHHHHHHHHHHHHhCCchhHH---HHHHHHHHHHHHHhhHH
Confidence              223333333332222    23568888999999999 999999999999999886543   33444445566666665


Q ss_pred             HH
Q 013489          239 IY  240 (442)
Q Consensus       239 i~  240 (442)
                      .|
T Consensus       268 ~~  269 (275)
T 1xnf_A          268 DL  269 (275)
T ss_dssp             --
T ss_pred             HH
Confidence            55

>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=98.99  E-value=6.1e-10  Score=97.17  Aligned_cols=52  Identities=23%  Similarity=0.374  Sum_probs=49.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+++++++|+++|+.||.|..|+++.++.+|+++|||||+|.
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~  154 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD  154 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEEC
Confidence            3479999999999999999999999999999999999889999999999996

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=98.99  E-value=8.8e-10  Score=93.25  Aligned_cols=53  Identities=28%  Similarity=0.339  Sum_probs=50.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|++||.|.++.++.++.+|+++|||||+|.
T Consensus        85 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~  137 (166)
T 3md3_A           85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFT  137 (166)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeC
Confidence            44679999999999999999999999999999999999889999999999995

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.99  E-value=1.9e-10  Score=88.04  Aligned_cols=48  Identities=19%  Similarity=0.284  Sum_probs=42.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|+.||.|..+     ..+|+++|||||+|.
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~   61 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFK   61 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEEC
Confidence            456799999999999999999999999987665     368999999999995

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.98  E-value=9.2e-10  Score=83.08  Aligned_cols=45  Identities=20%  Similarity=0.286  Sum_probs=41.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+.+|++||.|.+|+++        +|||||+|.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~   50 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIE   50 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEES
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEEC
Confidence            345799999999999999999999999999999987        589999995

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=98.97  E-value=6.3e-10  Score=92.75  Aligned_cols=48  Identities=15%  Similarity=0.294  Sum_probs=44.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||||||+++++++|+.+|++||.|.+|+++.+     ++|||||+|.
T Consensus        71 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~  118 (150)
T 2i2y_A           71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFE  118 (150)
T ss_dssp             TTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEEC
Confidence            45679999999999999999999999999999999887     5899999995

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=98.97  E-value=1.3e-07  Score=87.50  Aligned_cols=213  Identities=10%  Similarity=0.045  Sum_probs=145.1

Q ss_pred             ChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHh--------cCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcC--
Q 013489           19 DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAIT--------DFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNC--   88 (442)
Q Consensus        19 ~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~--------~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~--   88 (442)
                      ++.....|...+......|+++.+..+|++++.        ..|....+|...+..+.. .+..+.+...|++++...  
T Consensus        23 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~-~g~~~~A~~~~~~al~~~~~  101 (311)
T 3nf1_A           23 IPARLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRD-QNKYKDAANLLNDALAIREK  101 (311)
T ss_dssp             SCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence            566788899999988999999999999999998        356667777777776554 456677999999999864  


Q ss_pred             ------CCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCC-----hhhHHHHHHHHHHHHHHHHHHhhccCccchhhhH
Q 013489           89 ------PWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA-----FSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDY  157 (442)
Q Consensus        89 ------p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~-----~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~  157 (442)
                            |....+|..... +....++.+.+...|++++...     ..... ....+......+ ..         ..++
T Consensus       102 ~~~~~~~~~~~~~~~l~~-~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~-~~~~~~~la~~~-~~---------~~~~  169 (311)
T 3nf1_A          102 TLGKDHPAVAATLNNLAV-LYGKRGKYKEAEPLCKRALEIREKVLGKDHPD-VAKQLNNLALLC-QN---------QGKY  169 (311)
T ss_dssp             HHCTTCHHHHHHHHHHHH-HHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHH-HHHHHHHHHHHH-HT---------TTCH
T ss_pred             HhCCCChHHHHHHHHHHH-HHHHcCcHHHHHHHHHHHHHHHHHhcCCCChH-HHHHHHHHHHHH-HH---------cCCH
Confidence                  444456666555 4445788999999999998642     11111 111111111011 01         1345


Q ss_pred             HHHHHHHHHHHHHHhhhhcC-chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-----------------------
Q 013489          158 SLIRETFQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS-----------------------  213 (442)
Q Consensus       158 ~~~r~~~~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~-----------------------  213 (442)
                      ......|++++......... .+....++...+.+....| +++.|..+|++++...                       
T Consensus       170 ~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~  248 (311)
T 3nf1_A          170 EEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQG-KFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEERE  248 (311)
T ss_dssp             HHHHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHH
Confidence            56667777777765544322 3445678888899999999 9999999999999753                       


Q ss_pred             --------------------------hhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          214 --------------------------GAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       214 --------------------------~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                                                |....+|...+.+....|+++.|..+|++|+.
T Consensus       249 ~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          249 ECKGKQKDGTSFGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             HC-------CCSCCCC---------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HhcCchhhHHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                                      44445666666666666777777777777664

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=98.97  E-value=3.9e-10  Score=88.30  Aligned_cols=48  Identities=6%  Similarity=0.067  Sum_probs=42.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVG-GVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+++++++|+++|++|| .|..+.++.+    +++|||||+|.
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~   75 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFP   75 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEEC
Confidence            357999999999999999999999999 8999988643    48999999995

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=98.97  E-value=1.2e-07  Score=91.27  Aligned_cols=123  Identities=11%  Similarity=0.035  Sum_probs=79.1

Q ss_pred             HHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH------HHHHHHHHHHHHhc
Q 013489          157 YSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM------LEAWQSYISMEIEL  230 (442)
Q Consensus       157 ~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~------~~~w~~~~~~e~~~  230 (442)
                      +......|++++...... ........++...+.+....| +++.|..+|++++...+..      ..+|...+.+....
T Consensus       203 ~~~A~~~~~~al~~~~~~-~~~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~  280 (406)
T 3sf4_A          203 FRDAVIAHEQRLLIAKEF-GDKAAERRAYSNLGNAYIFLG-EFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLL  280 (406)
T ss_dssp             HHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHhc-CCcHHHHHHHHHHHHHHHHcC-ChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHh
Confidence            334444555555544321 112223457777888888888 9999999999999885543      56788888888899


Q ss_pred             ccHHHHHHHHHHHHhcccCCCChHH---HHHHHHHHHHHhCCHhhHHHHHHhhc
Q 013489          231 DHINEARSIYKRCYSKRFTGTGSED---ICHAWLRFEREYGTLEDFDHSVQKVT  281 (442)
Q Consensus       231 g~~~~ar~i~~ral~~~~~~~~~~~---i~~~~~~fE~~~G~~~~~~~~~~~~~  281 (442)
                      |+++.|...|++++...-....+..   ++......-...|+.+.-.....++.
T Consensus       281 g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  334 (406)
T 3sf4_A          281 QDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHL  334 (406)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            9999999999999864212222222   33344444455677655544444443

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.97  E-value=1.6e-09  Score=82.92  Aligned_cols=46  Identities=13%  Similarity=0.238  Sum_probs=42.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+++++++|+.+|++||.|.+|.++.+      +|||||+|.
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~   61 (97)
T 1why_A           16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYE   61 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEEC
Confidence            3469999999999999999999999999999998764      689999995

>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=98.96  E-value=1.1e-09  Score=93.40  Aligned_cols=51  Identities=14%  Similarity=0.260  Sum_probs=49.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||+.+++++|+++|++||.|.+++++.++.+|+++|||||+|.
T Consensus        94 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~  144 (172)
T 2g4b_A           94 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV  144 (172)
T ss_dssp             TTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEES
T ss_pred             CCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeC
Confidence            579999999999999999999999999999999999889999999999995

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=98.96  E-value=3.8e-07  Score=88.31  Aligned_cols=210  Identities=11%  Similarity=0.012  Sum_probs=123.2

Q ss_pred             cchhhHHHHHHHHHHHcCCCcH----HHHHHHHHHHHHccCCHHHHHHHHHHHHhC------ChhhHHHHHHHHHH----
Q 013489           71 LKVGNVVRDVYSRATKNCPWVG----ELWVRSLLSLERSRASEEEISTVFEKSLLC------AFSTFEEYLDLFLT----  136 (442)
Q Consensus        71 ~~~~~~~~~v~erAl~~~p~s~----~lW~~y~~~le~~~~~~~~~~~i~~~al~~------~~~~~~~~~~~~~~----  136 (442)
                      .++.+.+...|++|+...|...    .+|......+. ..++.+.+...|++++..      .+.....+..+-..    
T Consensus        61 ~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~lg~~~~-~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~  139 (411)
T 4a1s_A           61 AGDCRAGVAFFQAAIQAGTEDLRTLSAIYSQLGNAYF-YLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNLGNTLKVM  139 (411)
T ss_dssp             TTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHH-HHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             hCcHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHH-HCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHC
Confidence            3566789999999999999875    35666555333 468899999999998864      12111111111110    


Q ss_pred             -----HHHHHHHHhhc----cC---ccc---hhhhHHHHHHH-----------------HHHHHHHHhhhhc------Cc
Q 013489          137 -----RIDGLRRRILF----SG---EVE---GVLDYSLIRET-----------------FQRASDYLSEQMK------NT  178 (442)
Q Consensus       137 -----~~~~l~rr~~~----~~---~~~---~~~~~~~~r~~-----------------~~~a~~~l~~~~~------~~  178 (442)
                           ...++.+-+..    ..   ...   ....+......                 ++.|+.++..++.      ..
T Consensus       140 g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~  219 (411)
T 4a1s_A          140 GRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLMRDLGDR  219 (411)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTCH
T ss_pred             CCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHcCCH
Confidence                 01111100000    00   000   00011111222                 5555555544332      12


Q ss_pred             hhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHH------HHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCC
Q 013489          179 DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAML------EAWQSYISMEIELDHINEARSIYKRCYSKRFTGTG  252 (442)
Q Consensus       179 ~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~------~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~  252 (442)
                      +....++...+.+....| +++.|...|++++...+...      .+|...+.+....|+++.|...|++++...-....
T Consensus       220 ~~~~~~~~~la~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~  298 (411)
T 4a1s_A          220 GAQGRACGNLGNTYYLLG-DFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGE  298 (411)
T ss_dssp             HHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHcC-ChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCC
Confidence            334457777888888888 99999999999999865432      37888888888999999999999999974211122


Q ss_pred             h---HHHHHHHHHHHHHhCCHhhHHHHHHhhch
Q 013489          253 S---EDICHAWLRFEREYGTLEDFDHSVQKVTP  282 (442)
Q Consensus       253 ~---~~i~~~~~~fE~~~G~~~~~~~~~~~~~~  282 (442)
                      +   ..++..........|+.+.-...++++..
T Consensus       299 ~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  331 (411)
T 4a1s_A          299 REVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLA  331 (411)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            2   23444445555666776665555555443

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=98.95  E-value=5.5e-10  Score=86.33  Aligned_cols=45  Identities=18%  Similarity=0.241  Sum_probs=42.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ++|||+|||+++++++|+.+|++||.|.+|.++.+     ++|||||+|.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~   45 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFE   45 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEEC
Confidence            48999999999999999999999999999999887     7899999995

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=98.95  E-value=8.5e-10  Score=97.83  Aligned_cols=51  Identities=20%  Similarity=0.270  Sum_probs=47.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||+++++++|+.+|+.||.|.+|+++.++.+|+++|||||+|.
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~   78 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYE   78 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEES
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeC
Confidence            469999999999999999999999999999999999889999999999995

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=98.94  E-value=2.9e-09  Score=92.94  Aligned_cols=53  Identities=13%  Similarity=0.253  Sum_probs=50.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|++||.|.+|+++.++.+|+++|||||+|.
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~  164 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV  164 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEEC
Confidence            45679999999999999999999999999999999999889999999999995

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=98.93  E-value=2.8e-09  Score=83.72  Aligned_cols=45  Identities=20%  Similarity=0.327  Sum_probs=41.2

Q ss_pred             CCCceEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLK-ATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+. +++++|+.+|++||.|.+|.+        ++|||||+|.
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~   70 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYS   70 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECS
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEEC
Confidence            34579999999999 999999999999999999988        5799999995

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.93  E-value=5.7e-10  Score=87.77  Aligned_cols=46  Identities=9%  Similarity=0.187  Sum_probs=42.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +.++|||+|||+.+++++|+.+|++||.|.+|.|+.      ++|||||+|.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~   54 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFL   54 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeC
Confidence            456999999999999999999999999999998874      5799999995

>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=98.93  E-value=6.4e-10  Score=94.34  Aligned_cols=51  Identities=25%  Similarity=0.376  Sum_probs=48.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||+.+++++|+++|++||.|.+++++.++.+|+++|||||+|.
T Consensus        87 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~  137 (167)
T 2cjk_A           87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYD  137 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEES
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEEC
Confidence            358999999999999999999999999999999999889999999999995

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.93  E-value=2.5e-09  Score=81.34  Aligned_cols=47  Identities=21%  Similarity=0.235  Sum_probs=41.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||||||+++++++|+.+|+.||.|.+|  +.++.+|+   ||||+|.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~   53 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMG   53 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEEC
Confidence            34699999999999999999999999999987  66666776   9999995

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.93  E-value=1.1e-09  Score=85.90  Aligned_cols=46  Identities=22%  Similarity=0.377  Sum_probs=42.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||..+++++|+.+|+.||.|.+|+|+.+      +|||||+|.
T Consensus        24 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~   69 (109)
T 1x4g_A           24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFS   69 (109)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEES
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEEC
Confidence            4569999999999999999999999999999999886      799999995

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=98.91  E-value=1.7e-09  Score=82.72  Aligned_cols=45  Identities=27%  Similarity=0.380  Sum_probs=40.6

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINL-KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+ .+++++|+.+|++||.|.+|.+.        +|||||+|.
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~   53 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFD   53 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEES
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEEC
Confidence            3456999999999 99999999999999999999984        699999995

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.91  E-value=2.4e-09  Score=81.08  Aligned_cols=45  Identities=20%  Similarity=0.194  Sum_probs=40.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|++||.|.+|.+++        |||||+|.
T Consensus         8 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~   52 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHME   52 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEEC
Confidence            4457999999999999999999999999999999873        49999995

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=98.91  E-value=2.4e-10  Score=94.52  Aligned_cols=53  Identities=19%  Similarity=0.236  Sum_probs=43.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEE--EeeC---CCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIR--ILHD---KFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~--~~~~---~~~g~~~g~~fv~f~  441 (442)
                      ...++|||||||+.+++++|+.+|+.||.|..+.  ++.+   ..+|+++|||||+|.
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~  100 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLP  100 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeC
Confidence            3456999999999999999999999999988751  1111   258999999999995

>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=98.91  E-value=4.1e-07  Score=80.62  Aligned_cols=190  Identities=8%  Similarity=-0.017  Sum_probs=131.9

Q ss_pred             hhhHHHHHHhhcCC-CCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHH
Q 013489            3 NARAHLEEQISRQD-LSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVY   81 (442)
Q Consensus         3 ~~r~~yE~~l~~~~-~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~   81 (442)
                      +|...|+.+|...| .    +...|...+......|+++.+...|++++..+|.+..+|...+..+.. .++.+.+...|
T Consensus        25 ~A~~~~~~al~~~~~~----~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~-~~~~~~A~~~~   99 (228)
T 4i17_A           25 VAFEKYSEYLKLTNNQ----DSVTAYNCGVCADNIKKYKEAADYFDIAIKKNYNLANAYIGKSAAYRD-MKNNQEYIATL   99 (228)
T ss_dssp             HHHHHHHHHHHHTTTC----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCSHHHHHHHHHHHHHH-TTCHHHHHHHH
T ss_pred             HHHHHHHHHHhccCCC----CcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCcchHHHHHHHHHHHHH-cccHHHHHHHH
Confidence            46778899998876 4    455676677777889999999999999999999999999999987764 45667899999


Q ss_pred             HHHHHcCCCcHHH-------HHHHHHHHHHccCCHHHHHHHHHHHHhCChh--hHHHHHHHHHHHHHHHHHHhhccCccc
Q 013489           82 SRATKNCPWVGEL-------WVRSLLSLERSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRILFSGEVE  152 (442)
Q Consensus        82 erAl~~~p~s~~l-------W~~y~~~le~~~~~~~~~~~i~~~al~~~~~--~~~~~~~~~~~~~~~l~rr~~~~~~~~  152 (442)
                      ++++...|.+..+       |..... +....+..+.+...|++++...+.  ....+..+-..+..             
T Consensus       100 ~~al~~~p~~~~~~~~~~~~~~~~g~-~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~-------------  165 (228)
T 4i17_A          100 TEGIKAVPGNATIEKLYAIYYLKEGQ-KFQQAGNIEKAEENYKHATDVTSKKWKTDALYSLGVLFYN-------------  165 (228)
T ss_dssp             HHHHHHSTTCHHHHHHHHHHHHHHHH-HHHHTTCHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHHHH-------------
T ss_pred             HHHHHHCCCcHHHHHHHHHHHHHHhH-HHHHhccHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHH-------------
Confidence            9999999998844       555444 334468899999999999998776  44444333322210             


Q ss_pred             hhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHH
Q 013489          153 GVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISME  227 (442)
Q Consensus       153 ~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e  227 (442)
                            .-...++++.....       ..  ...+........+ .++.|...|+++++..|++..++.....+.
T Consensus       166 ------~~~~~~~~a~~~~~-------~~--~~~~~~~~~~~~~-~~~~A~~~~~~a~~l~p~~~~~~~~l~~i~  224 (228)
T 4i17_A          166 ------NGADVLRKATPLAS-------SN--KEKYASEKAKADA-AFKKAVDYLGEAVTLSPNRTEIKQMQDQVK  224 (228)
T ss_dssp             ------HHHHHHHHHGGGTT-------TC--HHHHHHHHHHHHH-HHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             ------HHHHHHHHHHhccc-------CC--HHHHHHHHHHHHH-HHHHHHHHHHHHhhcCCCCHHHHHHHHHHH
Confidence                  00112233322211       11  1112222333444 688999999999999999887766555543

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=98.90  E-value=7.4e-10  Score=87.75  Aligned_cols=46  Identities=15%  Similarity=0.284  Sum_probs=41.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++++++|+++|++||.|.+|.|+.+       |||||+|.
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~   59 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFV   59 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEEC
Confidence            34679999999999999999999999999999999876       89999996

>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=98.90  E-value=2.8e-09  Score=90.41  Aligned_cols=52  Identities=27%  Similarity=0.455  Sum_probs=49.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||..+++++|+.+|++||.|..++++.++.+|+++|||||+|.
T Consensus        88 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~  139 (168)
T 1b7f_A           88 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYN  139 (168)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEEC
Confidence            4569999999999999999999999999999999999889999999999995

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=98.90  E-value=1.1e-06  Score=81.82  Aligned_cols=253  Identities=10%  Similarity=-0.061  Sum_probs=152.9

Q ss_pred             HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCH----HHHHHHHHHHHHhcchhhHHHHHHHHHHHcC------CCcH
Q 013489           23 FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS----DLWLDYTQYLDKTLKVGNVVRDVYSRATKNC------PWVG   92 (442)
Q Consensus        23 ~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~----~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~------p~s~   92 (442)
                      ...|...+......|+++.+..+|++++...|.++    .+|...+.... ..++.+.+...|++|+...      |...
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            34566666666788999999999999999999985    45555555444 3456678999999998763      2234


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh--hHHHHHHHHHHHHHHHHHHhhc---c-C-------ccchhhhHHH
Q 013489           93 ELWVRSLLSLERSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRILF---S-G-------EVEGVLDYSL  159 (442)
Q Consensus        93 ~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~--~~~~~~~~~~~~~~~l~rr~~~---~-~-------~~~~~~~~~~  159 (442)
                      .+|......+ ...+..+.+...|++++.....  ........+.... .+......   . .       ..+....+..
T Consensus        84 ~~~~~l~~~~-~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~  161 (338)
T 3ro2_A           84 KASGNLGNTL-KVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLG-NVYHAKGKSFGCPGPQDTGEFPEDVRNALQA  161 (338)
T ss_dssp             HHHHHHHHHH-HHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHHHHHHHTSSSSSCC----CCHHHHHHHHH
T ss_pred             HHHHHHHHHH-HHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHH-HHHHHcCcccccchhhhhhhhhhhHHHHHHH
Confidence            5666655533 3468899999999999864322  1111111111111 11001100   0 0       0000011333


Q ss_pred             HHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH------HHHHHHHHHHHHhcccH
Q 013489          160 IRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM------LEAWQSYISMEIELDHI  233 (442)
Q Consensus       160 ~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~------~~~w~~~~~~e~~~g~~  233 (442)
                      ....+++++...... ...+....++...+.+....| +++.|..++++++...+..      ..+|...+.+....|++
T Consensus       162 A~~~~~~a~~~~~~~-~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  239 (338)
T 3ro2_A          162 AVDLYEENLSLVTAL-GDRAAQGRAFGNLGNTHYLLG-NFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEF  239 (338)
T ss_dssp             HHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHHHHHHHHHhc-CCHHHHHHHHHHHHHHHHHhC-CHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCH
Confidence            344444444443222 122334557777888888889 9999999999999874432      23788888888889999


Q ss_pred             HHHHHHHHHHHhcccCCCChHH---HHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          234 NEARSIYKRCYSKRFTGTGSED---ICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       234 ~~ar~i~~ral~~~~~~~~~~~---i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                      +.|..+|++++........+..   ++..........|+.+.-...+.++
T Consensus       240 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  289 (338)
T 3ro2_A          240 ETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKH  289 (338)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            9999999999864222222322   3334444555567766554444444

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=98.89  E-value=1.8e-07  Score=92.48  Aligned_cols=191  Identities=15%  Similarity=0.068  Sum_probs=128.7

Q ss_pred             HhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHH--hcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHH---ccCC
Q 013489           34 QSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDK--TLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER---SRAS  108 (442)
Q Consensus        34 ~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~--~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~---~~~~  108 (442)
                      ...+++++|...|+++|..+|.++..|..+......  ..+..+.+...|++|+...|....+|..+...+..   ..+.
T Consensus       149 ~~~~~y~~A~~~~~kal~~~p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~p~~~~~~~~l~~~~~~~~~~~~~  228 (472)
T 4g1t_A          149 CGGNQNERAKVCFEKALEKKPKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLNPDNQYLKVLLALKLHKMREEGEE  228 (472)
T ss_dssp             HCTTHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHCSSCHHHHHHHHHHHHHCC-----
T ss_pred             HccccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHhhhhH
Confidence            344678999999999999999999999988765442  22344568899999999999998888776543332   2345


Q ss_pred             HHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHH
Q 013489          109 EEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYW  188 (442)
Q Consensus       109 ~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~  188 (442)
                      .+.+..+|++++...+.....+..+-..+.     ..         .++......|++|+..       .|....++...
T Consensus       229 ~~~a~~~~~~al~~~~~~~~~~~~lg~~~~-----~~---------~~~~~A~~~~~~al~~-------~p~~~~~~~~l  287 (472)
T 4g1t_A          229 EGEGEKLVEEALEKAPGVTDVLRSAAKFYR-----RK---------DEPDKAIELLKKALEY-------IPNNAYLHCQI  287 (472)
T ss_dssp             -CHHHHHHHHHHHHCSSCHHHHHHHHHHHH-----HT---------TCHHHHHHHHHHHHHH-------STTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCccHHHHHHHHHHHHH-----Hc---------CchHHHHHHHHHHHHh-------CCChHHHHHHH
Confidence            678999999999876664443332221111     11         2333333444444432       33333333333


Q ss_pred             HHHHH-------------------HcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          189 AHLEQ-------------------SMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       189 a~~e~-------------------~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      +.++.                   ... ..+.|...|++++..+|.....|...+.+....|+++.|..+|++++..
T Consensus       288 g~~y~~~~~~~~~~~~~~~~~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~  363 (472)
T 4g1t_A          288 GCCYRAKVFQVMNLRENGMYGKRKLLE-LIGHAVAHLKKADEANDNLFRVCSILASLHALADQYEEAEYYFQKEFSK  363 (472)
T ss_dssp             HHHHHHHHHHHHHC------CHHHHHH-HHHHHHHHHHHHHHHCTTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHh-hHHHHHHHHHHHhhcCCchhhhhhhHHHHHHHhccHHHHHHHHHHHHhc
Confidence            32221                   112 3568888999999999999999999999999999999999999999974

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.89  E-value=2.1e-09  Score=81.11  Aligned_cols=45  Identities=18%  Similarity=0.259  Sum_probs=40.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++++++|+.+|++||.|.+|+++.        |||||+|.
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~   51 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHME   51 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEEC
Confidence            3456999999999999999999999999999999873        49999996

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.88  E-value=1.4e-09  Score=84.92  Aligned_cols=45  Identities=9%  Similarity=0.121  Sum_probs=40.2

Q ss_pred             CceEEE--cCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFL--SNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v--~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..+|||  ||||+++++++|+++|++||.|.+|.|+.+      ||||||+|.
T Consensus        25 t~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~   71 (114)
T 2cq2_A           25 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYR   71 (114)
T ss_dssp             CSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEES
T ss_pred             CCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEEC
Confidence            458999  779999999999999999999999987642      799999995

>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=98.88  E-value=2.5e-09  Score=90.48  Aligned_cols=52  Identities=29%  Similarity=0.422  Sum_probs=49.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||..+++++|+.+|++||.|.+++++.++.+|+++|||||+|.
T Consensus        87 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~  138 (167)
T 1fxl_A           87 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFD  138 (167)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeC
Confidence            3468999999999999999999999999999999999889999999999995

>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=98.88  E-value=1.9e-09  Score=92.12  Aligned_cols=51  Identities=31%  Similarity=0.431  Sum_probs=47.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+.+++++|+++|++||.|.+++++.+ .+|+++|||||+|.
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~-~~g~~~g~afV~f~  144 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFT  144 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC-TTSCEEEEEEEEES
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEEC-CCCCEEEEEEEEEC
Confidence            4569999999999999999999999999999999999 47999999999995

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=98.87  E-value=2.9e-09  Score=94.34  Aligned_cols=51  Identities=18%  Similarity=0.292  Sum_probs=48.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||..+++++|+++|+.||.|.+|+++.++.+|+++|||||+|.
T Consensus       125 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~  175 (216)
T 2qfj_A          125 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYE  175 (216)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEec
Confidence            459999999999999999999999999999999999889999999999995

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.86  E-value=6.4e-09  Score=79.92  Aligned_cols=45  Identities=16%  Similarity=0.313  Sum_probs=40.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccC--CCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDV--GGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~--G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|++|  |.|.+|.++        +|||||+|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~   59 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFS   59 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEES
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeC
Confidence            345799999999999999999999999  899988764        579999995

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=98.86  E-value=1e-06  Score=84.68  Aligned_cols=255  Identities=9%  Similarity=-0.063  Sum_probs=154.0

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCH----HHHHHHHHHHHHhcchhhHHHHHHHHHHHcC------CCc
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS----DLWLDYTQYLDKTLKVGNVVRDVYSRATKNC------PWV   91 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~----~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~------p~s   91 (442)
                      ....|...+......|+++.+..+|++++...|.++    .+|...+.... ..++.+.+...|++|+...      |..
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            344666777777889999999999999999999885    45666665544 3456678999999998763      223


Q ss_pred             HHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh--hHHHHHHHHHH--HHHHHHHHh---hccCccc-----hhhhHHH
Q 013489           92 GELWVRSLLSLERSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLT--RIDGLRRRI---LFSGEVE-----GVLDYSL  159 (442)
Q Consensus        92 ~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~--~~~~~~~~~~~--~~~~l~rr~---~~~~~~~-----~~~~~~~  159 (442)
                      ..+|...... ....++.+.+...|++++.....  ........+..  .+-...-+.   .....+.     ....+..
T Consensus        87 ~~~~~~la~~-~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~  165 (406)
T 3sf4_A           87 AKASGNLGNT-LKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQA  165 (406)
T ss_dssp             HHHHHHHHHH-HHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHH
T ss_pred             HHHHHHHHHH-HHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHH
Confidence            3456555543 33468899999999999864332  11111111111  110010000   0000000     0011333


Q ss_pred             HHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH------HHHHHHHHHHHHhcccH
Q 013489          160 IRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM------LEAWQSYISMEIELDHI  233 (442)
Q Consensus       160 ~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~------~~~w~~~~~~e~~~g~~  233 (442)
                      ....+.+++.+.... ...+....++...+.+....| +++.|...|++++...+..      ..+|...+.+....|++
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            444445555443322 122334567788888988899 9999999999999884432      23788888888889999


Q ss_pred             HHHHHHHHHHHhcccCCCChHH---HHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          234 NEARSIYKRCYSKRFTGTGSED---ICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       234 ~~ar~i~~ral~~~~~~~~~~~---i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                      +.|..+|++++...-....+..   ++..........|+.+.-...+.++
T Consensus       244 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  293 (406)
T 3sf4_A          244 ETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKH  293 (406)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHH
Confidence            9999999999964212222222   3333344445556665544444443

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=98.85  E-value=2.2e-09  Score=80.57  Aligned_cols=46  Identities=4%  Similarity=0.122  Sum_probs=41.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|++| .|.++++.      +++|||||+|.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~   48 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLL   48 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEEC
Confidence            345799999999999999999999999 99999884      57899999995

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=98.85  E-value=3.4e-09  Score=82.12  Aligned_cols=44  Identities=20%  Similarity=0.237  Sum_probs=40.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+++++++|+.+|++||.|.+|+++        +|||||+|.
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~   53 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFD   53 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeC
Confidence            35699999999999999999999999999999886        469999995

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=98.84  E-value=2.6e-09  Score=79.93  Aligned_cols=47  Identities=21%  Similarity=0.298  Sum_probs=42.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccC----C-------CeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDV----G-------GVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~----G-------~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++++++|+.+|++|    |       .|.+++++.+      +|||||+|.
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~   61 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFR   61 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcC
Confidence            345799999999999999999999999    8       8999988765      799999995

>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=98.84  E-value=1.8e-08  Score=85.93  Aligned_cols=165  Identities=13%  Similarity=0.059  Sum_probs=117.4

Q ss_pred             HHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHH
Q 013489           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLE  103 (442)
Q Consensus        24 ~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le  103 (442)
                      +.+...+......|+++.+..+|++++..+|.++..|..++..+... +..+.+...|++++...| ...++........
T Consensus         7 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~-g~~~~A~~~~~~a~~~~p-~~~~~~~~~~~~~   84 (176)
T 2r5s_A            7 EQLLKQVSELLQQGEHAQALNVIQTLSDELQSRGDVKLAKADCLLET-KQFELAQELLATIPLEYQ-DNSYKSLIAKLEL   84 (176)
T ss_dssp             TTHHHHHHHHHHTTCHHHHHHHHHTSCHHHHTSHHHHHHHHHHHHHT-TCHHHHHHHHTTCCGGGC-CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHC-CCHHHHHHHHHHhhhccC-ChHHHHHHHHHHH
Confidence            34556666666788999999999999999999999999888877644 456778888998888888 5544332211000


Q ss_pred             HccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHH
Q 013489          104 RSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLR  183 (442)
Q Consensus       104 ~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~  183 (442)
                      ........+.                                                ..|++++..       .|....
T Consensus        85 ~~~~~~~~a~------------------------------------------------~~~~~al~~-------~P~~~~  109 (176)
T 2r5s_A           85 HQQAAESPEL------------------------------------------------KRLEQELAA-------NPDNFE  109 (176)
T ss_dssp             HHHHTSCHHH------------------------------------------------HHHHHHHHH-------STTCHH
T ss_pred             HhhcccchHH------------------------------------------------HHHHHHHHh-------CCCCHH
Confidence            0000000011                                                223333332       344556


Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH--HHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          184 LYAYWAHLEQSMGKDMVSARGVWERLLKISGAM--LEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~--~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      .+..++.+....| +++.|...|++++...|+.  ...|..++.+....|+.+.|...|.+++..
T Consensus       110 ~~~~la~~~~~~g-~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~~al~~  173 (176)
T 2r5s_A          110 LACELAVQYNQVG-RDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYRRQLYS  173 (176)
T ss_dssp             HHHHHHHHHHHTT-CHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcc-cHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHHHHHHH
Confidence            7888888888888 9999999999999998875  558999999999999999999999999863

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.84  E-value=1.1e-06  Score=79.60  Aligned_cols=186  Identities=11%  Similarity=-0.032  Sum_probs=130.0

Q ss_pred             HhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCC---HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCc---HHH
Q 013489           21 EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVS---SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV---GEL   94 (442)
Q Consensus        21 ~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~---~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s---~~l   94 (442)
                      .+.+.+...+......|+++.+..+|++++..+|.+   ...|...+..+.. .++.+.+...|++++...|.+   ...
T Consensus        13 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~-~~~~~~A~~~~~~~l~~~p~~~~~~~a   91 (261)
T 3qky_A           13 SSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYGRTHEWAADAQFYLARAYYQ-NKEYLLAASEYERFIQIYQIDPRVPQA   91 (261)
T ss_dssp             SSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGCSCSTTHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCTTHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHH-hCcHHHHHHHHHHHHHHCCCCchhHHH
Confidence            356677777777788999999999999999999998   7788777766554 456678999999999998854   344


Q ss_pred             HHHHHHHHHH-------ccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHH
Q 013489           95 WVRSLLSLER-------SRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRA  167 (442)
Q Consensus        95 W~~y~~~le~-------~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a  167 (442)
                      |......+..       ..+..+.+...|++++...|........  ..++                          ...
T Consensus        92 ~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a--~~~~--------------------------~~~  143 (261)
T 3qky_A           92 EYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRYPNHELVDDA--TQKI--------------------------REL  143 (261)
T ss_dssp             HHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCTTCTTHHHH--HHHH--------------------------HHH
T ss_pred             HHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHCcCchhHHHH--HHHH--------------------------HHH
Confidence            4444443322       0466788888999988755542110000  0000                          000


Q ss_pred             HHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchh---HHHHHHHHHHHHHhc----------ccHH
Q 013489          168 SDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA---MLEAWQSYISMEIEL----------DHIN  234 (442)
Q Consensus       168 ~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~---~~~~w~~~~~~e~~~----------g~~~  234 (442)
                      ..          .....+...+.+....| +++.|...|++++..+|+   ....|...+......          |+++
T Consensus       144 ~~----------~~~~~~~~la~~~~~~g-~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~  212 (261)
T 3qky_A          144 RA----------KLARKQYEAARLYERRE-LYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYR  212 (261)
T ss_dssp             HH----------HHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHH
T ss_pred             HH----------HHHHHHHHHHHHHHHcc-CHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHH
Confidence            00          01113455677777888 999999999999999887   456777777766554          8899


Q ss_pred             HHHHHHHHHHhc
Q 013489          235 EARSIYKRCYSK  246 (442)
Q Consensus       235 ~ar~i~~ral~~  246 (442)
                      .|...|++++..
T Consensus       213 ~A~~~~~~~~~~  224 (261)
T 3qky_A          213 RAVELYERLLQI  224 (261)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999999973

>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=98.82  E-value=2.5e-06  Score=77.81  Aligned_cols=198  Identities=12%  Similarity=-0.003  Sum_probs=136.5

Q ss_pred             hHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh---cchhhHHHHHHHHHHHcCCCcHHHHH
Q 013489           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKT---LKVGNVVRDVYSRATKNCPWVGELWV   96 (442)
Q Consensus        20 ~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~---~~~~~~~~~v~erAl~~~p~s~~lW~   96 (442)
                      +++...|..........|+++.+...|++++.  |.++..|......+...   .++.+.+...|++|+..-  ....|.
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            34677888888888889999999999999999  77888888887766640   456678999999999864  566777


Q ss_pred             HHHHHHHH---ccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhh
Q 013489           97 RSLLSLER---SRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSE  173 (442)
Q Consensus        97 ~y~~~le~---~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~  173 (442)
                      .....+..   ..++.+.+...|++++..+..  ..+..+-..+.     .-   ...  ..++......|++|+.    
T Consensus        79 ~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~--~a~~~lg~~~~-----~~---~~~--~~~~~~A~~~~~~a~~----  142 (273)
T 1ouv_A           79 LLGNLYYSGQGVSQNTNKALQYYSKACDLKYA--EGCASLGGIYH-----DG---KVV--TRDFKKAVEYFTKACD----  142 (273)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCH--HHHHHHHHHHH-----HC---SSS--CCCHHHHHHHHHHHHH----
T ss_pred             HHHHHHhCCCCcccCHHHHHHHHHHHHHcCCc--cHHHHHHHHHH-----cC---CCc--ccCHHHHHHHHHHHHh----
Confidence            65553332   157889999999999987532  22222221111     10   000  1233344444555444    


Q ss_pred             hhcCchhhHHHHHHHHHHHHH----cCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHh----cccHHHHHHHHHHHHh
Q 013489          174 QMKNTDGLLRLYAYWAHLEQS----MGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE----LDHINEARSIYKRCYS  245 (442)
Q Consensus       174 ~~~~~~~~~~l~~~~a~~e~~----~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~----~g~~~~ar~i~~ral~  245 (442)
                         ..+  ...+..++.+...    .+ +++.|...|++++...  +...+..+..+...    .++++.|...|++++.
T Consensus       143 ---~~~--~~a~~~lg~~~~~~~~~~~-~~~~A~~~~~~a~~~~--~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~  214 (273)
T 1ouv_A          143 ---LND--GDGCTILGSLYDAGRGTPK-DLKKALASYDKACDLK--DSPGCFNAGNMYHHGEGATKNFKEALARYSKACE  214 (273)
T ss_dssp             ---TTC--HHHHHHHHHHHHHTSSSCC-CHHHHHHHHHHHHHTT--CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHH
T ss_pred             ---cCc--HHHHHHHHHHHHcCCCCCC-CHHHHHHHHHHHHHCC--CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHh
Confidence               222  3356666777666    66 9999999999999873  35667777777777    8899999999999997

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.82  E-value=4.6e-07  Score=84.36  Aligned_cols=104  Identities=13%  Similarity=0.074  Sum_probs=56.7

Q ss_pred             hHHHHHHHHHHHHhcCCh-hhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc-chhhHHHHHHHHHHHcCCCcHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDP-GRVQLLYERAITDFPVSSDLWLDYTQYLDKTL-KVGNVVRDVYSRATKNCPWVGELWVRSL   99 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~-~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~-~~~~~~~~v~erAl~~~p~s~~lW~~y~   99 (442)
                      .+..-+.|+.-....|.. +++..+++.+|..+|.+..+|..-...+.... ...+.....++.++...|.+..+|....
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            344444444444444433 46666666666666666666666555554333 2445566666666666666666666655


Q ss_pred             HHH----HHcc--CCHHHHHHHHHHHHhCChh
Q 013489          100 LSL----ERSR--ASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus       100 ~~l----e~~~--~~~~~~~~i~~~al~~~~~  125 (442)
                      ..+    ....  +..++....+++++...+.
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            544    2211  3344455566666655444

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=98.81  E-value=4.7e-09  Score=87.23  Aligned_cols=48  Identities=19%  Similarity=0.225  Sum_probs=42.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...+|||+||++.+++++|+.+|++||.|.+|.|+.+    +++|||||+|.
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~   92 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYA   92 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEES
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEEC
Confidence            3458999999999999999999999999999998754    25799999995

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.81  E-value=1.1e-08  Score=78.30  Aligned_cols=45  Identities=20%  Similarity=0.181  Sum_probs=39.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+||  ++++++|+.+|++||.|.+|.|.      +++|||||+|.
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~   57 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYE   57 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEES
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEEC
Confidence            34579999996  89999999999999999999884      56899999995

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.81  E-value=3.9e-09  Score=80.63  Aligned_cols=48  Identities=21%  Similarity=0.171  Sum_probs=42.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEE-EeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIR-ILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~-~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+++++++|+.+|++||.|.+|+ ++.++.+|+    |||+|.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~----afV~f~   62 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYS   62 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEES
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEEC
Confidence            456999999999999999999999999999995 888865554    999995

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.79  E-value=2.6e-09  Score=81.08  Aligned_cols=45  Identities=20%  Similarity=0.245  Sum_probs=38.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCC-eeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGG-VSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~-i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+++++++|+.+|++||. |..+.+.       ++|||||+|.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~   52 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYP   52 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEEC
Confidence            4569999999999999999999999999 6666552       4799999995

>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=98.79  E-value=7.1e-07  Score=81.01  Aligned_cols=162  Identities=12%  Similarity=0.073  Sum_probs=109.1

Q ss_pred             HhcCChhhHHHHHHHHHhc--------CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcC--------CCcHHHHHH
Q 013489           34 QSSGDPGRVQLLYERAITD--------FPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNC--------PWVGELWVR   97 (442)
Q Consensus        34 ~~~g~~~~~~~lyERal~~--------~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~--------p~s~~lW~~   97 (442)
                      ...|+++.+..+|++|+..        .|....+|...+..+.. .+..+.+...|++|+...        |....+|..
T Consensus        12 ~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~   90 (283)
T 3edt_B           12 SGLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRD-QNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNN   90 (283)
T ss_dssp             -CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHH-cccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHH
Confidence            3467888999999999873        35556677777766554 456677999999999864        444566776


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHhCC--------hhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHH
Q 013489           98 SLLSLERSRASEEEISTVFEKSLLCA--------FSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASD  169 (442)
Q Consensus        98 y~~~le~~~~~~~~~~~i~~~al~~~--------~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~  169 (442)
                      ... +....++.+.+...|++++...        +.....+..+-..+     ..         ..++......|++++.
T Consensus        91 l~~-~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~-----~~---------~g~~~~A~~~~~~al~  155 (283)
T 3edt_B           91 LAV-LYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLC-----QN---------QGKAEEVEYYYRRALE  155 (283)
T ss_dssp             HHH-HHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-----HT---------TTCHHHHHHHHHHHHH
T ss_pred             HHH-HHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHH-----HH---------cCCHHHHHHHHHHHHH
Confidence            665 4445788999999999998641        21112121111111     01         1345566677777777


Q ss_pred             HHhhhhcC-chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh
Q 013489          170 YLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI  212 (442)
Q Consensus       170 ~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~  212 (442)
                      ........ .+....++...+.+....| +++.|..+|++++..
T Consensus       156 ~~~~~~~~~~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~~l~~  198 (283)
T 3edt_B          156 IYATRLGPDDPNVAKTKNNLASCYLKQG-KYQDAETLYKEILTR  198 (283)
T ss_dssp             HHHHHSCTTCHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHH
T ss_pred             HHHHhcCCCCHHHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHH
Confidence            65544332 3445678888999999999 999999999999986

>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=98.77  E-value=7.9e-09  Score=94.51  Aligned_cols=50  Identities=18%  Similarity=0.177  Sum_probs=47.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..+|||+|||+.+++++|+.+|+.||.|.+|.++.+ .+|+++|||||+|.
T Consensus        96 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~  145 (261)
T 3sde_A           96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFA  145 (261)
T ss_dssp             SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEES
T ss_pred             CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeC
Confidence            459999999999999999999999999999999999 69999999999996

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.76  E-value=1.1e-06  Score=77.11  Aligned_cols=171  Identities=8%  Similarity=-0.032  Sum_probs=113.6

Q ss_pred             HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHH----------------HHHHHHHhcchhhHHHHHHHHHHH
Q 013489           23 FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLD----------------YTQYLDKTLKVGNVVRDVYSRATK   86 (442)
Q Consensus        23 ~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~----------------Y~~~l~~~~~~~~~~~~v~erAl~   86 (442)
                      .+.+..-+......|+++.+...|+++|..+|.++..|..                .+..+. ..+..+.+...|++|+.
T Consensus         4 ~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~-~~g~~~~A~~~~~~al~   82 (208)
T 3urz_A            4 VDEMLQKVSAAIEAGQNGQAVSYFRQTIALNIDRTEMYYWTNVDKNSEISSKLATELALAYK-KNRNYDKAYLFYKELLQ   82 (208)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHhhhcchhhhhHHHHHHHHHHHH-HCCCHHHHHHHHHHHHH
Confidence            3455555555667899999999999999999999999887                665554 34567889999999999


Q ss_pred             cCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHH
Q 013489           87 NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQR  166 (442)
Q Consensus        87 ~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~  166 (442)
                      ..|.+...|......+. ..+..+.+...|++++...|.....+..+-..+...-                   ......
T Consensus        83 ~~p~~~~~~~~lg~~~~-~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~-------------------~~~~~~  142 (208)
T 3urz_A           83 KAPNNVDCLEACAEMQV-CRGQEKDALRMYEKILQLEADNLAANIFLGNYYYLTA-------------------EQEKKK  142 (208)
T ss_dssp             HCTTCHHHHHHHHHHHH-HHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-------------------HHHHHH
T ss_pred             HCCCCHHHHHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHh-------------------HHHHHH
Confidence            99999999999877554 4788999999999999888776554443332221000                   011112


Q ss_pred             HHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH
Q 013489          167 ASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM  216 (442)
Q Consensus       167 a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~  216 (442)
                      +...+.......+... .|..........+ +++.|...|+++++.+|+.
T Consensus       143 ~~~~~~~~~~~~~~~~-a~~~~g~~~~~~~-~~~~A~~~~~~al~l~P~~  190 (208)
T 3urz_A          143 LETDYKKLSSPTKMQY-ARYRDGLSKLFTT-RYEKARNSLQKVILRFPST  190 (208)
T ss_dssp             HHHHHC---CCCHHHH-HHHHHHHHHHHHH-THHHHHHHHHHHTTTSCCH
T ss_pred             HHHHHHHHhCCCchhH-HHHHHHHHHHHcc-CHHHHHHHHHHHHHhCCCH
Confidence            2222222222222211 2222233334455 7888999999999888874

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=98.75  E-value=1.2e-08  Score=81.63  Aligned_cols=47  Identities=19%  Similarity=0.216  Sum_probs=41.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcce-EEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVV-QSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~-~fv~f~  441 (442)
                      .-..|||+||++.+++++|+.+|++||.|.+|.++.+     ++|| |||+|.
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~   74 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYA   74 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEES
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEEC
Confidence            3458999999999999999999999999999988764     3688 999995

>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=98.74  E-value=1.2e-08  Score=94.39  Aligned_cols=51  Identities=14%  Similarity=0.195  Sum_probs=48.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||+.+++++|+.+|+.||.|.+++++.++.+|+++|||||+|.
T Consensus        95 ~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~  145 (284)
T 3smz_A           95 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYM  145 (284)
T ss_dssp             SCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEEC
Confidence            369999999999999999999999999999999999889999999999995

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.73  E-value=2.7e-07  Score=85.39  Aligned_cols=168  Identities=15%  Similarity=0.016  Sum_probs=105.1

Q ss_pred             CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHH
Q 013489           54 PVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDL  133 (442)
Q Consensus        54 p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~  133 (442)
                      |.+.+.++..+..+... ++.+.+...|++++...|.....|......+. ..+..+++..+|++++...+......+..
T Consensus       114 p~~~~~~~~~a~~~~~~-g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~-~~g~~~~A~~~l~~~~~~~p~~~~~~~~~  191 (287)
T 3qou_A          114 PREEELXAQQAMQLMQE-SNYTDALPLLXDAWQLSNQNGEIGLLLAETLI-ALNRSEDAEAVLXTIPLQDQDTRYQGLVA  191 (287)
T ss_dssp             CCHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHTTSCHHHHHHHHHHHH-HTTCHHHHHHHHTTSCGGGCSHHHHHHHH
T ss_pred             CCchhhHHHHHHHHHhC-CCHHHHHHHHHHHHHhCCcchhHHHHHHHHHH-HCCCHHHHHHHHHhCchhhcchHHHHHHH
Confidence            55556665555544432 34455666777777766766666666665333 35666666666666665443311111110


Q ss_pred             HHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc
Q 013489          134 FLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS  213 (442)
Q Consensus       134 ~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~  213 (442)
                      .   +.... .                 .....|+..+...+...|....++..++.++...| +++.|...|.+++..+
T Consensus       192 ~---~~l~~-~-----------------~~~~~a~~~l~~al~~~P~~~~~~~~la~~l~~~g-~~~~A~~~l~~~l~~~  249 (287)
T 3qou_A          192 Q---IELLX-Q-----------------AADTPEIQQLQQQVAENPEDAALATQLALQLHQVG-RNEEALELLFGHLRXD  249 (287)
T ss_dssp             H---HHHHH-H-----------------HTSCHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHC
T ss_pred             H---HHHHh-h-----------------cccCccHHHHHHHHhcCCccHHHHHHHHHHHHHcc-cHHHHHHHHHHHHhcc
Confidence            0   00000 0                 00111222222222234556678888898888888 8999999999999999


Q ss_pred             hhH--HHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          214 GAM--LEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       214 ~~~--~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      |++  ...|..++.+....|+.+.|...|.+++.
T Consensus       250 p~~~~~~a~~~l~~~~~~~g~~~~a~~~~r~al~  283 (287)
T 3qou_A          250 LTAADGQTRXTFQEILAALGTGDALASXYRRQLY  283 (287)
T ss_dssp             TTGGGGHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             cccccchHHHHHHHHHHHcCCCCcHHHHHHHHHH
Confidence            887  78999999999999999999999999886

>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=98.73  E-value=1.4e-08  Score=94.03  Aligned_cols=50  Identities=24%  Similarity=0.351  Sum_probs=45.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHH----HHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLR----RFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~----~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++++++|+    .+|+.||.|.+|+++.   +|+++|||||+|.
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~   60 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFK   60 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEEC
Confidence            346799999999999999977    8999999999998875   7889999999996

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.73  E-value=3.1e-08  Score=78.80  Aligned_cols=45  Identities=18%  Similarity=0.093  Sum_probs=39.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcce-EEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVV-QSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~-~fv~f~  441 (442)
                      ...|||+|||+.+++++|+.+|++||.|.+|+|+..      .|| |||+|.
T Consensus        25 vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~   70 (124)
T 2e5i_A           25 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFE   70 (124)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEES
T ss_pred             EEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEEC
Confidence            346899999999999999999999999999998652      286 999995

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=98.72  E-value=1e-08  Score=90.76  Aligned_cols=48  Identities=19%  Similarity=0.272  Sum_probs=44.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+|||+|||+.+++++|+.+|+.||.|.+|+|+.|+  +.++|||||+|.
T Consensus       104 ~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~  151 (213)
T 4f02_A          104 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFE  151 (213)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEES
T ss_pred             ccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeC
Confidence            489999999999999999999999999999999983  457999999995

>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=98.72  E-value=8.9e-08  Score=99.88  Aligned_cols=174  Identities=14%  Similarity=0.009  Sum_probs=126.4

Q ss_pred             HhcCChhhHHHHHHHHH--------hcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHc
Q 013489           34 QSSGDPGRVQLLYERAI--------TDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERS  105 (442)
Q Consensus        34 ~~~g~~~~~~~lyERal--------~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~  105 (442)
                      ...|+++.+...|++++        ..+|.+...|...+..+... +..+.+...|++|+...|....+|......+. .
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~-g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~-~  479 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDL-GDVAKATRKLDDLAERVGWRWRLVWYRAVAEL-L  479 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH-H
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhc-CCHHHHHHHHHHHhccCcchHHHHHHHHHHHH-H
Confidence            56789999999999999        88999999999988766644 45677999999999999999999998776444 4


Q ss_pred             cCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHH
Q 013489          106 RASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLY  185 (442)
Q Consensus       106 ~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~  185 (442)
                      .++.+++...|++|+...+.....+..+-..+.     ..         .++.. ...|++|+..       .+.....|
T Consensus       480 ~g~~~~A~~~~~~al~l~P~~~~~~~~lg~~~~-----~~---------g~~~~-~~~~~~al~~-------~P~~~~a~  537 (681)
T 2pzi_A          480 TGDYDSATKHFTEVLDTFPGELAPKLALAATAE-----LA---------GNTDE-HKFYQTVWST-------NDGVISAA  537 (681)
T ss_dssp             HTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHH-----HH---------TCCCT-TCHHHHHHHH-------CTTCHHHH
T ss_pred             cCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHH-----Hc---------CChHH-HHHHHHHHHh-------CCchHHHH
Confidence            688999999999999877764443332222111     11         12222 3455555553       34455678


Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhccc
Q 013489          186 AYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDH  232 (442)
Q Consensus       186 ~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~  232 (442)
                      ...+.+....| +++.|...|++++...|++...|...+......|.
T Consensus       538 ~~lg~~~~~~g-~~~~A~~~~~~al~l~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          538 FGLARARSAEG-DRVGAVRTLDEVPPTSRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HHHHHHHHHTT-CHHHHHHHHHTSCTTSTTHHHHHHHHHHHTC----
T ss_pred             HHHHHHHHHcC-CHHHHHHHHHhhcccCcccHHHHHHHHHHHHccCC
Confidence            88888888888 88889999999888888888888777776654443

>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=98.71  E-value=8.3e-07  Score=74.97  Aligned_cols=151  Identities=13%  Similarity=0.040  Sum_probs=114.6

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (442)
                      +...|+.++...|.    +...|...+......|+++.+..+|++++...|.+..+|...+..+... ++.+.+...|++
T Consensus        27 A~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~-~~~~~A~~~~~~  101 (186)
T 3as5_A           27 AVMLLEQVYDADAF----DVDVALHLGIAYVKTGAVDRGTELLERSLADAPDNVKVATVLGLTYVQV-QKYDLAVPLLIK  101 (186)
T ss_dssp             HHHHHTTTCCTTSC----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCcc----ChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHh-cCHHHHHHHHHH
Confidence            44555555555543    6778888888888899999999999999999999999999998877644 456779999999


Q ss_pred             HHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHH
Q 013489           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRET  163 (442)
Q Consensus        84 Al~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~  163 (442)
                      ++...|....+|...+..+.. .++.+.+...|++++...+.                                      
T Consensus       102 ~~~~~~~~~~~~~~~a~~~~~-~~~~~~A~~~~~~~~~~~~~--------------------------------------  142 (186)
T 3as5_A          102 VAEANPINFNVRFRLGVALDN-LGRFDEAIDSFKIALGLRPN--------------------------------------  142 (186)
T ss_dssp             HHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTT--------------------------------------
T ss_pred             HHhcCcHhHHHHHHHHHHHHH-cCcHHHHHHHHHHHHhcCcc--------------------------------------
Confidence            999999998888887764443 57777777777776643222                                      


Q ss_pred             HHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH
Q 013489          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM  216 (442)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~  216 (442)
                                       ...++...+.+....| +++.|..+|++++...|++
T Consensus       143 -----------------~~~~~~~la~~~~~~~-~~~~A~~~~~~~~~~~~~~  177 (186)
T 3as5_A          143 -----------------EGKVHRAIAFSYEQMG-RHEEALPHFKKANELDEGA  177 (186)
T ss_dssp             -----------------CHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHCC
T ss_pred             -----------------chHHHHHHHHHHHHcC-CHHHHHHHHHHHHHcCCCc
Confidence                             1234555666666777 8888888888888876653

>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=98.71  E-value=8.8e-07  Score=92.46  Aligned_cols=169  Identities=14%  Similarity=0.169  Sum_probs=126.7

Q ss_pred             cCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHH
Q 013489           52 DFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYL  131 (442)
Q Consensus        52 ~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~  131 (442)
                      .+|.+.+.|......+... +..+.+...|++|+...|.....|......+.. .+..+++...|++|+...+.      
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 SCPTHADSLNNLANIKREQ-GNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQ-QGKLQEALMHYKEAIRISPT------   75 (723)
T ss_dssp             --CHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTT------
T ss_pred             CCCCcHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHhCCC------
Confidence            4677788888887766644 455778888888888888888888887664443 57777777777776654332      


Q ss_pred             HHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 013489          132 DLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLK  211 (442)
Q Consensus       132 ~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~  211 (442)
                                                                       ....|...+.+....| +++.|.+.|+++++
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                                                             2335555666667788 99999999999999


Q ss_pred             hchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhhc
Q 013489          212 ISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVT  281 (442)
Q Consensus       212 ~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~~  281 (442)
                      .+|++...|...+......|+++.|...|++|+.  +.++.+ ..+......-...|+.++...+.+++.
T Consensus       106 l~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~--l~P~~~-~a~~~L~~~l~~~g~~~~A~~~~~kal  172 (723)
T 4gyw_A          106 INPAFADAHSNLASIHKDSGNIPEAIASYRTALK--LKPDFP-DAYCNLAHCLQIVCDWTDYDERMKKLV  172 (723)
T ss_dssp             HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCSCCH-HHHHHHHHHHHHTTCCTTHHHHHHHHH
T ss_pred             hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--hCCCCh-HHHhhhhhHHHhcccHHHHHHHHHHHH
Confidence            9999999999999999999999999999999997  455555 455566666667787766655555543

>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=98.71  E-value=1.1e-08  Score=95.25  Aligned_cols=53  Identities=8%  Similarity=0.139  Sum_probs=44.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          387 GFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       387 ~~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...+.++|||+|||+++++++|+.+|+.||.|.+|+|+.++ .| ++|||||+|.
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~-~~g~afV~f~   89 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL-KK-NFRFARIEFA   89 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECT-TS-SSEEEEEEES
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CC-CcEEEEEEEC
Confidence            34567899999999999999999999999999999999985 33 5899999996

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=98.69  E-value=3e-06  Score=78.49  Aligned_cols=187  Identities=12%  Similarity=-0.010  Sum_probs=130.1

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (442)
                      +...|+..|....  +|++...|...+......|+++.+..+|++     |.+...|...+..+... +..+.+...|++
T Consensus        84 A~~~l~~ll~~~~--~P~~~~~~~~la~~~~~~g~~~~Al~~l~~-----~~~~~~~~~l~~~~~~~-g~~~~A~~~l~~  155 (291)
T 3mkr_A           84 IVAELDREMSRSV--DVTNTTFLLMAASIYFYDQNPDAALRTLHQ-----GDSLECMAMTVQILLKL-DRLDLARKELKK  155 (291)
T ss_dssp             HHHHHHHHHHSCC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHTT-----CCSHHHHHHHHHHHHHT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHhccc--CCCCHHHHHHHHHHHHHCCCHHHHHHHHhC-----CCCHHHHHHHHHHHHHC-CCHHHHHHHHHH
Confidence            4567777776531  123677888888888899999999999998     89999999988877644 456789999999


Q ss_pred             HHHcCCCcHHHH--HHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHH
Q 013489           84 ATKNCPWVGELW--VRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIR  161 (442)
Q Consensus        84 Al~~~p~s~~lW--~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r  161 (442)
                      ++...|......  ..|+. +....+..+++..+|++++...+.....+..+-..+.     +.         .++....
T Consensus       156 ~~~~~p~~~~~~l~~a~~~-l~~~~~~~~eA~~~~~~~l~~~p~~~~~~~~la~~~~-----~~---------g~~~eA~  220 (291)
T 3mkr_A          156 MQDQDEDATLTQLATAWVS-LAAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHM-----AQ---------GRWEAAE  220 (291)
T ss_dssp             HHHHCTTCHHHHHHHHHHH-HHHCTTHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHH-----HT---------TCHHHHH
T ss_pred             HHhhCcCcHHHHHHHHHHH-HHhCchHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH-----Hc---------CCHHHHH
Confidence            999999875322  22333 2233577899999999999876654443332222111     11         2333334


Q ss_pred             HHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHH
Q 013489          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAW  220 (442)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w  220 (442)
                      ..|++++.       ..+.....|...+.+....|+..+.+..++++++..+|+++.+.
T Consensus       221 ~~l~~al~-------~~p~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~~P~~~~~~  272 (291)
T 3mkr_A          221 GVLQEALD-------KDSGHPETLINLVVLSQHLGKPPEVTNRYLSQLKDAHRSHPFIK  272 (291)
T ss_dssp             HHHHHHHH-------HCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             HHHHHHHH-------hCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhCCCChHHH
Confidence            44444444       35566678888888888889555568899999999999987643

>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=1.4e-05  Score=72.62  Aligned_cols=210  Identities=10%  Similarity=-0.081  Sum_probs=144.2

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHh----cCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh---cchhh
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQS----SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKT---LKVGN   75 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~----~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~---~~~~~   75 (442)
                      ++...|+.++.  +.    +...|.........    .++++.+...|++++...  ++..|......+...   .++.+
T Consensus        24 ~A~~~~~~a~~--~~----~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~--~~~a~~~lg~~~~~g~~~~~~~~   95 (273)
T 1ouv_A           24 QAKKYFEKACD--LK----ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN--YSNGCHLLGNLYYSGQGVSQNTN   95 (273)
T ss_dssp             HHHHHHHHHHH--TT----CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT--CHHHHHHHHHHHHHTSSSCCCHH
T ss_pred             HHHHHHHHHHH--CC----CHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC--CHHHHHHHHHHHhCCCCcccCHH
Confidence            35567777776  22    45577777777777    899999999999999875  788888887766541   45667


Q ss_pred             HHHHHHHHHHHcCCCcHHHHHHHHHHHHHc---cCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccc
Q 013489           76 VVRDVYSRATKNCPWVGELWVRSLLSLERS---RASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVE  152 (442)
Q Consensus        76 ~~~~v~erAl~~~p~s~~lW~~y~~~le~~---~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~  152 (442)
                      .+...|++|+..  .....|......+...   .++.+.+...|++++..+....  +..+-..+.     .-   ... 
T Consensus        96 ~A~~~~~~a~~~--~~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~a--~~~lg~~~~-----~~---~~~-  162 (273)
T 1ouv_A           96 KALQYYSKACDL--KYAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLNDGDG--CTILGSLYD-----AG---RGT-  162 (273)
T ss_dssp             HHHHHHHHHHHT--TCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTTCHHH--HHHHHHHHH-----HT---SSS-
T ss_pred             HHHHHHHHHHHc--CCccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcCcHHH--HHHHHHHHH-----cC---CCC-
Confidence            899999999986  3566777766544431   5788999999999998764322  222111111     00   000 


Q ss_pred             hhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHH----cCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHH
Q 013489          153 GVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQS----MGKDMVSARGVWERLLKISGAMLEAWQSYISMEI  228 (442)
Q Consensus       153 ~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~----~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~  228 (442)
                       ..++......|++++.       ..+  ...+...+.+...    .+ +++.|...|++++...+  ...+.....+..
T Consensus       163 -~~~~~~A~~~~~~a~~-------~~~--~~a~~~lg~~~~~g~~~~~-~~~~A~~~~~~a~~~~~--~~a~~~l~~~~~  229 (273)
T 1ouv_A          163 -PKDLKKALASYDKACD-------LKD--SPGCFNAGNMYHHGEGATK-NFKEALARYSKACELEN--GGGCFNLGAMQY  229 (273)
T ss_dssp             -CCCHHHHHHHHHHHHH-------TTC--HHHHHHHHHHHHHTCSSCC-CHHHHHHHHHHHHHTTC--HHHHHHHHHHHH
T ss_pred             -CCCHHHHHHHHHHHHH-------CCC--HHHHHHHHHHHHcCCCCCc-cHHHHHHHHHHHHhCCC--HHHHHHHHHHHH
Confidence             1233344444444443       222  3456667777777    67 99999999999998855  556777777777


Q ss_pred             h----cccHHHHHHHHHHHHhc
Q 013489          229 E----LDHINEARSIYKRCYSK  246 (442)
Q Consensus       229 ~----~g~~~~ar~i~~ral~~  246 (442)
                      .    .++++.|...|++|+..
T Consensus       230 ~g~~~~~~~~~A~~~~~~a~~~  251 (273)
T 1ouv_A          230 NGEGVTRNEKQAIENFKKGCKL  251 (273)
T ss_dssp             TTSSSSCCSTTHHHHHHHHHHH
T ss_pred             cCCCcccCHHHHHHHHHHHHHc
Confidence            7    78999999999999973

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=98.67  E-value=1.6e-08  Score=90.61  Aligned_cols=48  Identities=23%  Similarity=0.306  Sum_probs=44.2

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINL-KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+ ++++++|+.+|+.||.|.+|+++.++     +|||||+|.
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~   80 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMA   80 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEES
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEEC
Confidence            3457999999999 99999999999999999999999884     799999995

>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=98.66  E-value=2.5e-08  Score=91.13  Aligned_cols=48  Identities=27%  Similarity=0.400  Sum_probs=43.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..+.++|||||||+++|+++|+.+|+.||.|.+|.++.      ++|||||+|.
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~   66 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLE   66 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET------TTTEEEEECS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCcEEEEEEC
Confidence            35567999999999999999999999999999999864      3799999995

>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=98.65  E-value=3.7e-07  Score=75.65  Aligned_cols=126  Identities=10%  Similarity=-0.001  Sum_probs=98.3

Q ss_pred             chhhHHHHHHhhc---CCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHH
Q 013489            2 CNARAHLEEQISR---QDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVR   78 (442)
Q Consensus         2 ~~~r~~yE~~l~~---~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~   78 (442)
                      +..+..+|.+|..   ....++++...|..++......|+++.+...|+++|..+|.++..|......+.. .++.+.+.
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            3456666666633   2223456677788888888899999999999999999999999999999987764 45667899


Q ss_pred             HHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHH
Q 013489           79 DVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFE  128 (442)
Q Consensus        79 ~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~  128 (442)
                      ..|++|+...|....+|......+.......+.++..+++|+...|.+..
T Consensus        86 ~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P~~~~  135 (150)
T 4ga2_A           86 ECYRRSVELNPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFPGSPA  135 (150)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHSTTCHH
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCcCCHH
Confidence            99999999999999999998876655433345566677999987776433

>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=98.65  E-value=1.5e-08  Score=88.87  Aligned_cols=49  Identities=14%  Similarity=0.182  Sum_probs=44.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCe--eEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGV--SSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i--~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..+|||+|||+++++++|+++|++||.|  .+++++.++  |+++|||||+|.
T Consensus       123 ~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~  173 (205)
T 3tyt_A          123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWD  173 (205)
T ss_dssp             CSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECS
T ss_pred             cceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeC
Confidence            4699999999999999999999999999  899998874  666799999995

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.65  E-value=1.2e-06  Score=70.28  Aligned_cols=109  Identities=17%  Similarity=0.029  Sum_probs=95.3

Q ss_pred             CChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHH
Q 013489           18 SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVR   97 (442)
Q Consensus        18 ~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~   97 (442)
                      .||+..+.|.+-.....+.|+++.+...|+++|..+|.++.+|...+..+.. .+..+.+...|++|+...|.....|..
T Consensus         8 inP~~a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~-~~~~~~A~~~~~~al~~~p~~~~a~~~   86 (126)
T 4gco_A            8 INPELAQEEKNKGNEYFKKGDYPTAMRHYNEAVKRDPENAILYSNRAACLTK-LMEFQRALDDCDTCIRLDSKFIKGYIR   86 (126)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             HCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHhhHHHh-hccHHHHHHHHHHHHHhhhhhhHHHHH
Confidence            4677888999999888899999999999999999999999999999887764 456678999999999999999999999


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHhCChhhHH
Q 013489           98 SLLSLERSRASEEEISTVFEKSLLCAFSTFE  128 (442)
Q Consensus        98 y~~~le~~~~~~~~~~~i~~~al~~~~~~~~  128 (442)
                      ....+.. .+..+++...|++++...|....
T Consensus        87 lg~~~~~-~~~~~~A~~~~~~al~l~P~~~~  116 (126)
T 4gco_A           87 KAACLVA-MREWSKAQRAYEDALQVDPSNEE  116 (126)
T ss_dssp             HHHHHHH-TTCHHHHHHHHHHHHHHCTTCHH
T ss_pred             HHHHHHH-CCCHHHHHHHHHHHHHHCcCCHH
Confidence            8875554 78899999999999998777544

>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=98.65  E-value=7e-07  Score=90.94  Aligned_cols=164  Identities=12%  Similarity=-0.062  Sum_probs=89.0

Q ss_pred             CChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHH
Q 013489           37 GDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVF  116 (442)
Q Consensus        37 g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~  116 (442)
                      |+++.+...|++++..+|.+...|...+..+... ++.+.+...|++|+...|.....|..+...+. ..++.+++...|
T Consensus         3 g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~-g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~-~~g~~~~A~~~~   80 (568)
T 2vsy_A            3 ADGPRELLQLRAAVRHRPQDFVAWLMLADAELGM-GDTTAGEMAVQRGLALHPGHPEAVARLGRVRW-TQQRHAEAAVLL   80 (568)
T ss_dssp             ------------------CCHHHHHHHHHHHHHH-TCHHHHHHHHHHHHTTSTTCHHHHHHHHHHHH-HTTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH-HCCCHHHHHHHH
Confidence            5666777777777777777777777777655533 34566777777777777777777777665443 356677777777


Q ss_pred             HHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHc-
Q 013489          117 EKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSM-  195 (442)
Q Consensus       117 ~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~-  195 (442)
                      ++++...+.....+..+-..+.     ..         .++......|++++.       ..+.....+..++.+.... 
T Consensus        81 ~~al~~~p~~~~~~~~la~~~~-----~~---------g~~~~A~~~~~~al~-------~~p~~~~~~~~l~~~~~~~~  139 (568)
T 2vsy_A           81 QQASDAAPEHPGIALWLGHALE-----DA---------GQAEAAAAAYTRAHQ-------LLPEEPYITAQLLNWRRRLC  139 (568)
T ss_dssp             HHHHHHCTTCHHHHHHHHHHHH-----HT---------TCHHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHhcCCCCHHHHHHHHHHHH-----Hc---------CCHHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHhh
Confidence            7777655544332222211110     00         222222333333333       2344456777888888888 


Q ss_pred             --CCCHHHHHHHHHHHHHhchhHHHHHHHHH
Q 013489          196 --GKDMVSARGVWERLLKISGAMLEAWQSYI  224 (442)
Q Consensus       196 --~~~~~~ar~i~~~~l~~~~~~~~~w~~~~  224 (442)
                        + +.+.|...|++++...|+....|...+
T Consensus       140 ~~g-~~~~A~~~~~~al~~~p~~~~~~~~l~  169 (568)
T 2vsy_A          140 DWR-ALDVLSAQVRAAVAQGVGAVEPFAFLS  169 (568)
T ss_dssp             CCT-THHHHHHHHHHHHHHTCCCSCHHHHTT
T ss_pred             ccc-cHHHHHHHHHHHHhcCCcccChHHHhC
Confidence              7 899999999999999887766554333

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.64  E-value=3.2e-06  Score=78.62  Aligned_cols=220  Identities=9%  Similarity=0.047  Sum_probs=166.0

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcC--ChhhHHHHHHHHHhcCCCCHHHHHHHHHHH----HHhc--chhh
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSG--DPGRVQLLYERAITDFPVSSDLWLDYTQYL----DKTL--KVGN   75 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g--~~~~~~~lyERal~~~p~~~~lW~~Y~~~l----~~~~--~~~~   75 (442)
                      +-..++.+|..+|.    ++.+|..=.......|  .++.++.+++.+|..+|.+..+|..-...+    ....  ...+
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            45677888888876    8899988888777778  899999999999999999999999988777    3221  3456


Q ss_pred             HHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHH--HHHHHHHHHHhCChhhH--HHHHHHHHHHHHHHHHHhhccCcc
Q 013489           76 VVRDVYSRATKNCPWVGELWVRSLLSLERSRASEE--EISTVFEKSLLCAFSTF--EEYLDLFLTRIDGLRRRILFSGEV  151 (442)
Q Consensus        76 ~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~--~~~~i~~~al~~~~~~~--~~~~~~~~~~~~~l~rr~~~~~~~  151 (442)
                      .....+++++...|.+..+|....-.+.. .+..+  .....+++++...+.+.  |.+..+.+.       +.      
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-FDLHNDAKELSFVDKVIDTDLKNNSAWSHRFFLLF-------SK------  193 (306)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCTTCHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-------SS------
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHH-hcccChHHHHHHHHHHHHhCCCCHHHHHHHHHHHH-------hc------
Confidence            68899999999999999999998766665 34444  66678888887776643  333322210       00      


Q ss_pred             chhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc---hhHHHHHHHHHHHHH
Q 013489          152 EGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS---GAMLEAWQSYISMEI  228 (442)
Q Consensus       152 ~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~---~~~~~~w~~~~~~e~  228 (442)
                         .. ......++++++++..++...+.....|.+..-+....|...+.+..+.++++...   +.+...|.-.++...
T Consensus       194 ---~~-~~~~~~~~eEl~~~~~aI~~~p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~  269 (306)
T 3dra_A          194 ---KH-LATDNTIDEELNYVKDKIVKCPQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYT  269 (306)
T ss_dssp             ---GG-GCCHHHHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHH
T ss_pred             ---cc-cchhhhHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHH
Confidence               00 01234588899988888876777778998888888888866777888888887764   666777777777777


Q ss_pred             hcccHHHHHHHHHHHHh
Q 013489          229 ELDHINEARSIYKRCYS  245 (442)
Q Consensus       229 ~~g~~~~ar~i~~ral~  245 (442)
                      ..|+.+.|..+|+++..
T Consensus       270 ~~~~~~~A~~~~~~l~~  286 (306)
T 3dra_A          270 QQKKYNESRTVYDLLKS  286 (306)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHh
Confidence            78999999999999875

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=98.64  E-value=2.1e-08  Score=89.15  Aligned_cols=48  Identities=17%  Similarity=0.238  Sum_probs=43.4

Q ss_pred             CCCCceEEEcCCCCCC---------CHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKA---------TYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~---------~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....++|||||||..+         ++++|+.+|++||.|.+|+|+.+      +|||||+|.
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~  187 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFK  187 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEES
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeC
Confidence            4567899999999998         79999999999999999999863      799999996

>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=98.64  E-value=3.8e-09  Score=90.31  Aligned_cols=52  Identities=19%  Similarity=0.211  Sum_probs=45.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+.+|..||.+.. .++.+..+|+++|||||+|.
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~   62 (175)
T 1fje_B           11 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFE   62 (175)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEEC
Confidence            45679999999999999999999999998877 34455578999999999996

>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=98.62  E-value=2.8e-08  Score=92.37  Aligned_cols=53  Identities=13%  Similarity=0.189  Sum_probs=47.2

Q ss_pred             CCCceEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEeeCCC-CCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLK-ATYEDLRRFFSDVGGVSSIRILHDKF-TGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~-~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+. +++++|+.+|+.||.|.+|+++.++. ||+++|||||+|.
T Consensus       208 ~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~  262 (292)
T 2ghp_A          208 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFE  262 (292)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEES
T ss_pred             CCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeC
Confidence            34569999999999 99999999999999999999999865 5999999999996

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.61  E-value=5.8e-08  Score=71.95  Aligned_cols=39  Identities=26%  Similarity=0.323  Sum_probs=34.1

Q ss_pred             eEEEcCCCCCCCHHH----HHHHhccC-CCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINLKATYED----LRRFFSDV-GGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~----l~~~f~~~-G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .|||+|||+.+++++    |+.+|++| |.|.+|       ||   |||||.|.
T Consensus        11 ~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~   54 (96)
T 2diu_A           11 LLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFI   54 (96)
T ss_dssp             EEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEES
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEEC
Confidence            499999999999987    55899999 499988       44   99999995

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=98.61  E-value=8e-08  Score=74.34  Aligned_cols=51  Identities=12%  Similarity=-0.023  Sum_probs=43.3

Q ss_pred             CceEEEcCCCC-----CCCHHHHHHHhccCCCeeEEEEeeCCCC-CCCcceEEEEee
Q 013489          391 ECTAFLSNINL-----KATYEDLRRFFSDVGGVSSIRILHDKFT-GKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~-----~~~~~~l~~~f~~~G~i~~~~~~~~~~~-g~~~g~~fv~f~  441 (442)
                      .++|+|+|+..     +-++++|+..|++||.|.+|.|+.++.+ |+++|||||+|.
T Consensus         8 s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~   64 (105)
T 2pe8_A            8 TKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFE   64 (105)
T ss_dssp             CSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEES
T ss_pred             CCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEEC
Confidence            45999999963     2378999999999999999999998654 789999999995

>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=98.60  E-value=5.2e-08  Score=83.13  Aligned_cols=48  Identities=19%  Similarity=0.284  Sum_probs=42.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|++||.|..+     ..+|+++|||||+|.
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~  144 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFK  144 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECS
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEEC
Confidence            345799999999999999999999999987655     378999999999995

>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=98.59  E-value=5.3e-08  Score=90.13  Aligned_cols=51  Identities=12%  Similarity=0.074  Sum_probs=47.3

Q ss_pred             CCceEEEcCCCCCC-CHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKA-TYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~-~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+.+ ++++|+.+|+.||.|.+++|+.++ +|+++|||||+|.
T Consensus       183 ~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~  234 (284)
T 3smz_A          183 HSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYE  234 (284)
T ss_dssp             SCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECS
T ss_pred             CccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeC
Confidence            45699999999995 999999999999999999999994 8999999999995

>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=98.57  E-value=8.7e-07  Score=73.23  Aligned_cols=116  Identities=8%  Similarity=-0.051  Sum_probs=97.4

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ++...|+.+|...|    ++...|..++......|+++.+...|++++..+|.++..|......+.. .+..+.+...|+
T Consensus         5 ~~~~~~~~al~~~p----~~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~-~g~~~~A~~~~~   79 (148)
T 2vgx_A            5 SGGGTIAMLNEISS----DTLEQLYSLAFNQYQSGXYEDAHXVFQALCVLDHYDSRFFLGLGACRQA-MGQYDLAIHSYS   79 (148)
T ss_dssp             -CCCSHHHHTTCCH----HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHH
T ss_pred             chhhhHHHHHcCCH----hhHHHHHHHHHHHHHcCChHHHHHHHHHHHHcCcccHHHHHHHHHHHHH-HhhHHHHHHHHH
Confidence            34556777876654    4888999999999999999999999999999999999999998876664 456678999999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCh
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAF  124 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~  124 (442)
                      +|+...|.....|......+. ..+..+++...|++++...+
T Consensus        80 ~al~l~p~~~~~~~~lg~~~~-~~g~~~~A~~~~~~al~~~p  120 (148)
T 2vgx_A           80 YGAVMDIXEPRFPFHAAECLL-QXGELAEAESGLFLAQELIA  120 (148)
T ss_dssp             HHHHHSTTCTHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHT
T ss_pred             HHHhcCCCCchHHHHHHHHHH-HcCCHHHHHHHHHHHHHHCc
Confidence            999999999999988776444 47889999999999997544

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.57  E-value=2e-05  Score=69.74  Aligned_cols=183  Identities=11%  Similarity=-0.013  Sum_probs=120.2

Q ss_pred             HHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCH---HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHH---HHHH
Q 013489           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS---DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGE---LWVR   97 (442)
Q Consensus        24 ~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~---~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~---lW~~   97 (442)
                      ..|...+......|+++.+...|++++..+|.++   ..|...+..+.. .++.+.+...|++++...|.+..   .|..
T Consensus         5 ~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~-~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~   83 (225)
T 2yhc_A            5 NEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYK-NADLPLAQAAIDRFIRLNPTHPNIDYVMYM   83 (225)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCTTHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHh-cCCHHHHHHHHHHHHHHCcCCCcHHHHHHH
Confidence            3455555555678999999999999999988764   566666554443 45667899999999999998754   2322


Q ss_pred             HHHHHHH-----------------ccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHH
Q 013489           98 SLLSLER-----------------SRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLI  160 (442)
Q Consensus        98 y~~~le~-----------------~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~  160 (442)
                      ....+..                 ..+..+.+...|++++...|........  ..++..                   +
T Consensus        84 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P~~~~a~~a--~~~l~~-------------------~  142 (225)
T 2yhc_A           84 RGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYPNSQYTTDA--TKRLVF-------------------L  142 (225)
T ss_dssp             HHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTCTTCTTHHHH--HHHHHH-------------------H
T ss_pred             HHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHCcCChhHHHH--HHHHHH-------------------H
Confidence            2222211                 1234556666677766554432110000  000000                   0


Q ss_pred             HHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHH---HHHHHHHHHHHhcccHHHHH
Q 013489          161 RETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAML---EAWQSYISMEIELDHINEAR  237 (442)
Q Consensus       161 r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~---~~w~~~~~~e~~~g~~~~ar  237 (442)
                      ..                 .........+.+....| ++..|...|++++..+|++.   +.|...+......|+.+.|.
T Consensus       143 ~~-----------------~~~~~~~~~a~~~~~~~-~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~  204 (225)
T 2yhc_A          143 KD-----------------RLAKYEYSVAEYYTERG-AWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAE  204 (225)
T ss_dssp             HH-----------------HHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HH-----------------HHHHHHHHHHHHHHHcC-cHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHH
Confidence            00                 00012234566777788 99999999999999988764   67889999999999999999


Q ss_pred             HHHHHHHhc
Q 013489          238 SIYKRCYSK  246 (442)
Q Consensus       238 ~i~~ral~~  246 (442)
                      ..|+++...
T Consensus       205 ~~~~~l~~~  213 (225)
T 2yhc_A          205 KVAKIIAAN  213 (225)
T ss_dssp             HHHHHHHHC
T ss_pred             HHHHHHHhh
Confidence            999998863

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.56  E-value=1.1e-06  Score=72.97  Aligned_cols=106  Identities=8%  Similarity=-0.080  Sum_probs=93.2

Q ss_pred             CChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHH
Q 013489           18 SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVR   97 (442)
Q Consensus        18 ~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~   97 (442)
                      .+|++.+.|..........|+++.+..+|++++..+|.++..|......+.. .+..+.+...|++|+...|.+...|..
T Consensus        31 l~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~-~g~~~~Ai~~~~~al~l~P~~~~~~~~  109 (151)
T 3gyz_A           31 IPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQI-KEQFQQAADLYAVAFALGKNDYTPVFH  109 (151)
T ss_dssp             SCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHSSSCCHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-HccHHHHHHHHHHHHhhCCCCcHHHHH
Confidence            3567899999999989999999999999999999999999999999886664 456678999999999999999999999


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHhCChh
Q 013489           98 SLLSLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus        98 y~~~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                      ....+. ..+..+++...|++++...++
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            877555 478999999999999986654

>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=98.54  E-value=6.7e-07  Score=82.50  Aligned_cols=194  Identities=11%  Similarity=-0.034  Sum_probs=136.7

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~  101 (442)
                      +...|...+......|+++.+..+|+++|..+|.+..+|...+..+.. .+..+.+...|++|+...|....+|......
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~-~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~   81 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLK-MQQPEQALADCRRALELDGQSVKAHFFLGQC   81 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHH-TTCHHHHHHHHHHHTTSCTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHH-hcCHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            456778888888889999999999999999999999999999987664 4566789999999999999999999988775


Q ss_pred             HHHccCCHHHHHHHHHHHHhCChhhHHHHH-HHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchh
Q 013489          102 LERSRASEEEISTVFEKSLLCAFSTFEEYL-DLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDG  180 (442)
Q Consensus       102 le~~~~~~~~~~~i~~~al~~~~~~~~~~~-~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~  180 (442)
                      +.. .+..+++...|++++...+.....+. .++...                       +..-......+...  ..+.
T Consensus        82 ~~~-~g~~~~A~~~~~~al~l~p~~~~~~~~~~~~~~-----------------------~~~~~~~~~~~~~~--~~~~  135 (281)
T 2c2l_A           82 QLE-MESYDEAIANLQRAYSLAKEQRLNFGDDIPSAL-----------------------RIAKKKRWNSIEER--RIHQ  135 (281)
T ss_dssp             HHH-TTCHHHHHHHHHHHHHHHHHTTCCCCSHHHHHH-----------------------HHHHHHHHHHHHHT--CCCC
T ss_pred             HHH-cCCHHHHHHHHHHHHHhCccchhhHHHHHHHHH-----------------------HHHHHHHHHHHHHH--HHhh
Confidence            554 68899999999999976543210000 011000                       00000000001111  1112


Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhc-ccHHHHHHHHHHHHh
Q 013489          181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIEL-DHINEARSIYKRCYS  245 (442)
Q Consensus       181 ~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~-g~~~~ar~i~~ral~  245 (442)
                      ...+...+..+.  .| +.+.|.+.|++++...|++..+......+.... +.++.++.+|.++..
T Consensus       136 ~~~i~~~l~~l~--~~-~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~  198 (281)
T 2c2l_A          136 ESELHSYLTRLI--AA-ERERELEECQRNHEGHEDDGHIRAQQACIEAKHDKYMADMDELFSQVDE  198 (281)
T ss_dssp             CCHHHHHHHHHH--HH-HHHHHHTTTSGGGTTTSCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             hHHHHHHHHHHH--HH-HHHHHHHHHHhhhccccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            223444444443  35 789999999999999998888777777777666 578899999999875

>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=98.52  E-value=3.8e-05  Score=71.93  Aligned_cols=198  Identities=9%  Similarity=-0.003  Sum_probs=134.7

Q ss_pred             HHHHHHHHHhcCCh-hhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcch---------hhHHHHHHHHHHHcCCCcHHHH
Q 013489           26 YMIYLKYEQSSGDP-GRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKV---------GNVVRDVYSRATKNCPWVGELW   95 (442)
Q Consensus        26 w~~y~~~e~~~g~~-~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~---------~~~~~~v~erAl~~~p~s~~lW   95 (442)
                      -+.++--....|+. +++..+++.+|..+|.+..+|..--..+......         .+.....++.++...|.+..+|
T Consensus        32 ~~~~~~~~~~~~e~s~eaL~~t~~~L~~nP~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~PKny~aW  111 (331)
T 3dss_A           32 ATQAVFQKRQAGELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTW  111 (331)
T ss_dssp             HHHHHHHHHHTTCCSHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhCCCCHHHH
Confidence            33344334456665 4899999999999999999999887766543321         3457788999999999999999


Q ss_pred             HHHHHHHHHccC-CHHHHHHHHHHHHhCChhh--HHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHh
Q 013489           96 VRSLLSLERSRA-SEEEISTVFEKSLLCAFST--FEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLS  172 (442)
Q Consensus        96 ~~y~~~le~~~~-~~~~~~~i~~~al~~~~~~--~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~  172 (442)
                      ....-.+..... ..+.....+.+++...+.+  .|.+..+....+                ..      .++.+++++.
T Consensus       112 ~hR~wlL~~l~~~~~~~EL~~~~k~l~~dprNy~AW~~R~~vl~~l----------------~~------~~~eel~~~~  169 (331)
T 3dss_A          112 HHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQA----------------AV------APAEELAFTD  169 (331)
T ss_dssp             HHHHHHHHHCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT----------------TC------CHHHHHHHHH
T ss_pred             HHHHHHHhccCcccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHh----------------Cc------CHHHHHHHHH
Confidence            998876766443 3677778899999877664  343333222111                00      1234455555


Q ss_pred             hhhcCchhhHHHHHHHHHHHHHcC-------------CCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhc---------
Q 013489          173 EQMKNTDGLLRLYAYWAHLEQSMG-------------KDMVSARGVWERLLKISGAMLEAWQSYISMEIEL---------  230 (442)
Q Consensus       173 ~~~~~~~~~~~l~~~~a~~e~~~~-------------~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~---------  230 (442)
                      ..+..++.....|.+-..+...+.             +.++.+.+.+.+++..+|++...|...--+....         
T Consensus       170 ~~I~~~p~N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~P~d~SaW~Y~r~ll~~~~~~~~~~~~  249 (331)
T 3dss_A          170 SLITRNFSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGAGSGRCELSVE  249 (331)
T ss_dssp             HHHHHCSCCHHHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHSSSCGGGCCHH
T ss_pred             HHHHHCCCCHHHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhccCccccchH
Confidence            555445666667877666555542             1367889999999999999999997655544433         


Q ss_pred             --ccHHHHHHHHHHHHh
Q 013489          231 --DHINEARSIYKRCYS  245 (442)
Q Consensus       231 --g~~~~ar~i~~ral~  245 (442)
                        +-++++...++.++.
T Consensus       250 ~~~~l~~el~~~~elle  266 (331)
T 3dss_A          250 KSTVLQSELESCKELQE  266 (331)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence              236778888888886

>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=98.51  E-value=5.7e-05  Score=70.78  Aligned_cols=246  Identities=9%  Similarity=-0.031  Sum_probs=158.3

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCC----------hhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcc-
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGD----------PGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLK-   72 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~----------~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~-   72 (442)
                      +-..++.+|..+|.    ++.+|.-=-......+.          +.....+++.+|..+|.+..+|..-.-.+..... 
T Consensus        49 aL~~t~~~L~~nP~----~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~PKny~aW~hR~wlL~~l~~~  124 (331)
T 3dss_A           49 VLELTSQILGANPD----FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEP  124 (331)
T ss_dssp             HHHHHHHHHTTCTT----CHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHCSSC
T ss_pred             HHHHHHHHHHHCch----hHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHhccCcc
Confidence            34567777777775    88888755444443332          4677888999999999999999988876664432 


Q ss_pred             hhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhh--HHHHHHHHHHHHHHHHHHhhccCc
Q 013489           73 VGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFST--FEEYLDLFLTRIDGLRRRILFSGE  150 (442)
Q Consensus        73 ~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~--~~~~~~~~~~~~~~l~rr~~~~~~  150 (442)
                      ..+.....+++++...|.....|......+.......++....+.+++...+.+  .|.+....+..       +.....
T Consensus       125 ~~~~EL~~~~k~l~~dprNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p~N~SAW~~R~~ll~~-------l~~~~~  197 (331)
T 3dss_A          125 NWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQ-------LHPQPD  197 (331)
T ss_dssp             CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHH-------HSCCC-
T ss_pred             cHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-------hhhccc
Confidence            245688999999999999999999877666654433566777788888776663  44444332211       110000


Q ss_pred             cchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcC----------CCHHHHHHHHHHHHHhchhHHHHH
Q 013489          151 VEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMG----------KDMVSARGVWERLLKISGAMLEAW  220 (442)
Q Consensus       151 ~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~----------~~~~~ar~i~~~~l~~~~~~~~~w  220 (442)
                      ..  .........++++++++..++...|.....|.+..-+.....          +-++.+.+.+++++...|++.-..
T Consensus       198 ~~--~~~~~~~~~~~eEle~~~~ai~~~P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~~~~elle~~pd~~w~l  275 (331)
T 3dss_A          198 SG--PQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELESCKELQELEPENKWCL  275 (331)
T ss_dssp             -------CCCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             cc--cccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhccCccccchHHHHHHHHHHHHHHHHHhhCcccchHH
Confidence            00  000000245677777777777666666778876544444331          136789999999999999885455


Q ss_pred             HHHHHHHHh---cccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhC
Q 013489          221 QSYISMEIE---LDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYG  268 (442)
Q Consensus       221 ~~~~~~e~~---~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G  268 (442)
                      +..+.+...   .|..+.++..+.+.+.  +++--.    ..|.+++..+.
T Consensus       276 ~~~~~~~~~~~~~~~~~~~~~~l~~l~~--~Dp~r~----~~y~d~~~~~~  320 (331)
T 3dss_A          276 LTIILLMRALDPLLYEKETLQYFSTLKA--VDPMRA----AYLDDLRSKFL  320 (331)
T ss_dssp             HHHHHHHHHHCTTTTHHHHHHHHHHHHH--HCGGGH----HHHHHHHHHHH
T ss_pred             HHHHHHHHhhcccccHHHHHHHHHHHHH--hCcchh----hHHHHHHHHHH
Confidence            555544432   4677889999999885  332222    36666666543

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.51  E-value=2.1e-06  Score=70.12  Aligned_cols=113  Identities=9%  Similarity=-0.059  Sum_probs=92.9

Q ss_pred             HHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHH
Q 013489            7 HLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATK   86 (442)
Q Consensus         7 ~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~   86 (442)
                      .|+.+|..    +|++...|...+......|+++.+..+|++++..+|.++.+|......+.. .+..+.+...|++|+.
T Consensus         6 ~l~~al~~----~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~-~g~~~~A~~~~~~al~   80 (142)
T 2xcb_A            6 TLAMLRGL----SEDTLEQLYALGFNQYQAGKWDDAQKIFQALCMLDHYDARYFLGLGACRQS-LGLYEQALQSYSYGAL   80 (142)
T ss_dssp             ---CCTTC----CHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHH
T ss_pred             hHHHHHcC----CHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHH-HhhHHHHHHHHHHHHh
Confidence            44555544    355888999999988899999999999999999999999999998886664 4566789999999999


Q ss_pred             cCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh
Q 013489           87 NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus        87 ~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                      ..|....+|......+. ..++.+.+...|++++...+.
T Consensus        81 ~~p~~~~~~~~lg~~~~-~~g~~~~A~~~~~~al~~~p~  118 (142)
T 2xcb_A           81 MDINEPRFPFHAAECHL-QLGDLDGAESGFYSARALAAA  118 (142)
T ss_dssp             HCTTCTHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHHT
T ss_pred             cCCCCcHHHHHHHHHHH-HcCCHHHHHHHHHHHHHhCCC
Confidence            99999999988776444 478899999999999976543

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=98.50  E-value=4.1e-05  Score=70.32  Aligned_cols=180  Identities=12%  Similarity=0.099  Sum_probs=123.8

Q ss_pred             cCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHc--------CCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCC
Q 013489           52 DFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKN--------CPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA  123 (442)
Q Consensus        52 ~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~--------~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~  123 (442)
                      .+|....+|...+..+... ++.+.+..+|++++..        .|....+|......+ ...+..+.+...|++++...
T Consensus        22 ~~~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~-~~~g~~~~A~~~~~~al~~~   99 (311)
T 3nf1_A           22 EIPARLRTLHNLVIQYASQ-GRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVY-RDQNKYKDAANLLNDALAIR   99 (311)
T ss_dssp             TSCHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHH-HHCCCHHHHHHHHHHHHHHH
Confidence            3566667777777666543 4567799999999984        455556677666533 44788999999999998641


Q ss_pred             -----hhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcC-chhhHHHHHHHHHHHHHcCC
Q 013489          124 -----FSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGK  197 (442)
Q Consensus       124 -----~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~  197 (442)
                           .... .....+....... ..         ..++......|++++......... .+....++...+.+....| 
T Consensus       100 ~~~~~~~~~-~~~~~~~~l~~~~-~~---------~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~-  167 (311)
T 3nf1_A          100 EKTLGKDHP-AVAATLNNLAVLY-GK---------RGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQG-  167 (311)
T ss_dssp             HHHHCTTCH-HHHHHHHHHHHHH-HT---------TTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTT-
T ss_pred             HHHhCCCCh-HHHHHHHHHHHHH-HH---------cCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcC-
Confidence                 1100 1111111111011 01         134555666777777765443322 2445677888899988888 


Q ss_pred             CHHHHHHHHHHHHHh--------chhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          198 DMVSARGVWERLLKI--------SGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       198 ~~~~ar~i~~~~l~~--------~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      +++.|..+|++++..        .|....+|...+.+....|+++.|..+|++++.
T Consensus       168 ~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  223 (311)
T 3nf1_A          168 KYEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILT  223 (311)
T ss_dssp             CHHHHHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            999999999999998        677778999999999999999999999999996

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.49  E-value=9.7e-06  Score=73.34  Aligned_cols=95  Identities=7%  Similarity=-0.072  Sum_probs=71.1

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCH---HHHHHHHHHHHHh-------cc
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS---DLWLDYTQYLDKT-------LK   72 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~---~lW~~Y~~~l~~~-------~~   72 (442)
                      +|...|+..|...|. ++.....|...+......|+++.+...|+++|..+|.++   ..|...+..+...       .+
T Consensus        33 ~A~~~~~~~l~~~p~-~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~~~~~  111 (261)
T 3qky_A           33 RAIEYFKAVFTYGRT-HEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAEYERAMCYYKLSPPYELDQT  111 (261)
T ss_dssp             HHHHHHHHHGGGCSC-STTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCCCTTSCCH
T ss_pred             HHHHHHHHHHHhCCC-CcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHHhcccccccch
Confidence            467789999988775 122266788888878889999999999999999988664   4455444443320       45


Q ss_pred             hhhHHHHHHHHHHHcCCCcHHHHHHH
Q 013489           73 VGNVVRDVYSRATKNCPWVGELWVRS   98 (442)
Q Consensus        73 ~~~~~~~v~erAl~~~p~s~~lW~~y   98 (442)
                      ..+.+...|++++...|.+...+...
T Consensus       112 ~~~~A~~~~~~~l~~~p~~~~~~~a~  137 (261)
T 3qky_A          112 DTRKAIEAFQLFIDRYPNHELVDDAT  137 (261)
T ss_dssp             HHHHHHHHHHHHHHHCTTCTTHHHHH
T ss_pred             hHHHHHHHHHHHHHHCcCchhHHHHH
Confidence            66789999999999999887666554

>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=98.49  E-value=2.8e-06  Score=71.97  Aligned_cols=118  Identities=12%  Similarity=0.028  Sum_probs=100.2

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchh--hHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVG--NVVRDV   80 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~--~~~~~v   80 (442)
                      ++...|+.++...|.    +...|..++......|+++.+...|++++..+|.++.+|..++..+....+..  +.+...
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            456788999988875    67889999999999999999999999999999999999999998744334454  779999


Q ss_pred             HHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh
Q 013489           81 YSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus        81 ~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                      |++++...|....+|......+. ..++.+.+...|++++...+.
T Consensus       104 ~~~al~~~p~~~~~~~~la~~~~-~~g~~~~A~~~~~~al~~~p~  147 (177)
T 2e2e_A          104 IDKALALDSNEITALMLLASDAF-MQANYAQAIELWQKVMDLNSP  147 (177)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHTCCT
T ss_pred             HHHHHHhCCCcHHHHHHHHHHHH-HcccHHHHHHHHHHHHhhCCC
Confidence            99999999999999988777444 468899999999999987665

>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=98.47  E-value=1.3e-05  Score=63.43  Aligned_cols=92  Identities=16%  Similarity=0.186  Sum_probs=49.7

Q ss_pred             HHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHc
Q 013489           26 YMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERS  105 (442)
Q Consensus        26 w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~  105 (442)
                      |...+......|+++.+..+|++++...|.+...|...+...... ++.+.+...|++++...|....+|..++..+. .
T Consensus         4 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~-~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~-~   81 (136)
T 2fo7_A            4 WYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQ-GDYDEAIEYYQKALELDPRSAEAWYNLGNAYY-K   81 (136)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-T
T ss_pred             HHHHHHHHHHcCcHHHHHHHHHHHHHcCCcchhHHHHHHHHHHHh-cCHHHHHHHHHHHHHHCCCchHHHHHHHHHHH-H
Confidence            444455555566677777777777766666666666655544432 33455666666666666655555544443222 2


Q ss_pred             cCCHHHHHHHHHHH
Q 013489          106 RASEEEISTVFEKS  119 (442)
Q Consensus       106 ~~~~~~~~~i~~~a  119 (442)
                      .++.+.+..+|+++
T Consensus        82 ~~~~~~A~~~~~~~   95 (136)
T 2fo7_A           82 QGDYDEAIEYYQKA   95 (136)
T ss_dssp             TTCHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHH
Confidence            33444444444443

>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=98.47  E-value=2.2e-06  Score=70.84  Aligned_cols=98  Identities=16%  Similarity=0.070  Sum_probs=84.1

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      +|...|+.+|...|.    +...|..+.......|+++.+...|+++|..+|.++..|...+..+...+...+.+...++
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            467789999988876    7889999999999999999999999999999999999999999887766554454555679


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLLSLER  104 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~  104 (442)
                      +|++..|.+..+|......+..
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            9999999999999887776654

>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=98.46  E-value=3.2e-07  Score=84.68  Aligned_cols=48  Identities=15%  Similarity=0.253  Sum_probs=43.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||..+++++|+.+|+.||.|.+|+++.++     +|||||+|.
T Consensus       205 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~  252 (282)
T 3pgw_A          205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFD  252 (282)
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeC
Confidence            446799999999999999999999999999999999763     689999996

>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=98.45  E-value=3.8e-06  Score=85.45  Aligned_cols=122  Identities=10%  Similarity=0.055  Sum_probs=92.9

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      +|...|+.+|...|.    +...|..++......|+++.+...|++++..+|.+...|..++..+... ++.+.+...|+
T Consensus         7 ~A~~~~~~al~~~p~----~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~-g~~~~A~~~~~   81 (568)
T 2vsy_A            7 RELLQLRAAVRHRPQ----DFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQ-QRHAEAAVLLQ   81 (568)
T ss_dssp             --------------C----CHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTSTTCHHHHHHHHHHHHHT-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC----CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHC-CCHHHHHHHHH
Confidence            456778888877765    6788999999888999999999999999999999999999999877644 56678999999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHH
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEY  130 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~  130 (442)
                      +|+...|.+...|..+...+. ..++.+++...|++++...+.....+
T Consensus        82 ~al~~~p~~~~~~~~la~~~~-~~g~~~~A~~~~~~al~~~p~~~~~~  128 (568)
T 2vsy_A           82 QASDAAPEHPGIALWLGHALE-DAGQAEAAAAAYTRAHQLLPEEPYIT  128 (568)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             HHHhcCCCCHHHHHHHHHHHH-HcCCHHHHHHHHHHHHHhCCCCHHHH
Confidence            999999999999999877444 47889999999999998776654433

>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=98.45  E-value=4.3e-05  Score=71.99  Aligned_cols=195  Identities=14%  Similarity=0.125  Sum_probs=137.3

Q ss_pred             hHHHHHHHHHHHHh-cCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQS-SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (442)
Q Consensus        22 ~~~~w~~y~~~e~~-~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~  100 (442)
                      ++..-+.|+.-... .+..+++..+++++|..+|.+..+|..-...+...+...+.....++.++...|.+..+|.....
T Consensus        52 ~y~~~~~~~r~~~~~~e~se~AL~lt~~~L~~nP~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPKny~aW~hR~w  131 (349)
T 3q7a_A           52 EYKDAMDYFRAIAAKEEKSERALELTEIIVRMNPAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLKSYQVWHHRLL  131 (349)
T ss_dssp             HHHHHHHHHHHHHHTTCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCchhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCCcHHHHHHHHH
Confidence            44444444444444 44557899999999999999999999888877754435677899999999999999999999887


Q ss_pred             HHHHccC-CHHHHHHHHHHHHhCChhh--HHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcC
Q 013489          101 SLERSRA-SEEEISTVFEKSLLCAFST--FEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKN  177 (442)
Q Consensus       101 ~le~~~~-~~~~~~~i~~~al~~~~~~--~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~  177 (442)
                      .+....+ ..++....+.+++...+.+  .|.+..+.+..+...       ..    .+    ...+.++++++...+..
T Consensus       132 lL~~l~~~~~~~EL~~~~k~L~~dpkNy~AW~~R~wvl~~l~~~-------~~----~~----~~~~~eELe~~~k~I~~  196 (349)
T 3q7a_A          132 LLDRISPQDPVSEIEYIHGSLLPDPKNYHTWAYLHWLYSHFSTL-------GR----IS----EAQWGSELDWCNEMLRV  196 (349)
T ss_dssp             HHHHHCCSCCHHHHHHHHHHTSSCTTCHHHHHHHHHHHHHHHHT-------TC----CC----HHHHHHHHHHHHHHHHH
T ss_pred             HHHHhcCCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccc-------cc----cc----hhhHHHHHHHHHHHHHh
Confidence            7776523 5566667899999887764  344443332222110       00    01    13345566666666655


Q ss_pred             chhhHHHHHHHHHHHHHcCCC------HHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcc
Q 013489          178 TDGLLRLYAYWAHLEQSMGKD------MVSARGVWERLLKISGAMLEAWQSYISMEIELD  231 (442)
Q Consensus       178 ~~~~~~l~~~~a~~e~~~~~~------~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g  231 (442)
                      ++.....|.+-..+....++.      ++.+.+.+.+++..+|++...|...--+....|
T Consensus       197 dp~N~SAW~~R~~lL~~l~~~~~~~~~~~eELe~~~~aI~~~P~n~SaW~Ylr~Ll~~~~  256 (349)
T 3q7a_A          197 DGRNNSAWGWRWYLRVSRPGAETSSRSLQDELIYILKSIHLIPHNVSAWNYLRGFLKHFS  256 (349)
T ss_dssp             CTTCHHHHHHHHHHHTTSTTCCCCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcC
Confidence            666677888877776666621      678999999999999999999987776666555

>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=98.45  E-value=2.9e-06  Score=72.03  Aligned_cols=117  Identities=8%  Similarity=-0.075  Sum_probs=90.2

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ++...|+.+|...|.    +...|..++......|+++.+...|++++...| ++.++................+...|+
T Consensus        24 ~A~~~~~~al~~~P~----~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p-~~~~~~~~~~~~~~~~~~~~~a~~~~~   98 (176)
T 2r5s_A           24 QALNVIQTLSDELQS----RGDVKLAKADCLLETKQFELAQELLATIPLEYQ-DNSYKSLIAKLELHQQAAESPELKRLE   98 (176)
T ss_dssp             HHHHHHHTSCHHHHT----SHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGC-CHHHHHHHHHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHHHHCCC----cHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccC-ChHHHHHHHHHHHHhhcccchHHHHHH
Confidence            355667777766654    788999999999999999999999999999999 887665544332211111123678999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                      +++...|.+..+|..+...+.. .++.+++...|++++...+.
T Consensus        99 ~al~~~P~~~~~~~~la~~~~~-~g~~~~A~~~~~~~l~~~p~  140 (176)
T 2r5s_A           99 QELAANPDNFELACELAVQYNQ-VGRDEEALELLWNILKVNLG  140 (176)
T ss_dssp             HHHHHSTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCTT
T ss_pred             HHHHhCCCCHHHHHHHHHHHHH-cccHHHHHHHHHHHHHhCcc
Confidence            9999999999999998875554 78889999999999876543

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.43  E-value=7.4e-07  Score=68.03  Aligned_cols=36  Identities=14%  Similarity=0.090  Sum_probs=32.7

Q ss_pred             CCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          401 LKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       401 ~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..+++++|+.+|++||.|.+|+|+     ++++|||||+|.
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~   62 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFA   62 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEES
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEEC
Confidence            468999999999999999999988     468999999995

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=98.42  E-value=1.9e-07  Score=87.53  Aligned_cols=45  Identities=11%  Similarity=0.142  Sum_probs=39.5

Q ss_pred             CceEEEcC--CCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSN--INLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~n--l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..+|||||  |++.+++++|+++|++||.|.+|.++.      +||||||+|.
T Consensus        18 s~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~   64 (345)
T 3tht_A           18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYR   64 (345)
T ss_dssp             CSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEES
T ss_pred             CCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEEC
Confidence            45999999  589999999999999999999987653      4799999995

>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=98.41  E-value=3.4e-06  Score=87.86  Aligned_cols=165  Identities=10%  Similarity=-0.028  Sum_probs=122.1

Q ss_pred             CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHH--------HcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCh
Q 013489           53 FPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRAT--------KNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAF  124 (442)
Q Consensus        53 ~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl--------~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~  124 (442)
                      +|.++..+....    ...++.+.+...|++|+        ...|.+..+|......+. ..++.+++...|++++...+
T Consensus       390 ~p~~~~a~~~~a----~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~-~~g~~~~A~~~~~~al~~~p  464 (681)
T 2pzi_A          390 DPTDVAASVLQA----TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALL-DLGDVAKATRKLDDLAERVG  464 (681)
T ss_dssp             CTTSTTHHHHHH----TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHH-HHTCHHHHHHHHHHHHHHHC
T ss_pred             CCCCcchHHhhc----ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHH-hcCCHHHHHHHHHHHhccCc
Confidence            455555444322    23456678999999999        788999999998877444 36889999999999998766


Q ss_pred             hhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHH
Q 013489          125 STFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARG  204 (442)
Q Consensus       125 ~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~  204 (442)
                      ..+..+..+-..+.     ..         .++......|++|+.       ..+.....|...+.+....| +++. ..
T Consensus       465 ~~~~a~~~lg~~~~-----~~---------g~~~~A~~~~~~al~-------l~P~~~~~~~~lg~~~~~~g-~~~~-~~  521 (681)
T 2pzi_A          465 WRWRLVWYRAVAEL-----LT---------GDYDSATKHFTEVLD-------TFPGELAPKLALAATAELAG-NTDE-HK  521 (681)
T ss_dssp             CCHHHHHHHHHHHH-----HH---------TCHHHHHHHHHHHHH-------HSTTCSHHHHHHHHHHHHHT-CCCT-TC
T ss_pred             chHHHHHHHHHHHH-----Hc---------CCHHHHHHHHHHHHH-------hCCCChHHHHHHHHHHHHcC-ChHH-HH
Confidence            65544433222221     00         233344444555544       34555678888999988999 8888 99


Q ss_pred             HHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          205 VWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       205 i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      .|+++++.+|++...|...+......|+++.|...|++|+.
T Consensus       522 ~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~  562 (681)
T 2pzi_A          522 FYQTVWSTNDGVISAAFGLARARSAEGDRVGAVRTLDEVPP  562 (681)
T ss_dssp             HHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHTSCT
T ss_pred             HHHHHHHhCCchHHHHHHHHHHHHHcCCHHHHHHHHHhhcc
Confidence            99999999999999999999999999999999999999986

>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=98.39  E-value=4.5e-06  Score=70.67  Aligned_cols=145  Identities=14%  Similarity=0.149  Sum_probs=98.2

Q ss_pred             cCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCH--HHHH
Q 013489           36 SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASE--EEIS  113 (442)
Q Consensus        36 ~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~--~~~~  113 (442)
                      .|+++.+..+|++++..+|.+...|...+..+... ++.+.+...|++++...|.+..+|..+...+....+..  +.+.
T Consensus        23 ~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~-~~~~~A~~~~~~al~~~p~~~~~~~~la~~l~~~~~~~~~~~A~  101 (177)
T 2e2e_A           23 QQNPEAQLQALQDKIRANPQNSEQWALLGEYYLWQ-NDYSNSLLAYRQALQLRGENAELYAALATVLYYQASQHMTAQTR  101 (177)
T ss_dssp             ----CCCCHHHHHHHHHCCSCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHTTTCCCHHHH
T ss_pred             ccCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCcchHHHH
Confidence            46788899999999999999999999988876643 45677999999999999988888888777534334554  6666


Q ss_pred             HHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHH
Q 013489          114 TVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQ  193 (442)
Q Consensus       114 ~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~  193 (442)
                      ..|++++...+.                                                       ...+|...+.++.
T Consensus       102 ~~~~~al~~~p~-------------------------------------------------------~~~~~~~la~~~~  126 (177)
T 2e2e_A          102 AMIDKALALDSN-------------------------------------------------------EITALMLLASDAF  126 (177)
T ss_dssp             HHHHHHHHHCTT-------------------------------------------------------CHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCC-------------------------------------------------------cHHHHHHHHHHHH
Confidence            666665543222                                                       2234555566666


Q ss_pred             HcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHH
Q 013489          194 SMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCY  244 (442)
Q Consensus       194 ~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral  244 (442)
                      ..| +++.|...|++++...|++...+.-       ...+..++.+.....
T Consensus       127 ~~g-~~~~A~~~~~~al~~~p~~~~~~~~-------~~~i~~~~~~~~~~~  169 (177)
T 2e2e_A          127 MQA-NYAQAIELWQKVMDLNSPRINRTQL-------VESINMAKLLQRRSD  169 (177)
T ss_dssp             HTT-CHHHHHHHHHHHHHTCCTTSCHHHH-------HHHHHHHHHHHHHHH
T ss_pred             Hcc-cHHHHHHHHHHHHhhCCCCccHHHH-------HHHHHHHHHhcCCCC
Confidence            677 8888888888888887776443221       123445555555544

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=98.36  E-value=9.9e-07  Score=76.75  Aligned_cols=47  Identities=28%  Similarity=0.320  Sum_probs=42.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVG-GVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||..+++++|+++|+.|| .|.+|+++.+     .+|||||+|.
T Consensus       119 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~  166 (198)
T 1qm9_A          119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMG  166 (198)
T ss_dssp             CCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECS
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeC
Confidence            467999999999999999999999999 9999998765     2799999995

>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=98.36  E-value=7.9e-05  Score=67.18  Aligned_cols=159  Identities=14%  Similarity=0.128  Sum_probs=113.1

Q ss_pred             chhhHHHHHHHHHHHcC--------CCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCC--------hhhHHHHHHHHH
Q 013489           72 KVGNVVRDVYSRATKNC--------PWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA--------FSTFEEYLDLFL  135 (442)
Q Consensus        72 ~~~~~~~~v~erAl~~~--------p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~--------~~~~~~~~~~~~  135 (442)
                      ++.+.+...|++|+..+        |....+|...... ....+..+.+...|++++...        +.....+..+-.
T Consensus        15 ~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~-~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~   93 (283)
T 3edt_B           15 VPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALV-YRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAV   93 (283)
T ss_dssp             SCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHH-HHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHH-HHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHH
Confidence            45566888888888743        4445667666653 344788999999999998641        111111111111


Q ss_pred             HHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcC-chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh--
Q 013489          136 TRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI--  212 (442)
Q Consensus       136 ~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~--  212 (442)
                      .+     ..         ..++......|.+++......... .+....++...+.+....| +++.|..+|++++..  
T Consensus        94 ~~-----~~---------~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g-~~~~A~~~~~~al~~~~  158 (283)
T 3edt_B           94 LY-----GK---------RGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQG-KAEEVEYYYRRALEIYA  158 (283)
T ss_dssp             HH-----HT---------TTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTT-CHHHHHHHHHHHHHHHH
T ss_pred             HH-----HH---------hccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHHHH
Confidence            11     01         135556667778887776555443 3455678888999998889 999999999999998  


Q ss_pred             ------chhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          213 ------SGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       213 ------~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                            .|....+|..++.+....|+++.|..+|++++..
T Consensus       159 ~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~  198 (283)
T 3edt_B          159 TRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILTR  198 (283)
T ss_dssp             HHSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence                  6777789999999999999999999999999963

>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=98.33  E-value=1.9e-06  Score=81.68  Aligned_cols=84  Identities=6%  Similarity=-0.014  Sum_probs=50.6

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHH
Q 013489          184 LYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRF  263 (442)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~f  263 (442)
                      +|...+.+....+ +++.|...|++++..+|++...|...+......|+++.|...|++|+..  .++.+ .++......
T Consensus       198 ~~~nla~~~~~~g-~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~-~a~~~l~~~  273 (336)
T 1p5q_A          198 SHLNLAMCHLKLQ-AFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQL--YPNNK-AAKTQLAVC  273 (336)
T ss_dssp             HHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSSCH-HHHHHHHHH
T ss_pred             HHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CCCCH-HHHHHHHHH
Confidence            3444555555666 6777777777777777777777777777777777777777777777752  33333 344344444


Q ss_pred             HHHhCCHh
Q 013489          264 EREYGTLE  271 (442)
Q Consensus       264 E~~~G~~~  271 (442)
                      ....|..+
T Consensus       274 ~~~~~~~~  281 (336)
T 1p5q_A          274 QQRIRRQL  281 (336)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            44444443

>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=98.32  E-value=2.3e-05  Score=62.08  Aligned_cols=100  Identities=12%  Similarity=-0.010  Sum_probs=87.4

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~  101 (442)
                      ....|...+......|+++.+...|+++|..+|.++.+|...+..+.. .+..+.+...|++|+...|.....|......
T Consensus         3 ~a~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~a~~~~~-~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~   81 (126)
T 3upv_A            3 KAEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAK-LMSFPEAIADCNKAIEKDPNFVRAYIRKATA   81 (126)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHH-hcCHHHHHHHHHHHHHhCCCcHHHHHHHHHH
Confidence            556788888888899999999999999999999999999999987764 4566789999999999999999999998775


Q ss_pred             HHHccCCHHHHHHHHHHHHhCC
Q 013489          102 LERSRASEEEISTVFEKSLLCA  123 (442)
Q Consensus       102 le~~~~~~~~~~~i~~~al~~~  123 (442)
                      +. ..+..+++...|++++...
T Consensus        82 ~~-~~~~~~~A~~~~~~al~~~  102 (126)
T 3upv_A           82 QI-AVKEYASALETLDAARTKD  102 (126)
T ss_dssp             HH-HTTCHHHHHHHHHHHHHHH
T ss_pred             HH-HHhCHHHHHHHHHHHHHhC
Confidence            54 4788999999999999765

>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=98.32  E-value=1.9e-05  Score=62.35  Aligned_cols=116  Identities=15%  Similarity=0.129  Sum_probs=96.1

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ++...|+.++...|.    +...|..++......|+++.+..+|++++...|.+..+|..++..+.. .++.+.+...|+
T Consensus        19 ~A~~~~~~~~~~~~~----~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~A~~~~~   93 (136)
T 2fo7_A           19 EAIEYYQKALELDPR----SAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYK-QGDYDEAIEYYQ   93 (136)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHT-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCc----chhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHH-hcCHHHHHHHHH
Confidence            456778888877664    567888888888888999999999999999999999999998886664 456678999999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCh
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAF  124 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~  124 (442)
                      +++...|....+|...+..+. ..++.+.+...|++++...+
T Consensus        94 ~~~~~~~~~~~~~~~la~~~~-~~~~~~~A~~~~~~~~~~~~  134 (136)
T 2fo7_A           94 KALELDPRSAEAWYNLGNAYY-KQGDYDEAIEYYQKALELDP  134 (136)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHH-TTTCHHHHHHHHHHHHHHST
T ss_pred             HHHHhCCCChHHHHHHHHHHH-HHccHHHHHHHHHHHHccCC
Confidence            999999999999988777444 47888999999999886543

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.30  E-value=1.2e-05  Score=67.11  Aligned_cols=104  Identities=13%  Similarity=0.025  Sum_probs=90.7

Q ss_pred             hHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHH
Q 013489           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSL   99 (442)
Q Consensus        20 ~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~   99 (442)
                      +.+...|..........|+++.+..+|+++|..+|.+..+|......+.. .+..+.+...|++|+...|.....|..+.
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            45677899999988999999999999999999999999999999987764 45667899999999999999999999988


Q ss_pred             HHHHHccCCHHHHHHHHHHHHhCChh
Q 013489          100 LSLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus       100 ~~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                      ..+.. .++.+.+...|++++...+.
T Consensus        87 ~~~~~-~g~~~~A~~~~~~al~~~p~  111 (164)
T 3sz7_A           87 LARFD-MADYKGAKEAYEKGIEAEGN  111 (164)
T ss_dssp             HHHHH-TTCHHHHHHHHHHHHHHHSS
T ss_pred             HHHHH-ccCHHHHHHHHHHHHHhCCC
Confidence            75554 78899999999999976555

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.30  E-value=3.4e-05  Score=67.31  Aligned_cols=115  Identities=9%  Similarity=-0.033  Sum_probs=88.0

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHH----------------HHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMI----------------YLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQY   66 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~----------------y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~   66 (442)
                      +|...|+.+|...|.    +...|..                .+......|+++.+...|+++|..+|.++..|...+..
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            456778888877653    7777777                77777889999999999999999999999999999987


Q ss_pred             HHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHc-cCCHHHHHHHHHHHHhC
Q 013489           67 LDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERS-RASEEEISTVFEKSLLC  122 (442)
Q Consensus        67 l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~-~~~~~~~~~i~~~al~~  122 (442)
                      +... +..+.+...|++++...|.....|......+... ......+...|.+++..
T Consensus        98 ~~~~-g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~~~  153 (208)
T 3urz_A           98 QVCR-GQEKDALRMYEKILQLEADNLAANIFLGNYYYLTAEQEKKKLETDYKKLSSP  153 (208)
T ss_dssp             HHHH-TCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHC---CC
T ss_pred             HHHc-CCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhCC
Confidence            7754 4567899999999999999999998877644322 12234456667776643

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=98.28  E-value=1.6e-06  Score=77.37  Aligned_cols=47  Identities=28%  Similarity=0.320  Sum_probs=42.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVG-GVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+.+++++|+++|+.|| .|.+|+++.+     ++|||||+|.
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~  197 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMG  197 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEES
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEEC
Confidence            357999999999999999999999999 9999998664     3799999995

>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=98.27  E-value=3.8e-05  Score=59.22  Aligned_cols=103  Identities=17%  Similarity=0.062  Sum_probs=88.4

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~  101 (442)
                      ....|...+......|+++.+..+|++++...|.+..+|...+..+... ++.+.+...|++++...|....+|..+...
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~-~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~   81 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKK-GDYQKAYEDGCKTVDLKPDWGKGYSRKAAA   81 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHhh-ccHHHHHHHHHHHHHhCcccHHHHHHHHHH
Confidence            4567888888888899999999999999999999999999998876644 566789999999999999999999988875


Q ss_pred             HHHccCCHHHHHHHHHHHHhCChhh
Q 013489          102 LERSRASEEEISTVFEKSLLCAFST  126 (442)
Q Consensus       102 le~~~~~~~~~~~i~~~al~~~~~~  126 (442)
                      +.. .+..+.+...|++++...+..
T Consensus        82 ~~~-~~~~~~A~~~~~~~~~~~~~~  105 (118)
T 1elw_A           82 LEF-LNRFEEAKRTYEEGLKHEANN  105 (118)
T ss_dssp             HHH-TTCHHHHHHHHHHHHTTCTTC
T ss_pred             HHH-HhhHHHHHHHHHHHHHcCCCC
Confidence            554 788999999999999877654

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=98.27  E-value=0.00023  Score=68.10  Aligned_cols=224  Identities=10%  Similarity=-0.007  Sum_probs=137.3

Q ss_pred             hhhHHHHHHhhcCCC--CChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCH-------HHHHHHHHHHHHhcch
Q 013489            3 NARAHLEEQISRQDL--SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS-------DLWLDYTQYLDKTLKV   73 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~--~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~-------~lW~~Y~~~l~~~~~~   73 (442)
                      +|...|+.++.....  .++.....|...+......|+++.+...|++|+...+...       ..+...+.... ..+.
T Consensus       121 ~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~-~~g~  199 (383)
T 3ulq_A          121 SAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLFATNFL-DLKQ  199 (383)
T ss_dssp             HHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHHHHHHH-HTTC
T ss_pred             HHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHHHHH-HhcC
Confidence            355677777754221  1123456777777777888999999999999998644332       23333333222 3456


Q ss_pred             hhHHHHHHHHHHHcCCCcH------HHHHHHHHHHHHccCCHHHHHHHHHHHHhC-----C-hhhHHHHHHHHHHHHHHH
Q 013489           74 GNVVRDVYSRATKNCPWVG------ELWVRSLLSLERSRASEEEISTVFEKSLLC-----A-FSTFEEYLDLFLTRIDGL  141 (442)
Q Consensus        74 ~~~~~~v~erAl~~~p~s~------~lW~~y~~~le~~~~~~~~~~~i~~~al~~-----~-~~~~~~~~~~~~~~~~~l  141 (442)
                      .+.+...|++|+..+|...      .+|..... +....++.+.+...|++|+..     . +.....+..+-..+.   
T Consensus       200 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~-~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~---  275 (383)
T 3ulq_A          200 YEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGL-CKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHY---  275 (383)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHH---
T ss_pred             HHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHH-HHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHH---
Confidence            6789999999998664322      34555333 444578889999999999862     2 222222222111110   


Q ss_pred             HHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCC---HHHHHHHHHHHHHhchhHHH
Q 013489          142 RRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKD---MVSARGVWERLLKISGAMLE  218 (442)
Q Consensus       142 ~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~---~~~ar~i~~~~l~~~~~~~~  218 (442)
                        ..         .++......+++|+.......  .+.....+...+.+....+ +   +..|..++++. ...+....
T Consensus       276 --~~---------g~~~~A~~~~~~al~~~~~~~--~~~~~~~~~~l~~~~~~~~-~~~~~~~al~~~~~~-~~~~~~~~  340 (383)
T 3ulq_A          276 --KL---------GKIDKAHEYHSKGMAYSQKAG--DVIYLSEFEFLKSLYLSGP-DEEAIQGFFDFLESK-MLYADLED  340 (383)
T ss_dssp             --HT---------TCHHHHHHHHHHHHHHHHHHT--CHHHHHHHHHHHHHHTSSC-CHHHHHHHHHHHHHT-TCHHHHHH
T ss_pred             --HC---------CCHHHHHHHHHHHHHHHHHcC--CHHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHC-cCHHHHHH
Confidence              11         344555566677666543321  1222222344566666666 6   66666666665 23455567


Q ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          219 AWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       219 ~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      ++...+.+....|+++.|...|++|+..
T Consensus       341 ~~~~la~~y~~~g~~~~A~~~~~~al~~  368 (383)
T 3ulq_A          341 FAIDVAKYYHERKNFQKASAYFLKVEQV  368 (383)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            8888999999999999999999999863

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.27  E-value=3.2e-05  Score=61.22  Aligned_cols=105  Identities=16%  Similarity=0.054  Sum_probs=90.7

Q ss_pred             hHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHH
Q 013489           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSL   99 (442)
Q Consensus        20 ~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~   99 (442)
                      +.....|...+......|+++.+..+|++++...|.+..+|...+..+.. .++.+.+...|++++...|....+|..+.
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~-~~~~~~A~~~~~~a~~~~~~~~~~~~~la   91 (133)
T 2lni_A           13 PDLALMVKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTK-LLEFQLALKDCEECIQLEPTFIKGYTRKA   91 (133)
T ss_dssp             SCHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTCTTCHHHHHHHHHHHTT-TTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHH-hccHHHHHHHHHHHHHhCCCchHHHHHHH
Confidence            45778899999999999999999999999999999999999999887653 45667899999999999999999999988


Q ss_pred             HHHHHccCCHHHHHHHHHHHHhCChhh
Q 013489          100 LSLERSRASEEEISTVFEKSLLCAFST  126 (442)
Q Consensus       100 ~~le~~~~~~~~~~~i~~~al~~~~~~  126 (442)
                      ..+. ..+..+.+...|++++...+..
T Consensus        92 ~~~~-~~~~~~~A~~~~~~~~~~~p~~  117 (133)
T 2lni_A           92 AALE-AMKDYTKAMDVYQKALDLDSSC  117 (133)
T ss_dssp             HHHH-HTTCHHHHHHHHHHHHHHCGGG
T ss_pred             HHHH-HHhhHHHHHHHHHHHHHhCCCc
Confidence            7554 4688999999999999776653

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=98.26  E-value=0.00027  Score=67.16  Aligned_cols=229  Identities=11%  Similarity=-0.033  Sum_probs=117.4

Q ss_pred             hhhHHHHHHhhcCCCCChH-hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHH------HHHHHHHHHhcchhh
Q 013489            3 NARAHLEEQISRQDLSDSE-KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLW------LDYTQYLDKTLKVGN   75 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~-~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW------~~Y~~~l~~~~~~~~   75 (442)
                      .++..++.+|...+..++. ....+..........|+++.+...|++++...|.....+      ..... +....++.+
T Consensus        32 ~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~-~~~~~G~~~  110 (373)
T 1hz4_A           32 EAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSE-ILFAQGFLQ  110 (373)
T ss_dssp             HHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HHHHTTCHH
T ss_pred             HHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHH-HHHHCCCHH
Confidence            3566777777766542221 112344445555667888888888888887654333221      11122 222345566


Q ss_pred             HHHHHHHHHHHcCC--------CcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh-hHHHHHHHHHHHHHHHHHHhh
Q 013489           76 VVRDVYSRATKNCP--------WVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFS-TFEEYLDLFLTRIDGLRRRIL  146 (442)
Q Consensus        76 ~~~~v~erAl~~~p--------~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~-~~~~~~~~~~~~~~~l~rr~~  146 (442)
                      .+...|++++...+        .....+..... +....++.+++...+++++..... ........+... ..+...  
T Consensus       111 ~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~-~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l-a~~~~~--  186 (373)
T 1hz4_A          111 TAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQ-LLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAML-IQCSLA--  186 (373)
T ss_dssp             HHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHH-HHHHHH--
T ss_pred             HHHHHHHHHHHHHHHhccccCcHHHHHHHHHHH-HHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHH-HHHHHH--
Confidence            78888888887542        12223333333 333467888888888888854321 000011111000 000000  


Q ss_pred             ccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHH--HHHHHHHHHcCCCHHHHHHHHHHHHHhchhH----HHHH
Q 013489          147 FSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLY--AYWAHLEQSMGKDMVSARGVWERLLKISGAM----LEAW  220 (442)
Q Consensus       147 ~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~--~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~----~~~w  220 (442)
                             ..++......++++.......  ..+......  ...+.+....| +++.|+..+.+++...+..    ...+
T Consensus       187 -------~g~~~~A~~~l~~a~~~~~~~--~~~~~~~~~~~~~~~~~~~~~g-~~~~A~~~~~~a~~~~~~~~~~~~~~~  256 (373)
T 1hz4_A          187 -------RGDLDNARSQLNRLENLLGNG--KYHSDWISNANKVRVIYWQMTG-DKAAAANWLRHTAKPEFANNHFLQGQW  256 (373)
T ss_dssp             -------HTCHHHHHHHHHHHHHHHTTS--CCCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHSCCCCCTTCGGGHHHH
T ss_pred             -------cCCHHHHHHHHHHHHHHHhcc--CcchhHHHHHHHHHHHHHHHCC-CHHHHHHHHHhCCCCCCCcchhhHHHH
Confidence                   023334444455554432211  011111111  11223344566 7888888888877654321    2345


Q ss_pred             HHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          221 QSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       221 ~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      ..++......|+++.|..++++++..
T Consensus       257 ~~la~~~~~~g~~~~A~~~l~~a~~~  282 (373)
T 1hz4_A          257 RNIARAQILLGEFEPAEIVLEELNEN  282 (373)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            66677777778888888888887753

>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=98.26  E-value=2.7e-05  Score=66.26  Aligned_cols=117  Identities=12%  Similarity=0.136  Sum_probs=86.2

Q ss_pred             chhhHHHHHHhhc--CCCCChHhHHHHHHHHHHHHhc---CCh---hhHH-HHHHHHHhcCCC---------CHHHHHHH
Q 013489            2 CNARAHLEEQISR--QDLSDSEKFQQYMIYLKYEQSS---GDP---GRVQ-LLYERAITDFPV---------SSDLWLDY   63 (442)
Q Consensus         2 ~~~r~~yE~~l~~--~~~~~~~~~~~w~~y~~~e~~~---g~~---~~~~-~lyERal~~~p~---------~~~lW~~Y   63 (442)
                      ...|..||..|..  ...  .+-++.|..||.|....   |..   .... .++|||+..+-.         ...+|+.|
T Consensus         9 ~~~r~~fE~~l~~~l~~~--dDPL~~w~~YIkW~ee~yP~g~~~~~s~L~~~lLErc~~~F~~~~rYkND~RYLklWl~Y   86 (202)
T 3esl_A            9 NQTKIAYEQRLLNDLEDM--DDPLDLFLDYMIWISTSYIEVDSESGQEVLRSTMERCLIYIQDMETYRNDPRFLKIWIWY   86 (202)
T ss_dssp             HHHHHHHHHHHHHTGGGC--SCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHTTCGGGTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccccC--CCchHHHHHHHHHHHHhCCCCCCcchhchHHHHHHHHHHHhcccccccCCHHHHHHHHHH
Confidence            3578999999988  332  23478899999998754   332   2344 799999985443         34799999


Q ss_pred             HHHHHHhcchhhHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCC
Q 013489           64 TQYLDKTLKVGNVVRDVYSRATKN--CPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA  123 (442)
Q Consensus        64 ~~~l~~~~~~~~~~~~v~erAl~~--~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~  123 (442)
                      +.++..  ++......+|....++  .-....+|..|+.++|. .++...+..||+.+++..
T Consensus        87 a~~~~~--~~~~~p~~if~~L~~~~IG~~~AlfYe~wA~~lE~-~g~~~~A~~Vy~~GI~~~  145 (202)
T 3esl_A           87 INLFLS--NNFHESENTFKYMFNKGIGTKLSLFYEEFSKLLEN-AQFFLEAKVLLELGAENN  145 (202)
T ss_dssp             HHHHST--TCHHHHHHHHHHHHHHTSSTTBHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHTT
T ss_pred             HHhhcc--cccCCHHHHHHHHHHCCCcHHHHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHcC
Confidence            998621  1122356788877773  35678999999999997 688999999999999764

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.26  E-value=4.7e-05  Score=69.43  Aligned_cols=187  Identities=7%  Similarity=-0.082  Sum_probs=131.2

Q ss_pred             hcCChhhHHHHHHHHHhcCCCCHHHHHHH-------HHHHHHhcchhhHHHHHHHHHHHcCCC-----------------
Q 013489           35 SSGDPGRVQLLYERAITDFPVSSDLWLDY-------TQYLDKTLKVGNVVRDVYSRATKNCPW-----------------   90 (442)
Q Consensus        35 ~~g~~~~~~~lyERal~~~p~~~~lW~~Y-------~~~l~~~~~~~~~~~~v~erAl~~~p~-----------------   90 (442)
                      ..+++..+...|.+++..+|...+.|+..       ...+..... ...+...+.|++..-|.                 
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 LPMSEARSLDLFTEITNYDESACDAWIGRIRCGDTDRVTLFRAWY-SRRNFGQLSGSVQISMSTLNARIAIGGLYGDITY   96 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHTTCCCHHHHHHHHH-TGGGTTHHHHTTTCCGGGGCCEEECCTTTCCCEE
T ss_pred             cCCCHHHHHHHHHHHHHhChhhhHHHHhHHHccCCcHHHHHHHHH-HHHHHHHHHHHhcCChhhhhhhhccCCccccccc
Confidence            46899999999999999999999999999       444443222 23345677777763332                 


Q ss_pred             ----cHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHH
Q 013489           91 ----VGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQR  166 (442)
Q Consensus        91 ----s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~  166 (442)
                          -..++..|+..+-. .+..+++..+|..++..++... .   .|..-+-++  +.         .+       +..
T Consensus        97 ~v~~r~dl~LayA~~L~~-~g~y~eA~~~l~~~~~~~p~~~-~---~~~~a~l~~--~~---------~r-------~~d  153 (282)
T 4f3v_A           97 PVTSPLAITMGFAACEAA-QGNYADAMEALEAAPVAGSEHL-V---AWMKAVVYG--AA---------ER-------WTD  153 (282)
T ss_dssp             ECSSHHHHHHHHHHHHHH-HTCHHHHHHHHTSSCCTTCHHH-H---HHHHHHHHH--HT---------TC-------HHH
T ss_pred             ccCCHhHHHHHHHHHHHH-CCCHHHHHHHHHHHHhcCCchH-H---HHHHHHHHH--Hc---------CC-------HHH
Confidence                14688889885554 6889999999998776555433 1   111111001  00         22       344


Q ss_pred             HHHHHhhhhcCchhh--HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc--hh-HHHHHHHHHHHHHhcccHHHHHHHHH
Q 013489          167 ASDYLSEQMKNTDGL--LRLYAYWAHLEQSMGKDMVSARGVWERLLKIS--GA-MLEAWQSYISMEIELDHINEARSIYK  241 (442)
Q Consensus       167 a~~~l~~~~~~~~~~--~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~--~~-~~~~w~~~~~~e~~~g~~~~ar~i~~  241 (442)
                      ++.++.......++.  ..++.+.......+| +++.|...|++++...  |. ..+.++......+..|+.+.|+.+|+
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            455554443322232  347788888888999 9999999999999653  66 67899999999999999999999999


Q ss_pred             HHHhc
Q 013489          242 RCYSK  246 (442)
Q Consensus       242 ral~~  246 (442)
                      +++..
T Consensus       233 ~a~a~  237 (282)
T 4f3v_A          233 WLQTT  237 (282)
T ss_dssp             HHHHH
T ss_pred             HHHhc
Confidence            99973

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.26  E-value=2.1e-06  Score=67.28  Aligned_cols=48  Identities=23%  Similarity=0.275  Sum_probs=38.5

Q ss_pred             CCceEEEcCCCCCCC-----------HHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKAT-----------YEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~-----------~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|+|.||.....           +++|+.+|++||.|.+|.| .++   .++|||||+|.
T Consensus        14 ~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~   72 (112)
T 2dit_A           14 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFR   72 (112)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECS
T ss_pred             CceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEEC
Confidence            356999999944432           5799999999999999955 553   27999999995

>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=98.26  E-value=4.6e-05  Score=62.94  Aligned_cols=110  Identities=15%  Similarity=0.274  Sum_probs=82.0

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhc---CChh-hHHHHHHHHHhcCCCCH---------HHHHHHHHHHHHh
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS---GDPG-RVQLLYERAITDFPVSS---------DLWLDYTQYLDKT   70 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~---g~~~-~~~~lyERal~~~p~~~---------~lW~~Y~~~l~~~   70 (442)
                      .|..||..|.....  .+-++.|..||.|....   |... ....++|||+..+..+.         .+|+.|+.+.   
T Consensus         2 ~r~~fE~~i~~~~g--dDPL~~w~~yIkW~e~~~p~~~~~s~L~~lLErc~~~f~~~~~YknD~RyLklWl~ya~~~---   76 (164)
T 2wvi_A            2 QKRAFEYEIRFYTG--NDPLDVWDRYISWTEQNYPQGGKESNMSTLLERAVEALQGEKRYYSDPRFLNLWLKLGRLC---   76 (164)
T ss_dssp             CTHHHHHHCCCCCS--SCTHHHHHHHHHHHHHHCCC----CCHHHHHHHHHHHTTTCGGGTTCHHHHHHHHHHHHHC---
T ss_pred             hHHHHHHHHhhcCC--CCChHHHHHHHHHHHHHCcCCCccchHHHHHHHHHHHhhhhhhhccCHHHHHHHHHHHHhc---
Confidence            47789999974333  23478899999998753   3332 45779999999765443         6999999874   


Q ss_pred             cchhhHHHHHHHHHHH--cCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCC
Q 013489           71 LKVGNVVRDVYSRATK--NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA  123 (442)
Q Consensus        71 ~~~~~~~~~v~erAl~--~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~  123 (442)
                       .+   ...+|....+  ..-....+|..|+.++|. .++...+..||..++...
T Consensus        77 -~~---p~~if~~L~~~~IG~~~AlfY~~wA~~lE~-~~~~~~A~~Iy~~Gi~~~  126 (164)
T 2wvi_A           77 -NE---PLDMYSYLHNQGIGVSLAQFYISWAEEYEA-RENFRKADAIFQEGIQQK  126 (164)
T ss_dssp             -SC---HHHHHHHHHHTTSSTTBHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHTT
T ss_pred             -CC---HHHHHHHHHHCCcchhhHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHcC
Confidence             22   3567777776  346678999999999997 689999999999999764

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.26  E-value=9.5e-05  Score=68.19  Aligned_cols=213  Identities=12%  Similarity=0.118  Sum_probs=127.5

Q ss_pred             ChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCC------cHHHHHHHHHHHHHccCCHHH
Q 013489           38 DPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPW------VGELWVRSLLSLERSRASEEE  111 (442)
Q Consensus        38 ~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~------s~~lW~~y~~~le~~~~~~~~  111 (442)
                      +++.+..+|+++...              + ...+..+.+...|.+|+...+.      ....|..... +....++.++
T Consensus        32 ~~~~A~~~~~~a~~~--------------~-~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~-~~~~~g~~~~   95 (292)
T 1qqe_A           32 KFEEAADLCVQAATI--------------Y-RLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYK-CFKSGGNSVN   95 (292)
T ss_dssp             HHHHHHHHHHHHHHH--------------H-HHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HHHHTTCHHH
T ss_pred             cHHHHHHHHHHHHHH--------------H-HHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH-HHHHCCCHHH
Confidence            378888889888431              1 2335567788899999886422      2356666555 4444688899


Q ss_pred             HHHHHHHHHhCChh--hHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHH
Q 013489          112 ISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWA  189 (442)
Q Consensus       112 ~~~i~~~al~~~~~--~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a  189 (442)
                      +...|++|+...+.  ........+.. +..+....        ..++......|++|+.+....- .......++...+
T Consensus        96 A~~~~~~Al~l~~~~g~~~~~a~~~~~-lg~~~~~~--------lg~~~~A~~~~~~Al~~~~~~~-~~~~~~~~~~~lg  165 (292)
T 1qqe_A           96 AVDSLENAIQIFTHRGQFRRGANFKFE-LGEILEND--------LHDYAKAIDCYELAGEWYAQDQ-SVALSNKCFIKCA  165 (292)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHH-HHHHHHHT--------TCCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHH-HHHHHHHh--------hcCHHHHHHHHHHHHHHHHhCC-ChHHHHHHHHHHH
Confidence            99999999865322  11111111111 11110010        0344455566777776543210 1111245778889


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHhchhHH-------HHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHH----HHH
Q 013489          190 HLEQSMGKDMVSARGVWERLLKISGAML-------EAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSED----ICH  258 (442)
Q Consensus       190 ~~e~~~~~~~~~ar~i~~~~l~~~~~~~-------~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~----i~~  258 (442)
                      .+....| +++.|..+|++++...|+..       ..|...+.+....|+++.|...|++++..  .++.+..    ++.
T Consensus       166 ~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~~~~~~~l~  242 (292)
T 1qqe_A          166 DLKALDG-QYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSE--DPNFADSRESNFLK  242 (292)
T ss_dssp             HHHHHTT-CHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC-----------HHHHH
T ss_pred             HHHHHhC-CHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCCCCcHHHHHHH
Confidence            9999999 99999999999999866432       26777778888889999999999999862  2222211    111


Q ss_pred             HHHHHHHHhCCHhhHHHHHHhh
Q 013489          259 AWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       259 ~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                      ...... ..|+.+.++.++...
T Consensus       243 ~l~~~~-~~~~~~~~~~A~~~~  263 (292)
T 1qqe_A          243 SLIDAV-NEGDSEQLSEHCKEF  263 (292)
T ss_dssp             HHHHHH-HTTCTTTHHHHHHHH
T ss_pred             HHHHHH-HcCCHHHHHHHHHHh
Confidence            111111 236777777777655

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=98.25  E-value=1.5e-07  Score=72.74  Aligned_cols=45  Identities=4%  Similarity=0.078  Sum_probs=38.4

Q ss_pred             EcCCCCCCCHHHHHHHh------------ccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          396 LSNINLKATYEDLRRFF------------SDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       396 v~nl~~~~~~~~l~~~f------------~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +++||+.+++++|++.|            ++||.|.+|.|+.++ +|+++|||||+|.
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~   76 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFR   76 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEES
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEEC
Confidence            56788888888777766            999999999999984 6899999999995

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.24  E-value=5.2e-05  Score=59.55  Aligned_cols=105  Identities=16%  Similarity=0.046  Sum_probs=89.9

Q ss_pred             hHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHH
Q 013489           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSL   99 (442)
Q Consensus        20 ~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~   99 (442)
                      +.+...|...+......|+++.+..+|++++...|.+..+|...+..+.. .++.+.+...|++++...|....+|....
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            45677888888888889999999999999999999999999999887764 45667899999999999999999998887


Q ss_pred             HHHHHccCCHHHHHHHHHHHHhCChhh
Q 013489          100 LSLERSRASEEEISTVFEKSLLCAFST  126 (442)
Q Consensus       100 ~~le~~~~~~~~~~~i~~~al~~~~~~  126 (442)
                      ..+. ..++.+.+...|++++...+..
T Consensus        88 ~~~~-~~~~~~~A~~~~~~~~~~~p~~  113 (131)
T 2vyi_A           88 LALS-SLNKHVEAVAYYKKALELDPDN  113 (131)
T ss_dssp             HHHH-HTTCHHHHHHHHHHHHHHSTTC
T ss_pred             HHHH-HhCCHHHHHHHHHHHHhcCccc
Confidence            7554 4788999999999999876654

>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=98.24  E-value=4.4e-05  Score=71.89  Aligned_cols=222  Identities=9%  Similarity=-0.036  Sum_probs=142.9

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcC-ChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcc-hhhHHHHHH
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSG-DPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLK-VGNVVRDVY   81 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g-~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~-~~~~~~~v~   81 (442)
                      +-..++.+|..+|.    ++.+|..=.......| +++..+.+++.+|..+|.+..+|..-.-.+....+ ..+.....+
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            44567888888876    8899987777777777 58999999999999999999999998877765523 556778999


Q ss_pred             HHHHHcCCCcHHHHHHHHHHHHHccCCH-------HHHHHHHHHHHhCChhh--HHHHHHHHHHHHHHHHHHhhccCccc
Q 013489           82 SRATKNCPWVGELWVRSLLSLERSRASE-------EEISTVFEKSLLCAFST--FEEYLDLFLTRIDGLRRRILFSGEVE  152 (442)
Q Consensus        82 erAl~~~p~s~~lW~~y~~~le~~~~~~-------~~~~~i~~~al~~~~~~--~~~~~~~~~~~~~~l~rr~~~~~~~~  152 (442)
                      ++++...|.+...|....-.+.......       .+....+++++...+.+  .|.+..+.+..       .....   
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 HGSLLPDPKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDGRNNSAWGWRWYLRVS-------RPGAE---  218 (349)
T ss_dssp             HHHTSSCTTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHTT-------STTCC---
T ss_pred             HHHHHhCCCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHh-------ccccc---
Confidence            9999999999999988665444322211       24555667777666553  33333222111       10000   


Q ss_pred             hhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCC-------------------HHHHHHHHHHHHHhc
Q 013489          153 GVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKD-------------------MVSARGVWERLLKIS  213 (442)
Q Consensus       153 ~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~-------------------~~~ar~i~~~~l~~~  213 (442)
                        .    ....++++++++..++...+.....|.+..-+....+..                   .....++...++...
T Consensus       219 --~----~~~~~~eELe~~~~aI~~~P~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  292 (349)
T 3q7a_A          219 --T----SSRSLQDELIYILKSIHLIPHNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDP  292 (349)
T ss_dssp             --C----CHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCCC-C
T ss_pred             --c----chHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHHhcc
Confidence              0    024466777777666665666677888876666666533                   222222322222221


Q ss_pred             ------hhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          214 ------GAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       214 ------~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                            +.+.-++--.+++....|+.++|..+|+....
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                  23444566666666677888999999999765

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=98.24  E-value=0.0004  Score=66.38  Aligned_cols=201  Identities=12%  Similarity=0.027  Sum_probs=123.2

Q ss_pred             HHHHHHhcCChhhHHHHHHHHHhc---CCCC---HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcH-------HHH
Q 013489           29 YLKYEQSSGDPGRVQLLYERAITD---FPVS---SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVG-------ELW   95 (442)
Q Consensus        29 y~~~e~~~g~~~~~~~lyERal~~---~p~~---~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~-------~lW   95 (442)
                      .+.+....|+++.+...|++|+..   .+..   ..+|...+.... ..++.+.+...|.+|+..++...       .++
T Consensus       109 ~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~-~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  187 (383)
T 3ulq_A          109 RGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYY-YMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCH  187 (383)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHHHHHHHhCccchHHHHHHH
Confidence            344456679999999999999986   3332   345555555444 34566789999999999764332       233


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCChhh--HHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhh
Q 013489           96 VRSLLSLERSRASEEEISTVFEKSLLCAFST--FEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSE  173 (442)
Q Consensus        96 ~~y~~~le~~~~~~~~~~~i~~~al~~~~~~--~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~  173 (442)
                      ..... +....+..+.+...|++|+......  .......+. .+..+....         .++......|++|+.+...
T Consensus       188 ~~lg~-~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~-~lg~~y~~~---------g~~~~A~~~~~~al~~~~~  256 (383)
T 3ulq_A          188 SLFAT-NFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLY-NIGLCKNSQ---------SQYEDAIPYFKRAIAVFEE  256 (383)
T ss_dssp             HHHHH-HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH-HHHHHHHHT---------TCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHH-HHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHH-HHHHHHHHC---------CCHHHHHHHHHHHHHHHHh
Confidence            33333 4445788999999999999643221  111111111 111111111         3455555666666665433


Q ss_pred             hhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhch-----hHHHHHHHHHHHHHhccc---HHHHHHHHHHH
Q 013489          174 QMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG-----AMLEAWQSYISMEIELDH---INEARSIYKRC  243 (442)
Q Consensus       174 ~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~-----~~~~~w~~~~~~e~~~g~---~~~ar~i~~ra  243 (442)
                      .. ..+.....+...+.+....| +++.|...+++++...+     .....+.....+....|+   +..|..+++++
T Consensus       257 ~~-~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~  332 (383)
T 3ulq_A          257 SN-ILPSLPQAYFLITQIHYKLG-KIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESK  332 (383)
T ss_dssp             TT-CGGGHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHT
T ss_pred             hc-cchhHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHC
Confidence            21 11445677888899989999 99999999999998742     222233445555566677   66666666665

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.23  E-value=1.5e-05  Score=63.75  Aligned_cols=93  Identities=13%  Similarity=-0.044  Sum_probs=81.4

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      +|...|+.+|...|.    +...|...+......|+++.+...|+++|..+|.++..|...+..+.. .+..+.+...|+
T Consensus        31 ~A~~~~~~al~~~p~----~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~-~~~~~~A~~~~~  105 (126)
T 4gco_A           31 TAMRHYNEAVKRDPE----NAILYSNRAACLTKLMEFQRALDDCDTCIRLDSKFIKGYIRKAACLVA-MREWSKAQRAYE  105 (126)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC----CHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHH-CCCHHHHHHHHH
Confidence            467789999988876    788999999999999999999999999999999999999999987764 456688999999


Q ss_pred             HHHHcCCCcHHHHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLL  100 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~  100 (442)
                      +|+...|....++..+..
T Consensus       106 ~al~l~P~~~~a~~~l~~  123 (126)
T 4gco_A          106 DALQVDPSNEEAREGVRN  123 (126)
T ss_dssp             HHHHHCTTCHHHHHHHHH
T ss_pred             HHHHHCcCCHHHHHHHHH
Confidence            999999999888877543

>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=98.21  E-value=3.6e-05  Score=62.65  Aligned_cols=110  Identities=14%  Similarity=0.231  Sum_probs=85.0

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhc---CChhhHHHHHHHHHhcCCCC---------HHHHHHHHHHHHHh
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS---GDPGRVQLLYERAITDFPVS---------SDLWLDYTQYLDKT   70 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~---g~~~~~~~lyERal~~~p~~---------~~lW~~Y~~~l~~~   70 (442)
                      ..|..||..|......|  -++.|..||.|....   |. .....++|||+..+..+         ..+|+.|+.+..  
T Consensus         8 ~~~~~fE~~i~~y~gdD--PL~~w~~YI~W~e~~~P~g~-~~l~~lLErc~~~f~~~~~YknD~RyLklWl~ya~~~~--   82 (152)
T 4a1g_A            8 NVLQMLEAHMQSYKGND--PLGEWERYIQWVEENFPENK-EYLITLLEHLMKEFLDKKKYHNDPRFISYCLKFAEYNS--   82 (152)
T ss_dssp             HHHHHHHHHTTSCCSSC--HHHHHHHHHHHHHTTCSSCT-HHHHHHHHHHHHHHTTCGGGTTCHHHHHHHHHHHTTBS--
T ss_pred             HHHHHHHHHHHhCCCCC--CHHHHHHHHHHHHHHcCCCc-hhHHHHHHHHHHHhcccccccCCHHHHHHHHHHHHhcC--
Confidence            36788999998864323  477899999999864   33 34678999999865433         369999998632  


Q ss_pred             cchhhHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCC
Q 013489           71 LKVGNVVRDVYSRATKN--CPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA  123 (442)
Q Consensus        71 ~~~~~~~~~v~erAl~~--~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~  123 (442)
                        +   ...+|....++  .-....+|..|+.++|. .++...+..||+.+++..
T Consensus        83 --d---p~~if~~L~~~~IG~~~AlfYe~wA~~lE~-~g~~~~A~~Vy~~Gi~~~  131 (152)
T 4a1g_A           83 --D---LHQFFEFLYNHGIGTLSSPLYIAWAGHLEA-QGELQHASAVLQRGIQNQ  131 (152)
T ss_dssp             --C---HHHHHHHHHTTTTTTTBHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHTT
T ss_pred             --C---HHHHHHHHHHCCCcHHHHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHcC
Confidence              2   46788887773  35678999999999997 689999999999999764

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.19  E-value=0.0001  Score=65.02  Aligned_cols=177  Identities=11%  Similarity=-0.026  Sum_probs=108.4

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHH---HHHHHHHHHH----------
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDL---WLDYTQYLDK----------   69 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~l---W~~Y~~~l~~----------   69 (442)
                      +|...|+..|...|.. +.....|...+......|+++.+...|++++..+|.++.+   |..-......          
T Consensus        22 ~A~~~~~~~~~~~p~~-~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~~g~~~~~~~~~~~~~~~  100 (225)
T 2yhc_A           22 QAITQLEALDNRYPFG-PYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFF  100 (225)
T ss_dssp             HHHHHHHHHHHHCTTS-TTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHC-------
T ss_pred             HHHHHHHHHHHhCCCC-hHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHHHHHHHHHhhhhhhhhhhh
Confidence            4677899999877642 2234567777777788999999999999999999998753   3222221111          


Q ss_pred             -------hcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHH
Q 013489           70 -------TLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLR  142 (442)
Q Consensus        70 -------~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~  142 (442)
                             ..+..+.+...|++++...|.+...|..+......        ......        ....+...  +   . 
T Consensus       101 ~~~~~~~~~~~~~~A~~~~~~~l~~~P~~~~a~~a~~~l~~~--------~~~~~~--------~~~~~a~~--~---~-  158 (225)
T 2yhc_A          101 GVDRSDRDPQQARAAFSDFSKLVRGYPNSQYTTDATKRLVFL--------KDRLAK--------YEYSVAEY--Y---T-  158 (225)
T ss_dssp             -------CCHHHHHHHHHHHHHHTTCTTCTTHHHHHHHHHHH--------HHHHHH--------HHHHHHHH--H---H-
T ss_pred             ccchhhcCcHHHHHHHHHHHHHHHHCcCChhHHHHHHHHHHH--------HHHHHH--------HHHHHHHH--H---H-
Confidence                   12456779999999999999998777654431111        000000        00000000  0   0 


Q ss_pred             HHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHH
Q 013489          143 RRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAML  217 (442)
Q Consensus       143 rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~  217 (442)
                       +         ..++......|++++....    ..+...+.+...+......| +.+.|...++.+....|++.
T Consensus       159 -~---------~~~~~~A~~~~~~~l~~~p----~~~~~~~a~~~l~~~~~~~g-~~~~A~~~~~~l~~~~~~~~  218 (225)
T 2yhc_A          159 -E---------RGAWVAVVNRVEGMLRDYP----DTQATRDALPLMENAYRQMQ-MNAQAEKVAKIIAANSSNTL  218 (225)
T ss_dssp             -H---------HTCHHHHHHHHHHHHHHST----TSHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHCCSCCC
T ss_pred             -H---------cCcHHHHHHHHHHHHHHCc----CCCccHHHHHHHHHHHHHcC-CcHHHHHHHHHHHhhCCCch
Confidence             0         0233333344444443211    12223467888888888999 99999999999988777643

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.18  E-value=1.2e-05  Score=61.59  Aligned_cols=103  Identities=17%  Similarity=0.143  Sum_probs=86.8

Q ss_pred             HhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCC--cHHHHHHH
Q 013489           21 EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPW--VGELWVRS   98 (442)
Q Consensus        21 ~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~--s~~lW~~y   98 (442)
                      .+...|...+......|+++.+..+|++++...|.+..+|..++..+... +..+.+...|++++...|.  ...+|...
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~-~~~~~A~~~~~~a~~~~~~~~~~~~~~~l   82 (112)
T 2kck_A            4 QNPEEYYLEGVLQYDAGNYTESIDLFEKAIQLDPEESKYWLMKGKALYNL-ERYEEAVDCYNYVINVIEDEYNKDVWAAK   82 (112)
T ss_dssp             SSTTGGGGHHHHHHSSCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHTSCCTTCHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHc-cCHHHHHHHHHHHHHhCcccchHHHHHHH
Confidence            35567777888788899999999999999999999999999998877644 4567899999999999999  99999988


Q ss_pred             HHHHHHcc-CCHHHHHHHHHHHHhCChh
Q 013489           99 LLSLERSR-ASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus        99 ~~~le~~~-~~~~~~~~i~~~al~~~~~  125 (442)
                      ... .... +..+.+...|++++...+.
T Consensus        83 ~~~-~~~~~~~~~~A~~~~~~~~~~~p~  109 (112)
T 2kck_A           83 ADA-LRYIEGKEVEAEIAEARAKLEHHH  109 (112)
T ss_dssp             HHH-HTTCSSCSHHHHHHHHHHGGGCCC
T ss_pred             HHH-HHHHhCCHHHHHHHHHHHhhcccC
Confidence            774 4457 8889999999999876543

>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=98.18  E-value=1.1e-05  Score=66.35  Aligned_cols=77  Identities=1%  Similarity=-0.157  Sum_probs=51.7

Q ss_pred             HHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhC
Q 013489           44 LLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLC  122 (442)
Q Consensus        44 ~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~  122 (442)
                      ..|++++..+|.+...|...+..+... +..+.+...|++++...|....+|......+. ..+..+++...|++++..
T Consensus         8 ~~~~~al~~~p~~~~~~~~~g~~~~~~-g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~-~~g~~~~A~~~~~~al~l   84 (148)
T 2vgx_A            8 GTIAMLNEISSDTLEQLYSLAFNQYQS-GXYEDAHXVFQALCVLDHYDSRFFLGLGACRQ-AMGQYDLAIHSYSYGAVM   84 (148)
T ss_dssp             CSHHHHTTCCHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHH
T ss_pred             hhHHHHHcCCHhhHHHHHHHHHHHHHc-CChHHHHHHHHHHHHcCcccHHHHHHHHHHHH-HHhhHHHHHHHHHHHHhc
Confidence            357777777777777777777666543 34566777888888877877777776655333 356666666666666543

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=98.18  E-value=1.9e-06  Score=66.49  Aligned_cols=51  Identities=24%  Similarity=0.018  Sum_probs=41.6

Q ss_pred             CceEEEcCC--CCCCC--------HHHHHHHhccCCCeeEEEEeeCCCC--CCCcceEEEEee
Q 013489          391 ECTAFLSNI--NLKAT--------YEDLRRFFSDVGGVSSIRILHDKFT--GKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl--~~~~~--------~~~l~~~f~~~G~i~~~~~~~~~~~--g~~~g~~fv~f~  441 (442)
                      .+.|.+.|+  |....        .++|+..|++||.|.+|.|++++.+  ++++|||||+|.
T Consensus         5 s~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~   67 (105)
T 3v4m_A            5 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFT   67 (105)
T ss_dssp             CSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEES
T ss_pred             CeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEEC
Confidence            458899997  33333        3689999999999999999998654  478999999996

>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=98.17  E-value=0.00029  Score=57.97  Aligned_cols=104  Identities=10%  Similarity=-0.089  Sum_probs=88.3

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~  101 (442)
                      ....|...+......|+++.+...|++++...|.+..+|...+..+.. .++.+.+...|++++...|....+|......
T Consensus        12 ~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~-~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~   90 (166)
T 1a17_A           12 RAEELKTQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLR-TECYGYALGDATRAIELDKKYIKGYYRRAAS   90 (166)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHH-cCCHHHHHHHHHHHHHhCcccHHHHHHHHHH
Confidence            455788888888889999999999999999999999999999887664 4566789999999999999999999988775


Q ss_pred             HHHccCCHHHHHHHHHHHHhCChhhH
Q 013489          102 LERSRASEEEISTVFEKSLLCAFSTF  127 (442)
Q Consensus       102 le~~~~~~~~~~~i~~~al~~~~~~~  127 (442)
                      +. ..+..+.+...|++++...+...
T Consensus        91 ~~-~~~~~~~A~~~~~~a~~~~p~~~  115 (166)
T 1a17_A           91 NM-ALGKFRAALRDYETVVKVKPHDK  115 (166)
T ss_dssp             HH-HTTCHHHHHHHHHHHHHHSTTCH
T ss_pred             HH-HhccHHHHHHHHHHHHHhCCCCH
Confidence            54 47889999999999998766543

>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=98.17  E-value=2.7e-05  Score=62.42  Aligned_cols=102  Identities=13%  Similarity=-0.075  Sum_probs=88.5

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~  101 (442)
                      +...|...+......|+++.+..+|+++|..+|.+..+|..++..+.. .++.+.+...|++++...|.....|......
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            667899999988999999999999999999999999999999987764 4566789999999999999999999998875


Q ss_pred             HHHccCCHHHHHHHHHHHHhCChh
Q 013489          102 LERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus       102 le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                      +.. .++.+.+...|++++...+.
T Consensus        87 ~~~-~~~~~~A~~~~~~a~~~~p~  109 (137)
T 3q49_B           87 QLE-MESYDEAIANLQRAYSLAKE  109 (137)
T ss_dssp             HHH-TTCHHHHHHHHHHHHHHHHH
T ss_pred             HHH-HhhHHHHHHHHHHHHHHChh
Confidence            554 78899999999999975443

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.17  E-value=2.3e-05  Score=62.10  Aligned_cols=99  Identities=10%  Similarity=-0.026  Sum_probs=81.0

Q ss_pred             HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHH
Q 013489           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER  104 (442)
Q Consensus        25 ~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~  104 (442)
                      .|...+......|+++.+...|+++|..+|.+...|......+.. .+..+.+...|++|+...|.....|......+. 
T Consensus        19 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~-~g~~~~A~~~~~~al~l~P~~~~~~~~la~~~~-   96 (121)
T 1hxi_A           19 NPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAE-NEKDGLAIIALNHARMLDPKDIAVHAALAVSHT-   96 (121)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH-
Confidence            466666667788999999999999999999999999998887664 456677999999999999999999988776444 


Q ss_pred             ccCCHHHHHHHHHHHHhCChh
Q 013489          105 SRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus       105 ~~~~~~~~~~i~~~al~~~~~  125 (442)
                      ..+..+++...|++++...+.
T Consensus        97 ~~g~~~~A~~~~~~al~~~P~  117 (121)
T 1hxi_A           97 NEHNANAALASLRAWLLSQPQ  117 (121)
T ss_dssp             HHHHHHHHHHHHHHHHC----
T ss_pred             HcCCHHHHHHHHHHHHHhCcC
Confidence            367788999999999976553

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.15  E-value=1.7e-05  Score=64.53  Aligned_cols=77  Identities=4%  Similarity=-0.158  Sum_probs=48.9

Q ss_pred             HHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhC
Q 013489           44 LLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLC  122 (442)
Q Consensus        44 ~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~  122 (442)
                      ..|++++...|.+...|...+..+... +..+.+...|++++...|....+|......+. ..+..+.+...|++++..
T Consensus         5 ~~l~~al~~~p~~~~~~~~~a~~~~~~-g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~-~~g~~~~A~~~~~~al~~   81 (142)
T 2xcb_A            5 GTLAMLRGLSEDTLEQLYALGFNQYQA-GKWDDAQKIFQALCMLDHYDARYFLGLGACRQ-SLGLYEQALQSYSYGALM   81 (142)
T ss_dssp             ----CCTTCCHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHH
T ss_pred             hhHHHHHcCCHHHHHHHHHHHHHHHHH-ccHHHHHHHHHHHHHhCCccHHHHHHHHHHHH-HHhhHHHHHHHHHHHHhc
Confidence            356777777777777777776655543 44566777888888877877777777655333 356666666666666543

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.15  E-value=0.00014  Score=67.02  Aligned_cols=168  Identities=9%  Similarity=-0.084  Sum_probs=115.1

Q ss_pred             HcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHH
Q 013489           86 KNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQ  165 (442)
Q Consensus        86 ~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~  165 (442)
                      ...|.....+......+. ..++.+.+..+|++++...+.....++.+-..+.                     ..+.++
T Consensus       111 ~~lp~~~~~~~~~a~~~~-~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~---------------------~~g~~~  168 (287)
T 3qou_A          111 XVLPREEELXAQQAMQLM-QESNYTDALPLLXDAWQLSNQNGEIGLLLAETLI---------------------ALNRSE  168 (287)
T ss_dssp             HHSCCHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHTTSCHHHHHHHHHHHH---------------------HTTCHH
T ss_pred             HHcCCchhhHHHHHHHHH-hCCCHHHHHHHHHHHHHhCCcchhHHHHHHHHHH---------------------HCCCHH
Confidence            345888888877776444 3688999999999999887776554433332211                     113356


Q ss_pred             HHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          166 RASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       166 ~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      +|...+.......+.....+..........+ ..+.|...|++++..+|++..+|..++......|+++.|...|.+++.
T Consensus       169 ~A~~~l~~~~~~~p~~~~~~~~~~~~l~~~~-~~~~a~~~l~~al~~~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~  247 (287)
T 3qou_A          169 DAEAVLXTIPLQDQDTRYQGLVAQIELLXQA-ADTPEIQQLQQQVAENPEDAALATQLALQLHQVGRNEEALELLFGHLR  247 (287)
T ss_dssp             HHHHHHTTSCGGGCSHHHHHHHHHHHHHHHH-TSCHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCchhhcchHHHHHHHHHHHHhhc-ccCccHHHHHHHHhcCCccHHHHHHHHHHHHHcccHHHHHHHHHHHHh
Confidence            6777766655433332222222222233444 567789999999999999999999999999999999999999999998


Q ss_pred             cccCCCChHHHHHHHHHHHHHhCCHhhHHHHH
Q 013489          246 KRFTGTGSEDICHAWLRFEREYGTLEDFDHSV  277 (442)
Q Consensus       246 ~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~  277 (442)
                      .. +.......+..........|..+......
T Consensus       248 ~~-p~~~~~~a~~~l~~~~~~~g~~~~a~~~~  278 (287)
T 3qou_A          248 XD-LTAADGQTRXTFQEILAALGTGDALASXY  278 (287)
T ss_dssp             HC-TTGGGGHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             cc-cccccchHHHHHHHHHHHcCCCCcHHHHH
Confidence            42 32222567788888888888765544333

>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=98.15  E-value=0.00065  Score=61.51  Aligned_cols=184  Identities=15%  Similarity=0.132  Sum_probs=113.9

Q ss_pred             HHHHHHHHhcCCCCHH-------HHHHHHH-HHHHhc------------chhhHHHHHHHHHHHcCCCcHHHHHHHHHHH
Q 013489           43 QLLYERAITDFPVSSD-------LWLDYTQ-YLDKTL------------KVGNVVRDVYSRATKNCPWVGELWVRSLLSL  102 (442)
Q Consensus        43 ~~lyERal~~~p~~~~-------lW~~Y~~-~l~~~~------------~~~~~~~~v~erAl~~~p~s~~lW~~y~~~l  102 (442)
                      ..+||-.|..+|.+..       +...|+. |+....            .+...+..+|.||....          ++.|
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            5678999999999874       6777766 444211            12345677777776621          2234


Q ss_pred             HHccCCHH-HHH----HHHHHHH-hCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhc
Q 013489          103 ERSRASEE-EIS----TVFEKSL-LCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMK  176 (442)
Q Consensus       103 e~~~~~~~-~~~----~i~~~al-~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~  176 (442)
                      +..+..+. .++    .-+..++ .+.+..+...+-.-..+....  .. ....+.........+..+++|+++      
T Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~dve~L~W~ai~~ss~a--~~-~~gg~~Al~~l~~A~a~lerAleL------  192 (301)
T 3u64_A          122 ETAYPGFTREVFSGDEQRLHKVLSRCTRVDVGTLYWVGTGYVAAF--AL-TPLGSALPDTVHAAVMMLERACDL------  192 (301)
T ss_dssp             HHHSTTHHHHHTSSCHHHHHHHHTTCCGGGHHHHHHHHHHHHHHH--TT-SCTTSCCHHHHHHHHHHHHHHHHH------
T ss_pred             HHhCccHHHHHHhcchhhHHHHHHHcCccccHHHHHHHHHHHHHH--hc-CCCChHHHHhHHHHHHHHHHHHHh------
Confidence            43323222 111    2244444 234443333221111111111  11 112223334555666777777774      


Q ss_pred             Cchh--hHHHHHHHHHHHHHc----CCCHHHHHHHHHHHHHhchhH-HHHHHHHHHHHHhc-ccHHHHHHHHHHHHhc
Q 013489          177 NTDG--LLRLYAYWAHLEQSM----GKDMVSARGVWERLLKISGAM-LEAWQSYISMEIEL-DHINEARSIYKRCYSK  246 (442)
Q Consensus       177 ~~~~--~~~l~~~~a~~e~~~----~~~~~~ar~i~~~~l~~~~~~-~~~w~~~~~~e~~~-g~~~~ar~i~~ral~~  246 (442)
                       .+.  .-..|..++.++...    +++.++|+..|+++|..+|+. ...+..|++|.... |+.+.++..+++|+..
T Consensus       193 -DP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a  269 (301)
T 3u64_A          193 -WPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAI  269 (301)
T ss_dssp             -CTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHC
T ss_pred             -CCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHHcC
Confidence             333  224788888888885    459999999999999999976 99999999999875 8999999999999973

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.14  E-value=0.00013  Score=56.70  Aligned_cols=103  Identities=15%  Similarity=0.132  Sum_probs=87.6

Q ss_pred             HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHH
Q 013489           23 FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSL  102 (442)
Q Consensus        23 ~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~l  102 (442)
                      ...|...+......|+++.+..+|++++...|.+..+|..++..+... +..+.+...|++++...|....+|...+..+
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            567888888888899999999999999999999999999998877644 5667899999999999999999998887755


Q ss_pred             HHccCCHHHHHHHHHHHHhCChhhH
Q 013489          103 ERSRASEEEISTVFEKSLLCAFSTF  127 (442)
Q Consensus       103 e~~~~~~~~~~~i~~~al~~~~~~~  127 (442)
                      . ..++.+.+...|++++...+...
T Consensus        88 ~-~~~~~~~A~~~~~~~~~~~~~~~  111 (125)
T 1na0_A           88 Y-KQGDYDEAIEYYQKALELDPNNA  111 (125)
T ss_dssp             H-HTTCHHHHHHHHHHHHHHCTTCH
T ss_pred             H-HhcCHHHHHHHHHHHHHhCCCcH
Confidence            4 46889999999999998766543

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.14  E-value=2.6e-06  Score=66.81  Aligned_cols=47  Identities=19%  Similarity=0.175  Sum_probs=42.5

Q ss_pred             CCCceEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLK-ATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...+.|||+||+.. ++.++|+.+|+.||.|..|.++.+..      .|||.|.
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~   63 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFK   63 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEES
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEEC
Confidence            45679999999999 99999999999999999999999853      5999995

>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=98.13  E-value=2.3e-05  Score=74.12  Aligned_cols=151  Identities=8%  Similarity=-0.012  Sum_probs=94.7

Q ss_pred             ChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCc---------------HHHHHHHHHHH
Q 013489           38 DPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV---------------GELWVRSLLSL  102 (442)
Q Consensus        38 ~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s---------------~~lW~~y~~~l  102 (442)
                      +++.+...|++++...|.+...|......+... +..+.+...|++|+...|..               ..+|..+...+
T Consensus       128 ~~~~A~~~~~~a~~~~p~~a~~~~~~g~~~~~~-g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~  206 (336)
T 1p5q_A          128 SFEKAKESWEMNSEEKLEQSTIVKERGTVYFKE-GKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCH  206 (336)
T ss_dssp             EEECCCCGGGCCHHHHHHHHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ecccccchhcCCHHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHH
Confidence            334444445555555555555555555544432 23344555555555555554               46777766533


Q ss_pred             HHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhH
Q 013489          103 ERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLL  182 (442)
Q Consensus       103 e~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~  182 (442)
                      . ..+..+++...|++++...+..                                                       .
T Consensus       207 ~-~~g~~~~A~~~~~~al~~~p~~-------------------------------------------------------~  230 (336)
T 1p5q_A          207 L-KLQAFSAAIESCNKALELDSNN-------------------------------------------------------E  230 (336)
T ss_dssp             H-HTTCHHHHHHHHHHHHHHCTTC-------------------------------------------------------H
T ss_pred             H-HcCCHHHHHHHHHHHHHhCCCc-------------------------------------------------------H
Confidence            3 4677888888888877643331                                                       1


Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHH-HHHHHHHHhc
Q 013489          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEA-RSIYKRCYSK  246 (442)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~a-r~i~~ral~~  246 (442)
                      ..|...+.+....| +++.|...|++++...|++..+|.....+....|+++.+ +.+|++++..
T Consensus       231 ~a~~~lg~~~~~~g-~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~~~~  294 (336)
T 1p5q_A          231 KGLSRRGEAHLAVN-DFELARADFQKVLQLYPNNKAAKTQLAVCQQRIRRQLAREKKLYANMFER  294 (336)
T ss_dssp             HHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCC-CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            23334445556667 888888888888888888888888888888888877766 6677777653

>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=98.12  E-value=0.001  Score=61.05  Aligned_cols=162  Identities=11%  Similarity=-0.028  Sum_probs=95.4

Q ss_pred             hhhHHHHHHHHHHHcCCCcHH-----HHHHHHHHHHHccCCHHHHHHHHHHHHhCChh--hHHHHHHHHHHHHHHHHHHh
Q 013489           73 VGNVVRDVYSRATKNCPWVGE-----LWVRSLLSLERSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRI  145 (442)
Q Consensus        73 ~~~~~~~v~erAl~~~p~s~~-----lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~--~~~~~~~~~~~~~~~l~rr~  145 (442)
                      +.+.+..+|++++...+....     .|...+..+....++.+.+...|++|+.....  .....+.++. .+..+....
T Consensus        90 ~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~-~lg~~y~~~  168 (293)
T 3u3w_A           90 RYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIEN-AIANIYAEN  168 (293)
T ss_dssp             CHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHH-HHHHHHHHT
T ss_pred             hHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHH-HHHHHHHHc
Confidence            445566666666665554433     13332333443344666677777777753221  1110011110 000110011


Q ss_pred             hccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH------HHH
Q 013489          146 LFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM------LEA  219 (442)
Q Consensus       146 ~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~------~~~  219 (442)
                               .++......|++|+..+.......+....++...+.+....| +++.|...+++++...+..      ..+
T Consensus       169 ---------g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~-~y~~A~~~~~~al~~~~~~~~~~~~~~~  238 (293)
T 3u3w_A          169 ---------GYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDS-RYEESLYQVNKAIEISCRINSMALIGQL  238 (293)
T ss_dssp             ---------TCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHTTBCTTHHHH
T ss_pred             ---------CCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHh-HHHHHHHHHHHHHHHHHHcCcHHHHHHH
Confidence                     234444555666665544332223334567788888888999 9999999999999885433      568


Q ss_pred             HHHHHHHHHhcc-cHHHHHHHHHHHHh
Q 013489          220 WQSYISMEIELD-HINEARSIYKRCYS  245 (442)
Q Consensus       220 w~~~~~~e~~~g-~~~~ar~i~~ral~  245 (442)
                      |..........| +++.|...|++|+.
T Consensus       239 ~~~lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          239 YYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            888888888889 57999999999985

>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=98.10  E-value=0.00015  Score=73.46  Aligned_cols=176  Identities=10%  Similarity=0.048  Sum_probs=129.5

Q ss_pred             HhcCC-hhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcch---------hhHHHHHHHHHHHcCCCcHHHHHHHHHHHH
Q 013489           34 QSSGD-PGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKV---------GNVVRDVYSRATKNCPWVGELWVRSLLSLE  103 (442)
Q Consensus        34 ~~~g~-~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~---------~~~~~~v~erAl~~~p~s~~lW~~y~~~le  103 (442)
                      ...|. .++|..+|+++|..+|.+..+|..-...+.....+         .+.+...+++++...|.+..+|....-.+.
T Consensus        39 ~~~~~~~eeal~~~~~~l~~nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK~y~aW~hR~w~l~  118 (567)
T 1dce_A           39 RQAGELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLS  118 (567)
T ss_dssp             HHTTCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHcCCCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            33444 46889999999999999999999887777654332         566889999999999999999999877666


Q ss_pred             HccC--CHHHHHHHHHHHHhCChhhH--HHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCch
Q 013489          104 RSRA--SEEEISTVFEKSLLCAFSTF--EEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTD  179 (442)
Q Consensus       104 ~~~~--~~~~~~~i~~~al~~~~~~~--~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~  179 (442)
                      . .+  ..++....+++++...+.++  |.+..+....       +.               ..+++++++...++..++
T Consensus       119 ~-l~~~~~~~el~~~~k~l~~d~~N~~aW~~R~~~l~~-------l~---------------~~~~~el~~~~~~I~~~p  175 (567)
T 1dce_A          119 R-LPEPNWARELELCARFLEADERNFHCWDYRRFVAAQ-------AA---------------VAPAEELAFTDSLITRNF  175 (567)
T ss_dssp             T-CSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-------TC---------------CCHHHHHHHHHTTTTTTC
T ss_pred             H-cccccHHHHHHHHHHHHhhccccccHHHHHHHHHHH-------cC---------------CChHHHHHHHHHHHHHCC
Confidence            5 45  45778899999998777643  3333222111       10               024567777777777677


Q ss_pred             hhHHHHHHHHHHHHHcC-------------CCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhccc
Q 013489          180 GLLRLYAYWAHLEQSMG-------------KDMVSARGVWERLLKISGAMLEAWQSYISMEIELDH  232 (442)
Q Consensus       180 ~~~~l~~~~a~~e~~~~-------------~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~  232 (442)
                      .....|.+-..+...++             +.++.+.+.+.+++..+|++..+|..+.-+....+.
T Consensus       176 ~n~saW~~r~~ll~~l~~~~~~~~~~~~~~~~~~eel~~~~~ai~~~P~~~saW~y~~~ll~~~~~  241 (567)
T 1dce_A          176 SNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEP  241 (567)
T ss_dssp             CCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCCCC
T ss_pred             CCccHHHHHHHHHHhhcccccccccccccHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHHhcCCC
Confidence            77778888776665541             146899999999999999999999988777765554

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.08  E-value=9.3e-05  Score=61.13  Aligned_cols=108  Identities=8%  Similarity=-0.019  Sum_probs=82.2

Q ss_pred             HHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhccc
Q 013489          169 DYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRF  248 (442)
Q Consensus       169 ~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~  248 (442)
                      ..+...+...|.....|...+......| +++.|..+|++++..+|++..+|..........|+++.|...|++|+.  +
T Consensus        23 ~~l~~al~l~p~~~~~~~~lg~~~~~~g-~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~--l   99 (151)
T 3gyz_A           23 ATLKDINAIPDDMMDDIYSYAYDFYNKG-RIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFA--L   99 (151)
T ss_dssp             CCTGGGCCSCHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--H
T ss_pred             CCHHHHhCCCHHHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHh--h
Confidence            3445555556777778888888888888 899999999999999999999999999999999999999999999997  4


Q ss_pred             CCCChHHHHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          249 TGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       249 ~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                      .++.+. .|......-...|+.+.-..+++++
T Consensus       100 ~P~~~~-~~~~lg~~~~~lg~~~eA~~~~~~a  130 (151)
T 3gyz_A          100 GKNDYT-PVFHTGQCQLRLKAPLKAKECFELV  130 (151)
T ss_dssp             SSSCCH-HHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             CCCCcH-HHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            556664 3434444455567766555444443

>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=98.07  E-value=0.00024  Score=60.47  Aligned_cols=102  Identities=11%  Similarity=0.261  Sum_probs=78.9

Q ss_pred             HHHHHHHHHHh--hhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh-ch-hHHHHHHHHHHHHHhcccHHHHH
Q 013489          162 ETFQRASDYLS--EQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI-SG-AMLEAWQSYISMEIELDHINEAR  237 (442)
Q Consensus       162 ~~~~~a~~~l~--~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~-~~-~~~~~w~~~~~~e~~~g~~~~ar  237 (442)
                      ..+++|+..+.  ..+.+.+..+++|+.||++.  ..++...++.+|.-+... -+ ..+.+|..|+.+....|++..|.
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            56677777653  33445666789999999865  122578999999999987 44 44679999999999999999999


Q ss_pred             HHHHHHHhcccCCCChHHHHHHHHHHHHHh
Q 013489          238 SIYKRCYSKRFTGTGSEDICHAWLRFEREY  267 (442)
Q Consensus       238 ~i~~ral~~~~~~~~~~~i~~~~~~fE~~~  267 (442)
                      .||+.++.+..  ...+.|-.++.+|++..
T Consensus       136 ~Vy~~GI~~~A--~P~~rL~~~~~~F~~R~  163 (202)
T 3esl_A          136 VLLELGAENNC--RPYNRLLRSLSNYEDRL  163 (202)
T ss_dssp             HHHHHHHHTTC--BSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCC--ccHHHHHHHHHHHHHHH
Confidence            99999998642  23567888999998774

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=98.07  E-value=0.01  Score=58.74  Aligned_cols=46  Identities=9%  Similarity=-0.010  Sum_probs=23.4

Q ss_pred             CHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhc-----ccHHHHHHHHHHHHh
Q 013489          198 DMVSARGVWERLLKISGAMLEAWQSYISMEIEL-----DHINEARSIYKRCYS  245 (442)
Q Consensus       198 ~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~-----g~~~~ar~i~~ral~  245 (442)
                      +.+.|...|++++...  +...+.....+....     ++++.|...|++|+.
T Consensus       274 d~~~A~~~~~~a~~~~--~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~  324 (490)
T 2xm6_A          274 EPLKALEWYRKSAEQG--NSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAE  324 (490)
T ss_dssp             CHHHHHHHHHHHHTTT--CHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcC--CHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHh
Confidence            5666666666665441  223333333333333     456666666666654

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.07  E-value=0.0013  Score=60.41  Aligned_cols=162  Identities=10%  Similarity=-0.036  Sum_probs=96.8

Q ss_pred             hhhHHHHHHHHHHHcCCCcHH-----HHHHHHHHHHHccCCHHHHHHHHHHHHhCChhh--HHHHHHHHHHHHHHHHHHh
Q 013489           73 VGNVVRDVYSRATKNCPWVGE-----LWVRSLLSLERSRASEEEISTVFEKSLLCAFST--FEEYLDLFLTRIDGLRRRI  145 (442)
Q Consensus        73 ~~~~~~~v~erAl~~~p~s~~-----lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~--~~~~~~~~~~~~~~l~rr~  145 (442)
                      +.+.+...|.+++...|....     .|..++..+....++.+.+...|++++......  .......+.. +..+....
T Consensus        90 ~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~-lg~~y~~~  168 (293)
T 2qfc_A           90 RYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENA-IANIYAEN  168 (293)
T ss_dssp             CHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHHHHH-HHHHHHHT
T ss_pred             hHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHHHHH-HHHHHHHc
Confidence            445567777777776554321     333334334444567777777788877532210  0000111100 00110011


Q ss_pred             hccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchh------HHHH
Q 013489          146 LFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA------MLEA  219 (442)
Q Consensus       146 ~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~------~~~~  219 (442)
                               .++......|++|+...............++...+.+....| +++.|...+++++...++      ...+
T Consensus       169 ---------~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~-~y~~Al~~~~kal~~~~~~~~~~~~~~~  238 (293)
T 2qfc_A          169 ---------GYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDS-RYEESLYQVNKAIEISCRINSMALIGQL  238 (293)
T ss_dssp             ---------TCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHTTBCSSHHHH
T ss_pred             ---------CCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHh-hHHHHHHHHHHHHHHHHhcCcHHHHHHH
Confidence                     344455566666665544322111112357777888888889 999999999999988543      2568


Q ss_pred             HHHHHHHHHhcccHHHH-HHHHHHHHh
Q 013489          220 WQSYISMEIELDHINEA-RSIYKRCYS  245 (442)
Q Consensus       220 w~~~~~~e~~~g~~~~a-r~i~~ral~  245 (442)
                      +.....+....|+++.| ...|++|+.
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            88888888899999999 888999985

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=98.03  E-value=0.0097  Score=58.84  Aligned_cols=111  Identities=10%  Similarity=-0.088  Sum_probs=55.4

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHh----cCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh---cchhh
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQS----SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKT---LKVGN   75 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~----~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~---~~~~~   75 (442)
                      ++...|+.++...      +...+..+......    .++++.+...|++++..  .++..+..........   .++.+
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            3455666665442      22333334433333    45666666667666654  3455555555444321   23445


Q ss_pred             HHHHHHHHHHHcCCCcHHHHHHHHHHHHH---ccCCHHHHHHHHHHHHhCC
Q 013489           76 VVRDVYSRATKNCPWVGELWVRSLLSLER---SRASEEEISTVFEKSLLCA  123 (442)
Q Consensus        76 ~~~~v~erAl~~~p~s~~lW~~y~~~le~---~~~~~~~~~~i~~~al~~~  123 (442)
                      .+...|++|+..  .....|......+..   ..++.+.+...|++++..+
T Consensus       169 ~A~~~~~~a~~~--~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~  217 (490)
T 2xm6_A          169 MAREWYSKAAEQ--GNVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSG  217 (490)
T ss_dssp             HHHHHHHHHHHT--TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHC--CCHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC
Confidence            566666666663  233444443332222   0345556666666666543

>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=98.02  E-value=0.00011  Score=60.69  Aligned_cols=111  Identities=12%  Similarity=-0.170  Sum_probs=86.3

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      .+...|+.++...|.    +...|..++......|+++.+...|++++..+|.+...|...+..+... +..+.+...|+
T Consensus        31 ~A~~~~~~al~~~~~----~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~-~~~~~A~~~~~  105 (166)
T 1a17_A           31 NAIKFYSQAIELNPS----NAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMAL-GKFRAALRDYE  105 (166)
T ss_dssp             HHHHHHHHHHHHSTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC----ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHh-ccHHHHHHHHH
Confidence            466788888888775    6778999999888999999999999999999999999999998877644 56678999999


Q ss_pred             HHHHcCCCcHHHHHHHHHHH-HHccCCHHHHHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLLSL-ERSRASEEEISTVFEK  118 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~l-e~~~~~~~~~~~i~~~  118 (442)
                      +++...|....+|..+.... ....+..+++...+++
T Consensus       106 ~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~  142 (166)
T 1a17_A          106 TVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEH  142 (166)
T ss_dssp             HHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHcccc
Confidence            99999999988886554321 1123344444444444

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=98.02  E-value=4.1e-06  Score=66.02  Aligned_cols=51  Identities=14%  Similarity=0.102  Sum_probs=41.7

Q ss_pred             CceEEEcCCCC--C---CCHHHHHHHhccCCCeeEEEEeeCCC----CCCCcceEEEEee
Q 013489          391 ECTAFLSNINL--K---ATYEDLRRFFSDVGGVSSIRILHDKF----TGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~--~---~~~~~l~~~f~~~G~i~~~~~~~~~~----~g~~~g~~fv~f~  441 (442)
                      .++|++.|+-.  +   --+++|+..|++||.|.+|.|+.++.    +++++|||||+|.
T Consensus        20 s~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~   79 (118)
T 3ue2_A           20 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFS   79 (118)
T ss_dssp             CCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEES
T ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEEC
Confidence            34899999832  1   23689999999999999999999854    4678899999996

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.01  E-value=0.0016  Score=59.84  Aligned_cols=208  Identities=10%  Similarity=-0.057  Sum_probs=127.8

Q ss_pred             hHHHHHHHHHhcCCCCHHHHHHHHHHHHHh-cchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHH
Q 013489           41 RVQLLYERAITDFPVSSDLWLDYTQYLDKT-LKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKS  119 (442)
Q Consensus        41 ~~~~lyERal~~~p~~~~lW~~Y~~~l~~~-~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~a  119 (442)
                      .+..++..|-...+.+..+| .|.   ... .+..+.+...|++|..               +....+..+++...|++|
T Consensus         3 ~a~~~~~~a~k~~~~~~~~~-~~~---~~~~~~~~~~A~~~~~~a~~---------------~~~~~g~~~~A~~~~~~a   63 (292)
T 1qqe_A            3 DPVELLKRAEKKGVPSSGFM-KLF---SGSDSYKFEEAADLCVQAAT---------------IYRLRKELNLAGDSFLKA   63 (292)
T ss_dssp             CHHHHHHHHHHHSSCCCTHH-HHH---SCCSHHHHHHHHHHHHHHHH---------------HHHHTTCTHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhCcCCCcc-hhc---CCCCCccHHHHHHHHHHHHH---------------HHHHcCCHHHHHHHHHHH
Confidence            45667777777777766777 443   211 1235668888888833               122357888899999998


Q ss_pred             HhCChh--hHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHc-C
Q 013489          120 LLCAFS--TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSM-G  196 (442)
Q Consensus       120 l~~~~~--~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~-~  196 (442)
                      +.....  ........+... ..+....         .++......|++|+.+.... .........+...+.+.... |
T Consensus        64 l~~~~~~~~~~~~a~~~~~l-g~~~~~~---------g~~~~A~~~~~~Al~l~~~~-g~~~~~a~~~~~lg~~~~~~lg  132 (292)
T 1qqe_A           64 ADYQKKAGNEDEAGNTYVEA-YKCFKSG---------GNSVNAVDSLENAIQIFTHR-GQFRRGANFKFELGEILENDLH  132 (292)
T ss_dssp             HHHHHHTTCHHHHHHHHHHH-HHHHHHT---------TCHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHhCCHHHHHHHHHHH-HHHHHHC---------CCHHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHHhhc
Confidence            864211  111111111111 1111111         34555566777777765321 11222345777788888885 8


Q ss_pred             CCHHHHHHHHHHHHHhchhH------HHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChH---H---HHHHHHHHH
Q 013489          197 KDMVSARGVWERLLKISGAM------LEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSE---D---ICHAWLRFE  264 (442)
Q Consensus       197 ~~~~~ar~i~~~~l~~~~~~------~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~---~---i~~~~~~fE  264 (442)
                       +++.|...|++++..+|..      ..+|...+.+....|+++.|..+|++++...  ++.+.   .   .+......-
T Consensus       133 -~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~~~~~~~~~lg~~~  209 (292)
T 1qqe_A          133 -DYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSS--MGNRLSQWSLKDYFLKKGLCQ  209 (292)
T ss_dssp             -CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT--SSCTTTGGGHHHHHHHHHHHH
T ss_pred             -CHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH--hcCCcccHHHHHHHHHHHHHH
Confidence             9999999999999987643      4678899999999999999999999999742  22221   1   233333334


Q ss_pred             HHhCCHhhHHHHHHhhc
Q 013489          265 REYGTLEDFDHSVQKVT  281 (442)
Q Consensus       265 ~~~G~~~~~~~~~~~~~  281 (442)
                      ...|+.+.-..+++++.
T Consensus       210 ~~~g~~~~A~~~~~~al  226 (292)
T 1qqe_A          210 LAATDAVAAARTLQEGQ  226 (292)
T ss_dssp             HHTTCHHHHHHHHHGGG
T ss_pred             HHcCCHHHHHHHHHHHH
Confidence            45677766666666554

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.99  E-value=0.00013  Score=58.94  Aligned_cols=104  Identities=13%  Similarity=-0.016  Sum_probs=88.3

Q ss_pred             hHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCC---HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHH
Q 013489           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVS---SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWV   96 (442)
Q Consensus        20 ~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~---~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~   96 (442)
                      +.+...|...+......|+++.+..+|++++...|.+   ..+|..++..+.. .++.+.+...|++++...|....+|.
T Consensus        25 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~a~~~~~-~~~~~~A~~~~~~~~~~~~~~~~~~~  103 (148)
T 2dba_A           25 ASSVEQLRKEGNELFKCGDYGGALAAYTQALGLDATPQDQAVLHRNRAACHLK-LEDYDKAETEASKAIEKDGGDVKALY  103 (148)
T ss_dssp             CCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHTSCCHHHHH
T ss_pred             hHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHH-HccHHHHHHHHHHHHhhCccCHHHHH
Confidence            3467789999998889999999999999999999987   8888888876654 45667899999999999999999998


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCChh
Q 013489           97 RSLLSLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus        97 ~y~~~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                      .+...+.. .+..+.+...|++++...+.
T Consensus       104 ~~a~~~~~-~~~~~~A~~~~~~al~~~p~  131 (148)
T 2dba_A          104 RRSQALEK-LGRLDQAVLDLQRCVSLEPK  131 (148)
T ss_dssp             HHHHHHHH-HTCHHHHHHHHHHHHHHCSS
T ss_pred             HHHHHHHH-cCCHHHHHHHHHHHHHcCCC
Confidence            87775544 68899999999999977655

>4aez_C MAD3, mitotic spindle checkpoint component MAD3; cell cycle, KEN-BOX, D-BOX, APC/C; 2.30A {Schizosaccharomyces pombe}

Probab=97.98  E-value=0.00011  Score=63.57  Aligned_cols=112  Identities=17%  Similarity=0.319  Sum_probs=84.4

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhc---CC--hhhHHHHHHHHHhcCCCC---------HHHHHHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS---GD--PGRVQLLYERAITDFPVS---------SDLWLDYTQYLD   68 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~---g~--~~~~~~lyERal~~~p~~---------~~lW~~Y~~~l~   68 (442)
                      ..|..||..|.....+ .+-++.|..||.|....   |.  -.....++|||+..+..+         ..+|+.|+.+. 
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            4688999999873111 12478899999998764   32  224678999999976554         36999999863 


Q ss_pred             HhcchhhHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCC
Q 013489           69 KTLKVGNVVRDVYSRATKN--CPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCA  123 (442)
Q Consensus        69 ~~~~~~~~~~~v~erAl~~--~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~  123 (442)
                         .+   ...+|....++  .-....+|..|+.++|. .++...+..||+.+++..
T Consensus       131 ---~~---p~~if~~L~~~~IG~~~AlfYe~wA~~lE~-~g~~~~A~~Vy~~Gi~~~  180 (223)
T 4aez_C          131 ---DE---PVELFSFLAHHHIGQESSIFYEEYANYFES-RGLFQKADEVYQKGKRMK  180 (223)
T ss_dssp             ---SC---HHHHHHHHHHTTCSTTBHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHT
T ss_pred             ---CC---HHHHHHHHHHCCcchhHHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHcC
Confidence               22   45788877773  35678999999999997 689999999999999653

>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=97.97  E-value=0.0001  Score=56.63  Aligned_cols=93  Identities=13%  Similarity=-0.058  Sum_probs=80.0

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ++...|+.++...|.    +...|..++......|+++.+..+|++++...|.++.+|..++..+.. .+..+.+...|+
T Consensus        22 ~A~~~~~~~~~~~~~----~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~-~~~~~~A~~~~~   96 (118)
T 1elw_A           22 DALQCYSEAIKLDPH----NHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEF-LNRFEEAKRTYE   96 (118)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCC----cHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCcccHHHHHHHHHHHHH-HhhHHHHHHHHH
Confidence            456778888887775    677899999888889999999999999999999999999999887764 456678999999


Q ss_pred             HHHHcCCCcHHHHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLL  100 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~  100 (442)
                      +++...|....+|..+..
T Consensus        97 ~~~~~~~~~~~~~~~l~~  114 (118)
T 1elw_A           97 EGLKHEANNPQLKEGLQN  114 (118)
T ss_dssp             HHHTTCTTCHHHHHHHHH
T ss_pred             HHHHcCCCCHHHHHHHHH
Confidence            999999999988887665

>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=97.97  E-value=9.7e-05  Score=58.35  Aligned_cols=93  Identities=13%  Similarity=-0.077  Sum_probs=80.4

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      +|...|+.+|...|.    +...|...+......|+++.+...|+++|..+|.++..|...+..+.. .+..+.+...|+
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            467789999988875    678899999999999999999999999999999999999999987764 456678999999


Q ss_pred             HHHHcC------CCcHHHHHHHHH
Q 013489           83 RATKNC------PWVGELWVRSLL  100 (442)
Q Consensus        83 rAl~~~------p~s~~lW~~y~~  100 (442)
                      +++...      |....+|.....
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            999998      888788777554

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=97.97  E-value=0.0014  Score=62.59  Aligned_cols=235  Identities=14%  Similarity=-0.028  Sum_probs=132.0

Q ss_pred             HHHHHHhcCChhhHHHHHHHHHhcCC---CC---HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCc-------HHHH
Q 013489           29 YLKYEQSSGDPGRVQLLYERAITDFP---VS---SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV-------GELW   95 (442)
Q Consensus        29 y~~~e~~~g~~~~~~~lyERal~~~p---~~---~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s-------~~lW   95 (442)
                      ...+....|+++.+...|++|+...+   ..   ..++...+.... ..++.+.+...|++|+..++..       ...+
T Consensus       107 ~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~-~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  185 (378)
T 3q15_A          107 RGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYY-HMKQTHVSMYHILQALDIYQNHPLYSIRTIQSL  185 (378)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHH-HcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHH
Confidence            34445678999999999999987532   22   233433333333 3456678999999999866432       2234


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCChh--hHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhh
Q 013489           96 VRSLLSLERSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSE  173 (442)
Q Consensus        96 ~~y~~~le~~~~~~~~~~~i~~~al~~~~~--~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~  173 (442)
                      ..... +....+..+.+...|++|+.....  ........+ ..+..+....         .++......|++|+.+...
T Consensus       186 ~~lg~-~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~-~~lg~~y~~~---------~~~~~A~~~~~~al~~~~~  254 (378)
T 3q15_A          186 FVIAG-NYDDFKHYDKALPHLEAALELAMDIQNDRFIAISL-LNIANSYDRS---------GDDQMAVEHFQKAAKVSRE  254 (378)
T ss_dssp             HHHHH-HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHH-HHHHHHHHHH---------TCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHH-HHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHH-HHHHHHHHHC---------CCHHHHHHHHHHHHHHHHh
Confidence            44333 444578899999999999964221  111111111 1111111111         3444455566666665433


Q ss_pred             hhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhch-----hHHHHHHHHHHHHHhccc---HHHHHHHHHHHHh
Q 013489          174 QMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG-----AMLEAWQSYISMEIELDH---INEARSIYKRCYS  245 (442)
Q Consensus       174 ~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~-----~~~~~w~~~~~~e~~~g~---~~~ar~i~~ral~  245 (442)
                      .  ..+.....+...+.+....| +.+.|...+++++...+     ...........+....|+   +..|..++++.-.
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  23334667777888888888 99999999999998732     223333333334444566   6666666665211


Q ss_pred             cccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhhch
Q 013489          246 KRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTP  282 (442)
Q Consensus       246 ~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~~~  282 (442)
                          ......++.....+-...|+.+.-.....++..
T Consensus       332 ----~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          332 ----HAYIEACARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             ----HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ----hhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                111223444455555566766554444444433

>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=97.95  E-value=0.00019  Score=56.34  Aligned_cols=102  Identities=12%  Similarity=-0.038  Sum_probs=84.6

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCc-------HHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV-------GEL   94 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s-------~~l   94 (442)
                      ....|...+......|+++.+..+|++++...|.+..+|...+..+... ++.+.+...|++++...|..       ..+
T Consensus         3 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~-~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~   81 (131)
T 1elr_A            3 QALKEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEK-GDYNKCRELCEKAIEVGRENREDYRQIAKA   81 (131)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHHHHSTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHh-ccHHHHHHHHHHHHhhccccchhHHHHHHH
Confidence            4567888888888899999999999999999999999999998876644 45677999999999987765       677


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCChh
Q 013489           95 WVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus        95 W~~y~~~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                      |......+. ..++.+.+...|++++...+.
T Consensus        82 ~~~la~~~~-~~~~~~~A~~~~~~~~~~~~~  111 (131)
T 1elr_A           82 YARIGNSYF-KEEKYKDAIHFYNKSLAEHRT  111 (131)
T ss_dssp             HHHHHHHHH-HTTCHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHHHHH-HhccHHHHHHHHHHHHHhCCC
Confidence            877776444 468899999999999976543

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=97.93  E-value=5.1e-05  Score=59.99  Aligned_cols=85  Identities=8%  Similarity=-0.043  Sum_probs=69.8

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      +|...|+.+|...|.    +...|..........|+++.+...|+++|..+|.+...|...+..+... +..+.+...|+
T Consensus        35 ~A~~~~~~al~~~P~----~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~la~~~~~~-g~~~~A~~~~~  109 (121)
T 1hxi_A           35 EAALAFEAVCQKEPE----REEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNE-HNANAALASLR  109 (121)
T ss_dssp             HHHHHHHHHHHHSTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCC----CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc-CCHHHHHHHHH
Confidence            467789999998876    7889999999999999999999999999999999999999988876644 45677999999


Q ss_pred             HHHHcCCCcH
Q 013489           83 RATKNCPWVG   92 (442)
Q Consensus        83 rAl~~~p~s~   92 (442)
                      +++...|...
T Consensus       110 ~al~~~P~~~  119 (121)
T 1hxi_A          110 AWLLSQPQYE  119 (121)
T ss_dssp             HHHC------
T ss_pred             HHHHhCcCCC
Confidence            9999888653

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=97.93  E-value=0.00013  Score=57.68  Aligned_cols=96  Identities=17%  Similarity=-0.017  Sum_probs=81.2

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ++...|+.++...|.    +...|..++......|+++.+..+|++++...|.+..+|..++..+.. .++.+.+...|+
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            466788888887765    677899999988899999999999999999999999999999887664 456678999999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLLSLE  103 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le  103 (442)
                      +++...|....+|..+...+.
T Consensus       109 ~~~~~~p~~~~~~~~l~~~~~  129 (133)
T 2lni_A          109 KALDLDSSCKEAADGYQRCMM  129 (133)
T ss_dssp             HHHHHCGGGTHHHHHHHHHHH
T ss_pred             HHHHhCCCchHHHHHHHHHHH
Confidence            999999988888887766443

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=97.93  E-value=0.0002  Score=56.13  Aligned_cols=96  Identities=15%  Similarity=-0.043  Sum_probs=81.3

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      .+...|+.++...|.    +...|..++......|+++.+..+|++++...|.+..+|...+..+.. .++.+.+...|+
T Consensus        30 ~A~~~~~~~~~~~~~----~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~A~~~~~  104 (131)
T 2vyi_A           30 AAVHFYGKAIELNPA----NAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPAYSKAYGRMGLALSS-LNKHVEAVAYYK  104 (131)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCC----CHHHHHHHHHHHHHhhchHHHHHHHHHHHhcCccCHHHHHHHHHHHHH-hCCHHHHHHHHH
Confidence            356678888877765    677899999988899999999999999999999999999999887664 456678999999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLLSLE  103 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le  103 (442)
                      +++...|.+..+|..+...+.
T Consensus       105 ~~~~~~p~~~~~~~~l~~~~~  125 (131)
T 2vyi_A          105 KALELDPDNETYKSNLKIAEL  125 (131)
T ss_dssp             HHHHHSTTCHHHHHHHHHHHH
T ss_pred             HHHhcCccchHHHHHHHHHHH
Confidence            999999999888888776444

>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=97.90  E-value=0.00035  Score=56.87  Aligned_cols=83  Identities=12%  Similarity=0.148  Sum_probs=63.6

Q ss_pred             hcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh-ch-hHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCC
Q 013489          175 MKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI-SG-AMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTG  252 (442)
Q Consensus       175 ~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~-~~-~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~  252 (442)
                      +.+.+..+++|+.||++   .. +   ++.+|.-+... -+ ..+.+|..|+.+....|++..|..||+.++++..  ..
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 YHNDPRFISYCLKFAEY---NS-D---LHQFFEFLYNHGIGTLSSPLYIAWAGHLEAQGELQHASAVLQRGIQNQA--EP  134 (152)
T ss_dssp             GTTCHHHHHHHHHHHTT---BS-C---HHHHHHHHHTTTTTTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC--BS
T ss_pred             ccCCHHHHHHHHHHHHh---cC-C---HHHHHHHHHHCCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC--cc
Confidence            33456677899999855   23 3   78899888877 34 4467999999999999999999999999998632  23


Q ss_pred             hHHHHHHHHHHHHH
Q 013489          253 SEDICHAWLRFERE  266 (442)
Q Consensus       253 ~~~i~~~~~~fE~~  266 (442)
                      .+.|-.++.+|.+.
T Consensus       135 ~~rL~~~~~~F~~R  148 (152)
T 4a1g_A          135 REFLQQQYRLFQTR  148 (152)
T ss_dssp             HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHH
Confidence            55677888888765

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=97.89  E-value=0.00013  Score=60.75  Aligned_cols=81  Identities=12%  Similarity=0.106  Sum_probs=66.4

Q ss_pred             HHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHH
Q 013489          165 QRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCY  244 (442)
Q Consensus       165 ~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral  244 (442)
                      +.|+.++..++...+....+|...+.+....+ +++.|...|++++..+|++..+|..+.......|+++.|...|++++
T Consensus        28 ~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g-~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al  106 (164)
T 3sz7_A           28 SKAIDLYTQALSIAPANPIYLSNRAAAYSASG-QHEKAAEDAELATVVDPKYSKAWSRLGLARFDMADYKGAKEAYEKGI  106 (164)
T ss_dssp             HHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCcCHHHHHHHHHHHHHcc-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            44444444444334556678888898888888 89999999999999999999999999999999999999999999999


Q ss_pred             hc
Q 013489          245 SK  246 (442)
Q Consensus       245 ~~  246 (442)
                      ..
T Consensus       107 ~~  108 (164)
T 3sz7_A          107 EA  108 (164)
T ss_dssp             HH
T ss_pred             Hh
Confidence            73

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=97.88  E-value=0.0028  Score=60.38  Aligned_cols=223  Identities=9%  Similarity=-0.022  Sum_probs=134.0

Q ss_pred             hhhHHHHHHhhcCCCC--ChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCH-------HHHHHHHHHHHHhcch
Q 013489            3 NARAHLEEQISRQDLS--DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS-------DLWLDYTQYLDKTLKV   73 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~--~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~-------~lW~~Y~~~l~~~~~~   73 (442)
                      +|...|+.++......  ++.....+...+......|+++.+...|++|+...+...       ..+...+.... ..+.
T Consensus       119 ~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~y~-~~~~  197 (378)
T 3q15_A          119 EAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNYD-DFKH  197 (378)
T ss_dssp             HHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHHH-HTTC
T ss_pred             HHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHH-HhCC
Confidence            4566778887553211  233455777777777889999999999999998654322       23333333333 3456


Q ss_pred             hhHHHHHHHHHHHcCC---Cc---HHHHHHHHHHHHHccCCHHHHHHHHHHHHh-----CChhhHHHHHHHHHHHHHHHH
Q 013489           74 GNVVRDVYSRATKNCP---WV---GELWVRSLLSLERSRASEEEISTVFEKSLL-----CAFSTFEEYLDLFLTRIDGLR  142 (442)
Q Consensus        74 ~~~~~~v~erAl~~~p---~s---~~lW~~y~~~le~~~~~~~~~~~i~~~al~-----~~~~~~~~~~~~~~~~~~~l~  142 (442)
                      .+.+...|++|+..++   ..   ..++..... +....+..+.+...|++++.     ..+.....+..+-..+     
T Consensus       198 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~-~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~-----  271 (378)
T 3q15_A          198 YDKALPHLEAALELAMDIQNDRFIAISLLNIAN-SYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTL-----  271 (378)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHH-----
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-HHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHH-----
Confidence            7889999999998653   22   123433333 44457889999999999997     3332222222111111     


Q ss_pred             HHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCC---HHHHHHHHHHHHHhchhHHHH
Q 013489          143 RRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKD---MVSARGVWERLLKISGAMLEA  219 (442)
Q Consensus       143 rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~---~~~ar~i~~~~l~~~~~~~~~  219 (442)
                      .+.         .++......+++|+......-  .+.....+.....+....+ +   +..|..++++ ....+....+
T Consensus       272 ~~~---------g~~~~A~~~~~~al~~~~~~~--~~~~~~~~~~l~~ly~~~~-~~~~~~~al~~~~~-~~~~~~~~~~  338 (378)
T 3q15_A          272 CKA---------GQTQKAFQFIEEGLDHITARS--HKFYKELFLFLQAVYKETV-DERKIHDLLSYFEK-KNLHAYIEAC  338 (378)
T ss_dssp             HHT---------TCHHHHHHHHHHHHHHCCTTC--CSCHHHHHHHHHHHHSSSC-CHHHHHHHHHHHHH-TTCHHHHHHH
T ss_pred             HHC---------CCHHHHHHHHHHHHHHHHHcC--CHHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHh-CCChhHHHHH
Confidence            011         344455566666666543211  1222223333444444444 5   5556655555 1224555668


Q ss_pred             HHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          220 WQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       220 w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      +...+.+....|+++.|...|++++.
T Consensus       339 ~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          339 ARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            88899999999999999999999986

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.88  E-value=0.00018  Score=58.05  Aligned_cols=97  Identities=10%  Similarity=-0.118  Sum_probs=80.5

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ++...|+.++...|. ++.....|..++......|+++.+...|++++...|.+..+|..++..+... ++.+.+...|+
T Consensus        46 ~A~~~~~~a~~~~~~-~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~-~~~~~A~~~~~  123 (148)
T 2dba_A           46 GALAAYTQALGLDAT-PQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDGGDVKALYRRSQALEKL-GRLDQAVLDLQ  123 (148)
T ss_dssp             HHHHHHHHHHTSCCC-HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccc-chHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCccCHHHHHHHHHHHHHc-CCHHHHHHHHH
Confidence            466788888887764 1112678999999888999999999999999999999999999998876644 45677999999


Q ss_pred             HHHHcCCCcHHHHHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~  101 (442)
                      +++...|....+|..+...
T Consensus       124 ~al~~~p~~~~~~~~l~~~  142 (148)
T 2dba_A          124 RCVSLEPKNKVFQEALRNI  142 (148)
T ss_dssp             HHHHHCSSCHHHHHHHHHH
T ss_pred             HHHHcCCCcHHHHHHHHHH
Confidence            9999999999999886653

>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=97.82  E-value=0.0019  Score=55.66  Aligned_cols=147  Identities=7%  Similarity=-0.065  Sum_probs=105.4

Q ss_pred             HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHH
Q 013489           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER  104 (442)
Q Consensus        25 ~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~  104 (442)
                      .+...+......|+++.+...|++++   +.++.+|...+..+.. .++.+.+...|++|+...|.....|......+. 
T Consensus         8 ~~~~~g~~~~~~~~~~~A~~~~~~a~---~~~~~~~~~lg~~~~~-~g~~~~A~~~~~~al~~~~~~~~~~~~lg~~~~-   82 (213)
T 1hh8_A            8 SLWNEGVLAADKKDWKGALDAFSAVQ---DPHSRICFNIGCMYTI-LKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYY-   82 (213)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHTSS---SCCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHc---CCChHHHHHHHHHHHH-cCCHHHHHHHHHHHHHhCccchHHHHHHHHHHH-
Confidence            34445555567899999999999997   3377899888876664 456678999999999999999999988877444 


Q ss_pred             ccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHH
Q 013489          105 SRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRL  184 (442)
Q Consensus       105 ~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l  184 (442)
                      ..++.+.+...|++++...+....                          ..             +........+....+
T Consensus        83 ~~~~~~~A~~~~~~al~~~~~~~~--------------------------~~-------------~~~~~~~~~~~~~~~  123 (213)
T 1hh8_A           83 QTEKYDLAIKDLKEALIQLRGNQL--------------------------ID-------------YKILGLQFKLFACEV  123 (213)
T ss_dssp             HTTCHHHHHHHHHHHHHTTTTCSE--------------------------EE-------------CGGGTBCCEEEHHHH
T ss_pred             HcccHHHHHHHHHHHHHhCCCccH--------------------------HH-------------HHHhccccCccchHH
Confidence            478889999999998875443100                          00             000000112233456


Q ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH
Q 013489          185 YAYWAHLEQSMGKDMVSARGVWERLLKISGAM  216 (442)
Q Consensus       185 ~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~  216 (442)
                      |...+.+....| +++.|...|++++...|+.
T Consensus       124 ~~~l~~~~~~~g-~~~~A~~~~~~al~~~p~~  154 (213)
T 1hh8_A          124 LYNIAFMYAKKE-EWKKAEEQLALATSMKSEP  154 (213)
T ss_dssp             HHHHHHHHHHTT-CHHHHHHHHHHHHTTCCSG
T ss_pred             HHHHHHHHHHcc-CHHHHHHHHHHHHHcCccc
Confidence            777777778888 8999999999999988764

>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=97.82  E-value=0.0044  Score=57.26  Aligned_cols=180  Identities=13%  Similarity=0.083  Sum_probs=106.7

Q ss_pred             cCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCc------HHHHHHHHHHHHHccCCH
Q 013489           36 SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV------GELWVRSLLSLERSRASE  109 (442)
Q Consensus        36 ~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s------~~lW~~y~~~le~~~~~~  109 (442)
                      .++++.+..+|+++..               +....+..+.+...|.+|+...+..      ...|..... +....++.
T Consensus        29 ~~~~~~A~~~~~~a~~---------------~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~-~~~~~g~~   92 (307)
T 2ifu_A           29 KPDYDSAASEYAKAAV---------------AFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGM-MLKDLQRM   92 (307)
T ss_dssp             SCCHHHHHHHHHHHHH---------------HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HHHHTTCG
T ss_pred             CCCHHHHHHHHHHHHH---------------HHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-HHHhCCCH
Confidence            3567777777777632               1112344556777777777654321      224444333 33345677


Q ss_pred             HHHHHHHHHHHhCChh--hHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHH
Q 013489          110 EEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAY  187 (442)
Q Consensus       110 ~~~~~i~~~al~~~~~--~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~  187 (442)
                      +++...|++|+.....  ........+... ..+.         .. .++......|++|+.+.... ........++..
T Consensus        93 ~~A~~~~~~Al~l~~~~g~~~~~a~~~~~l-g~~~---------~~-g~~~~A~~~~~~Al~~~~~~-~~~~~~~~~~~~  160 (307)
T 2ifu_A           93 PEAVQYIEKASVMYVENGTPDTAAMALDRA-GKLM---------EP-LDLSKAVHLYQQAAAVFENE-ERLRQAAELIGK  160 (307)
T ss_dssp             GGGHHHHHHHHHHHHTTTCHHHHHHHHHHH-HHHH---------TT-TCHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHHH---------Hc-CCHHHHHHHHHHHHHHHHhC-CChhHHHHHHHH
Confidence            7788888888753211  111111111110 0000         01 24445556667776655331 111123467778


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhchhH------HHHHHHHHHHHHhcccHHHHHHHHHHHH
Q 013489          188 WAHLEQSMGKDMVSARGVWERLLKISGAM------LEAWQSYISMEIELDHINEARSIYKRCY  244 (442)
Q Consensus       188 ~a~~e~~~~~~~~~ar~i~~~~l~~~~~~------~~~w~~~~~~e~~~g~~~~ar~i~~ral  244 (442)
                      .+.+....| +++.|...|++++...+..      ...|+..+.+....|+++.|...|++++
T Consensus       161 lg~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          161 ASRLLVRQQ-KFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHHHHHTT-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHcC-CHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            888988999 9999999999999985432      2367777777777899999999999998

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=97.81  E-value=0.0004  Score=53.73  Aligned_cols=93  Identities=13%  Similarity=0.052  Sum_probs=78.9

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ++...|+.++...|.    +...|..++......|+++.+..+|++++...|.+..+|...+..+.. .++.+.+...|+
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            466788888887765    667898999888899999999999999999999999999998887664 456678999999


Q ss_pred             HHHHcCCCcHHHHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLL  100 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~  100 (442)
                      +++...|....++.....
T Consensus       102 ~~~~~~~~~~~~~~~l~~  119 (125)
T 1na0_A          102 KALELDPNNAEAKQNLGN  119 (125)
T ss_dssp             HHHHHCTTCHHHHHHHHH
T ss_pred             HHHHhCCCcHHHHHHHHH
Confidence            999999998888777654

>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=97.81  E-value=0.00011  Score=60.55  Aligned_cols=89  Identities=9%  Similarity=-0.080  Sum_probs=65.7

Q ss_pred             ChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcc---------hhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcc--
Q 013489           38 DPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLK---------VGNVVRDVYSRATKNCPWVGELWVRSLLSLERSR--  106 (442)
Q Consensus        38 ~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~---------~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~--  106 (442)
                      .++.++..|++++..+|.+.+.|..+...+.....         ..+.+...|++|+...|.....|......+....  
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            45678888889998889999888888876654321         1356888899999988888888877665444321  


Q ss_pred             --------CCHHHHHHHHHHHHhCChhh
Q 013489          107 --------ASEEEISTVFEKSLLCAFST  126 (442)
Q Consensus       107 --------~~~~~~~~i~~~al~~~~~~  126 (442)
                              ++++++...|++|+...|..
T Consensus        97 ~P~~~~a~g~~~eA~~~~~kAl~l~P~~  124 (158)
T 1zu2_A           97 TPDETEAKHNFDLATQFFQQAVDEQPDN  124 (158)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             CcchhhhhccHHHHHHHHHHHHHhCCCC
Confidence                    46788888899998877663

>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=0.015  Score=54.83  Aligned_cols=235  Identities=12%  Similarity=0.070  Sum_probs=135.5

Q ss_pred             HHHHHHhcCChhhHHHHHHHHHhcCCCCHHH-H----HHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHH----HHH-H
Q 013489           29 YLKYEQSSGDPGRVQLLYERAITDFPVSSDL-W----LDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGEL----WVR-S   98 (442)
Q Consensus        29 y~~~e~~~g~~~~~~~lyERal~~~p~~~~l-W----~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~l----W~~-y   98 (442)
                      ........|+++.+..++++++...|..... |    ......+. ..++.+.+...|++|+...|..+..    |.. .
T Consensus        20 ~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~-~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~   98 (373)
T 1hz4_A           20 RAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLH-CKGELTRSLALMQQTEQMARQHDVWHYALWSLIQ   98 (373)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHH-HHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHH-hcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHH
Confidence            3334456899999999999999988765432 2    12222222 3356677999999999876543322    211 1


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHhCChh------hHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHh
Q 013489           99 LLSLERSRASEEEISTVFEKSLLCAFS------TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLS  172 (442)
Q Consensus        99 ~~~le~~~~~~~~~~~i~~~al~~~~~------~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~  172 (442)
                      +..+....++.+.+...|++++.....      .........+..   +...         ..++......+.+++....
T Consensus        99 la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~---~~~~---------~g~~~~A~~~~~~al~~~~  166 (373)
T 1hz4_A           99 QSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQ---LLWA---------WARLDEAEASARSGIEVLS  166 (373)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHH---HHHH---------TTCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHH---HHHH---------hcCHHHHHHHHHHHHHHhh
Confidence            223444578899999999998853211      001111111111   1001         1345555566666666543


Q ss_pred             hhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchh--HHHHHHH-----HHHHHHhcccHHHHHHHHHHHHh
Q 013489          173 EQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA--MLEAWQS-----YISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       173 ~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~--~~~~w~~-----~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ..-  .+.....+...+.+....| +++.|...+++++...+.  ....|..     .+.+....|+++.|+..+.+++.
T Consensus       167 ~~~--~~~~~~~~~~la~~~~~~g-~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~  243 (373)
T 1hz4_A          167 SYQ--PQQQLQCLAMLIQCSLARG-DLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAK  243 (373)
T ss_dssp             TSC--GGGGHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCC
T ss_pred             ccC--cHHHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCC
Confidence            211  1123456777888888899 999999999999976321  1123332     23345578999999999999986


Q ss_pred             cccCCC-C-hHHHHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          246 KRFTGT-G-SEDICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       246 ~~~~~~-~-~~~i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                      .. +.+ . ....+..........|+.+.-...+.++
T Consensus       244 ~~-~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a  279 (373)
T 1hz4_A          244 PE-FANNHFLQGQWRNIARAQILLGEFEPAEIVLEEL  279 (373)
T ss_dssp             CC-CTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             CC-CCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            32 111 1 1223344445555667766554444443

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=97.80  E-value=8.5e-05  Score=67.74  Aligned_cols=197  Identities=8%  Similarity=-0.053  Sum_probs=130.8

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHH-------HHHHhcCChhhHHHHHHHHHhcCCCC-------------------
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYL-------KYEQSSGDPGRVQLLYERAITDFPVS-------------------   56 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~-------~~e~~~g~~~~~~~lyERal~~~p~~-------------------   56 (442)
                      .++..|..++..+|.    ..+.|...+       ......+....+...+.|++...|..                   
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            578899999999886    788999994       43333334455666788888754421                   


Q ss_pred             --HHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHH
Q 013489           57 --SDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLF  134 (442)
Q Consensus        57 --~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~  134 (442)
                        .++++.|+..+... +..+.+..+|+..+...|.....|.. .. +....+..+.+...|+.++..+.+....-..++
T Consensus       100 ~r~dl~LayA~~L~~~-g~y~eA~~~l~~~~~~~p~~~~~~~~-a~-l~~~~~r~~dA~~~l~~a~~~~d~~~~~~a~~~  176 (282)
T 4f3v_A          100 SPLAITMGFAACEAAQ-GNYADAMEALEAAPVAGSEHLVAWMK-AV-VYGAAERWTDVIDQVKSAGKWPDKFLAGAAGVA  176 (282)
T ss_dssp             SHHHHHHHHHHHHHHH-TCHHHHHHHHTSSCCTTCHHHHHHHH-HH-HHHHTTCHHHHHHHHTTGGGCSCHHHHHHHHHH
T ss_pred             CHhHHHHHHHHHHHHC-CCHHHHHHHHHHHHhcCCchHHHHHH-HH-HHHHcCCHHHHHHHHHHhhccCCcccHHHHHHH
Confidence              47888899887754 45677999999888777754423332 22 333468889999999988766533211111222


Q ss_pred             HHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcC-c-hh-hHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 013489          135 LTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKN-T-DG-LLRLYAYWAHLEQSMGKDMVSARGVWERLLK  211 (442)
Q Consensus       135 ~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~-~-~~-~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~  211 (442)
                      +..   +.                .-...|++|+.++.+.... . +. ..+.+...+.....+| +.+.|+.+|++++.
T Consensus       177 LG~---al----------------~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lG-r~deA~~~l~~a~a  236 (282)
T 4f3v_A          177 HGV---AA----------------ANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQG-NESAAVALLEWLQT  236 (282)
T ss_dssp             HHH---HH----------------HHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHH
T ss_pred             HHH---HH----------------HHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcC-CHHHHHHHHHHHHh
Confidence            111   10                1113456666666655432 2 33 4568888888889999 99999999999999


Q ss_pred             hchhHHHHHHHHHHHH
Q 013489          212 ISGAMLEAWQSYISME  227 (442)
Q Consensus       212 ~~~~~~~~w~~~~~~e  227 (442)
                      .+|+ ..+|....+..
T Consensus       237 ~~P~-~~~~~aL~~~~  251 (282)
T 4f3v_A          237 THPE-PKVAAALKDPS  251 (282)
T ss_dssp             HSCC-HHHHHHHHCTT
T ss_pred             cCCc-HHHHHHHhCCC
Confidence            9999 87777665543

>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=97.80  E-value=0.00039  Score=60.14  Aligned_cols=102  Identities=4%  Similarity=-0.127  Sum_probs=86.6

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcH---------
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVG---------   92 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~---------   92 (442)
                      +...|...+......|+++.+...|++++..+|.+...|...+..+.. .+..+.+...|++++...|...         
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            456898899888899999999999999999999999999999987764 4566789999999999888755         


Q ss_pred             -------HHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh
Q 013489           93 -------ELWVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus        93 -------~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                             .+|......+. ..++.+.+...|++++...+.
T Consensus       115 ~~~~~~~~~~~~l~~~~~-~~g~~~~A~~~~~~al~~~p~  153 (213)
T 1hh8_A          115 QFKLFACEVLYNIAFMYA-KKEEWKKAEEQLALATSMKSE  153 (213)
T ss_dssp             CCEEEHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCCS
T ss_pred             ccCccchHHHHHHHHHHH-HccCHHHHHHHHHHHHHcCcc
Confidence                   78887776444 478899999999999987664

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.79  E-value=9.3e-05  Score=57.82  Aligned_cols=89  Identities=11%  Similarity=0.065  Sum_probs=46.6

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (442)
                      |...|+.+|...+ .+|.+...|...+......|+++.+...|+++|..+|.++.+|..++..+... +..+.+...|++
T Consensus         9 A~~~~~~al~~~~-~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~-g~~~~A~~~~~~   86 (117)
T 3k9i_A            9 AVPYYEKAIASGL-QGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPNHQALRVFYAMVLYNL-GRYEQGVELLLK   86 (117)
T ss_dssp             CHHHHHHHHSSCC-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCC-CCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHc-CCHHHHHHHHHH
Confidence            4445555554421 12334555555555555555666666666666666666655555555544432 333445555666


Q ss_pred             HHHcCCCcHHH
Q 013489           84 ATKNCPWVGEL   94 (442)
Q Consensus        84 Al~~~p~s~~l   94 (442)
                      ++...|.+..+
T Consensus        87 al~~~p~~~~~   97 (117)
T 3k9i_A           87 IIAETSDDETI   97 (117)
T ss_dssp             HHHHHCCCHHH
T ss_pred             HHHhCCCcHHH
Confidence            65555555443

>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=97.77  E-value=0.00031  Score=55.88  Aligned_cols=101  Identities=11%  Similarity=-0.079  Sum_probs=78.6

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcH-------HH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVG-------EL   94 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~-------~l   94 (442)
                      ....|.+........|+++.++..|++||..+|.+..+|...+..+.. .+..+.+...|++|+...|...       .+
T Consensus         7 ~A~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~p~~~~~~~nlg~~~~~-~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~   85 (127)
T 4gcn_A            7 AAIAEKDLGNAAYKQKDFEKAHVHYDKAIELDPSNITFYNNKAAVYFE-EKKFAECVQFCEKAVEVGRETRADYKLIAKA   85 (127)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHHH-hhhHHHHHHHHHHHHHhCcccchhhHHHHHH
Confidence            345688888888889999999999999999999999999988876664 4566789999999999766432       23


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCh
Q 013489           95 WVRSLLSLERSRASEEEISTVFEKSLLCAF  124 (442)
Q Consensus        95 W~~y~~~le~~~~~~~~~~~i~~~al~~~~  124 (442)
                      |..... .....+..+.+...|++++...+
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            433333 33446888999999999997544

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.76  E-value=0.00036  Score=54.04  Aligned_cols=81  Identities=11%  Similarity=-0.005  Sum_probs=38.6

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (442)
                      +...|+.+|...|.    +...|..++......|+++.+...|++++..+|.+...|..++..+... ++.+.+...|++
T Consensus         4 a~~~~~~al~~~p~----~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~-g~~~~A~~~~~~   78 (115)
T 2kat_A            4 ITERLEAMLAQGTD----NMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPTYSVAWKWLGKTLQGQ-GDRAGARQAWES   78 (115)
T ss_dssp             HHHHHHHHHTTTCC----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCC----cHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHc-CCHHHHHHHHHH
Confidence            34445555544443    3444555554444555555555555555555555555555444433322 233444555555


Q ss_pred             HHHcCC
Q 013489           84 ATKNCP   89 (442)
Q Consensus        84 Al~~~p   89 (442)
                      ++...|
T Consensus        79 al~~~~   84 (115)
T 2kat_A           79 GLAAAQ   84 (115)
T ss_dssp             HHHHHH
T ss_pred             HHHhcc
Confidence            554433

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.74  E-value=0.00014  Score=56.80  Aligned_cols=82  Identities=12%  Similarity=0.105  Sum_probs=69.0

Q ss_pred             HHHHHHHHhhhhcC---chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHH
Q 013489          164 FQRASDYLSEQMKN---TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIY  240 (442)
Q Consensus       164 ~~~a~~~l~~~~~~---~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~  240 (442)
                      +++|+.++..++..   .+....+|...+.+....| +++.|...|++++..+|++..+|..++......|+++.|...|
T Consensus         6 ~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~-~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~   84 (117)
T 3k9i_A            6 EAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLG-EYRKAEAVLANGVKQFPNHQALRVFYAMVLYNLGRYEQGVELL   84 (117)
T ss_dssp             -CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHcCCHHHHHHHH
Confidence            33444555555544   3556788999999999999 9999999999999999999999999999999999999999999


Q ss_pred             HHHHhc
Q 013489          241 KRCYSK  246 (442)
Q Consensus       241 ~ral~~  246 (442)
                      ++++..
T Consensus        85 ~~al~~   90 (117)
T 3k9i_A           85 LKIIAE   90 (117)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            999974

>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=97.74  E-value=5.8e-05  Score=74.58  Aligned_cols=83  Identities=6%  Similarity=0.026  Sum_probs=51.8

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHH
Q 013489          184 LYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRF  263 (442)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~f  263 (442)
                      +|...+.....++ +++.|...|++++..+|++...|...+......|+++.|+..|++|+..  .++.+ .++......
T Consensus       319 ~~~nla~~~~~~g-~~~~A~~~~~~al~~~p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l--~P~~~-~a~~~l~~~  394 (457)
T 1kt0_A          319 AFLNLAMCYLKLR-EYTKAVECCDKALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNK-AARLQISMC  394 (457)
T ss_dssp             HHHHHHHHHHHTT-CHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--C-----CHHHHHHHH
T ss_pred             HHHHHHHHHHHhc-CHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCH-HHHHHHHHH
Confidence            4444555556666 7777777788877777777777777777777777777788778777752  22322 234344444


Q ss_pred             HHHhCCH
Q 013489          264 EREYGTL  270 (442)
Q Consensus       264 E~~~G~~  270 (442)
                      ....|..
T Consensus       395 ~~~~~~~  401 (457)
T 1kt0_A          395 QKKAKEH  401 (457)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            4444443

>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=97.73  E-value=0.0011  Score=56.89  Aligned_cols=103  Identities=12%  Similarity=-0.130  Sum_probs=86.2

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCH----------------HHHHHHHHHHHHhcchhhHHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS----------------DLWLDYTQYLDKTLKVGNVVRDVYSRAT   85 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~----------------~lW~~Y~~~l~~~~~~~~~~~~v~erAl   85 (442)
                      ....|...+......|+++.+..+|++++...|.++                .+|...+..+.. .+..+.+...|++|+
T Consensus        37 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~-~~~~~~A~~~~~~al  115 (198)
T 2fbn_A           37 SAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNK-NKDYPKAIDHASKVL  115 (198)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHH-hcCHHHHHHHHHHHH
Confidence            455788888888889999999999999999998887                788888776654 456678999999999


Q ss_pred             HcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhh
Q 013489           86 KNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFST  126 (442)
Q Consensus        86 ~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~  126 (442)
                      ...|.....|......+. ..++.+.+...|++++...+..
T Consensus       116 ~~~p~~~~~~~~lg~~~~-~~~~~~~A~~~~~~al~~~p~~  155 (198)
T 2fbn_A          116 KIDKNNVKALYKLGVANM-YFGFLEEAKENLYKAASLNPNN  155 (198)
T ss_dssp             HHSTTCHHHHHHHHHHHH-HHTCHHHHHHHHHHHHHHSTTC
T ss_pred             HhCcccHHHHHHHHHHHH-HcccHHHHHHHHHHHHHHCCCc
Confidence            999999999988877554 4788999999999999876654

>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=97.72  E-value=0.00025  Score=56.51  Aligned_cols=93  Identities=14%  Similarity=-0.068  Sum_probs=78.3

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      .+...|+.+|...|.    +...|..++......|+++.+...|++++..+|.++..|...+..+... ++.+.+...|.
T Consensus        27 ~A~~~~~~al~~~~~----~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~-~~~~~A~~~~~  101 (137)
T 3q49_B           27 EAAACYGRAITRNPL----VAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQLEM-ESYDEAIANLQ  101 (137)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHhhCcC----cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHH-hhHHHHHHHHH
Confidence            456788888888775    6789999999999999999999999999999999999999999877644 56678999999


Q ss_pred             HHHHcCCC-----cHHHHHHHHH
Q 013489           83 RATKNCPW-----VGELWVRSLL  100 (442)
Q Consensus        83 rAl~~~p~-----s~~lW~~y~~  100 (442)
                      +++...|.     ...+|.....
T Consensus       102 ~a~~~~p~~~~~~~~~~~~~l~~  124 (137)
T 3q49_B          102 RAYSLAKEQRLNFGDDIPSALRI  124 (137)
T ss_dssp             HHHHHHHHTTCCCTTHHHHHHHH
T ss_pred             HHHHHChhHHHHHHHHHHHHHHH
Confidence            99998776     5667666544

>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=97.72  E-value=0.0008  Score=61.61  Aligned_cols=171  Identities=13%  Similarity=0.019  Sum_probs=113.7

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      +|...|+.+|...|.    +...|..++......|+++.+...|++++..+|.+...|...+..+.. .+..+.+...|+
T Consensus        22 ~A~~~~~~al~~~p~----~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~-~g~~~~A~~~~~   96 (281)
T 2c2l_A           22 EAAACYGRAITRNPL----VAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQLE-MESYDEAIANLQ   96 (281)
T ss_dssp             HHHHHHHHHHHHCSC----CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHH-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCc----cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-cCCHHHHHHHHH
Confidence            467789999988876    778899999998999999999999999999999999999999887664 456678999999


Q ss_pred             HHHHcCCCc-----HHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh--hHHHHHHHHHHHHHHHHHHhhccCccchhh
Q 013489           83 RATKNCPWV-----GELWVRSLLSLERSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRILFSGEVEGVL  155 (442)
Q Consensus        83 rAl~~~p~s-----~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~--~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~  155 (442)
                      +|+...|..     ..+|..... ...     .....   ......+.  .+..++..                      
T Consensus        97 ~al~l~p~~~~~~~~~~~~~~~~-~~~-----~~~~~---~~~~~~~~~~~i~~~l~~----------------------  145 (281)
T 2c2l_A           97 RAYSLAKEQRLNFGDDIPSALRI-AKK-----KRWNS---IEERRIHQESELHSYLTR----------------------  145 (281)
T ss_dssp             HHHHHHHHTTCCCCSHHHHHHHH-HHH-----HHHHH---HHHTCCCCCCHHHHHHHH----------------------
T ss_pred             HHHHhCccchhhHHHHHHHHHHH-HHH-----HHHHH---HHHHHHhhhHHHHHHHHH----------------------
Confidence            999977743     356655422 111     01111   11111111  11111111                      


Q ss_pred             hHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh
Q 013489          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI  212 (442)
Q Consensus       156 ~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~  212 (442)
                         .+...+++|+..+..++...+....+......+.....+.++.+..+|.++...
T Consensus       146 ---l~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~~  199 (281)
T 2c2l_A          146 ---LIAAERERELEECQRNHEGHEDDGHIRAQQACIEAKHDKYMADMDELFSQVDEK  199 (281)
T ss_dssp             ---HHHHHHHHHHTTTSGGGTTTSCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSCT
T ss_pred             ---HHHHHHHHHHHHHHhhhccccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence               112455667777766665444444455555556655543678899999988764

>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=97.72  E-value=0.0018  Score=59.93  Aligned_cols=207  Identities=9%  Similarity=0.004  Sum_probs=122.0

Q ss_pred             cCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHH
Q 013489           36 SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTV  115 (442)
Q Consensus        36 ~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i  115 (442)
                      .|+++.+..+++++....+.+         ++ ...++.+.+...|.++..               +....+..+.+...
T Consensus         4 ~~~~~eA~~~~~~a~k~~~~~---------~~-~~~~~~~~A~~~~~~a~~---------------~~~~~g~~~~A~~~   58 (307)
T 2ifu_A            4 AQKISEAHEHIAKAEKYLKTS---------FM-KWKPDYDSAASEYAKAAV---------------AFKNAKQLEQAKDA   58 (307)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCC---------SS-SCSCCHHHHHHHHHHHHH---------------HHHHTTCHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHcccc---------cc-CCCCCHHHHHHHHHHHHH---------------HHHHcCCHHHHHHH
Confidence            455677888888888766542         11 112345667778887732               22235778888888


Q ss_pred             HHHHHhCChh--hHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHH
Q 013489          116 FEKSLLCAFS--TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQ  193 (442)
Q Consensus       116 ~~~al~~~~~--~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~  193 (442)
                      |.+++.....  ........+.... .+....         .++......|++|+.+.... .+.......+...+.++.
T Consensus        59 ~~~al~~~~~~~~~~~~a~~~~~lg-~~~~~~---------g~~~~A~~~~~~Al~l~~~~-g~~~~~a~~~~~lg~~~~  127 (307)
T 2ifu_A           59 YLQEAEAHANNRSLFHAAKAFEQAG-MMLKDL---------QRMPEAVQYIEKASVMYVEN-GTPDTAAMALDRAGKLME  127 (307)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHH-HHHHHT---------TCGGGGHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHH-HHHHhC---------CCHHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHH
Confidence            9888864321  1111111111111 111111         22333446677777664321 112223467777788777


Q ss_pred             HcCCCHHHHHHHHHHHHHhchhH------HHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHH---H
Q 013489          194 SMGKDMVSARGVWERLLKISGAM------LEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRF---E  264 (442)
Q Consensus       194 ~~~~~~~~ar~i~~~~l~~~~~~------~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~f---E  264 (442)
                      . | +++.|...|++++..++..      ..++.....+....|+++.|..+|++++...........+...|+..   -
T Consensus       128 ~-g-~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~  205 (307)
T 2ifu_A          128 P-L-DLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQ  205 (307)
T ss_dssp             T-T-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             c-C-CHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHH
Confidence            6 6 9999999999999986532      46888999999999999999999999997421111222222333333   3


Q ss_pred             HHhCCHhhHHHHHHhh
Q 013489          265 REYGTLEDFDHSVQKV  280 (442)
Q Consensus       265 ~~~G~~~~~~~~~~~~  280 (442)
                      ...|+.+.-..+++++
T Consensus       206 ~~~g~~~~A~~~~~~a  221 (307)
T 2ifu_A          206 LHRADYVAAQKCVRES  221 (307)
T ss_dssp             HHTTCHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHH
Confidence            3347766655555554

>4aez_C MAD3, mitotic spindle checkpoint component MAD3; cell cycle, KEN-BOX, D-BOX, APC/C; 2.30A {Schizosaccharomyces pombe}

Probab=97.71  E-value=0.00033  Score=60.61  Aligned_cols=95  Identities=11%  Similarity=0.131  Sum_probs=70.6

Q ss_pred             HHHHHHHHHHh--hhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh-ch-hHHHHHHHHHHHHHhcccHHHHH
Q 013489          162 ETFQRASDYLS--EQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI-SG-AMLEAWQSYISMEIELDHINEAR  237 (442)
Q Consensus       162 ~~~~~a~~~l~--~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~-~~-~~~~~w~~~~~~e~~~g~~~~ar  237 (442)
                      .++++|+..+.  ..+.+.+..+++|+.|+++    .   +.++.+|.-+... -+ ..+.+|..|+.+....|++..|.
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            55667766653  2344566678999999864    2   2567899888877 44 44679999999999999999999


Q ss_pred             HHHHHHHhcccCCCChHHHHHHHHHHHH
Q 013489          238 SIYKRCYSKRFTGTGSEDICHAWLRFER  265 (442)
Q Consensus       238 ~i~~ral~~~~~~~~~~~i~~~~~~fE~  265 (442)
                      .||+.++.+...  ..+.|-.++.+|++
T Consensus       171 ~Vy~~Gi~~~A~--P~~rL~~~~~~F~~  196 (223)
T 4aez_C          171 EVYQKGKRMKAK--PFLRFQQKYQQFTH  196 (223)
T ss_dssp             HHHHHHHHHTCB--SHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCc--cHHHHHHHHHHHHH
Confidence            999999986422  24566677777764

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.70  E-value=0.0012  Score=54.54  Aligned_cols=104  Identities=11%  Similarity=-0.100  Sum_probs=86.8

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhc------------------CCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITD------------------FPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~------------------~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (442)
                      ....|..-.......|+++.+...|+++|..                  .|.+..+|...+..+.. .+..+.+...|++
T Consensus        10 ~a~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~-~~~~~~A~~~~~~   88 (162)
T 3rkv_A           10 SVEALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLN-IGDLHEAEETSSE   88 (162)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHH-HTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHh-cCcHHHHHHHHHH
Confidence            4567888888888899999999999999998                  66677888888776654 3566789999999


Q ss_pred             HHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhH
Q 013489           84 ATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTF  127 (442)
Q Consensus        84 Al~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~  127 (442)
                      |+...|.....|......+.. .+..+.+...|++++...|...
T Consensus        89 al~~~p~~~~a~~~~g~~~~~-~g~~~~A~~~~~~al~l~p~~~  131 (162)
T 3rkv_A           89 VLKREETNEKALFRRAKARIA-AWKLDEAEEDLKLLLRNHPAAA  131 (162)
T ss_dssp             HHHHSTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCGGGH
T ss_pred             HHhcCCcchHHHHHHHHHHHH-HhcHHHHHHHHHHHHhcCCCCH
Confidence            999999999999988775554 7889999999999998877644

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.67  E-value=0.0003  Score=54.51  Aligned_cols=75  Identities=11%  Similarity=0.002  Sum_probs=64.5

Q ss_pred             HHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          170 YLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       170 ~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      .+...+...+....+|..++.+....| +++.|...|++++..+|+....|..++.+....|+++.|+..|++++.
T Consensus         7 ~~~~al~~~p~~~~~~~~lg~~~~~~g-~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~   81 (115)
T 2kat_A            7 RLEAMLAQGTDNMLLRFTLGKTYAEHE-QFDAALPHLRAALDFDPTYSVAWKWLGKTLQGQGDRAGARQAWESGLA   81 (115)
T ss_dssp             HHHHHHTTTCCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCcHHHHHHHHHHHHHcc-CHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            333333334555678888999988889 999999999999999999999999999999999999999999999986

>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=97.67  E-value=0.00032  Score=69.18  Aligned_cols=105  Identities=12%  Similarity=-0.063  Sum_probs=87.0

Q ss_pred             HhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCC---------------HHHHHHHHHHHHHhcchhhHHHHHHHHHH
Q 013489           21 EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVS---------------SDLWLDYTQYLDKTLKVGNVVRDVYSRAT   85 (442)
Q Consensus        21 ~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~---------------~~lW~~Y~~~l~~~~~~~~~~~~v~erAl   85 (442)
                      .....|..........|+++.|...|++||..+|.+               ..+|..++..+.. .+..+.+...|++|+
T Consensus       266 ~~a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~-~g~~~~A~~~~~~al  344 (457)
T 1kt0_A          266 EQAAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLK-LREYTKAVECCDKAL  344 (457)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHH-hcCHHHHHHHHHHHH
Confidence            356688889998889999999999999999999988               6888888876664 456688999999999


Q ss_pred             HcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhH
Q 013489           86 KNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTF  127 (442)
Q Consensus        86 ~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~  127 (442)
                      ...|.....|......+.. .++.+.+...|++|+...+...
T Consensus       345 ~~~p~~~~a~~~~g~a~~~-~g~~~~A~~~~~~al~l~P~~~  385 (457)
T 1kt0_A          345 GLDSANEKGLYRRGEAQLL-MNEFESAKGDFEKVLEVNPQNK  385 (457)
T ss_dssp             HHSTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTC----
T ss_pred             hcCCccHHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhCCCCH
Confidence            9999999999888775554 6889999999999998877643

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.65  E-value=0.00046  Score=57.11  Aligned_cols=89  Identities=19%  Similarity=0.164  Sum_probs=72.0

Q ss_pred             hHHHHHHHHHHHHHHHhhhhcC-----------chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHH
Q 013489          156 DYSLIRETFQRASDYLSEQMKN-----------TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYI  224 (442)
Q Consensus       156 ~~~~~r~~~~~a~~~l~~~~~~-----------~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~  224 (442)
                      ++......|.+|+.++......           .+....+|...+......| +++.|...+++++..+|++...|...+
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            4455556667776664332210           2334568888899989999 999999999999999999999999999


Q ss_pred             HHHHhcccHHHHHHHHHHHHh
Q 013489          225 SMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       225 ~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ......|+++.|...|++++.
T Consensus       105 ~~~~~~g~~~~A~~~~~~al~  125 (162)
T 3rkv_A          105 KARIAAWKLDEAEEDLKLLLR  125 (162)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhcHHHHHHHHHHHHh
Confidence            999999999999999999997

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.65  E-value=0.00019  Score=67.79  Aligned_cols=149  Identities=11%  Similarity=-0.030  Sum_probs=64.8

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~  101 (442)
                      ....|..........|+++.|...|+++|..+|.+.. +.        ..+....+..    ++.     ..+|..+.. 
T Consensus       178 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~-~~--------~~~~~~~~~~----~l~-----~~~~~nla~-  238 (338)
T 2if4_A          178 AADRRKMDGNSLFKEEKLEEAMQQYEMAIAYMGDDFM-FQ--------LYGKYQDMAL----AVK-----NPCHLNIAA-  238 (338)
T ss_dssp             HHHHHHHHHHHTCSSSCCHHHHHHHHHHHHHSCHHHH-HT--------CCHHHHHHHH----HHH-----THHHHHHHH-
T ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhccchh-hh--------hcccHHHHHH----HHH-----HHHHHHHHH-
Confidence            3456777777677789999999999999998886541 00        0011111111    111     135555554 


Q ss_pred             HHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhh
Q 013489          102 LERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGL  181 (442)
Q Consensus       102 le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~  181 (442)
                      +....+..+.+...|++++...+...                                                      
T Consensus       239 ~~~~~g~~~~A~~~~~~al~~~p~~~------------------------------------------------------  264 (338)
T 2if4_A          239 CLIKLKRYDEAIGHCNIVLTEEEKNP------------------------------------------------------  264 (338)
T ss_dssp             HHHTTTCCHHHHHHHHHHHHHCTTCH------------------------------------------------------
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCCCH------------------------------------------------------
Confidence            33345667777777777775433211                                                      


Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHH-hcccHHHHHHHHHHHHh
Q 013489          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEI-ELDHINEARSIYKRCYS  245 (442)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~-~~g~~~~ar~i~~ral~  245 (442)
                       ..|...+..+...+ +++.|+..|++++...|++..+|..+..+.. ..+..+.++.+|.+++.
T Consensus       265 -~a~~~lg~a~~~~g-~~~~A~~~l~~al~l~p~~~~a~~~L~~l~~~~~~~~~~a~~~~~~~l~  327 (338)
T 2if4_A          265 -KALFRRGKAKAELG-QMDSARDDFRKAQKYAPDDKAIRRELRALAEQEKALYQKQKEMYKGIFK  327 (338)
T ss_dssp             -HHHHHHHHHHHTTT-CHHHHHHHHHHTTC-----------------------------------
T ss_pred             -HHHHHHHHHHHHcC-CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence             12333344444555 6777777777777666666666666665533 33456666667776665

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.64  E-value=0.00026  Score=53.76  Aligned_cols=66  Identities=8%  Similarity=0.022  Sum_probs=53.6

Q ss_pred             hhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchh--HHHHHHHHHHHHHhc-ccHHHHHHHHHHHHh
Q 013489          179 DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA--MLEAWQSYISMEIEL-DHINEARSIYKRCYS  245 (442)
Q Consensus       179 ~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~--~~~~w~~~~~~e~~~-g~~~~ar~i~~ral~  245 (442)
                      +....+|..++.+....+ +++.|...|++++...|+  ...+|...+.+.... |+++.|...|.+++.
T Consensus        37 ~~~~~~~~~~a~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~  105 (112)
T 2kck_A           37 PEESKYWLMKGKALYNLE-RYEEAVDCYNYVINVIEDEYNKDVWAAKADALRYIEGKEVEAEIAEARAKL  105 (112)
T ss_dssp             CCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHTSCCTTCHHHHHHHHHHHTTCSSCSHHHHHHHHHHGG
T ss_pred             cCCHHHHHHHHHHHHHcc-CHHHHHHHHHHHHHhCcccchHHHHHHHHHHHHHHhCCHHHHHHHHHHHhh
Confidence            344557777787777777 888888888888888888  788888888888888 888888888888886

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.63  E-value=0.00012  Score=69.11  Aligned_cols=117  Identities=11%  Similarity=-0.020  Sum_probs=66.7

Q ss_pred             hhhHHHHHHhhcCCCCChHhH-----------------HHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKF-----------------QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQ   65 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~-----------------~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~   65 (442)
                      +|...|+.+|...|.    +.                 ..|.+++......|+++.+...|+++|..+|.+...|...+.
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            466788888877663    32                 378888888889999999999999999999999999999988


Q ss_pred             HHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCh
Q 013489           66 YLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAF  124 (442)
Q Consensus        66 ~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~  124 (442)
                      .+.. .+..+.+...|++|+...|....+|..+........+..+..+.+|.+++...+
T Consensus       273 a~~~-~g~~~~A~~~l~~al~l~p~~~~a~~~L~~l~~~~~~~~~~a~~~~~~~l~~~p  330 (338)
T 2if4_A          273 AKAE-LGQMDSARDDFRKAQKYAPDDKAIRRELRALAEQEKALYQKQKEMYKGIFKGKD  330 (338)
T ss_dssp             HHHT-TTCHHHHHHHHHHTTC--------------------------------------
T ss_pred             HHHH-cCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCC
Confidence            7664 456688999999999999998888887665434444556677888888886544

>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=97.63  E-value=0.014  Score=50.54  Aligned_cols=61  Identities=11%  Similarity=-0.153  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHHH----cCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHh-cc-----cHHHHHHHHHHHHh
Q 013489          183 RLYAYWAHLEQS----MGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE-LD-----HINEARSIYKRCYS  245 (442)
Q Consensus       183 ~l~~~~a~~e~~----~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~-~g-----~~~~ar~i~~ral~  245 (442)
                      ..+..++.+...    .. +++.|...|++++.. +.+...+.....+... .|     +++.|...|++|+.
T Consensus       126 ~a~~~Lg~~y~~g~g~~~-d~~~A~~~~~~A~~~-~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~  196 (212)
T 3rjv_A          126 DAQMLLGLIYASGVHGPE-DDVKASEYFKGSSSL-SRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCL  196 (212)
T ss_dssp             HHHHHHHHHHHHTSSSSC-CHHHHHHHHHHHHHT-SCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCC-CHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHH
Confidence            344445555544    34 889999999999987 3333344445554432 23     89999999999986

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.62  E-value=0.0012  Score=51.79  Aligned_cols=97  Identities=7%  Similarity=-0.040  Sum_probs=76.7

Q ss_pred             HHHHHHHHhcCChhhHHHHHHHHHhcCCCCH---HHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCc---HHHHHHHHH
Q 013489           27 MIYLKYEQSSGDPGRVQLLYERAITDFPVSS---DLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV---GELWVRSLL  100 (442)
Q Consensus        27 ~~y~~~e~~~g~~~~~~~lyERal~~~p~~~---~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s---~~lW~~y~~  100 (442)
                      ...+......|+++.+...|++++..+|.++   ..|...+..... .++.+.+...|++++...|.+   ...|.....
T Consensus         6 ~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~~-~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~la~   84 (129)
T 2xev_A            6 YNVAFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYA-TRNFQLAEAQFRDLVSRYPTHDKAAGGLLKLGL   84 (129)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHH-hccHHHHHHHHHHHHHHCCCCcccHHHHHHHHH
Confidence            3344445678999999999999999999888   788877766554 456678999999999999988   677777666


Q ss_pred             HHHHccCCHHHHHHHHHHHHhCChh
Q 013489          101 SLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus       101 ~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                      .+. ..++.+.+...|++++...+.
T Consensus        85 ~~~-~~g~~~~A~~~~~~~~~~~p~  108 (129)
T 2xev_A           85 SQY-GEGKNTEAQQTLQQVATQYPG  108 (129)
T ss_dssp             HHH-HTTCHHHHHHHHHHHHHHSTT
T ss_pred             HHH-HcCCHHHHHHHHHHHHHHCCC
Confidence            444 478899999999999976554

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=97.61  E-value=0.021  Score=52.65  Aligned_cols=201  Identities=13%  Similarity=0.027  Sum_probs=124.1

Q ss_pred             HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCC--CcHHHHHHHHH
Q 013489           23 FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCP--WVGELWVRSLL  100 (442)
Q Consensus        23 ~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p--~s~~lW~~y~~  100 (442)
                      ......|+.|..  ++   +...|++.+...+.+.....-.+. +....++.+.+..++.+++..-|  .+.++....+.
T Consensus        71 ~~a~~~la~~~~--~~---a~~~l~~l~~~~~~~~~~~~~la~-i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vq  144 (310)
T 3mv2_B           71 GKVLDLYVQFLD--TK---NIEELENLLKDKQNSPYELYLLAT-AQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIE  144 (310)
T ss_dssp             HHHHHHHHHHHT--TT---CCHHHHHTTTTSCCCHHHHHHHHH-HHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHhc--cc---HHHHHHHHHhcCCCCcHHHHHHHH-HHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHH
Confidence            345556666553  21   667788888765555555553333 33345677889999999988776  67778877777


Q ss_pred             HHHHccCCHHHHHHHHHHHHhCChhhH----HHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhc
Q 013489          101 SLERSRASEEEISTVFEKSLLCAFSTF----EEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMK  176 (442)
Q Consensus       101 ~le~~~~~~~~~~~i~~~al~~~~~~~----~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~  176 (442)
                      .+.. .++.+.++.+++++....++..    ...+.+...|+....-    .             +.++.|..++.....
T Consensus       145 i~L~-~~r~d~A~k~l~~~~~~~~d~~~~~d~~l~~Laea~v~l~~g----~-------------~~~q~A~~~f~El~~  206 (310)
T 3mv2_B          145 VALL-NNNVSTASTIFDNYTNAIEDTVSGDNEMILNLAESYIKFATN----K-------------ETATSNFYYYEELSQ  206 (310)
T ss_dssp             HHHH-TTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHT----C-------------STTTHHHHHHHHHHT
T ss_pred             HHHH-CCCHHHHHHHHHHHHhcCccccccchHHHHHHHHHHHHHHhC----C-------------ccHHHHHHHHHHHHH
Confidence            4444 6888999999999877665211    1122233333322210    0             012333333333332


Q ss_pred             CchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc----------hhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          177 NTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS----------GAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       177 ~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~----------~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      ..+........|. ....+| +++.|.++++.+++.+          |+++.+....|.+....|+  .|..++.++.. 
T Consensus       207 ~~p~~~~~~lLln-~~~~~g-~~~eAe~~L~~l~~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~-  281 (310)
T 3mv2_B          207 TFPTWKTQLGLLN-LHLQQR-NIAEAQGIVELLLSDYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVK-  281 (310)
T ss_dssp             TSCSHHHHHHHHH-HHHHHT-CHHHHHHHHHHHHSHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHH-
T ss_pred             hCCCcccHHHHHH-HHHHcC-CHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHH-
Confidence            3332111111222 567778 9999999999887764          6788888899888888887  78889999886 


Q ss_pred             ccCCCCh
Q 013489          247 RFTGTGS  253 (442)
Q Consensus       247 ~~~~~~~  253 (442)
                       +.++.|
T Consensus       282 -~~P~hp  287 (310)
T 3mv2_B          282 -LDHEHA  287 (310)
T ss_dssp             -TTCCCH
T ss_pred             -hCCCCh
Confidence             344444

>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=97.60  E-value=0.00041  Score=59.64  Aligned_cols=99  Identities=7%  Similarity=-0.095  Sum_probs=79.7

Q ss_pred             hhhHHHHHHhhcCCCCChH-------------hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSE-------------KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDK   69 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~-------------~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~   69 (442)
                      +|...|+.+|...|.. ++             ....|..++......|+++.+...|+++|...|.+...|...+..+..
T Consensus        56 ~A~~~~~~al~~~~~~-~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~  134 (198)
T 2fbn_A           56 EAIVKYKEALDFFIHT-EEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMY  134 (198)
T ss_dssp             HHHHHHHHHHHTTTTC-TTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcc-cccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHH
Confidence            4566788888766531 10             026788888888889999999999999999999999999999887764


Q ss_pred             hcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHH
Q 013489           70 TLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLE  103 (442)
Q Consensus        70 ~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le  103 (442)
                       .++.+.+...|++|+...|....+|......+.
T Consensus       135 -~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~  167 (198)
T 2fbn_A          135 -FGFLEEAKENLYKAASLNPNNLDIRNSYELCVN  167 (198)
T ss_dssp             -HTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH
T ss_pred             -cccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHH
Confidence             456678999999999999999988888766443

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=97.59  E-value=0.036  Score=54.27  Aligned_cols=96  Identities=10%  Similarity=0.077  Sum_probs=52.3

Q ss_pred             HHHHHHHHHHhcC---ChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh---cchhhHHHHHHHHHHHcCCCcHHHHHHH
Q 013489           25 QYMIYLKYEQSSG---DPGRVQLLYERAITDFPVSSDLWLDYTQYLDKT---LKVGNVVRDVYSRATKNCPWVGELWVRS   98 (442)
Q Consensus        25 ~w~~y~~~e~~~g---~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~---~~~~~~~~~v~erAl~~~p~s~~lW~~y   98 (442)
                      .+..+.......|   +.+.+...|++++...|.....|.....++...   .++.+.+...|++|.   |.....+...
T Consensus       178 a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa---~g~~~a~~~L  254 (452)
T 3e4b_A          178 CYVELATVYQKKQQPEQQAELLKQMEAGVSRGTVTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA---PGYPASWVSL  254 (452)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG---GGSTHHHHHH
T ss_pred             HHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc---CCCHHHHHHH
Confidence            3334444334455   566666667777766666666555544444321   134455666676666   5555555554


Q ss_pred             HHHHH--HccCCHHHHHHHHHHHHhCC
Q 013489           99 LLSLE--RSRASEEEISTVFEKSLLCA  123 (442)
Q Consensus        99 ~~~le--~~~~~~~~~~~i~~~al~~~  123 (442)
                      ...+.  ...++.+++...|+++...+
T Consensus       255 g~~~~~~~~~~d~~~A~~~~~~Aa~~g  281 (452)
T 3e4b_A          255 AQLLYDFPELGDVEQMMKYLDNGRAAD  281 (452)
T ss_dssp             HHHHHHSGGGCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHhCCCCCCHHHHHHHHHHHHHCC
Confidence            44322  23455666666666666554

>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=97.58  E-value=0.00053  Score=56.54  Aligned_cols=86  Identities=9%  Similarity=-0.008  Sum_probs=70.7

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCC----------hhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc-
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGD----------PGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL-   71 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~----------~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~-   71 (442)
                      +++..|+.++..+|.    +.+.|.++.......+.          ++.++..|++||..+|.+.+.|......+...+ 
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            467788888888876    77888888887666654          459999999999999999999999988776543 


Q ss_pred             ---------chhhHHHHHHHHHHHcCCCcH
Q 013489           72 ---------KVGNVVRDVYSRATKNCPWVG   92 (442)
Q Consensus        72 ---------~~~~~~~~v~erAl~~~p~s~   92 (442)
                               ++.+.+...|++|+...|...
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                     356789999999999999763

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.56  E-value=0.00095  Score=52.40  Aligned_cols=63  Identities=6%  Similarity=-0.028  Sum_probs=56.7

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH---HHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM---LEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~---~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      ..+...+.+....| +++.|...|++++..+|++   ...|...+......|+++.|...|++++..
T Consensus        40 ~~~~~lg~~~~~~~-~~~~A~~~~~~~~~~~p~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           40 NALYWLGESYYATR-NFQLAEAQFRDLVSRYPTHDKAAGGLLKLGLSQYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhc-cHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            57777888888888 9999999999999999888   778888899888999999999999999973

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.54  E-value=0.0014  Score=47.83  Aligned_cols=80  Identities=14%  Similarity=0.056  Sum_probs=68.1

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~  101 (442)
                      ....|..........|+++.+...|++++...|.+..+|..+...+.. .++.+.+...|++++...|.....|..+...
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~-~~~~~~A~~~~~~a~~~~p~~~~~~~~l~~~   86 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYK-QGDYDEAIEYYQKALELDPNNAEAKQNLGNA   86 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHH-HhhHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            566788888888889999999999999999999999999998887664 4566789999999999999988888776654


Q ss_pred             H
Q 013489          102 L  102 (442)
Q Consensus       102 l  102 (442)
                      +
T Consensus        87 ~   87 (91)
T 1na3_A           87 K   87 (91)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=97.54  E-value=0.00091  Score=55.23  Aligned_cols=102  Identities=14%  Similarity=0.057  Sum_probs=83.1

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCC-------CHH-----HHHHHHHHHHHhcchhhHHHHHHHHHHHc--
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPV-------SSD-----LWLDYTQYLDKTLKVGNVVRDVYSRATKN--   87 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~-------~~~-----lW~~Y~~~l~~~~~~~~~~~~v~erAl~~--   87 (442)
                      ....|.....-....|+++.+...|++||..+|.       +..     +|.+-...+.. .+..+.+...|++||..  
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 GAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAG-LRSFDEALHSADKALHYFN   88 (159)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHhhh
Confidence            3456778888778899999999999999999998       444     88888876664 45667788999999998  


Q ss_pred             -----CCCcHHHH----HHHHHHHHHccCCHHHHHHHHHHHHhCChh
Q 013489           88 -----CPWVGELW----VRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus        88 -----~p~s~~lW----~~y~~~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                           .|.....|    ......+.. .+..+++...|++++...+.
T Consensus        89 ~~~e~~pd~~~A~~~~~~~rG~aL~~-lgr~eEAl~~y~kAlel~p~  134 (159)
T 2hr2_A           89 RRGELNQDEGKLWISAVYSRALALDG-LGRGAEAMPEFKKVVEMIEE  134 (159)
T ss_dssp             HHCCTTSTHHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCCchHHHHHHHHHhHHHHHHH-CCCHHHHHHHHHHHHhcCCC
Confidence                 99999999    776665554 78899999999999976543

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=97.54  E-value=0.0019  Score=63.55  Aligned_cols=80  Identities=10%  Similarity=0.072  Sum_probs=48.3

Q ss_pred             HHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHc---CCCHHHHHHHHHHHHHhchhHHHHHHHHHHH-H--HhcccHHHH
Q 013489          163 TFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSM---GKDMVSARGVWERLLKISGAMLEAWQSYISM-E--IELDHINEA  236 (442)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~---~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~-e--~~~g~~~~a  236 (442)
                      .+.+|+.++..+....+.....+...+.++..-   .++++.|...|++++   |.++..+..+..+ .  ...++++.|
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            445566666555544444444444444444322   137788888888877   5556666666665 3  345678888


Q ss_pred             HHHHHHHHh
Q 013489          237 RSIYKRCYS  245 (442)
Q Consensus       237 r~i~~ral~  245 (442)
                      ...|++|+.
T Consensus       271 ~~~~~~Aa~  279 (452)
T 3e4b_A          271 MKYLDNGRA  279 (452)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            888888775

>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=97.53  E-value=0.00091  Score=53.06  Aligned_cols=81  Identities=11%  Similarity=0.091  Sum_probs=59.0

Q ss_pred             HHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHH-------HHHHHHHHHHHhcccHHHH
Q 013489          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAML-------EAWQSYISMEIELDHINEA  236 (442)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~-------~~w~~~~~~e~~~g~~~~a  236 (442)
                      |++|+.++.+++...|....+|...+.+....| +++.|...|++++...|+..       .+|.....+....|+++.|
T Consensus        24 ~~~A~~~y~~Al~~~p~~~~~~~nlg~~~~~~~-~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A  102 (127)
T 4gcn_A           24 FEKAHVHYDKAIELDPSNITFYNNKAAVYFEEK-KFAECVQFCEKAVEVGRETRADYKLIAKAMSRAGNAFQKQNDLSLA  102 (127)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHhHHHHHHHhh-hHHHHHHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHcCCHHHH
Confidence            344444444444435556678888888888888 89999999999998866542       3566666777778899999


Q ss_pred             HHHHHHHHh
Q 013489          237 RSIYKRCYS  245 (442)
Q Consensus       237 r~i~~ral~  245 (442)
                      ...|++++.
T Consensus       103 ~~~~~kal~  111 (127)
T 4gcn_A          103 VQWFHRSLS  111 (127)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            999999886

>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=97.49  E-value=0.0036  Score=63.41  Aligned_cols=177  Identities=10%  Similarity=0.024  Sum_probs=119.0

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCC----------hhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcc-
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGD----------PGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLK-   72 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~----------~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~-   72 (442)
                      |-..|+.+|..+|.    ++.+|..=.......|.          ++.+...|+++|..+|.+..+|..-.-.+.. .+ 
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----FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSR-LPE  122 (567)
T ss_dssp             HHHHHHHHHHHCTT----CHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHT-CSS
T ss_pred             HHHHHHHHHHHCch----hHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-ccc
Confidence            34678888888876    88888765555555555          7889999999999999999999988766654 44 


Q ss_pred             -hhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhH--HHHHHHHHHHHHHHHHHhhcc-
Q 013489           73 -VGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTF--EEYLDLFLTRIDGLRRRILFS-  148 (442)
Q Consensus        73 -~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~--~~~~~~~~~~~~~l~rr~~~~-  148 (442)
                       ..+.+...+++++...|.....|......+.......++....+.+++...+.+.  |.+....+.       ++... 
T Consensus       123 ~~~~~el~~~~k~l~~d~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~n~saW~~r~~ll~-------~l~~~~  195 (567)
T 1dce_A          123 PNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLP-------QLHPQP  195 (567)
T ss_dssp             CCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHH-------HHSCCC
T ss_pred             ccHHHHHHHHHHHHhhccccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCCCccHHHHHHHHHH-------hhcccc
Confidence             3367889999999999999999998776666544367778888888888777643  333322211       11100 


Q ss_pred             Cccc-hhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcC
Q 013489          149 GEVE-GVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMG  196 (442)
Q Consensus       149 ~~~~-~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~  196 (442)
                      .... ....    ...++++++++..++...|.....|.+..-+....+
T Consensus       196 ~~~~~~~~~----~~~~~eel~~~~~ai~~~P~~~saW~y~~~ll~~~~  240 (567)
T 1dce_A          196 DSGPQGRLP----ENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAE  240 (567)
T ss_dssp             CSSSCCSSC----HHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCCC
T ss_pred             ccccccccc----HHHHHHHHHHHHHHHhhCCCCccHHHHHHHHHhcCC
Confidence            0000 0000    134566666666666545555668887766655444

>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=97.41  E-value=0.00044  Score=66.15  Aligned_cols=100  Identities=10%  Similarity=-0.095  Sum_probs=78.5

Q ss_pred             hhhHHHHHHhhcCCC------------CChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh
Q 013489            3 NARAHLEEQISRQDL------------SDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKT   70 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~------------~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~   70 (442)
                      +|...|+.+|...+.            .++.+...|.+++......|+++.|...|+++|..+|.+...|..++..+.. 
T Consensus       241 ~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~-  319 (370)
T 1ihg_A          241 MAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQG-  319 (370)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHH-
Confidence            356677777762110            1234677899999988899999999999999999999999999998877664 


Q ss_pred             cchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHH
Q 013489           71 LKVGNVVRDVYSRATKNCPWVGELWVRSLLSLE  103 (442)
Q Consensus        71 ~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le  103 (442)
                      .++.+.+...|++|+...|....+|..+...+.
T Consensus       320 ~g~~~eA~~~l~~Al~l~P~~~~~~~~l~~~~~  352 (370)
T 1ihg_A          320 LKEYDQALADLKKAQEIAPEDKAIQAELLKVKQ  352 (370)
T ss_dssp             TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            456678999999999999998888887665443

>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=97.40  E-value=0.00099  Score=52.00  Aligned_cols=80  Identities=11%  Similarity=0.120  Sum_probs=62.5

Q ss_pred             HHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH-------HHHHHHHHHHHHhcccHHHHH
Q 013489          165 QRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM-------LEAWQSYISMEIELDHINEAR  237 (442)
Q Consensus       165 ~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~-------~~~w~~~~~~e~~~g~~~~ar  237 (442)
                      +.|+.++...+...+....++...+.+....+ +++.|..+|++++...|+.       ..+|...+......|+++.|.
T Consensus        21 ~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~   99 (131)
T 1elr_A           21 DTALKHYDKAKELDPTNMTYITNQAAVYFEKG-DYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAI   99 (131)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHhcCCccHHHHHHHHHHHHHhc-cHHHHHHHHHHHHhhccccchhHHHHHHHHHHHHHHHHHhccHHHHH
Confidence            33334433333323445567888888888888 8999999999999997766       778888999888899999999


Q ss_pred             HHHHHHHh
Q 013489          238 SIYKRCYS  245 (442)
Q Consensus       238 ~i~~ral~  245 (442)
                      ..|++++.
T Consensus       100 ~~~~~~~~  107 (131)
T 1elr_A          100 HFYNKSLA  107 (131)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99999997

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.37  E-value=0.00071  Score=51.11  Aligned_cols=66  Identities=12%  Similarity=0.061  Sum_probs=60.0

Q ss_pred             hhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          179 DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       179 ~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      +....+|...+.+....| +++.|...|++++..+|+...+|..........|+++.|...|++++.
T Consensus         4 p~~~~~~~~lg~~~~~~g-~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   69 (100)
T 3ma5_A            4 PEDPFTRYALAQEHLKHD-NASRALALFEELVETDPDYVGTYYHLGKLYERLDRTDDAIDTYAQGIE   69 (100)
T ss_dssp             -CCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            344567888888888888 999999999999999999999999999999999999999999999996

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.35  E-value=0.0025  Score=48.35  Aligned_cols=69  Identities=13%  Similarity=0.000  Sum_probs=60.2

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCc
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWV   91 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s   91 (442)
                      +...|...+......|+++.+...|+++|...|.++.+|...+..+.. .+..+.+...|++|+...|..
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~-~g~~~~A~~~~~~al~~~p~~   71 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLITAQPQNPVGYSNKAMALIK-LGEYTQAIQMCQQGLRYTSTA   71 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTSCSST
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHH-hcCHHHHHHHHHHHHHhCCCc
Confidence            456788888888889999999999999999999999999999887664 456678999999999999987

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.32  E-value=0.00034  Score=52.94  Aligned_cols=69  Identities=12%  Similarity=0.146  Sum_probs=50.5

Q ss_pred             hHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCC
Q 013489           20 SEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCP   89 (442)
Q Consensus        20 ~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p   89 (442)
                      |++...|..++......|+++.+...|+++|..+|.++..|......+.. .+..+.+...|++|+...|
T Consensus         4 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~-~g~~~~A~~~~~~al~l~~   72 (100)
T 3ma5_A            4 PEDPFTRYALAQEHLKHDNASRALALFEELVETDPDYVGTYYHLGKLYER-LDRTDDAIDTYAQGIEVAR   72 (100)
T ss_dssp             -CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHH-cCCHHHHHHHHHHHHhhhh
Confidence            34666777777777778888888888888888888888888877766553 3455667788888877554

>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=97.28  E-value=0.0005  Score=68.18  Aligned_cols=91  Identities=11%  Similarity=-0.173  Sum_probs=54.6

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSR   83 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~er   83 (442)
                      |...|+.+|...|.    +...|..++......|+++.|...|++++..+|.+...|...+..+... +..+.+...|++
T Consensus        25 A~~~~~~Al~~~p~----~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~~~~-g~~~eA~~~~~~   99 (477)
T 1wao_1           25 AIKFYSQAIELNPS----NAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMAL-GKFRAALRDYET   99 (477)
T ss_dssp             HHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHH-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCc----cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc-CCHHHHHHHHHH
Confidence            45556666655553    4556666666666666666666666666666666666666665544432 344556666666


Q ss_pred             HHHcCCCcHHHHHHHH
Q 013489           84 ATKNCPWVGELWVRSL   99 (442)
Q Consensus        84 Al~~~p~s~~lW~~y~   99 (442)
                      |+...|.....|..+.
T Consensus       100 al~~~p~~~~~~~~l~  115 (477)
T 1wao_1          100 VVKVKPHDKDAKMKYQ  115 (477)
T ss_dssp             HHHHSTTCTTHHHHHH
T ss_pred             HHHhCCCCHHHHHHHH
Confidence            6666666555555543

>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=97.27  E-value=0.0028  Score=52.24  Aligned_cols=97  Identities=13%  Similarity=0.216  Sum_probs=72.4

Q ss_pred             HHHHHHHHHHh--hhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh-ch-hHHHHHHHHHHHHHhcccHHHHH
Q 013489          162 ETFQRASDYLS--EQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI-SG-AMLEAWQSYISMEIELDHINEAR  237 (442)
Q Consensus       162 ~~~~~a~~~l~--~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~-~~-~~~~~w~~~~~~e~~~g~~~~ar  237 (442)
                      .++++|+..+.  ..+.+.+..+++|+.|+++.   + +   ++.+|.-+... -+ ..+.+|..|+.+....|++..|.
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            45566666553  33445666789999998762   3 4   67788888877 34 45679999999999999999999


Q ss_pred             HHHHHHHhcccCCCChHHHHHHHHHHHHHh
Q 013489          238 SIYKRCYSKRFTGTGSEDICHAWLRFEREY  267 (442)
Q Consensus       238 ~i~~ral~~~~~~~~~~~i~~~~~~fE~~~  267 (442)
                      .||..++....  ...+.|-.++.+|+...
T Consensus       117 ~Iy~~Gi~~~A--~P~~~L~~~~~~F~~R~  144 (164)
T 2wvi_A          117 AIFQEGIQQKA--EPLERLQSQHRQFQARV  144 (164)
T ss_dssp             HHHHHHHHTTC--BSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCC--CcHHHHHHHHHHHHHHH
Confidence            99999998642  23567778888887654

>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=97.26  E-value=0.0087  Score=56.37  Aligned_cols=93  Identities=9%  Similarity=-0.054  Sum_probs=64.1

Q ss_pred             hhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHH
Q 013489          179 DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICH  258 (442)
Q Consensus       179 ~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~  258 (442)
                      +....++..++-.....| +++.|...+++++..+|+ ...|..........|+.+.|...|.+|+.  +.+..+...|.
T Consensus       274 ~~~a~~~~alal~~l~~g-d~d~A~~~l~rAl~Ln~s-~~a~~llG~~~~~~G~~~eA~e~~~~Alr--L~P~~~t~~~~  349 (372)
T 3ly7_A          274 NNLSIIYQIKAVSALVKG-KTDESYQAINTGIDLEMS-WLNYVLLGKVYEMKGMNREAADAYLTAFN--LRPGANTLYWI  349 (372)
T ss_dssp             TTCHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HSCSHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHhCC-CHHHHHHHHHHHHhcCCC-HHHHHHHHHHHHHCCCHHHHHHHHHHHHh--cCCCcChHHHH
Confidence            334456666665555667 999999999999999876 44556666677778999999999999997  44444443443


Q ss_pred             HHHHHHHHhCCHhhHHHHHH
Q 013489          259 AWLRFEREYGTLEDFDHSVQ  278 (442)
Q Consensus       259 ~~~~fE~~~G~~~~~~~~~~  278 (442)
                      .=+-|   |-+++.|.-+..
T Consensus       350 ~~l~F---~sn~~~i~~~~~  366 (372)
T 3ly7_A          350 ENGIF---QTSVPYVVPYLD  366 (372)
T ss_dssp             HHSSS---CCCHHHHCHHHH
T ss_pred             hCcee---ecchhhhHHHHH
Confidence            33333   556665554443

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=97.22  E-value=0.047  Score=46.03  Aligned_cols=90  Identities=16%  Similarity=0.165  Sum_probs=62.2

Q ss_pred             hHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhch---hH---HHHHHHHHHHHHh
Q 013489          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG---AM---LEAWQSYISMEIE  229 (442)
Q Consensus       156 ~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~---~~---~~~w~~~~~~e~~  229 (442)
                      ++......+.+++...............++...+.+....| +++.|...+++++...+   +.   ..++...+.....
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            44455566666666554221111133456777788888888 99999999999997632   21   2356777778888


Q ss_pred             cccHHHHHHHHHHHHhc
Q 013489          230 LDHINEARSIYKRCYSK  246 (442)
Q Consensus       230 ~g~~~~ar~i~~ral~~  246 (442)
                      .|+++.|...|++++..
T Consensus       160 ~g~~~~A~~~~~~al~~  176 (203)
T 3gw4_A          160 EKNLLEAQQHWLRARDI  176 (203)
T ss_dssp             TTCHHHHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHH
Confidence            89999999999999863

>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=97.20  E-value=0.0049  Score=55.82  Aligned_cols=116  Identities=11%  Similarity=0.097  Sum_probs=88.4

Q ss_pred             HHHHHhhcCCCCChHhHH--HHHHHHHHHH---hcCC------hhhHHHHHHHHHhcCCC--CHHHHHHHHHHHHHh---
Q 013489            7 HLEEQISRQDLSDSEKFQ--QYMIYLKYEQ---SSGD------PGRVQLLYERAITDFPV--SSDLWLDYTQYLDKT---   70 (442)
Q Consensus         7 ~yE~~l~~~~~~~~~~~~--~w~~y~~~e~---~~g~------~~~~~~lyERal~~~p~--~~~lW~~Y~~~l~~~---   70 (442)
                      .++.+|.....   ++.+  +|..-+....   ..|+      ...+...+||+|..+|.  +...|..+..+...-   
T Consensus       139 ~~~~~l~~~~~---~dve~L~W~ai~~ss~a~~~~gg~~Al~~l~~A~a~lerAleLDP~~~~GsA~~~LG~lY~~vPp~  215 (301)
T 3u64_A          139 RLHKVLSRCTR---VDVGTLYWVGTGYVAAFALTPLGSALPDTVHAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPES  215 (301)
T ss_dssp             HHHHHHTTCCG---GGHHHHHHHHHHHHHHHTTSCTTSCCHHHHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHHSCTT
T ss_pred             hHHHHHHHcCc---cccHHHHHHHHHHHHHHhcCCCChHHHHhHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHhCCCc
Confidence            45666655533   3333  5665555432   2243      35778899999999999  677999998876642   


Q ss_pred             -cchhhHHHHHHHHHHHcCCCc-HHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh
Q 013489           71 -LKVGNVVRDVYSRATKNCPWV-GELWVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus        71 -~~~~~~~~~v~erAl~~~p~s-~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                       .++.++++..|+||+...|.. ...+..|..++-+..++.+.+...+++++..++.
T Consensus       216 ~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a~p~  272 (301)
T 3u64_A          216 FGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAIDPE  272 (301)
T ss_dssp             TTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHCCGG
T ss_pred             cCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCC
Confidence             467889999999999999974 8999999998887668889999999999987765

>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=97.19  E-value=0.00026  Score=55.18  Aligned_cols=46  Identities=17%  Similarity=0.032  Sum_probs=35.0

Q ss_pred             ceEEEcCCCCCC----------CHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKA----------TYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~----------~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +.|.+.|+=..-          -+++|+..|++||.|.+|.|+++.    ++|||||+|.
T Consensus         8 ~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~   63 (114)
T 3s6e_A            8 QCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCP   63 (114)
T ss_dssp             SEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECS
T ss_pred             cEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEEC
Confidence            477788762221          235789999999999999987662    5899999995

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.15  E-value=0.007  Score=43.81  Aligned_cols=65  Identities=15%  Similarity=0.181  Sum_probs=58.4

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          181 LLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       181 ~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      ....|...+......+ +++.|...|++++...|+...+|..++.+....|+++.|...|++++..
T Consensus         8 ~~~~~~~la~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~   72 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQG-DYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL   72 (91)
T ss_dssp             HHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcc-CHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            3456777788888888 9999999999999999999999999999999999999999999999973

>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=97.15  E-value=0.11  Score=57.20  Aligned_cols=76  Identities=14%  Similarity=0.115  Sum_probs=51.0

Q ss_pred             cCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHH
Q 013489           36 SGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTV  115 (442)
Q Consensus        36 ~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i  115 (442)
                      .++.++|..+++|+     ..+.+|..|+......+ ..+.+...|.+|     ....-|..-+..+++ .+..+++-..
T Consensus      1089 i~nldrAiE~Aerv-----n~p~vWsqLAKAql~~G-~~kEAIdsYiKA-----dD~say~eVa~~~~~-lGkyEEAIey 1156 (1630)
T 1xi4_A         1089 IGNLDRAYEFAERC-----NEPAVWSQLAKAQLQKG-MVKEAIDSYIKA-----DDPSSYMEVVQAANT-SGNWEELVKY 1156 (1630)
T ss_pred             HhhHHHHHHHHHhc-----CCHHHHHHHHHHHHhCC-CHHHHHHHHHhc-----CChHHHHHHHHHHHH-cCCHHHHHHH
Confidence            34555555555544     66888888888777544 445677888877     455677776766665 5777888888


Q ss_pred             HHHHHhCC
Q 013489          116 FEKSLLCA  123 (442)
Q Consensus       116 ~~~al~~~  123 (442)
                      |..|....
T Consensus      1157 L~mArk~~ 1164 (1630)
T 1xi4_A         1157 LQMARKKA 1164 (1630)
T ss_pred             HHHHHhhc
Confidence            87777543

>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=97.15  E-value=0.0044  Score=59.16  Aligned_cols=102  Identities=12%  Similarity=-0.088  Sum_probs=85.2

Q ss_pred             HHHHHHHHHHHHhcCChhhHHHHHHHHHh----------------cCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHH
Q 013489           23 FQQYMIYLKYEQSSGDPGRVQLLYERAIT----------------DFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATK   86 (442)
Q Consensus        23 ~~~w~~y~~~e~~~g~~~~~~~lyERal~----------------~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~   86 (442)
                      ...|...+......|+++.|...|++||.                ..|.+..+|..++..+.. .+..+.+...|++|+.
T Consensus       223 a~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~-~g~~~~A~~~~~~al~  301 (370)
T 1ihg_A          223 SEDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLK-MSDWQGAVDSCLEALE  301 (370)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHh-ccCHHHHHHHHHHHHH
Confidence            34577777777889999999999999998                667778899998877664 4566789999999999


Q ss_pred             cCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhh
Q 013489           87 NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFST  126 (442)
Q Consensus        87 ~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~  126 (442)
                      ..|.....|..+...+.. .++.+++...|++|+...+..
T Consensus       302 ~~p~~~~a~~~lg~~~~~-~g~~~eA~~~l~~Al~l~P~~  340 (370)
T 1ihg_A          302 IDPSNTKALYRRAQGWQG-LKEYDQALADLKKAQEIAPED  340 (370)
T ss_dssp             TCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTC
T ss_pred             hCchhHHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhCCCC
Confidence            999999999988875554 688999999999999876653

>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=0.0042  Score=51.22  Aligned_cols=90  Identities=14%  Similarity=-0.006  Sum_probs=70.0

Q ss_pred             hhHHHHHHHHHHHHHHHhhhhc----C-chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh-------chhHHHHH--
Q 013489          155 LDYSLIRETFQRASDYLSEQMK----N-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI-------SGAMLEAW--  220 (442)
Q Consensus       155 ~~~~~~r~~~~~a~~~l~~~~~----~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~-------~~~~~~~w--  220 (442)
                      .++......|++|+.+......    . .+....+|...+.....+| +++.|...|+++|..       +|++...|  
T Consensus        25 g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lg-r~~eAl~~~~kAL~l~n~~~e~~pd~~~A~~~  103 (159)
T 2hr2_A           25 GEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLR-SFDEALHSADKALHYFNRRGELNQDEGKLWIS  103 (159)
T ss_dssp             TCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhhhccccCCCchHHHHHH
Confidence            3444555667777766533110    0 1112348888888888999 999999999999999       99999999  


Q ss_pred             --HHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          221 --QSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       221 --~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                        ..-.......|+++.|...|++|+.
T Consensus       104 ~~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A          104 AVYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence              8888999999999999999999997

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=97.01  E-value=0.046  Score=46.07  Aligned_cols=125  Identities=11%  Similarity=0.090  Sum_probs=80.3

Q ss_pred             hhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh---ch----hHHHHHHHHHHHH
Q 013489          155 LDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI---SG----AMLEAWQSYISME  227 (442)
Q Consensus       155 ~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~---~~----~~~~~w~~~~~~e  227 (442)
                      .++......|++++...... ...+....++...+.+....| +++.|...+++++..   .+    ....++.......
T Consensus        40 g~~~~A~~~~~~al~~~~~~-~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~  117 (203)
T 3gw4_A           40 DRFDEARASFQALQQQAQKS-GDHTAEHRALHQVGMVERMAG-NWDAARRCFLEERELLASLPEDPLAASANAYEVATVA  117 (203)
T ss_dssp             TCHHHHHHHHHHHHHHHHTT-CCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHHc-CCcHHHHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHH
Confidence            34555566677777655432 122334567777888888888 999999999999988   33    2244677788888


Q ss_pred             HhcccHHHHHHHHHHHHhcccCCCChHHHHH---HHHHHHHHhCCHhhHHHHHHhhc
Q 013489          228 IELDHINEARSIYKRCYSKRFTGTGSEDICH---AWLRFEREYGTLEDFDHSVQKVT  281 (442)
Q Consensus       228 ~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~---~~~~fE~~~G~~~~~~~~~~~~~  281 (442)
                      ...|+++.|...|++++...-....+.....   .........|+.+.-...+.+..
T Consensus       118 ~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  174 (203)
T 3gw4_A          118 LHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRAR  174 (203)
T ss_dssp             HHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence            8899999999999999963212223332222   22333444566655444444443

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.01  E-value=0.085  Score=42.07  Aligned_cols=88  Identities=11%  Similarity=0.012  Sum_probs=62.1

Q ss_pred             hHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhch------hHHHHHHHHHHHHHh
Q 013489          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG------AMLEAWQSYISMEIE  229 (442)
Q Consensus       156 ~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~------~~~~~w~~~~~~e~~  229 (442)
                      ++......+++++...... .+......++...+.+....| +++.|...+++++...+      ....++...+.+...
T Consensus        64 ~~~~A~~~~~~a~~~~~~~-~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~  141 (164)
T 3ro3_A           64 EFETASEYYKKTLLLARQL-KDRAVEAQSCYSLGNTYTLLQ-DYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTA  141 (164)
T ss_dssp             CHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHh-CCcHHHHHHHHHHHHHHHHHh-hHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHH
Confidence            3444455566666554332 112223456777888888888 99999999999997732      223467777778888


Q ss_pred             cccHHHHHHHHHHHHh
Q 013489          230 LDHINEARSIYKRCYS  245 (442)
Q Consensus       230 ~g~~~~ar~i~~ral~  245 (442)
                      .|+++.|...|++++.
T Consensus       142 ~g~~~~A~~~~~~a~~  157 (164)
T 3ro3_A          142 LGNHDQAMHFAEKHLE  157 (164)
T ss_dssp             HTCHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHH
Confidence            8999999999999986

>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=96.99  E-value=0.077  Score=52.67  Aligned_cols=98  Identities=9%  Similarity=-0.054  Sum_probs=63.6

Q ss_pred             HHHHHHHHHHhcCChhhHHHHHHHHHhc-CCCCHHHHHHHHHHHHHhc--------chhhHHHHHHHHHHHc-CCCcHHH
Q 013489           25 QYMIYLKYEQSSGDPGRVQLLYERAITD-FPVSSDLWLDYTQYLDKTL--------KVGNVVRDVYSRATKN-CPWVGEL   94 (442)
Q Consensus        25 ~w~~y~~~e~~~g~~~~~~~lyERal~~-~p~~~~lW~~Y~~~l~~~~--------~~~~~~~~v~erAl~~-~p~s~~l   94 (442)
                      .+..-|+..-+.|+++.|..+|+++... ...+...|...|..+....        ...+.+..+|++.... ++-+...
T Consensus        28 ~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~~t  107 (501)
T 4g26_A           28 LLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEAT  107 (501)
T ss_dssp             HHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCHHH
Confidence            4666677777889999999999988875 3446666766665443221        1234567777776662 3334566


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCC
Q 013489           95 WVRSLLSLERSRASEEEISTVFEKSLLCA  123 (442)
Q Consensus        95 W~~y~~~le~~~~~~~~~~~i~~~al~~~  123 (442)
                      |...|..+-+ .+..+.+..+|++....+
T Consensus       108 yn~lI~~~~~-~g~~~~A~~l~~~M~~~g  135 (501)
T 4g26_A          108 FTNGARLAVA-KDDPEMAFDMVKQMKAFG  135 (501)
T ss_dssp             HHHHHHHHHH-HTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHh-cCCHHHHHHHHHHHHHcC
Confidence            6766664544 577777888887766544

>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=96.94  E-value=0.0016  Score=64.49  Aligned_cols=91  Identities=12%  Similarity=-0.065  Sum_probs=78.5

Q ss_pred             HHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHH
Q 013489           33 EQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEI  112 (442)
Q Consensus        33 e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~  112 (442)
                      ....|+++.|..+|++||..+|.+..+|...+..+... +..+.+...|++|+...|.....|......+. ..+..+++
T Consensus        16 ~~~~g~~~~A~~~~~~Al~~~p~~~~~~~~lg~~~~~~-g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~~-~~g~~~eA   93 (477)
T 1wao_1           16 YFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRT-ECYGYALGDATRAIELDKKYIKGYYRRAASNM-ALGKFRAA   93 (477)
T ss_dssp             TTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHH-HHTCHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh-cCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH-HcCCHHHH
Confidence            34678999999999999999999999999999877644 56678999999999999999999998877544 47889999


Q ss_pred             HHHHHHHHhCChh
Q 013489          113 STVFEKSLLCAFS  125 (442)
Q Consensus       113 ~~i~~~al~~~~~  125 (442)
                      ...|++++...+.
T Consensus        94 ~~~~~~al~~~p~  106 (477)
T 1wao_1           94 LRDYETVVKVKPH  106 (477)
T ss_dssp             HHHHHHHHHHSTT
T ss_pred             HHHHHHHHHhCCC
Confidence            9999999987665

>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=96.93  E-value=0.15  Score=56.08  Aligned_cols=106  Identities=11%  Similarity=0.134  Sum_probs=70.4

Q ss_pred             HHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcC-CCHHHHHHHHHHHHHhch-----hHHHHHHHHHHHHHhccc
Q 013489          159 LIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMG-KDMVSARGVWERLLKISG-----AMLEAWQSYISMEIELDH  232 (442)
Q Consensus       159 ~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~-~~~~~ar~i~~~~l~~~~-----~~~~~w~~~~~~e~~~g~  232 (442)
                      .-++.|++|+.+++..+...+....+|..++.++.+.. +++..+.++|..-+...+     .+..+|.+++-+....|+
T Consensus      1291 e~~G~feEAI~LlE~aL~LeraH~gmftELaiLyaKy~peklmEhlk~f~~rini~k~~r~~e~~~lW~elv~LY~~~~e 1370 (1630)
T 1xi4_A         1291 QDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEE 1370 (1630)
T ss_pred             HHcCCHHHHHHHHHHHhccChhHhHHHHHHHHHHHhCCHHHHHHHHHHHHHhcccchHhHHHHHHHHHHHHHHHHHhccc
Confidence            34466788888888887766666677766666655542 145566666666666555     678899999999999999


Q ss_pred             HHHHHHHH-------------HHHHhcccCCCChHHHHHHHHHHHHHhC
Q 013489          233 INEARSIY-------------KRCYSKRFTGTGSEDICHAWLRFEREYG  268 (442)
Q Consensus       233 ~~~ar~i~-------------~ral~~~~~~~~~~~i~~~~~~fE~~~G  268 (442)
                      +++|...+             +..+.   ....+ .|+-.-++|--.++
T Consensus      1371 ~dnA~~tm~~h~~~a~~~~~Fk~~i~---kv~n~-elyykai~Fyl~~~ 1415 (1630)
T 1xi4_A         1371 YDNAIITMMNHPTDAWKEGQFKDIIT---KVANV-ELYYRAIQFYLEFK 1415 (1630)
T ss_pred             HHHHHHHHHhccHhhhhhHHHHHHhc---ccccH-HHHHHHHHHHHhhC
Confidence            99888433             33222   22334 45556677766555

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=96.91  E-value=0.014  Score=43.88  Aligned_cols=63  Identities=10%  Similarity=0.003  Sum_probs=57.2

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      ..|...+......| +++.|...|++++...|++..+|...+......|+++.|...|++++..
T Consensus         5 ~~~~~~g~~~~~~~-~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~   67 (111)
T 2l6j_A            5 EKQKEQGNSLFKQG-LYREAVHCYDQLITAQPQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRY   67 (111)
T ss_dssp             HHHHHHHHHHHTTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHcC-CHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            45666777777888 9999999999999999999999999999999999999999999999973

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=96.89  E-value=0.028  Score=45.01  Aligned_cols=89  Identities=9%  Similarity=0.004  Sum_probs=64.5

Q ss_pred             hHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchh------HHHHHHHHHHHHHh
Q 013489          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA------MLEAWQSYISMEIE  229 (442)
Q Consensus       156 ~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~------~~~~w~~~~~~e~~  229 (442)
                      ++......+.+++....... .......++...+.+....| +++.|...|++++...+.      ...++...+.+...
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            44455566666666554321 11223356777888888888 999999999999987433      24577788888888


Q ss_pred             cccHHHHHHHHHHHHhc
Q 013489          230 LDHINEARSIYKRCYSK  246 (442)
Q Consensus       230 ~g~~~~ar~i~~ral~~  246 (442)
                      .|+++.|...|++++..
T Consensus       102 ~~~~~~A~~~~~~a~~~  118 (164)
T 3ro3_A          102 LQDYEKAIDYHLKHLAI  118 (164)
T ss_dssp             TTCHHHHHHHHHHHHHH
T ss_pred             HhhHHHHHHHHHHHHHH
Confidence            99999999999999964

>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=96.87  E-value=0.093  Score=45.22  Aligned_cols=81  Identities=12%  Similarity=0.006  Sum_probs=55.7

Q ss_pred             CCHHHHHHHHHHHHHhch--hHHHHHHHHHHHHHh----cccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhC--
Q 013489          197 KDMVSARGVWERLLKISG--AMLEAWQSYISMEIE----LDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYG--  268 (442)
Q Consensus       197 ~~~~~ar~i~~~~l~~~~--~~~~~w~~~~~~e~~----~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G--  268 (442)
                      ++++.|...|++++...+  +.+..+..+..+...    .++++.|...|++|+..   ...+...+..-.-++...|  
T Consensus       103 ~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~---~~~~~a~~~Lg~~y~~g~gg~  179 (212)
T 3rjv_A          103 TDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSL---SRTGYAEYWAGMMFQQGEKGF  179 (212)
T ss_dssp             CCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHT---SCTTHHHHHHHHHHHHCBTTT
T ss_pred             cCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHc---CCCHHHHHHHHHHHHcCCCCC
Confidence            389999999999999866  457777777777766    56899999999999972   2334444444344444445  


Q ss_pred             CHhhHHHHHHhh
Q 013489          269 TLEDFDHSVQKV  280 (442)
Q Consensus       269 ~~~~~~~~~~~~  280 (442)
                      ...++..++.-.
T Consensus       180 ~~~d~~~A~~~~  191 (212)
T 3rjv_A          180 IEPNKQKALHWL  191 (212)
T ss_dssp             BCCCHHHHHHHH
T ss_pred             CCCCHHHHHHHH
Confidence            344455555443

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=96.82  E-value=0.1  Score=47.46  Aligned_cols=163  Identities=10%  Similarity=-0.009  Sum_probs=91.8

Q ss_pred             cCCHHHHHHHHHHHHhCChhhHH--HHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHH
Q 013489          106 RASEEEISTVFEKSLLCAFSTFE--EYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLR  183 (442)
Q Consensus       106 ~~~~~~~~~i~~~al~~~~~~~~--~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~  183 (442)
                      .++.+.+...+++++........  ....++. .+..+....         .++......|.+|+...... .+......
T Consensus        88 ~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~-~~~~~~~~~---------~~~~~A~~~~~~al~~~~~~-~~~~~~~~  156 (293)
T 2qfc_A           88 QKRYKEIYNKVWNELKKEEYHPEFQQFLQWQY-YVAAYVLKK---------VDYEYCILELKKLLNQQLTG-IDVYQNLY  156 (293)
T ss_dssp             TTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHH-HHHHHHHTS---------SCHHHHHHHHHHHHTTCCCS-SCTTHHHH
T ss_pred             hhhHHHHHHHHHHHhccccCChhHHHHHHHHH-HHHHHHhcC---------CCHHHHHHHHHHHHHHHhcC-CchHHHHH
Confidence            57888999999999875443211  1111111 111110000         12323333344444322110 11122355


Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHh---chhH----HHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCCh---
Q 013489          184 LYAYWAHLEQSMGKDMVSARGVWERLLKI---SGAM----LEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGS---  253 (442)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~~~~l~~---~~~~----~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~---  253 (442)
                      ++...+.++...| +++.|..+|++++..   .++.    ..++...+......|+++.|...|++|+......+..   
T Consensus       157 ~~~~lg~~y~~~~-~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~  235 (293)
T 2qfc_A          157 IENAIANIYAENG-YLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALI  235 (293)
T ss_dssp             HHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSH
T ss_pred             HHHHHHHHHHHcC-CHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHH
Confidence            7777888888888 999999999999954   4332    2578888888889999999999999999642111111   


Q ss_pred             HHHHHHHHHHHHHhCCHhhH-HHHHHhh
Q 013489          254 EDICHAWLRFEREYGTLEDF-DHSVQKV  280 (442)
Q Consensus       254 ~~i~~~~~~fE~~~G~~~~~-~~~~~~~  280 (442)
                      ..++..........|+.+.- ....+++
T Consensus       236 ~~~~~~lg~~y~~~g~~~~Ai~~~~~~A  263 (293)
T 2qfc_A          236 GQLYYQRGECLRKLEYEEAEIEDAYKKA  263 (293)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence            23333444444555665433 3334443

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.80  E-value=0.056  Score=51.90  Aligned_cols=200  Identities=11%  Similarity=0.026  Sum_probs=119.5

Q ss_pred             HhcCChhhHHHHHHHHHhcCCCCHH-----------------HHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHH---
Q 013489           34 QSSGDPGRVQLLYERAITDFPVSSD-----------------LWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGE---   93 (442)
Q Consensus        34 ~~~g~~~~~~~lyERal~~~p~~~~-----------------lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~---   93 (442)
                      .+.|++..|..+|..++...|...+                 .....+..+. ..++.+.+...|.+++...+....   
T Consensus        15 ~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~-~~~~~~~a~~~~~~~~~~~~~~~~~~~   93 (434)
T 4b4t_Q           15 VNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYV-TMGAKDKLREFIPHSTEYMMQFAKSKT   93 (434)
T ss_dssp             HHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHH-HHTCHHHHHHHHHHTHHHHHTSCHHHH
T ss_pred             HHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHH-HCCCHHHHHHHHHHHHHHHHHccchHH
Confidence            3478999999999999998776543                 2333333333 345667788999999886654322   


Q ss_pred             --HHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhH--HHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHH
Q 013489           94 --LWVRSLLSLERSRASEEEISTVFEKSLLCAFSTF--EEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASD  169 (442)
Q Consensus        94 --lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~--~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~  169 (442)
                        +-...+..+....+..+.+..++++++.......  .....++.... .+.         ...+++......+.++..
T Consensus        94 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la-~~~---------~~~g~~~~A~~~l~~~~~  163 (434)
T 4b4t_Q           94 VKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLA-TLH---------YQKKQYKDSLALINDLLR  163 (434)
T ss_dssp             HHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHH-HHH---------HHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHH-HHH---------HHccChHHHHHHHHHHHH
Confidence              1122233344445667778888888774321100  00001111000 000         011233344444444444


Q ss_pred             HHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhch---h--H--HHHHHHHHHHHHhcccHHHHHHHHHH
Q 013489          170 YLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISG---A--M--LEAWQSYISMEIELDHINEARSIYKR  242 (442)
Q Consensus       170 ~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~---~--~--~~~w~~~~~~e~~~g~~~~ar~i~~r  242 (442)
                      .+... .+.+..+.++...++++...+ ++++|+.++++++...+   +  .  ..++.....+....|++..|...|..
T Consensus       164 ~~~~~-~~~~~~~~~~~~~~~~~~~~~-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~  241 (434)
T 4b4t_Q          164 EFKKL-DDKPSLVDVHLLESKVYHKLR-NLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFE  241 (434)
T ss_dssp             HHTTS-SCSTHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHH
T ss_pred             HHHhc-ccchhHHHHHHHHHHHHHHhC-cHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence            33221 223445678888899999999 99999999999997632   1  1  34677777777778999999999988


Q ss_pred             HHhc
Q 013489          243 CYSK  246 (442)
Q Consensus       243 al~~  246 (442)
                      ++..
T Consensus       242 a~~~  245 (434)
T 4b4t_Q          242 SFES  245 (434)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8753

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.75  E-value=0.15  Score=48.93  Aligned_cols=163  Identities=9%  Similarity=0.012  Sum_probs=102.9

Q ss_pred             chhhHHHHHHHHHHHcCCCcHH-----------------HHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHH-HHHH
Q 013489           72 KVGNVVRDVYSRATKNCPWVGE-----------------LWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEE-YLDL  133 (442)
Q Consensus        72 ~~~~~~~~v~erAl~~~p~s~~-----------------lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~-~~~~  133 (442)
                      ++.+.+...|..++...|....                 ....... +....++.+++...+.+++......... ....
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            4556788999999987765321                 1222222 3445688888999998887532211011 1111


Q ss_pred             HHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh-
Q 013489          134 FLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI-  212 (442)
Q Consensus       134 ~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~-  212 (442)
                      ....++.+.    ..     ..+.......+..++...... ........++...+.+....| ++..|..+++.++.. 
T Consensus        97 ~~~~l~~~~----~~-----~~~~~~a~~~~~~~~~~~~~~-~~~~~~~~~~~~la~~~~~~g-~~~~A~~~l~~~~~~~  165 (434)
T 4b4t_Q           97 LKTLIEKFE----QV-----PDSLDDQIFVCEKSIEFAKRE-KRVFLKHSLSIKLATLHYQKK-QYKDSLALINDLLREF  165 (434)
T ss_dssp             HHHHHHHHC----SC-----CSCHHHHHHHHHHHHHHHHHS-SCCSSHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHH----hC-----CCCHHHHHHHHHHHHHHHHHh-CccHHHHHHHHHHHHHHHHcc-ChHHHHHHHHHHHHHH
Confidence            111111110    00     022334445556665554332 122334678888999999999 999999999999876 


Q ss_pred             -----chhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          213 -----SGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       213 -----~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                           .+..++++...+.+....|++.+|+.+|++++..
T Consensus       166 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~  204 (434)
T 4b4t_Q          166 KKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTA  204 (434)
T ss_dssp             TTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHH
Confidence                 2344678999999999999999999999999864

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.71  E-value=0.014  Score=43.17  Aligned_cols=63  Identities=17%  Similarity=0.060  Sum_probs=53.8

Q ss_pred             HHhcCChhhHHHHHHHHHhcCCCCHH-HHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHH
Q 013489           33 EQSSGDPGRVQLLYERAITDFPVSSD-LWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWV   96 (442)
Q Consensus        33 e~~~g~~~~~~~lyERal~~~p~~~~-lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~   96 (442)
                      ....|+++.+...|++++..+|.+.. +|...+..+... +..+.+...|++++...|.....|.
T Consensus        10 ~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~-~~~~~A~~~~~~al~~~p~~~~~~~   73 (99)
T 2kc7_A           10 LINQGDIENALQALEEFLQTEPVGKDEAYYLMGNAYRKL-GDWQKALNNYQSAIELNPDSPALQA   73 (99)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHCTTSTHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHhcCCCcHHHHH
Confidence            34578999999999999999999999 999988876644 4667899999999999999888773

>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=96.61  E-value=0.079  Score=51.23  Aligned_cols=81  Identities=10%  Similarity=0.123  Sum_probs=57.2

Q ss_pred             HHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcC-CCHHHHHHHHHHHHHhch-----hHHHHHHHHHHHHHhcccHHH
Q 013489          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMG-KDMVSARGVWERLLKISG-----AMLEAWQSYISMEIELDHINE  235 (442)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~-~~~~~ar~i~~~~l~~~~-----~~~~~w~~~~~~e~~~g~~~~  235 (442)
                      +.|++++.+++..+...+....+|..++-++.+.. +++....++|...+...|     .++.+|..++-+....+++++
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            45677888888887665556778888888777664 123344444444444455     567799999999999999998


Q ss_pred             HHHHHHH
Q 013489          236 ARSIYKR  242 (442)
Q Consensus       236 ar~i~~r  242 (442)
                      |...+-.
T Consensus       301 A~~tm~~  307 (449)
T 1b89_A          301 AIITMMN  307 (449)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            8865444

>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=96.59  E-value=0.1  Score=47.43  Aligned_cols=129  Identities=12%  Similarity=-0.005  Sum_probs=81.5

Q ss_pred             cCCHHHHHHHHHHHHhCChhhHHH--HHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHH
Q 013489          106 RASEEEISTVFEKSLLCAFSTFEE--YLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLR  183 (442)
Q Consensus       106 ~~~~~~~~~i~~~al~~~~~~~~~--~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~  183 (442)
                      .++.+.+..++++++.........  ++.++.. +..+.   ..      ..++......|++|+...... .+......
T Consensus        88 ~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~-l~~~~---~~------~~~~~~Ai~~~~~al~~~~~~-~~~~~~~~  156 (293)
T 3u3w_A           88 QKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYY-VAAYV---LK------KVDYEYCILELKKLLNQQLTG-IDVYQNLY  156 (293)
T ss_dssp             TTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHH-HHHHH---TT------SSCHHHHHHHHHHHHHTCCCC-SCTTHHHH
T ss_pred             HhhHHHHHHHHHHHhccccCChHHHHHHHHHHH-HHHHH---Hc------ccCHHHHHHHHHHHHHHhccc-ccHHHHHH
Confidence            588899999999999754432221  1212211 11110   00      023333444555555522110 11112345


Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHh-------chhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          184 LYAYWAHLEQSMGKDMVSARGVWERLLKI-------SGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       184 l~~~~a~~e~~~~~~~~~ar~i~~~~l~~-------~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      ++...+.++...| +++.|..+|++++..       .+....++...+.+....|+++.|...|++|+..
T Consensus       157 ~~~~lg~~y~~~g-~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~  225 (293)
T 3u3w_A          157 IENAIANIYAENG-YLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEI  225 (293)
T ss_dssp             HHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcC-CHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            6777888888888 999999999999964       2333458888999999999999999999999964

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=96.57  E-value=0.021  Score=42.43  Aligned_cols=67  Identities=12%  Similarity=-0.100  Sum_probs=57.9

Q ss_pred             hhHHHHHHHHHHHHHcCCC--HHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          180 GLLRLYAYWAHLEQSMGKD--MVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       180 ~~~~l~~~~a~~e~~~~~~--~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      ....++..++......++.  ...|+.++++++..+|+++..++.........|+++.|...+++++..
T Consensus         4 ~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A            4 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             CCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTC
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            3456888888887665522  689999999999999999999988999998999999999999999974

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.42  E-value=0.053  Score=39.90  Aligned_cols=63  Identities=14%  Similarity=0.077  Sum_probs=53.1

Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHhchhHHH-HHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChH
Q 013489          189 AHLEQSMGKDMVSARGVWERLLKISGAMLE-AWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSE  254 (442)
Q Consensus       189 a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~-~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~  254 (442)
                      +......| +++.|...|++++..+|++.. +|...+......|+++.|...|++++..  .++.+.
T Consensus         7 a~~~~~~~-~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~   70 (99)
T 2kc7_A            7 IKELINQG-DIENALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL--NPDSPA   70 (99)
T ss_dssp             HHHHHHHT-CHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTSTH
T ss_pred             HHHHHHcC-CHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCcHH
Confidence            34445667 899999999999999999998 9999999999999999999999999973  344443

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=96.40  E-value=0.21  Score=45.87  Aligned_cols=190  Identities=10%  Similarity=0.000  Sum_probs=112.8

Q ss_pred             hHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCC--CCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            5 RAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFP--VSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         5 r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p--~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ...|+..+...+.    ....+.-.+......|+++.+..+++++|...|  .+.++....+..+... +..+.++++++
T Consensus        86 ~~~l~~l~~~~~~----~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~-~r~d~A~k~l~  160 (310)
T 3mv2_B           86 IEELENLLKDKQN----SPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLN-NNVSTASTIFD  160 (310)
T ss_dssp             CHHHHHTTTTSCC----CHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHT-TCHHHHHHHHH
T ss_pred             HHHHHHHHhcCCC----CcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHC-CCHHHHHHHHH
Confidence            3456666655332    222334444555567999999999999999887  8889999998877754 45678999999


Q ss_pred             HHHHcCC---Cc-HHHHHHHHHH---HHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhh
Q 013489           83 RATKNCP---WV-GELWVRSLLS---LERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVL  155 (442)
Q Consensus        83 rAl~~~p---~s-~~lW~~y~~~---le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~  155 (442)
                      +.....|   |. ..+...++..   +-...+....+-.+|+.+....+. +.....++..   ++  +.         .
T Consensus       161 ~~~~~~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~~p~-~~~~~lLln~---~~--~~---------g  225 (310)
T 3mv2_B          161 NYTNAIEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQTFPT-WKTQLGLLNL---HL--QQ---------R  225 (310)
T ss_dssp             HHHHHSCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTTSCS-HHHHHHHHHH---HH--HH---------T
T ss_pred             HHHhcCccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhCCC-cccHHHHHHH---HH--Hc---------C
Confidence            9988888   22 2333333321   222234677889999997765443 2111112211   11  11         2


Q ss_pred             hHHHHHHHHHHHHHHHhhhhcC----chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHH
Q 013489          156 DYSLIRETFQRASDYLSEQMKN----TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLE  218 (442)
Q Consensus       156 ~~~~~r~~~~~a~~~l~~~~~~----~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~  218 (442)
                      ++......++...... ..+..    .+...+.....+-+....| +  .|.+++.++.+.+|+++-
T Consensus       226 ~~~eAe~~L~~l~~~~-p~~~~k~~~~p~~~~~LaN~i~l~~~lg-k--~a~~l~~qL~~~~P~hp~  288 (310)
T 3mv2_B          226 NIAEAQGIVELLLSDY-YSVEQKENAVLYKPTFLANQITLALMQG-L--DTEDLTNQLVKLDHEHAF  288 (310)
T ss_dssp             CHHHHHHHHHHHHSHH-HHTTTCHHHHSSHHHHHHHHHHHHHHTT-C--TTHHHHHHHHHTTCCCHH
T ss_pred             CHHHHHHHHHHHHHhc-ccccccccCCCCCHHHHHHHHHHHHHhC-h--HHHHHHHHHHHhCCCChH
Confidence            3333333333221110 00000    1234556666666777778 5  788999999999998765

>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=96.39  E-value=0.0029  Score=55.67  Aligned_cols=38  Identities=11%  Similarity=0.079  Sum_probs=32.7

Q ss_pred             CHHHHHHHhccCCCeeEEEEeeC----CCCCCCcceEEEEee
Q 013489          404 TYEDLRRFFSDVGGVSSIRILHD----KFTGKSRVVQSDIYT  441 (442)
Q Consensus       404 ~~~~l~~~f~~~G~i~~~~~~~~----~~~g~~~g~~fv~f~  441 (442)
                      .+++|+..|+.||.|.++.|+.+    +.+|+++|++||+|.
T Consensus       142 ~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~  183 (222)
T 3dxb_A          142 LEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFS  183 (222)
T ss_dssp             HHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEES
T ss_pred             HHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEEC
Confidence            56789999999999999999854    345699999999995

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=96.34  E-value=0.015  Score=43.25  Aligned_cols=68  Identities=12%  Similarity=-0.090  Sum_probs=29.0

Q ss_pred             CCCHHHHHHHHHHHHHhcc--hhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhC
Q 013489           54 PVSSDLWLDYTQYLDKTLK--VGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLC  122 (442)
Q Consensus        54 p~~~~lW~~Y~~~l~~~~~--~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~  122 (442)
                      |.++++|..|+..+.-..+  ..+.+..+|++|+..-|.+...+..... .....++...+...|++++..
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~-~~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIAN-DHFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHH-HHHHTTCHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHH-HHHHcCCHHHHHHHHHHHHhh
Confidence            4444555555444432211  1233444555555555544444433332 222234444455555554443

>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=96.20  E-value=0.53  Score=46.60  Aligned_cols=97  Identities=10%  Similarity=0.021  Sum_probs=73.5

Q ss_pred             hhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh-chhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHH
Q 013489          180 GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI-SGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICH  258 (442)
Q Consensus       180 ~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~-~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~  258 (442)
                      +....|...+....+.| +++.|.++|+.+... ..-+...|...+....+.|+++.|..+|+......+.+  ....|.
T Consensus       103 Pd~~tyn~lI~~~~~~g-~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~P--d~~ty~  179 (501)
T 4g26_A          103 PNEATFTNGARLAVAKD-DPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVP--EEPELA  179 (501)
T ss_dssp             CCHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCC--CHHHHH
T ss_pred             CCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCC--CHHHHH
Confidence            34446777777778888 899999999998876 33346678888888888899999999999988754433  245777


Q ss_pred             HHHHHHHHhCCHhhHHHHHHh
Q 013489          259 AWLRFEREYGTLEDFDHSVQK  279 (442)
Q Consensus       259 ~~~~fE~~~G~~~~~~~~~~~  279 (442)
                      ..+.--...|..+....++++
T Consensus       180 ~Li~~~~~~g~~d~A~~ll~~  200 (501)
T 4g26_A          180 ALLKVSMDTKNADKVYKTLQR  200 (501)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHhhCCCHHHHHHHHHH
Confidence            888888888888776665554

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.18  E-value=0.0066  Score=44.43  Aligned_cols=41  Identities=24%  Similarity=0.261  Sum_probs=33.1

Q ss_pred             eEEEcCCCC----CCCH----HHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINL----KATY----EDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~----~~~~----~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ||+|...|.    +.-.    .+|.+.|++||.|..++++.|+        +||+|.
T Consensus         9 tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~   57 (91)
T 2dnr_A            9 TVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFL   57 (91)
T ss_dssp             EEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEES
T ss_pred             eEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEEC
Confidence            899888762    2333    5788999999999999999973        899994

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=96.17  E-value=0.13  Score=50.72  Aligned_cols=89  Identities=11%  Similarity=0.057  Sum_probs=68.4

Q ss_pred             HHHHHHHHHHHHHHHhhhhcC-chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh--------chhHHHHHHHHHHHH
Q 013489          157 YSLIRETFQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI--------SGAMLEAWQSYISME  227 (442)
Q Consensus       157 ~~~~r~~~~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~--------~~~~~~~w~~~~~~e  227 (442)
                      +......+++++......+.. ++.....+...+.++...| +++.|..+++++|..        +|+-...+...+.+.
T Consensus       325 ~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g-~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~  403 (490)
T 3n71_A          325 YHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQ-AYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAGLTN  403 (490)
T ss_dssp             HHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhc-CHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence            444455566676666665554 3445677888899999999 999999999999976        344455778888888


Q ss_pred             HhcccHHHHHHHHHHHHhc
Q 013489          228 IELDHINEARSIYKRCYSK  246 (442)
Q Consensus       228 ~~~g~~~~ar~i~~ral~~  246 (442)
                      ...|+++.|..+|++|+..
T Consensus       404 ~~~G~~~eA~~~~~~Al~i  422 (490)
T 3n71_A          404 WHAGHIEVGHGMICKAYAI  422 (490)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHH
Confidence            8899999999999999953

>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=95.64  E-value=0.11  Score=50.48  Aligned_cols=89  Identities=13%  Similarity=0.110  Sum_probs=69.1

Q ss_pred             hHHHHHHHHHHHHHHHhhhhcC-chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh--------chhHHHHHHHHHHH
Q 013489          156 DYSLIRETFQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI--------SGAMLEAWQSYISM  226 (442)
Q Consensus       156 ~~~~~r~~~~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~--------~~~~~~~w~~~~~~  226 (442)
                      ++......+++++......+.. ++.....+...+.++...| +++.|..+++++|..        +|+-...+...+.+
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            3445556677777766666654 3344577778888999999 999999999999976        34445577888888


Q ss_pred             HHhcccHHHHHHHHHHHHh
Q 013489          227 EIELDHINEARSIYKRCYS  245 (442)
Q Consensus       227 e~~~g~~~~ar~i~~ral~  245 (442)
                      ...+|+++.|..+|++|+.
T Consensus       392 ~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          392 YMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHhccCHHHHHHHHHHHHH
Confidence            8899999999999999985

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=95.17  E-value=0.66  Score=45.71  Aligned_cols=127  Identities=12%  Similarity=0.018  Sum_probs=83.9

Q ss_pred             ccCCHHHHHHHHHHHHhC-----ChhhHH---HHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhc
Q 013489          105 SRASEEEISTVFEKSLLC-----AFSTFE---EYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMK  176 (442)
Q Consensus       105 ~~~~~~~~~~i~~~al~~-----~~~~~~---~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~  176 (442)
                      .++..+++..+++++|..     +....+   .+-.+-..+     ..         ..++......+++++......+.
T Consensus       321 ~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y-----~~---------~g~~~eA~~~~~~aL~i~~~~lG  386 (490)
T 3n71_A          321 SEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVL-----SY---------LQAYEEASHYARRMVDGYMKLYH  386 (490)
T ss_dssp             TTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHH-----HH---------TTCHHHHHHHHHHHHHHHHHHSC
T ss_pred             hCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHH-----HH---------hcCHHHHHHHHHHHHHHHHHHcC
Confidence            467888899999998842     332221   111111111     11         14666777888999988887777


Q ss_pred             Cch-hhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh--------chhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Q 013489          177 NTD-GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI--------SGAMLEAWQSYISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       177 ~~~-~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~--------~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      ..+ .....+...+.++...| +++.|..+|++++..        +|.-.++-..........+.+..|-.+|.++...
T Consensus       387 ~~Hp~~a~~l~nLa~~~~~~G-~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~  464 (490)
T 3n71_A          387 HNNAQLGMAVMRAGLTNWHAG-HIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREA  464 (490)
T ss_dssp             TTCHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            544 44567777899999999 999999999999976        2333444444444555566777888888877653

>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=94.96  E-value=2  Score=40.35  Aligned_cols=156  Identities=11%  Similarity=0.008  Sum_probs=78.4

Q ss_pred             HHHHHhcCCCCHHHHHHHHHHHHHh--c--chhhHHHHHHHHHHHcCCCcHHHHHHHHH--HHHHccC--C---HHHHHH
Q 013489           46 YERAITDFPVSSDLWLDYTQYLDKT--L--KVGNVVRDVYSRATKNCPWVGELWVRSLL--SLERSRA--S---EEEIST  114 (442)
Q Consensus        46 yERal~~~p~~~~lW~~Y~~~l~~~--~--~~~~~~~~v~erAl~~~p~s~~lW~~y~~--~le~~~~--~---~~~~~~  114 (442)
                      -+|+...-|.+.+.|-.|+.-....  .  .....++.+|++|+..-|.....|.....  .+....+  .   ...++.
T Consensus       183 ~~r~~~~~p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~lDP~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~  262 (372)
T 3ly7_A          183 QETLQKILPHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQSSPEFTYARAEKALVDIVRHSQHPLDEKQLAALNT  262 (372)
T ss_dssp             HHHHHHHSCSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHH
T ss_pred             HHHHhccCCCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhccCCCchhhHHHHHH
Confidence            4556666777777777776543321  1  12355788888888888887665554221  1111111  1   112222


Q ss_pred             HHHHHHhC--ChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHH
Q 013489          115 VFEKSLLC--AFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLE  192 (442)
Q Consensus       115 i~~~al~~--~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e  192 (442)
                      .+..+...  .+.....+..+-...  ..            ..++......+++|+..       ++. ...|...+.+.
T Consensus       263 a~~a~~a~~~~~~~a~~~~alal~~--l~------------~gd~d~A~~~l~rAl~L-------n~s-~~a~~llG~~~  320 (372)
T 3ly7_A          263 EIDNIVTLPELNNLSIIYQIKAVSA--LV------------KGKTDESYQAINTGIDL-------EMS-WLNYVLLGKVY  320 (372)
T ss_dssp             HHHHHHTCGGGTTCHHHHHHHHHHH--HH------------HTCHHHHHHHHHHHHHH-------CCC-HHHHHHHHHHH
T ss_pred             HHHHHHhcccCCcCHHHHHHHHHHH--Hh------------CCCHHHHHHHHHHHHhc-------CCC-HHHHHHHHHHH
Confidence            33322111  111111111000000  00            02333333444444443       222 33455667777


Q ss_pred             HHcCCCHHHHHHHHHHHHHhchhHHH-HHHHHH
Q 013489          193 QSMGKDMVSARGVWERLLKISGAMLE-AWQSYI  224 (442)
Q Consensus       193 ~~~~~~~~~ar~i~~~~l~~~~~~~~-~w~~~~  224 (442)
                      ...| +.+.|.+.|++++..+|.... .|.+-+
T Consensus       321 ~~~G-~~~eA~e~~~~AlrL~P~~~t~~~~~~l  352 (372)
T 3ly7_A          321 EMKG-MNREAADAYLTAFNLRPGANTLYWIENG  352 (372)
T ss_dssp             HHTT-CHHHHHHHHHHHHHHSCSHHHHHHHHHS
T ss_pred             HHCC-CHHHHHHHHHHHHhcCCCcChHHHHhCc
Confidence            7778 999999999999999887643 444433

>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=94.78  E-value=0.02  Score=42.11  Aligned_cols=41  Identities=12%  Similarity=0.136  Sum_probs=33.5

Q ss_pred             eEEEcCCCCC------CCH---HHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINLK------ATY---EDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~------~~~---~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ||+|..++..      ..+   .+|.+.|.+||.|..++++.|+        +||+|.
T Consensus        17 Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~   66 (95)
T 1ufw_A           17 TVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFA   66 (95)
T ss_dssp             EEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECS
T ss_pred             eEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEc
Confidence            9999988743      222   4688999999999999999984        899994

>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=94.11  E-value=0.098  Score=38.49  Aligned_cols=41  Identities=17%  Similarity=0.173  Sum_probs=34.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .||+-+.|.+....||..+|++||. ..|+++.|.       -|||.|.
T Consensus        17 HVf~l~FP~ewKt~DI~~lFs~fgg-v~I~WidDT-------sAlvvf~   57 (100)
T 1whv_A           17 HVLHVTFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLS   57 (100)
T ss_dssp             SEEEEECCTTCCHHHHHHHHTTTCS-CCCEEEETT-------EEEEECS
T ss_pred             eEEEEeCChhhhhHHHHHHhhccCC-EEEEEEcCC-------eEEEEec
Confidence            4555599999999999999999994 578999983       7888874

>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=93.84  E-value=1.2  Score=35.20  Aligned_cols=107  Identities=7%  Similarity=0.025  Sum_probs=65.6

Q ss_pred             HHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHh----cccHHHHHH
Q 013489          163 TFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE----LDHINEARS  238 (442)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~----~g~~~~ar~  238 (442)
                      .+++|+.++.++....+....    .+.+... +..++.|...|+++...  .+...+.....+...    .+++++|..
T Consensus        10 d~~~A~~~~~~aa~~g~~~a~----lg~~y~~-g~~~~~A~~~~~~Aa~~--g~~~a~~~Lg~~y~~G~g~~~d~~~A~~   82 (138)
T 1klx_A           10 DLKKAIQYYVKACELNEMFGC----LSLVSNS-QINKQKLFQYLSKACEL--NSGNGCRFLGDFYENGKYVKKDLRKAAQ   82 (138)
T ss_dssp             HHHHHHHHHHHHHHTTCTTHH----HHHHTCT-TSCHHHHHHHHHHHHHT--TCHHHHHHHHHHHHHCSSSCCCHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCHhhh----HHHHHHc-CCCHHHHHHHHHHHHcC--CCHHHHHHHHHHHHcCCCCCccHHHHHH
Confidence            344555555544443333222    4444433 34788899999999987  334445555555554    568999999


Q ss_pred             HHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          239 IYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       239 i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                      .|++|...    ..+...+..=.-++.-.|...++..++.-.
T Consensus        83 ~~~~Aa~~----g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~  120 (138)
T 1klx_A           83 YYSKACGL----NDQDGCLILGYKQYAGKGVVKNEKQAVKTF  120 (138)
T ss_dssp             HHHHHHHT----TCHHHHHHHHHHHHHTSSSCCCHHHHHHHH
T ss_pred             HHHHHHcC----CCHHHHHHHHHHHHCCCCCCcCHHHHHHHH
Confidence            99999863    445555554445555566666677666544

>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=93.77  E-value=0.37  Score=46.66  Aligned_cols=86  Identities=9%  Similarity=-0.044  Sum_probs=62.8

Q ss_pred             HHHHHHHHHHHHHhhhhcC-chhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh--------chhHHHHHHHHHHHHHh
Q 013489          159 LIRETFQRASDYLSEQMKN-TDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKI--------SGAMLEAWQSYISMEIE  229 (442)
Q Consensus       159 ~~r~~~~~a~~~l~~~~~~-~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~--------~~~~~~~w~~~~~~e~~  229 (442)
                      .....+++++......+.. ++.....+...+.++...| ++++|..+++++|..        +|+-...+...+.+...
T Consensus       305 ~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g-~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~l~nLa~~~~~  383 (429)
T 3qwp_A          305 QVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLG-LLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLH  383 (429)
T ss_dssp             HHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhc-cHHHHHHHHHHHHHhHHHHcCCCChHHHHHHHHHHHHHHh
Confidence            3334445554443333333 3344577777888888899 999999999999966        34444577888888888


Q ss_pred             cccHHHHHHHHHHHHh
Q 013489          230 LDHINEARSIYKRCYS  245 (442)
Q Consensus       230 ~g~~~~ar~i~~ral~  245 (442)
                      .|+++.|..+|++|+.
T Consensus       384 ~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          384 QGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             TTCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHH
Confidence            9999999999999985

>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=93.20  E-value=0.19  Score=37.15  Aligned_cols=41  Identities=17%  Similarity=0.152  Sum_probs=34.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .||+-+.|.+....||..+|++|| -..|+++.|.       -|||.|.
T Consensus         7 HV~~l~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~   47 (101)
T 3ctr_A            7 HVLHVTFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLS   47 (101)
T ss_dssp             EEEEEECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEE
T ss_pred             eEEEEeCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEec
Confidence            455559999999999999999999 5688999983       7888874

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=92.54  E-value=0.24  Score=37.26  Aligned_cols=47  Identities=15%  Similarity=0.097  Sum_probs=41.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccC-----CCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDV-----GGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~-----G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|-+-|||..++...++.+..++     |.|+.+-++.|      .|-|+|+|.
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD------H~GAivef~   70 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD------FNGAIIIFR   70 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT------TTEEEEECS
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC------CCceEEEEc
Confidence            345699999999999999999999999     99999999998      367899985

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=92.53  E-value=2.2  Score=34.49  Aligned_cols=90  Identities=11%  Similarity=-0.030  Sum_probs=59.2

Q ss_pred             hHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHhc-h-hHHHHHHHHHHHHHhcc
Q 013489          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMG--KDMVSARGVWERLLKIS-G-AMLEAWQSYISMEIELD  231 (442)
Q Consensus       156 ~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~--~~~~~ar~i~~~~l~~~-~-~~~~~w~~~~~~e~~~g  231 (442)
                      ++..++..|.+....       .+...+....|+-......  .++.++..+++.+++.. | ++.+.+...+-...+.|
T Consensus        13 ~l~~~~~~y~~e~~~-------~~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~LAv~~~kl~   85 (152)
T 1pc2_A           13 DLLKFEKKFQSEKAA-------GSVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLK   85 (152)
T ss_dssp             HHHHHHHHHHHHHHT-------TCCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHHcc-------CCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHcc
Confidence            344556666665441       2223334444444444332  14669999999999997 7 55677777776778899


Q ss_pred             cHHHHHHHHHHHHhcccCCCChH
Q 013489          232 HINEARSIYKRCYSKRFTGTGSE  254 (442)
Q Consensus       232 ~~~~ar~i~~ral~~~~~~~~~~  254 (442)
                      ++++|+..++++|.  ..+++.+
T Consensus        86 ~Y~~A~~y~~~lL~--ieP~n~Q  106 (152)
T 1pc2_A           86 EYEKALKYVRGLLQ--TEPQNNQ  106 (152)
T ss_dssp             CHHHHHHHHHHHHH--HCTTCHH
T ss_pred             CHHHHHHHHHHHHh--cCCCCHH
Confidence            99999999999997  3444443

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=91.81  E-value=1.4  Score=32.75  Aligned_cols=69  Identities=17%  Similarity=0.093  Sum_probs=45.4

Q ss_pred             HHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHH
Q 013489          157 YSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISM  226 (442)
Q Consensus       157 ~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~  226 (442)
                      +.....-|+.|+...............++..++......| +++.|..++++++...|++..+.....-+
T Consensus        21 y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g-~~~~A~~~~~~al~l~P~~~~~~~n~~~~   89 (104)
T 2v5f_A           21 YYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQG-DLDKALLLTKKLLELDPEHQRANGNLKYF   89 (104)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHcc-CHHHHHHHHHHHHhcCCCCHHHHhhHHHH
Confidence            3333344555555442221112345678888888888999 99999999999999999887665444433

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=91.67  E-value=3.1  Score=30.79  Aligned_cols=64  Identities=8%  Similarity=-0.011  Sum_probs=51.9

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHhc-------hhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCCh
Q 013489          187 YWAHLEQSMGKDMVSARGVWERLLKIS-------GAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGS  253 (442)
Q Consensus       187 ~~a~~e~~~~~~~~~ar~i~~~~l~~~-------~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~  253 (442)
                      ..+.+....+ ++..|..-|+.+++..       .....++..++......|+++.|..++++|+.  +.++.+
T Consensus        10 ~lG~~~~~~~-~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~--l~P~~~   80 (104)
T 2v5f_A           10 ELGKVAYTEA-DYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE--LDPEHQ   80 (104)
T ss_dssp             HHHHHHHHTT-CHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTTCH
T ss_pred             HHHHHHHHcc-chHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHh--cCCCCH
Confidence            3455666777 9999999999999873       24567899999999999999999999999997  344544

>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=90.93  E-value=12  Score=36.09  Aligned_cols=47  Identities=17%  Similarity=0.030  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh------------chhHHHHHHHHHHHHHh
Q 013489          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKI------------SGAMLEAWQSYISMEIE  229 (442)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~------------~~~~~~~w~~~~~~e~~  229 (442)
                      ..+|..++-++...+ +++.|....-.....            .+.+.++....+.|...
T Consensus       282 ~~~w~e~~~ly~~~~-e~d~A~~tm~~h~~~a~~~~~f~~~~~kv~n~elyYkai~fyl~  340 (449)
T 1b89_A          282 AHLWAELVFLYDKYE-EYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYLE  340 (449)
T ss_dssp             TTCHHHHHHHHHHTT-CHHHHHHHHHHSTTTTCCHHHHHHHHHHCSSTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhc-hHHHHHHHHHhCChhhhhhHHHHHHHhchhHHHHHHHHHHHHHh
Confidence            347777777777777 777776543332211            23345666666666653

>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=90.59  E-value=1.4  Score=42.51  Aligned_cols=91  Identities=11%  Similarity=0.114  Sum_probs=65.8

Q ss_pred             cCCCHHHHHHHHHHHHHh--------chhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc---ccCCCChHHHHHHHHHH
Q 013489          195 MGKDMVSARGVWERLLKI--------SGAMLEAWQSYISMEIELDHINEARSIYKRCYSK---RFTGTGSEDICHAWLRF  263 (442)
Q Consensus       195 ~~~~~~~ar~i~~~~l~~--------~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~---~~~~~~~~~i~~~~~~f  263 (442)
                      .| +++.|..+|+++|..        +|+-.......+......|+++.|..+|++++..   .+..+.| .+...+.++
T Consensus       311 ~g-~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp-~~a~~l~nL  388 (433)
T 3qww_A          311 YK-SPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSL-NVASMWLKL  388 (433)
T ss_dssp             TS-CHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCH-HHHHHHHHH
T ss_pred             cc-CHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCCh-HHHHHHHHH
Confidence            35 789999999999975        3444557777888888899999999999999954   3444555 566677777


Q ss_pred             HHHhCCHhhHHHHHHhhchhHHHH
Q 013489          264 EREYGTLEDFDHSVQKVTPRLEEL  287 (442)
Q Consensus       264 E~~~G~~~~~~~~~~~~~~~~~~~  287 (442)
                      -..|.+...+++|...+..+++..
T Consensus       389 a~~~~~qg~~~eA~~~~~~Al~i~  412 (433)
T 3qww_A          389 GRLYMGLENKAAGEKALKKAIAIM  412 (433)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHhccCHHHHHHHHHHHHHHH
Confidence            666665666666666655555443

>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=90.42  E-value=0.82  Score=33.41  Aligned_cols=50  Identities=6%  Similarity=0.008  Sum_probs=39.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCC--CcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGK--SRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~--~~g~~fv~f~  441 (442)
                      ++|-|.+||++.|++++.+.++..+.+.-...+..+.+.+  ..+-|||.|.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~   53 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFK   53 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEES
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeC
Confidence            4789999999999999999999998877777776654443  3357788885

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=88.87  E-value=2.2  Score=34.46  Aligned_cols=87  Identities=7%  Similarity=-0.124  Sum_probs=58.7

Q ss_pred             hhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc--chhhHHHHHHHHHHHcC-C-CcHHHHHHHHHHHHHccCCHHHHHH
Q 013489           39 PGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL--KVGNVVRDVYSRATKNC-P-WVGELWVRSLLSLERSRASEEEIST  114 (442)
Q Consensus        39 ~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~--~~~~~~~~v~erAl~~~-p-~s~~lW~~y~~~le~~~~~~~~~~~  114 (442)
                      ...++..|++.+...|.+.+...+|+--|.+..  .+......+|+..++.- | ...+.+....... -..++.+.++.
T Consensus        14 l~~~~~~y~~e~~~~~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~LAv~~-~kl~~Y~~A~~   92 (152)
T 1pc2_A           14 LLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGN-YRLKEYEKALK   92 (152)
T ss_dssp             HHHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHH-HHTSCHHHHHH
T ss_pred             HHHHHHHHHHHHccCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHH-HHccCHHHHHH
Confidence            345667788888888888888888887666432  13345777888888876 5 2223333323223 34688889999


Q ss_pred             HHHHHHhCChhh
Q 013489          115 VFEKSLLCAFST  126 (442)
Q Consensus       115 i~~~al~~~~~~  126 (442)
                      .++++|...|.+
T Consensus        93 y~~~lL~ieP~n  104 (152)
T 1pc2_A           93 YVRGLLQTEPQN  104 (152)
T ss_dssp             HHHHHHHHCTTC
T ss_pred             HHHHHHhcCCCC
Confidence            999999887764

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=88.25  E-value=1.9  Score=32.05  Aligned_cols=44  Identities=16%  Similarity=0.082  Sum_probs=34.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhcc-----CCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSD-----VGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~-----~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      -..+|.|.|||..+.++.|.-+|..     -|.|.++....        +-|+|+|.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~   55 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFR   55 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEES
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEc
Confidence            3569999999999999999999986     24666665422        57789885

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=86.42  E-value=0.44  Score=46.17  Aligned_cols=45  Identities=11%  Similarity=0.199  Sum_probs=35.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||. .|..+++.+|.+.|++||+|.++.+-.+  .|   -|+.|+|.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~--~g---~~~~vef~   97 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES--FG---LYAVVEFC   97 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS--SS---EEEEEECC
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc--CC---eEEEEEeC
Confidence            4699998 7999999999999999999999866543  23   59999996

>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=85.67  E-value=4.3  Score=39.09  Aligned_cols=92  Identities=10%  Similarity=0.046  Sum_probs=64.7

Q ss_pred             HcCCCHHHHHHHHHHHHHh--------chhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc---ccCCCChHHHHHHHHH
Q 013489          194 SMGKDMVSARGVWERLLKI--------SGAMLEAWQSYISMEIELDHINEARSIYKRCYSK---RFTGTGSEDICHAWLR  262 (442)
Q Consensus       194 ~~~~~~~~ar~i~~~~l~~--------~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~---~~~~~~~~~i~~~~~~  262 (442)
                      ..| .++.|..++++++..        +|....+....+......|+++.|..++++++..   .+..+.| .+...+.+
T Consensus       299 ~~g-~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp-~~a~~l~n  376 (429)
T 3qwp_A          299 AHW-KWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHP-VRGVQVMK  376 (429)
T ss_dssp             HTT-CHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCH-HHHHHHHH
T ss_pred             hhc-cHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCCh-HHHHHHHH
Confidence            345 899999999999965        3444567777788888899999999999999854   3555555 46666666


Q ss_pred             HHHHhCCHhhHHHHHHhhchhHHHH
Q 013489          263 FEREYGTLEDFDHSVQKVTPRLEEL  287 (442)
Q Consensus       263 fE~~~G~~~~~~~~~~~~~~~~~~~  287 (442)
                      +-..|.+...+++|...+...++..
T Consensus       377 La~~~~~~g~~~eA~~~~~~Al~i~  401 (429)
T 3qwp_A          377 VGKLQLHQGMFPQAMKNLRLAFDIM  401 (429)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHHH
Confidence            6666655555666665555544443

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=81.30  E-value=16  Score=34.53  Aligned_cols=57  Identities=16%  Similarity=0.138  Sum_probs=33.9

Q ss_pred             HHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHH
Q 013489           29 YLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATK   86 (442)
Q Consensus        29 y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~   86 (442)
                      .++.....|++..+....++++..+|.++.+|...+..+...+ ....+..+|++..+
T Consensus       177 ~~~~~l~~g~~~~a~~~l~~~~~~~P~~E~~~~~lm~al~~~G-r~~~Al~~y~~~r~  233 (388)
T 2ff4_A          177 KAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSD-RQSDALGAYRRVKT  233 (388)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTT-CHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcC-CHHHHHHHHHHHHH
Confidence            3333444566666666666667677777777776666665433 33446666666544

---

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	442
d2onda1	308	a.118.8.7 (A:242-549) Cleavage stimulation factor	1e-19
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	4e-06
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	0.001
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	0.004

>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 = 87.0 bits (214), Expect = 1e-19
 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 = 43.1 bits (101), Expect = 4e-06
 Identities = 18/60 (30%), Positives = 30/60 (50%)

Query: 374 KQPIKDAVPGRTKGFTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSR 433
           K P+++ V   +    D  T F   +  +    DL  FFS VG V  +RI+ D+ + +S+
Sbjct: 1   KSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 60

>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 = 35.3 bits (81), Expect = 0.001
 Identities = 12/41 (29%), Positives = 20/41 (48%)

Query: 392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKS 432
           C  F+  ++ + T E LR +F   G V    ++ D  T +S
Sbjct: 1   CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRS 41

>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 = 34.6 bits (79), Expect = 0.004
 Identities = 11/41 (26%), Positives = 18/41 (43%)

Query: 390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTG 430
             CT +   I    T + +R+ FS  G +  IR+  +K   
Sbjct: 17  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYS 57

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	442
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.97
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.89
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.55
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.54
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.53
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.52
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.5
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.5
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.49
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.49
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.47
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.47
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.47
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.47
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.46
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.46
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.46
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.46
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.45
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.45
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.45
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.45
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.44
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.43
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.43
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.43
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.41
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.41
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.41
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.4
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.4
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.4
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.38
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.37
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.37
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.35
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.33
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.33
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.32
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.31
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.31
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.3
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.29
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.29
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.27
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.26
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.26
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.25
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.24
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.24
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.23
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.22
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.22
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.2
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.16
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.15
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.15
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.15
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.15
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.14
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.12
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.12
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.11
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.08
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.08
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.07
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.05
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.03
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.01
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	98.99
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.99
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	98.99
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	98.99
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	98.97
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	98.97
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.97
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.96
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	98.96
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.95
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	98.94
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	98.93
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	98.93
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	98.92
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.89
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	98.89
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.88
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.88
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	98.87
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	98.78
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	98.76
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.76
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	98.72
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	98.66
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	98.45
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.44
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	98.44
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.36
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.21
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	98.2
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.2
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.11
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.03
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.99
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.98
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	97.93
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	97.81
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.79
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.75
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	97.64
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	97.57
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.51
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	97.49
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.48
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	97.41
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	97.41
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.37
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.35
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.33
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.25
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.21
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.21
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.2
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.14
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.08
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.05
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	96.75
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	96.68
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	96.65
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	96.61
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	96.54
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	96.36
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	95.93
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	95.72
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	95.59
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	92.47
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	92.26
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	90.59
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	90.42
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	89.54
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	88.99
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	87.4

>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=99.97  E-value=7.2e-30  Score=239.51  Aligned_cols=240  Identities=21%  Similarity=0.284  Sum_probs=191.4

Q ss_pred             hHhHHHHHHHHHHHHhcC--------ChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcc-------------hhhHHH
Q 013489           20 SEKFQQYMIYLKYEQSSG--------DPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLK-------------VGNVVR   78 (442)
Q Consensus        20 ~~~~~~w~~y~~~e~~~g--------~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~-------------~~~~~~   78 (442)
                      ...++.|+.||+||+.++        +.+||..+|||||..+|.++.+|+.|+.|+...++             ..+.++
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            456789999999998764        35789999999999999999999999999875432             235688


Q ss_pred             HHHHHHHHc-CCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhH
Q 013489           79 DVYSRATKN-CPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDY  157 (442)
Q Consensus        79 ~v~erAl~~-~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~  157 (442)
                      .+|+||+.. +|.+..+|..|+.+++. .+..+.++.+|++++...+...   ..+|..++.++++.          .++
T Consensus        85 ~i~~ral~~~~p~~~~l~~~ya~~~~~-~~~~~~a~~i~~~~l~~~~~~~---~~~w~~~~~~~~~~----------~~~  150 (308)
T d2onda1          85 NIYERAISTLLKKNMLLYFAYADYEES-RMKYEKVHSIYNRLLAIEDIDP---TLVYIQYMKFARRA----------EGI  150 (308)
T ss_dssp             HHHHHHHTTTTTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTSSSSCT---HHHHHHHHHHHHHH----------HCH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHHHh-cccHHHHHHHHHHHHHHhcCCh---HHHHHHHHHHHHHc----------CCh
Confidence            999999985 68899999999986554 7889999999999998765431   12344444444322          344


Q ss_pred             HHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHH
Q 013489          158 SLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEAR  237 (442)
Q Consensus       158 ~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar  237 (442)
                      ...+..|++|+.       ..+....+|..++.++....++++.|+.+|++++..+|++..+|+.|++|+...|++++||
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            455566666554       3455667899999998887669999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcc-cCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          238 SIYKRCYSKR-FTGTGSEDICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       238 ~i~~ral~~~-~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                      .+|++|+... .++.....||..|++||+.||+++++..+.+++
T Consensus       224 ~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~  267 (308)
T d2onda1         224 VLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRR  267 (308)
T ss_dssp             HHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            9999999842 111234579999999999999999988766554

>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=99.89  E-value=7.8e-22  Score=184.19  Aligned_cols=216  Identities=15%  Similarity=0.177  Sum_probs=171.7

Q ss_pred             hhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcC--------------ChhhHHHHHHHHHhc-CCCCHHHHHHHHHHHH
Q 013489            4 ARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSG--------------DPGRVQLLYERAITD-FPVSSDLWLDYTQYLD   68 (442)
Q Consensus         4 ~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g--------------~~~~~~~lyERal~~-~p~~~~lW~~Y~~~l~   68 (442)
                      .+..||++|...|.    ..++|..|+.|+...|              ..+.+..+|+|||.. +|.+..+|..|+.++.
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            45689999999887    7789999999986543              246788999999985 7899999999999887


Q ss_pred             HhcchhhHHHHHHHHHHHcCCCc-HHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhc
Q 013489           69 KTLKVGNVVRDVYSRATKNCPWV-GELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILF  147 (442)
Q Consensus        69 ~~~~~~~~~~~v~erAl~~~p~s-~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~  147 (442)
                      .. +..+.++.+|++++...|.. ..+|..|+.++.+ .+..+.++.+|++++...+.....++..-.     +..+.  
T Consensus       111 ~~-~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~-~~~~~~ar~i~~~al~~~~~~~~~~~~~a~-----~e~~~--  181 (308)
T d2onda1         111 SR-MKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARR-AEGIKSGRMIFKKAREDARTRHHVYVTAAL-----MEYYC--  181 (308)
T ss_dssp             HT-TCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHH-HHCHHHHHHHHHHHHTSTTCCTHHHHHHHH-----HHHHT--
T ss_pred             hc-ccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHH-cCChHHHHHHHHHHHHhCCCcHHHHHHHHH-----HHHHh--
Confidence            55 45678999999999999865 5689999986554 677899999999999887765443332111     10011  


Q ss_pred             cCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchh----HHHHHHHH
Q 013489          148 SGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA----MLEAWQSY  223 (442)
Q Consensus       148 ~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~----~~~~w~~~  223 (442)
                            ..+....+..|++++..       .+....+|..|++++...| ++++||.+|+++++.+|.    ...+|..|
T Consensus       182 ------~~~~~~a~~i~e~~l~~-------~p~~~~~w~~y~~~~~~~g-~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~  247 (308)
T d2onda1         182 ------SKDKSVAFKIFELGLKK-------YGDIPEYVLAYIDYLSHLN-EDNNTRVLFERVLTSGSLPPEKSGEIWARF  247 (308)
T ss_dssp             ------SCCHHHHHHHHHHHHHH-------HTTCHHHHHHHHHHHHTTC-CHHHHHHHHHHHHHSSSSCGGGCHHHHHHH
T ss_pred             ------ccCHHHHHHHHHHHHHh-------hhhhHHHHHHHHHHHHHcC-ChHHHHHHHHHHHHhCCCChHHHHHHHHHH
Confidence                  13455666777777764       3445679999999999999 999999999999998653    35699999


Q ss_pred             HHHHHhcccHHHHHHHHHHHHhc
Q 013489          224 ISMEIELDHINEARSIYKRCYSK  246 (442)
Q Consensus       224 ~~~e~~~g~~~~ar~i~~ral~~  246 (442)
                      +.||..+|+++.++++++|+...
T Consensus       248 ~~fE~~~G~~~~~~~~~~r~~~~  270 (308)
T d2onda1         248 LAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             HHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHH
Confidence            99999999999999999999873

>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=99.55  E-value=2.5e-15  Score=114.22  Aligned_cols=53  Identities=28%  Similarity=0.446  Sum_probs=50.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||||||+++++++|+.+|+.||.|.+|+|+.++.||+++|||||+|.
T Consensus        16 ~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~   68 (101)
T d2cq4a1          16 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC   68 (101)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEES
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEEC
Confidence            34579999999999999999999999999999999999999999999999995

>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=99.54  E-value=4.5e-15  Score=110.21  Aligned_cols=52  Identities=25%  Similarity=0.349  Sum_probs=49.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+++|+++|+.+|++||.|.+|+|+.|+.||++||||||+|.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~   58 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFT   58 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEES
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEEC
Confidence            3458999999999999999999999999999999999999999999999995

>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=99.53  E-value=2.5e-15  Score=108.13  Aligned_cols=50  Identities=26%  Similarity=0.517  Sum_probs=48.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      |+|||||||+++++++|+++|++||.|.+++|+.|+.||++||||||+|.
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~   50 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM   50 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEEC
Confidence            68999999999999999999999999999999999999999999999996

>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=99.52  E-value=4.4e-15  Score=106.11  Aligned_cols=49  Identities=24%  Similarity=0.368  Sum_probs=47.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +|||||||+++|+++|+++|++||.|.+|+|+.|+.||+++|||||+|.
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~   49 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFK   49 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEES
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEEC
Confidence            5899999999999999999999999999999999999999999999996

>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=99.50  E-value=1.1e-14  Score=106.78  Aligned_cols=51  Identities=24%  Similarity=0.343  Sum_probs=49.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||||||+++++++|+.+|+.||.|.+++|+.|+.||+++|||||+|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~   56 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA   56 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEc
Confidence            359999999999999999999999999999999999999999999999995

>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=99.50  E-value=2e-14  Score=107.58  Aligned_cols=52  Identities=17%  Similarity=0.280  Sum_probs=49.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||||||+++++++|+.+|++||.|.+|+|+.++.||+++|||||+|.
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~   59 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFL   59 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEES
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEEC
Confidence            3569999999999999999999999999999999999999999999999995

>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=99.49  E-value=2.5e-14  Score=109.23  Aligned_cols=53  Identities=25%  Similarity=0.378  Sum_probs=49.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||||||+.+++++|+++|+.||.|.+|+|+.|+.||+++|||||+|.
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~   60 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMA   60 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEES
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEEC
Confidence            34568999999999999999999999999999999999999999999999996

>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=99.49  E-value=1.6e-14  Score=103.49  Aligned_cols=49  Identities=27%  Similarity=0.476  Sum_probs=47.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +|||||||+++++++|+++|++||.|.+++|+.++.||+++|||||+|.
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~   49 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFK   49 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEES
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEEC
Confidence            4899999999999999999999999999999999999999999999996

>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=99.47  E-value=3.1e-14  Score=105.40  Aligned_cols=54  Identities=22%  Similarity=0.316  Sum_probs=50.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..+.++|||+|||+++++++|+++|++||.|.+|+++.|+.||+++|||||+|.
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~   57 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE   57 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEEC
Confidence            345679999999999999999999999999999999999999999999999995

>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=99.47  E-value=3e-14  Score=106.60  Aligned_cols=53  Identities=23%  Similarity=0.332  Sum_probs=50.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++||||||||+++++++|+.+|++||.|.+|+++.++.+|+++|||||+|.
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~   57 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYY   57 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEEC
Confidence            45679999999999999999999999999999999999999999999999995

>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=99.47  E-value=3e-14  Score=106.05  Aligned_cols=53  Identities=26%  Similarity=0.380  Sum_probs=50.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||.++++++|+++|++||.|.+|+|+.|+.+|+++|||||+|.
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~   58 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFH   58 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEEC
Confidence            45579999999999999999999999999999999999899999999999996

>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=99.47  E-value=2.3e-14  Score=109.11  Aligned_cols=51  Identities=18%  Similarity=0.348  Sum_probs=48.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||||||+++++++|+.+|++||.|.++.|+.|+.+++++|||||+|.
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~   70 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFS   70 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEEC
Confidence            368999999999999999999999999999999999999999999999995

>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=99.46  E-value=6.2e-12  Score=116.28  Aligned_cols=236  Identities=11%  Similarity=0.060  Sum_probs=147.5

Q ss_pred             HHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHH
Q 013489            7 HLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATK   86 (442)
Q Consensus         7 ~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~   86 (442)
                      .||.++.-.......+...+...+......|+++.|..+|+++|..+|.++..|...+..... .++.+.+...|.+|+.
T Consensus         3 ~~~~~~~~~~~n~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~-~~~~~~A~~~~~~al~   81 (323)
T d1fcha_           3 TYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAE-NEQELLAISALRRCLE   81 (323)
T ss_dssp             HHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHH
T ss_pred             chHHhHhhcccCCCcchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-cCChHHHHHHHHhhhc
Confidence            466666443221111222344556666778999999999999999999999999998876664 4566789999999999


Q ss_pred             cCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHH---------HH---------------HHHHHHHHHHH
Q 013489           87 NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEE---------YL---------------DLFLTRIDGLR  142 (442)
Q Consensus        87 ~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~---------~~---------------~~~~~~~~~l~  142 (442)
                      ..|.....|...+..+. ..+..+.+...|++++...+.....         ..               ..+......+.
T Consensus        82 ~~p~~~~~~~~la~~~~-~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~  160 (323)
T d1fcha_          82 LKPDNQTALMALAVSFT-NESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFL  160 (323)
T ss_dssp             HCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHH
T ss_pred             ccccccccccccccccc-ccccccccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHH
Confidence            99999999999877444 4688888999999988654331000         00               00000011111


Q ss_pred             HHh-hccCccch--hh---hHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH
Q 013489          143 RRI-LFSGEVEG--VL---DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM  216 (442)
Q Consensus       143 rr~-~~~~~~~~--~~---~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~  216 (442)
                      +-+ ..+...+.  +.   .+......++.|+.++...+...+....+|...+.+....| +++.|...|+++++..|++
T Consensus       161 ~al~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g-~~~~A~~~~~~al~~~p~~  239 (323)
T d1fcha_         161 AAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGN-QSEEAVAAYRRALELQPGY  239 (323)
T ss_dssp             HHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHhhcccccccchhhHHHHHHHHHHhhhhcccccccccccccccchhhhhhcccccc-cchhHHHHHHHHHHHhhcc
Confidence            000 00111100  00   01111122455666665555444555566777777777777 7777777777777777777


Q ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          217 LEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       217 ~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ...|..++......|+++.|...|++|+.
T Consensus       240 ~~a~~~lg~~~~~~g~~~~A~~~~~~al~  268 (323)
T d1fcha_         240 IRSRYNLGISCINLGAHREAVEHFLEALN  268 (323)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            77777777777777777777777777775

>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=99.46  E-value=3.6e-14  Score=104.35  Aligned_cols=51  Identities=29%  Similarity=0.432  Sum_probs=48.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +++|||||||+++++++|+++|++||.|.+++++.|+.+|+++|||||+|.
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~   56 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFD   56 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEc
Confidence            458999999999999999999999999999999999889999999999996

>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=99.46  E-value=4e-14  Score=103.68  Aligned_cols=51  Identities=25%  Similarity=0.386  Sum_probs=48.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||+.+++++|+++|++||.|.+|+|+.++.+|+++|||||+|.
T Consensus         9 ~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~   59 (83)
T d2cqca1           9 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE   59 (83)
T ss_dssp             GGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEES
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEEC
Confidence            469999999999999999999999999999999999999999999999996

>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=99.46  E-value=2.4e-14  Score=106.28  Aligned_cols=52  Identities=17%  Similarity=0.173  Sum_probs=49.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||||||+++++++|+++|++||.|.+|+|+.|+.+|+++|||||+|.
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~   55 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE   55 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCS
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEEC
Confidence            3469999999999999999999999999999999999999999999999995

>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=99.45  E-value=6.1e-14  Score=103.17  Aligned_cols=52  Identities=27%  Similarity=0.455  Sum_probs=49.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+++++++|+.+|++||.|.+++++.++.+|+++|||||+|.
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~   56 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYN   56 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEEC
Confidence            3458999999999999999999999999999999999999999999999995

>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=99.45  E-value=4.3e-14  Score=102.66  Aligned_cols=49  Identities=22%  Similarity=0.255  Sum_probs=47.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +|||||||+++++++|+.+|++||.|.+|+|+.|+.||+++|||||+|.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~   50 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQ   50 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEEC
Confidence            6999999999999999999999999999999999999999999999995

>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=99.45  E-value=4.5e-14  Score=103.73  Aligned_cols=50  Identities=14%  Similarity=0.265  Sum_probs=48.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+|||||||+++++++|+.+|+.||+|.+|+|+.|+.||+++|||||+|.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~   51 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV   51 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEES
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEEC
Confidence            47999999999999999999999999999999999999999999999995

>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=99.45  E-value=2e-11  Score=112.70  Aligned_cols=207  Identities=11%  Similarity=-0.003  Sum_probs=134.2

Q ss_pred             HHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHH--
Q 013489           59 LWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLT--  136 (442)
Q Consensus        59 lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~--  136 (442)
                      -|...+..+.. .++.+.+...|+++++..|.....|......+. ..+..+.+...|.+++...+.....+..+-..  
T Consensus        21 ~~~~~g~~~~~-~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~-~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~   98 (323)
T d1fcha_          21 QPFEEGLRRLQ-EGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQA-ENEQELLAISALRRCLELKPDNQTALMALAVSFT   98 (323)
T ss_dssp             SHHHHHHHHHH-TTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHH-cCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH-HcCChHHHHHHHHhhhcccccccccccccccccc
Confidence            34444444443 356688999999999999999999999876444 47889999999999998776644433322211  


Q ss_pred             -------HHHHHHHHhhc-cCc---------------c---chhhhHHHHHHHHHHHHHHHhhhhcCch--hhHHHHHHH
Q 013489          137 -------RIDGLRRRILF-SGE---------------V---EGVLDYSLIRETFQRASDYLSEQMKNTD--GLLRLYAYW  188 (442)
Q Consensus       137 -------~~~~l~rr~~~-~~~---------------~---~~~~~~~~~r~~~~~a~~~l~~~~~~~~--~~~~l~~~~  188 (442)
                             .+..+.+-+.. ...               .   ............+..+...+..++...+  ....+|...
T Consensus        99 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l  178 (323)
T d1fcha_          99 NESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGL  178 (323)
T ss_dssp             HTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHH
T ss_pred             ccccccccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhh
Confidence                   11112111100 000               0   0000011112334555555544433222  234577778


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhC
Q 013489          189 AHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYG  268 (442)
Q Consensus       189 a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G  268 (442)
                      +.+....| +++.|...|++++..+|+...+|...+.+....|+++.|...|++++.  +.++.+. .+......-...|
T Consensus       179 ~~~~~~~~-~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~--~~p~~~~-a~~~lg~~~~~~g  254 (323)
T d1fcha_         179 GVLFNLSG-EYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALE--LQPGYIR-SRYNLGISCINLG  254 (323)
T ss_dssp             HHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTTCHH-HHHHHHHHHHHHT
T ss_pred             HHHHHHHH-HHhhhhcccccccccccccccchhhhhhcccccccchhHHHHHHHHHH--HhhccHH-HHHHHHHHHHHCC
Confidence            88888888 999999999999999999999999999999999999999999999997  3445553 3333344444455


Q ss_pred             CHh
Q 013489          269 TLE  271 (442)
Q Consensus       269 ~~~  271 (442)
                      ..+
T Consensus       255 ~~~  257 (323)
T d1fcha_         255 AHR  257 (323)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            543

>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=99.44  E-value=8.8e-14  Score=105.48  Aligned_cols=53  Identities=23%  Similarity=0.356  Sum_probs=49.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||+|||+++++++|+++|..||.|.+|+|+.|+.||+++|||||+|.
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~   58 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFM   58 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEES
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEEC
Confidence            34568999999999999999999999999999999999999999999999995

>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=99.43  E-value=9.8e-14  Score=105.70  Aligned_cols=51  Identities=24%  Similarity=0.305  Sum_probs=48.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||+++++++|+++|+.||.|.++.++.++.+|+++|||||+|.
T Consensus        18 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~   68 (102)
T d2cpza1          18 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYD   68 (102)
T ss_dssp             TCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeC
Confidence            458999999999999999999999999999999999999999999999996

>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=99.43  E-value=6e-14  Score=102.52  Aligned_cols=51  Identities=22%  Similarity=0.262  Sum_probs=48.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~   52 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFT   52 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEES
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEEC
Confidence            458999999999999999999999999999999999899999999999995

>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=99.43  E-value=4.2e-11  Score=112.22  Aligned_cols=220  Identities=13%  Similarity=0.077  Sum_probs=167.4

Q ss_pred             hHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHH
Q 013489            5 RAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRA   84 (442)
Q Consensus         5 r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erA   84 (442)
                      ...++..+...|.    ....+...+......|+.+.+...++++|..+|.+...|..++..+... +..+.+...|+++
T Consensus       155 ~~~~~~~~~~~~~----~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~-~~~~~A~~~~~~~  229 (388)
T d1w3ba_         155 KACYLKAIETQPN----FAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEA-RIFDRAVAAYLRA  229 (388)
T ss_dssp             HHHHHHHHHHCTT----CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTT-TCTTHHHHHHHHH
T ss_pred             HHHHHHhhccCcc----hhHHHHhhcccccccCcHHHHHHHHHHHHHhCcccHHHHHHHhhhhhcc-ccHHHHHHHHHHh
Confidence            3445555655554    5667888888888899999999999999999999999999998877643 4567799999999


Q ss_pred             HHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHH
Q 013489           85 TKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETF  164 (442)
Q Consensus        85 l~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~  164 (442)
                      +...|.....|......+. ..+..+.+...|++++...+.....+..+-..+.     ..         .+       +
T Consensus       230 ~~~~~~~~~~~~~l~~~~~-~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~-----~~---------~~-------~  287 (388)
T d1w3ba_         230 LSLSPNHAVVHGNLACVYY-EQGLIDLAIDTYRRAIELQPHFPDAYCNLANALK-----EK---------GS-------V  287 (388)
T ss_dssp             HHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHH-----HH---------SC-------H
T ss_pred             HHHhhhHHHHHHHHHHHHH-HCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH-----Hc---------CC-------H
Confidence            9999998888887666444 4688899999999999887765444333222111     00         12       2


Q ss_pred             HHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHH
Q 013489          165 QRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCY  244 (442)
Q Consensus       165 ~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral  244 (442)
                      ..|+.++.......+....++...+.+....| +++.|...|+++++.+|++..+|...+......|+++.|...|++|+
T Consensus       288 ~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al  366 (388)
T d1w3ba_         288 AEAEDCYNTALRLCPTHADSLNNLANIKREQG-NIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAI  366 (388)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTT-CHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhccCCccchhhhHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            33444443333334555667888888888888 99999999999999999999999999999999999999999999999


Q ss_pred             hcccCCCChH
Q 013489          245 SKRFTGTGSE  254 (442)
Q Consensus       245 ~~~~~~~~~~  254 (442)
                      .  +.++.+.
T Consensus       367 ~--l~P~~~~  374 (388)
T d1w3ba_         367 R--ISPTFAD  374 (388)
T ss_dssp             T--TCTTCHH
T ss_pred             H--hCCCCHH
Confidence            7  3444443

>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=99.41  E-value=3.2e-14  Score=109.09  Aligned_cols=52  Identities=37%  Similarity=0.476  Sum_probs=49.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +.++|||+|||+++++++|+++|++||.|.+|+|+.++.||+++|||||+|.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~   58 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQ   58 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECS
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEEC
Confidence            3468999999999999999999999999999999999999999999999996

>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=99.41  E-value=1.6e-13  Score=100.19  Aligned_cols=50  Identities=24%  Similarity=0.395  Sum_probs=48.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ++|||||||+++++++|+++|++||.|.+|+++.++.+|+++|||||+|.
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~   52 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYI   52 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEEC
Confidence            48999999999999999999999999999999999889999999999995

>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=99.41  E-value=1.8e-13  Score=103.64  Aligned_cols=53  Identities=19%  Similarity=0.304  Sum_probs=50.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||||||+++++++|+.+|++||.|.++.++.++.+++++|||||+|.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~   58 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFM   58 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEES
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEc
Confidence            45679999999999999999999999999999999999889999999999995

>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=99.40  E-value=1.9e-13  Score=102.38  Aligned_cols=52  Identities=21%  Similarity=0.340  Sum_probs=47.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCC-CCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDK-FTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~-~~g~~~g~~fv~f~  441 (442)
                      ...+|||+|||+++++++|+.+|++||.|.+|+|+.++ .+|+++|||||+|.
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~   59 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFI   59 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEEC
Confidence            34589999999999999999999999999999999875 48999999999995

>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=99.40  E-value=1.9e-13  Score=99.02  Aligned_cols=50  Identities=24%  Similarity=0.402  Sum_probs=48.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ++|||||||+++|+++|+++|++||.|..+.++.++.+|+++|||||+|.
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~   52 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD   52 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEc
Confidence            58999999999999999999999999999999999999999999999995

>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=99.40  E-value=2.9e-13  Score=109.53  Aligned_cols=52  Identities=21%  Similarity=0.237  Sum_probs=49.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||||||+++++++|+.+|+.||.|.+|+|+.++.||+++|||||+|.
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~   92 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQ   92 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEEC
Confidence            3468999999999999999999999999999999999999999999999996

>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=99.38  E-value=2.9e-13  Score=99.28  Aligned_cols=50  Identities=14%  Similarity=0.305  Sum_probs=47.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||+++|+++|+.+|+.||.|.+|+|+.+ .+|+++|||||+|.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~-~~~~~kG~afV~f~   55 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFD   55 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEEC-TTCCEEEEEEEEES
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeee-ccCCcceEEEEEEc
Confidence            469999999999999999999999999999999988 59999999999996

>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=99.37  E-value=2.3e-13  Score=101.24  Aligned_cols=53  Identities=23%  Similarity=0.407  Sum_probs=49.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||||||+++++++|+.+|++||.|..+.++.++.+|+++|||||+|.
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~   55 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFE   55 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECS
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEEC
Confidence            35568999999999999999999999999999999998889999999999995

>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=99.37  E-value=2e-10  Score=107.53  Aligned_cols=267  Identities=13%  Similarity=0.092  Sum_probs=151.7

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      +|...|+.+|...|.    +...|...+......|+++.+..+|+++|..+|.+...|...+..+... +..+.+...|.
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            567889999988875    7788999999888999999999999999999999999999998877654 45577888999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccC---------------------------------CHHHHHHHHHHHHhCChhhHHH
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRA---------------------------------SEEEISTVFEKSLLCAFSTFEE  129 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~---------------------------------~~~~~~~i~~~al~~~~~~~~~  129 (442)
                      +++...|.....+............                                 ........+.+.+...+.....
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  171 (388)
T d1w3ba_          92 HALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQPNFAVA  171 (388)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHCTTCHHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhhhhHHHHHHhhccCcchhHH
Confidence            9888887766555444432221111                                 1111222233333222221111


Q ss_pred             HHHHHHH---------HHHHHHHHh-hccCccchhhhH---HHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcC
Q 013489          130 YLDLFLT---------RIDGLRRRI-LFSGEVEGVLDY---SLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMG  196 (442)
Q Consensus       130 ~~~~~~~---------~~~~l~rr~-~~~~~~~~~~~~---~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~  196 (442)
                      +..+-..         ....+.+-+ ..+...+.+...   ......+++|+..+.......+.....+...+.+....|
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            1110000         000010000 000110000000   000111234444444333323333445666666666666


Q ss_pred             CCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHH
Q 013489          197 KDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHS  276 (442)
Q Consensus       197 ~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~  276 (442)
                       +++.|..+|+++++.+|++..+|...+.+....|++..|..+|+.++..  .+..+ .++..........|+.+.-...
T Consensus       252 -~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~-~~~~~l~~~~~~~~~~~~A~~~  327 (388)
T d1w3ba_         252 -LIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRL--CPTHA-DSLNNLANIKREQGNIEEAVRL  327 (388)
T ss_dssp             -CHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH--CTTCH-HHHHHHHHHHHTTTCHHHHHHH
T ss_pred             -CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhcc--CCccc-hhhhHHHHHHHHCCCHHHHHHH
Confidence             7777777777777777777777777777777777777777777777752  22222 3444444444455555443333


Q ss_pred             HH
Q 013489          277 VQ  278 (442)
Q Consensus       277 ~~  278 (442)
                      ++
T Consensus       328 ~~  329 (388)
T d1w3ba_         328 YR  329 (388)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

>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=99.35  E-value=3.1e-13  Score=98.34  Aligned_cols=51  Identities=24%  Similarity=0.214  Sum_probs=41.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .|||||+|||+++++++|+++|++||.|..+.++.+..+|+++|||||+|.
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~   51 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVT   51 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECS
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEEC
Confidence            379999999999999999999999999998888888789999999999995

>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=99.33  E-value=1.7e-12  Score=98.45  Aligned_cols=52  Identities=31%  Similarity=0.412  Sum_probs=48.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||||||+++++++|+.+|++||.|..++++.+ .+|+++|||||+|.
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~   67 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARME   67 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeC
Confidence            44579999999999999999999999999999999998 68999999999995

>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=99.33  E-value=8.4e-13  Score=93.63  Aligned_cols=48  Identities=19%  Similarity=0.243  Sum_probs=46.6

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          394 AFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       394 v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      |||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~   48 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFD   48 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEES
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEEC
Confidence            799999999999999999999999999999999999999999999996

>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=99.32  E-value=7.1e-13  Score=95.47  Aligned_cols=48  Identities=17%  Similarity=0.349  Sum_probs=46.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +|||+|||+++++++|+++|++||.|.+++|+.+ .+|+++|||||+|.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~-~~g~~~g~afV~f~   49 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFE   49 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCS-SCCCSCCEEEEEES
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEe-eccccceeEEEEEC
Confidence            6999999999999999999999999999999999 59999999999996

>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=99.31  E-value=7.1e-13  Score=96.87  Aligned_cols=48  Identities=23%  Similarity=0.277  Sum_probs=45.1

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEE-EEeeCCCCCCCcceEEEEee
Q 013489          394 AFLSNINLKATYEDLRRFFSDVGGVSSI-RILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       394 v~v~nl~~~~~~~~l~~~f~~~G~i~~~-~~~~~~~~g~~~g~~fv~f~  441 (442)
                      |||||||+++++++|+++|++||.|.++ +++.++.+|+++|||||+|.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~   49 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFA   49 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBS
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEEC
Confidence            7999999999999999999999999764 78999899999999999995

>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=99.31  E-value=1.4e-12  Score=96.70  Aligned_cols=51  Identities=14%  Similarity=0.191  Sum_probs=45.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||||||.++++++|+++|++||.|.+|+++.++.++  +|||||+|.
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~   56 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFY   56 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEEC
Confidence            345699999999999999999999999999999999986554  799999995

>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=99.30  E-value=9.5e-13  Score=94.22  Aligned_cols=49  Identities=22%  Similarity=0.457  Sum_probs=47.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +|||||||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~   49 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFE   49 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECS
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEEC
Confidence            4899999999999999999999999999999999889999999999995

>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=99.29  E-value=7.7e-13  Score=97.26  Aligned_cols=52  Identities=15%  Similarity=0.200  Sum_probs=43.5

Q ss_pred             CCceEEEcCCCCCCC-HHHHHHHhccCCCeeEEEEeeC-CCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKAT-YEDLRRFFSDVGGVSSIRILHD-KFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~-~~~l~~~f~~~G~i~~~~~~~~-~~~g~~~g~~fv~f~  441 (442)
                      +.++|||+|||++++ +++|+++|++||.|.+|+|+.+ +.+|+++|||||+|.
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~   56 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFE   56 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEES
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEEC
Confidence            467999999999976 5679999999999999998764 568999999999995

>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=99.29  E-value=4.3e-12  Score=94.64  Aligned_cols=51  Identities=20%  Similarity=0.324  Sum_probs=45.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+++|+.||.|.+|+++.++  +.++|||||+|.
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~   59 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFE   59 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEEC
Confidence            345689999999999999999999999999999999984  347999999995

>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=99.27  E-value=1.4e-12  Score=95.73  Aligned_cols=48  Identities=31%  Similarity=0.367  Sum_probs=44.4

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCC---CCcceEEEEee
Q 013489          394 AFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTG---KSRVVQSDIYT  441 (442)
Q Consensus       394 v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g---~~~g~~fv~f~  441 (442)
                      |||||||+++++++|+.+|++||.|.+|.|+.++.++   +++|||||+|.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~   51 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYK   51 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEES
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEEC
Confidence            7999999999999999999999999999999987665   47999999995

>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=99.26  E-value=4e-12  Score=96.63  Aligned_cols=54  Identities=31%  Similarity=0.436  Sum_probs=47.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCee--------EEEEeeCCCCCCCcceEEEEee
Q 013489          388 FTDECTAFLSNINLKATYEDLRRFFSDVGGVS--------SIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       388 ~~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~--------~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +.+..+|||||||+.+++++|+++|..||.|.        .+.+..++.+|+++|||||+|.
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~   66 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE   66 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBS
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEec
Confidence            34567999999999999999999999999874        5677888889999999999995

>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=99.26  E-value=2.4e-12  Score=96.78  Aligned_cols=51  Identities=18%  Similarity=0.187  Sum_probs=46.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCC-eeEEEEeeCC-CCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGG-VSSIRILHDK-FTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~-i~~~~~~~~~-~~g~~~g~~fv~f~  441 (442)
                      +|+|||||||.++++++|+.+|+.||. |.++.++.++ .+|+++|||||+|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~   53 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYE   53 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEES
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEc
Confidence            478999999999999999999999995 8999999885 46899999999995

>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=99.25  E-value=7.5e-12  Score=95.56  Aligned_cols=50  Identities=22%  Similarity=0.403  Sum_probs=45.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCC-CCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDK-FTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~-~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||+++++++|+++|+.|| |.+++++.++ .+|+++|||||+|.
T Consensus        15 ~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~   65 (104)
T d1wi8a_          15 PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFE   65 (104)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEES
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEEC
Confidence            47999999999999999999999999 7788887764 47899999999996

>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=99.24  E-value=5.8e-13  Score=98.93  Aligned_cols=51  Identities=16%  Similarity=0.230  Sum_probs=47.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+++++++|+.+|+.||.|.+++|+.+ .+|+++|||||+|.
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~   62 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFE   62 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEES
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeC
Confidence            4569999999999999999999999999999998776 69999999999995

>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=99.24  E-value=5.7e-12  Score=93.18  Aligned_cols=48  Identities=19%  Similarity=0.272  Sum_probs=44.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+|||+|||+++++++|+++|++||.|.+++|+.++  +.++|||||+|.
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~   56 (89)
T d1cvja2           9 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFE   56 (89)
T ss_dssp             TEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEES
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEEC
Confidence            489999999999999999999999999999999984  447899999996

>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=99.23  E-value=7.3e-12  Score=97.37  Aligned_cols=48  Identities=23%  Similarity=0.385  Sum_probs=43.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +++|||||||+.+++++|+++|+.||.|.+|+++.   +|+++|||||+|.
T Consensus         7 ~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~   54 (114)
T d2f9da1           7 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYE   54 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEES
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEEC
Confidence            46999999999999999999999999999999875   4567999999996

>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=99.22  E-value=5e-12  Score=97.79  Aligned_cols=53  Identities=13%  Similarity=0.134  Sum_probs=46.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+++|+++|+++|+.||.+..+.++.+..+|+++|||||+|.
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~   68 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFR   68 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBS
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEEC
Confidence            35669999999999999999999999999877655555579999999999995

>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=99.22  E-value=1.7e-11  Score=93.41  Aligned_cols=52  Identities=19%  Similarity=0.228  Sum_probs=46.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +..+|||+|||+++++++|+++|..+|.|..+.++.+..+|+++|||||+|.
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~   65 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFA   65 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEES
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeC
Confidence            3448999999999999999999999999988666666689999999999996

>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=99.20  E-value=8.7e-12  Score=88.75  Aligned_cols=48  Identities=8%  Similarity=0.169  Sum_probs=43.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+|||+|||+++++++|+++|++||.|.+|+++.++.+  .+|||||+|.
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~--~~~~afV~F~   48 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFA   48 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEES
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEc
Confidence            38999999999999999999999999999999998533  4589999996

>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=99.16  E-value=1.4e-11  Score=90.78  Aligned_cols=47  Identities=23%  Similarity=0.328  Sum_probs=42.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||||||+++++++|+++|++||.|.+|+++.     .++|||||+|.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~   50 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFA   50 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEEC
Confidence            456999999999999999999999999999997654     46899999995

>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=99.15  E-value=4.5e-12  Score=96.49  Aligned_cols=52  Identities=19%  Similarity=0.218  Sum_probs=48.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||.++++++|+.+|+.||.|..+.++.+..+|+++|||||+|.
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~   68 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFP   68 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEec
Confidence            3569999999999999999999999999999999988789999999999995

>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=99.15  E-value=9.4e-12  Score=91.85  Aligned_cols=51  Identities=12%  Similarity=0.225  Sum_probs=45.3

Q ss_pred             CceEEEcCCCCCCCHHHH---HHHhccCCCeeEEEEeeCCCCCCC---cceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDL---RRFFSDVGGVSSIRILHDKFTGKS---RVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l---~~~f~~~G~i~~~~~~~~~~~g~~---~g~~fv~f~  441 (442)
                      ..+|||+|||+++++++|   .++|++||.|.+|.++.++.++.+   +|||||+|.
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~   64 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYI   64 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEES
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecc
Confidence            458999999999999999   678999999999999999777654   499999996

>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=99.15  E-value=1.7e-11  Score=93.28  Aligned_cols=51  Identities=14%  Similarity=0.100  Sum_probs=44.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..+|||+|||+++++++|+.+|+.||.|..+.++.+..+|+++|||||+|.
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~   58 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFK   58 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECS
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEEC
Confidence            458999999999999999999999999876444444479999999999996

>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=99.15  E-value=3.3e-11  Score=91.39  Aligned_cols=51  Identities=18%  Similarity=0.219  Sum_probs=45.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....+|||+|||+++|+++|+++|..|| +..|.++.+ .+|+++|||||+|.
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~-~~g~~~G~afVeF~   63 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIG-PDGRVTGEADVEFA   63 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEES-SSSCEEEEEEEECS
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEe-cCCcceEEEEEEEC
Confidence            3456999999999999999999999998 558888888 57999999999995

>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=99.14  E-value=8.5e-09  Score=94.80  Aligned_cols=204  Identities=9%  Similarity=0.043  Sum_probs=148.3

Q ss_pred             ChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHH
Q 013489           19 DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRS   98 (442)
Q Consensus        19 ~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y   98 (442)
                      +|+-.+++..+.....+.+..++|..+|++||..+|.+...|..-...+...+++.+.+...|++++...|.+..+|...
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            34545566656565667788999999999999999999999998888777655666789999999999999999999998


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCc
Q 013489           99 LLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNT  178 (442)
Q Consensus        99 ~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~  178 (442)
                      ...+.. .+..+++...|.+++...+.....+..+-..+     .++                ..++.|+.++..++...
T Consensus       119 ~~~~~~-l~~~~eAl~~~~kal~~dp~n~~a~~~~~~~~-----~~~----------------~~~~~Al~~~~~al~~~  176 (315)
T d2h6fa1         119 RVLVEW-LRDPSQELEFIADILNQDAKNYHAWQHRQWVI-----QEF----------------KLWDNELQYVDQLLKED  176 (315)
T ss_dssp             HHHHHH-HTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHH-----HHH----------------TCCTTHHHHHHHHHHHC
T ss_pred             hHHHHh-hccHHHHHHHHhhhhhhhhcchHHHHHHHHHH-----HHH----------------HhhHHHHHHHHHHHHHC
Confidence            765554 67788899999999988777554433222111     011                11233444444444435


Q ss_pred             hhhHHHHHHHHHHHHHcCC-----CHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          179 DGLLRLYAYWAHLEQSMGK-----DMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       179 ~~~~~l~~~~a~~e~~~~~-----~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      +.....|...+.+....++     ..+.|...+.+++..+|++..+|.....+.... ....+..++++++.
T Consensus       177 p~n~~a~~~r~~~l~~~~~~~~~~~~~~ai~~~~~al~~~P~~~~~~~~l~~ll~~~-~~~~~~~~~~~~~~  247 (315)
T d2h6fa1         177 VRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQDR-GLSKYPNLLNQLLD  247 (315)
T ss_dssp             TTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTTT-CGGGCHHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHccccchhhhhHHhHHHHHHHHHhCCCchHHHHHHHHHHHhc-ChHHHHHHHHHHHH
Confidence            5556677776666555542     257899999999999999999998877765443 45677788888876

>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=99.12  E-value=6e-11  Score=86.26  Aligned_cols=46  Identities=17%  Similarity=0.278  Sum_probs=42.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +++|||+|||.++++++|..+|+.||.|.+|+++.+     .+|||||+|.
T Consensus         8 ~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~   53 (83)
T d2b0ga1           8 NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFT   53 (83)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEES
T ss_pred             CCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecC
Confidence            459999999999999999999999999999999865     3789999995

>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=99.12  E-value=2.2e-11  Score=89.40  Aligned_cols=50  Identities=8%  Similarity=0.095  Sum_probs=44.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEE-EEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSI-RILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~-~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||+++++++|+++|+.||.|... .+..+ .+|+++|||||+|.
T Consensus         9 ~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~-~~g~~~G~afV~f~   59 (86)
T d2cqpa1           9 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFE   59 (86)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC-SSSCEEEEEEEEES
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeC-CCCCcceEEEEEEc
Confidence            4589999999999999999999999998764 55555 79999999999996

>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=99.11  E-value=1.2e-08  Score=90.25  Aligned_cols=217  Identities=11%  Similarity=0.043  Sum_probs=140.2

Q ss_pred             HHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHH
Q 013489            7 HLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATK   86 (442)
Q Consensus         7 ~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~   86 (442)
                      .++..|.+.+..+++...+|..........|+++.|...|+++|..+|.++..|...+..+.. .++.+.+...|++|+.
T Consensus        21 ~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~~~~a~~~lg~~~~~-~g~~~~A~~~~~~al~   99 (259)
T d1xnfa_          21 RMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQ-AGNFDAAYEAFDSVLE   99 (259)
T ss_dssp             HHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccCCCCHHHHhhhchHHHH-HHHHHHhhhhhhHHHH
Confidence            456666665544555667887778878889999999999999999999999999988876654 4566789999999999


Q ss_pred             cCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHH
Q 013489           87 NCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQR  166 (442)
Q Consensus        87 ~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~  166 (442)
                      ..|.....|......+. ..+..+.+...|++++...+......+.+.....     +.          +.......+..
T Consensus       100 ~~p~~~~a~~~lg~~~~-~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~-----~~----------~~~~~~~~~~~  163 (259)
T d1xnfa_         100 LDPTYNYAHLNRGIALY-YGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQ-----KL----------DEKQAKEVLKQ  163 (259)
T ss_dssp             HCTTCTHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-----HH----------CHHHHHHHHHH
T ss_pred             HHhhhhhhHHHHHHHHH-HHhhHHHHHHHHHHHHhhccccHHHHHHHHHHHH-----Hh----------hhHHHHHHHHH
Confidence            99999999988776444 4688899999999999876653322221111110     10          00000011111


Q ss_pred             HHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          167 ASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       167 a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ...   . ....+....+...+.......+ ....+...+...+...|+....|...+.+....|+++.|...|++|+.
T Consensus       164 ~~~---~-~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  237 (259)
T d1xnfa_         164 HFE---K-SDKEQWGWNIVEFYLGNISEQT-LMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVA  237 (259)
T ss_dssp             HHH---H-SCCCSTHHHHHHHHTTSSCHHH-HHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             Hhh---c-cchhhhhhhHHHHHHHHHHHHH-HHHHHHHHHHHhhhcCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            111   1 1111111111111100000011 234445555555555677778888888888889999999999999997

>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=99.08  E-value=1.2e-10  Score=87.06  Aligned_cols=50  Identities=12%  Similarity=0.305  Sum_probs=44.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +++++|||+|||+++++++|+++|++||.|..+.+..+   +.++|||||+|.
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~   61 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFE   61 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEEC
Confidence            45679999999999999999999999999999887554   457899999995

>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=99.08  E-value=1e-10  Score=85.50  Aligned_cols=46  Identities=20%  Similarity=0.292  Sum_probs=42.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||.++++++|+.+|++||.|.+|+++.+      +|||||+|.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~   52 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLE   52 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEEC
Confidence            4568999999999999999999999999999998865      589999995

>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=99.07  E-value=6.4e-11  Score=88.55  Aligned_cols=45  Identities=22%  Similarity=0.382  Sum_probs=42.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||||||..+++++|+.+|++||.|.+|+++.+      +|||||+|.
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~   62 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFS   62 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEES
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEEC
Confidence            468999999999999999999999999999999876      699999995

>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=99.05  E-value=5.9e-11  Score=91.67  Aligned_cols=46  Identities=9%  Similarity=0.192  Sum_probs=41.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||+.+++++|+.+|+.||.|..|.|.      +++|||||+|.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~   54 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFL   54 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEc
Confidence            45699999999999999999999999999999874      35799999996

>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=99.03  E-value=7.5e-11  Score=88.31  Aligned_cols=48  Identities=19%  Similarity=0.282  Sum_probs=42.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+.++|||||||+++++++|+++|++||.|..++     .+|+++|||||+|.
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~   61 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFK   61 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeC
Confidence            3457999999999999999999999999876653     47889999999995

>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=99.01  E-value=1.3e-10  Score=89.14  Aligned_cols=47  Identities=19%  Similarity=0.235  Sum_probs=43.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..+|||+|||+.+|+++|+++|++||.|.+|.++.++    ++|||||+|.
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~   53 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYA   53 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEES
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEEC
Confidence            4589999999999999999999999999999998763    5799999996

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.99  E-value=8.2e-11  Score=87.16  Aligned_cols=48  Identities=25%  Similarity=0.364  Sum_probs=41.7

Q ss_pred             CceEEEcCCCCCCCHHHHH----HHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLR----RFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~----~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +++|||||||+.+++++|+    .+|++||.|.+|++..   +|+++|||||+|.
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~   54 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFK   54 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEES
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEEC
Confidence            4699999999999999886    4689999999988743   6778999999995

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.99  E-value=1.2e-10  Score=85.51  Aligned_cols=42  Identities=14%  Similarity=0.294  Sum_probs=39.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +|||||||+++++++|+++|++||.|.+++++.+       |||||+|.
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~   43 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFV   43 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEES
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeC
Confidence            6999999999999999999999999999998764       89999995

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.99  E-value=6.3e-10  Score=83.30  Aligned_cols=46  Identities=13%  Similarity=0.270  Sum_probs=41.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+++|+.||.|.++.+..       +|||||+|.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~   58 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYL   58 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEEC
Confidence            3456899999999999999999999999999998864       489999996

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.99  E-value=4.6e-10  Score=82.42  Aligned_cols=45  Identities=11%  Similarity=0.035  Sum_probs=41.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||||||+.+++++|+++|++||.|.+++++.+      +|||||+|.
T Consensus         8 s~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~   52 (88)
T d2cq1a1           8 SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELA   52 (88)
T ss_dssp             CSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEES
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeC
Confidence            459999999999999999999999999999988765      589999995

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.97  E-value=2.3e-10  Score=87.88  Aligned_cols=46  Identities=24%  Similarity=0.314  Sum_probs=41.5

Q ss_pred             CceEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINL-KATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +++|||+|||+ .+++++|+.+|+.||.|.+|.|+.++     +|||||+|.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~   48 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMA   48 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEES
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEEC
Confidence            46999999965 58999999999999999999999873     799999996

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.97  E-value=3.3e-10  Score=84.86  Aligned_cols=45  Identities=20%  Similarity=0.339  Sum_probs=39.2

Q ss_pred             CCCceEEEcCCC-CCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNIN-LKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~-~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+||| ..+++.+|+.+|++||.|.+|+|        +||||||+|.
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~   58 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYV   58 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEES
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEEC
Confidence            344689999997 57889999999999999999988        3699999995

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.97  E-value=4.2e-10  Score=84.52  Aligned_cols=46  Identities=9%  Similarity=-0.004  Sum_probs=41.2

Q ss_pred             CCceEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLK-ATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .+++|||+|||.+ +|+++|..+|++||.|.+++++.+      +|||||+|.
T Consensus        17 ~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~   63 (99)
T d1x4fa1          17 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEME   63 (99)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECS
T ss_pred             CCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEec
Confidence            4569999999985 899999999999999999998865      589999995

>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=98.96  E-value=4.7e-10  Score=94.78  Aligned_cols=53  Identities=23%  Similarity=0.359  Sum_probs=49.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|||+|||+.+++++|+.+|+.||.|..+.++.++.+|+++|||||+|.
T Consensus        95 ~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~  147 (183)
T d1u1qa_          95 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD  147 (183)
T ss_dssp             CCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             cccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEEC
Confidence            34569999999999999999999999999999999999889999999999996

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.96  E-value=5e-10  Score=82.28  Aligned_cols=47  Identities=32%  Similarity=0.299  Sum_probs=41.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||||||+++++++|+++|+.||.|.++.+..+    +++|||||+|.
T Consensus        10 s~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~   56 (88)
T d2adca2          10 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMG   56 (88)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEES
T ss_pred             CCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEEC
Confidence            359999999999999999999999999988876543    45799999996

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.95  E-value=3.6e-11  Score=88.96  Aligned_cols=50  Identities=12%  Similarity=0.111  Sum_probs=43.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEe-----eCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRIL-----HDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~-----~~~~~g~~~g~~fv~f~  441 (442)
                      ++|||||||+++++++|+++|++||.|..+.++     .+..+++++|||||+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~   56 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFR   56 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEES
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeC
Confidence            589999999999999999999999988776654     34468899999999995

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.94  E-value=4.9e-10  Score=81.90  Aligned_cols=44  Identities=16%  Similarity=0.180  Sum_probs=39.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ++|||||||+++++++|+.+|++||.|..+.+.      +++|||||+|.
T Consensus         9 k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~   52 (86)
T d2cpda1           9 KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFS   52 (86)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEES
T ss_pred             CEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeC
Confidence            589999999999999999999999998877653      46799999995

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.93  E-value=1.4e-09  Score=82.55  Aligned_cols=46  Identities=7%  Similarity=0.029  Sum_probs=41.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...+|||+|||..+++++|..+|++||.|..+++.++      +|+|||+|.
T Consensus        14 ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~   59 (104)
T d1wexa_          14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFE   59 (104)
T ss_dssp             CCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeC
Confidence            3459999999999999999999999999999988754      689999995

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.93  E-value=1.3e-09  Score=81.48  Aligned_cols=45  Identities=13%  Similarity=0.248  Sum_probs=41.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|||+|||+++++++|+++|++||.|..++++++      +|||||+|.
T Consensus        17 s~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~   61 (97)
T d1whya_          17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYE   61 (97)
T ss_dssp             CSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEES
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccC
Confidence            469999999999999999999999999999998764      689999996

>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=98.92  E-value=1.9e-07  Score=86.06  Aligned_cols=233  Identities=8%  Similarity=-0.060  Sum_probs=152.4

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhc----------CChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc-
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS----------GDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL-   71 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~----------g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~-   71 (442)
                      ++...|+.+|..+|.    +..+|..-.......          |....+..+|+.+|..+|.++.+|......+.... 
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            567889999988876    777785433332222          23567889999999999999999998887665433 


Q ss_pred             chhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhcc-Cc
Q 013489           72 KVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFS-GE  150 (442)
Q Consensus        72 ~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~-~~  150 (442)
                      .+.+.+...+++++...|.....|...+.......+..+.+...+++++...+.....+..+...+.     +.... ..
T Consensus       123 ~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p~~~~a~~~l~~~~~-----~~~~~~~A  197 (334)
T d1dcea1         123 PNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLP-----QLHPQPDS  197 (334)
T ss_dssp             CCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHH-----HHSCCCCS
T ss_pred             ccHHHHHHHHHHHHhhCchhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCCCCHHHHHHHHHHHH-----HhcCHHHH
Confidence            2356788999999999999888887666556666788888999999999988876554433222111     11110 00


Q ss_pred             c---chhhh-----HHHHHHHH-----HHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHH
Q 013489          151 V---EGVLD-----YSLIRETF-----QRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAML  217 (442)
Q Consensus       151 ~---~~~~~-----~~~~r~~~-----~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~  217 (442)
                      .   ....+     ...+...+     +.+.......+...+.....+...+......+ +...|...+.+++..+|+..
T Consensus       198 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~a~~~~~~~l~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~p~~~  276 (334)
T d1dcea1         198 GPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEPLFRCELSVEKSTVLQ-SELESCKELQELEPENKWCL  276 (334)
T ss_dssp             SSCCSSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCCCCSSSCCCCHHHHHHHH-HHHHHHHHHHHHCTTCHHHH
T ss_pred             HHHHHHhHHhHHHHHHHHHHHHHhcchhHHHHHHHHHHHhCcchhhHHHHHHHHHHHHh-hHHHHHHHHHHHHhhCchHH
Confidence            0   00000     00000000     11222222222222221212222333334455 78889999999999999999


Q ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          218 EAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       218 ~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      .+|...+......|+++.|...|++|+.
T Consensus       277 ~~~~~l~~~~~~~~~~~eA~~~~~~ai~  304 (334)
T d1dcea1         277 LTIILLMRALDPLLYEKETLQYFSTLKA  304 (334)
T ss_dssp             HHHHHHHHHHCTGGGHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            9999999999999999999999999997

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.89  E-value=1.4e-09  Score=83.78  Aligned_cols=45  Identities=18%  Similarity=0.254  Sum_probs=41.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      -..+||||||+.+|+++|+.+|++||+|.+|+|+.+      +|||||.|.
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~   55 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFK   55 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEES
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEec
Confidence            347899999999999999999999999999999864      699999995

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.89  E-value=2.5e-10  Score=82.13  Aligned_cols=43  Identities=21%  Similarity=0.232  Sum_probs=38.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +|||||||+++++++|+++|++||.|.+++++.      ++|||||+|.
T Consensus         3 ~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~   45 (80)
T d2cqha1           3 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYP   45 (80)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCS
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEEC
Confidence            799999999999999999999999988766654      4799999995

>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=98.88  E-value=9.2e-08  Score=84.41  Aligned_cols=197  Identities=11%  Similarity=0.047  Sum_probs=127.3

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      +|...|+.+|.-.|.    +..+|...+......|+++.++..|+++|..+|.+...|...+..+... +..+.+...|+
T Consensus        55 ~A~~~~~~al~l~p~----~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~-g~~~~A~~~~~  129 (259)
T d1xnfa_          55 LARNDFSQALAIRPD----MPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYYG-GRDKLAQDDLL  129 (259)
T ss_dssp             HHHHHHHHHHHHCCC----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHT-TCHHHHHHHHH
T ss_pred             HHHHHHHHhhccCCC----CHHHHhhhchHHHHHHHHHHhhhhhhHHHHHHhhhhhhHHHHHHHHHHH-hhHHHHHHHHH
Confidence            567889999988876    7889999999899999999999999999999999999999998776644 45677999999


Q ss_pred             HHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHH-HHHHHHHHHHHHHHHHhhccCccchhhhHHHHH
Q 013489           83 RATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFE-EYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIR  161 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~-~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r  161 (442)
                      ++++..|.....+..... .....+.......+...........+. ..+..+.           ...  .       ..
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            999999987654333222 222223333333444443333322111 1111110           000  0       01


Q ss_pred             HHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHH
Q 013489          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISME  227 (442)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e  227 (442)
                      ..+..+...+.......+.....|...+.++...| +++.|...|++++..+|++. ++-.++.++
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            22333333222222112334457777888888888 99999999999999998764 233444444

>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=98.88  E-value=5.6e-08  Score=89.15  Aligned_cols=191  Identities=10%  Similarity=0.062  Sum_probs=138.8

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcC-ChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSG-DPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVY   81 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g-~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~   81 (442)
                      +|-..|+.+|..+|.    ++.+|..-.......| +.+.++..|+++|..+|.+..+|......+.. .+..+.+...|
T Consensus        61 ~Al~~~~~ai~lnP~----~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~~~~a~~~~~~~~~~-l~~~~eAl~~~  135 (315)
T d2h6fa1          61 RAFKLTRDAIELNAA----NYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVEW-LRDPSQELEFI  135 (315)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-HTCCTTHHHHH
T ss_pred             HHHHHHHHHHHHCCC----ChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHhhhhHHHHHhHHHHh-hccHHHHHHHH
Confidence            456778888888876    8899988887766655 68999999999999999999999999877664 45567799999


Q ss_pred             HHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHH
Q 013489           82 SRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIR  161 (442)
Q Consensus        82 erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r  161 (442)
                      .+|+...|.....|......+.. .+..+.+...|++++...+.....+..+....     .+....      .+    .
T Consensus       136 ~kal~~dp~n~~a~~~~~~~~~~-~~~~~~Al~~~~~al~~~p~n~~a~~~r~~~l-----~~~~~~------~~----~  199 (315)
T d2h6fa1         136 ADILNQDAKNYHAWQHRQWVIQE-FKLWDNELQYVDQLLKEDVRNNSVWNQRYFVI-----SNTTGY------ND----R  199 (315)
T ss_dssp             HHHHHHCTTCHHHHHHHHHHHHH-HTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHH-----HHTTCS------CS----H
T ss_pred             hhhhhhhhcchHHHHHHHHHHHH-HHhhHHHHHHHHHHHHHCCccHHHHHHHHHHH-----HHcccc------ch----h
Confidence            99999999999999998765544 67778899999999998777544433222111     111100      11    1


Q ss_pred             HHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH
Q 013489          162 ETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM  216 (442)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~  216 (442)
                      ..+++|+.++..++...|....+|.+...+....  ....+..+++.++...|+.
T Consensus       200 ~~~~~ai~~~~~al~~~P~~~~~~~~l~~ll~~~--~~~~~~~~~~~~~~l~~~~  252 (315)
T d2h6fa1         200 AVLEREVQYTLEMIKLVPHNESAWNYLKGILQDR--GLSKYPNLLNQLLDLQPSH  252 (315)
T ss_dssp             HHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTTT--CGGGCHHHHHHHHHHTTTC
T ss_pred             hhhHHhHHHHHHHHHhCCCchHHHHHHHHHHHhc--ChHHHHHHHHHHHHhCCCc
Confidence            3355566666555555566667887776664433  3678889999999886653

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.87  E-value=1.4e-09  Score=77.96  Aligned_cols=44  Identities=20%  Similarity=0.187  Sum_probs=38.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|+|  +|+++|+++|++||.|.+|++..+      +|||||+|.
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~   47 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYE   47 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECS
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEc
Confidence            34699999986  899999999999999999998754      689999995

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.78  E-value=4e-09  Score=74.53  Aligned_cols=41  Identities=10%  Similarity=0.064  Sum_probs=35.3

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          394 AFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       394 v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      |||||||+++++++|+++|++|| +..+.      +++++|||||+|.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~------~~~~~g~afv~f~   41 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCF------VDKYKGTAFVTLL   41 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEE------EETTTTEEEEEES
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-cccee------ecccceeEEEEEC
Confidence            79999999999999999999999 44443      3567899999995

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.76  E-value=1.4e-09  Score=79.59  Aligned_cols=44  Identities=5%  Similarity=0.123  Sum_probs=36.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          391 ECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..+|||+|||+++++++|+++|.+|| +..+.      +++++|||||+|.
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~------~~~~kg~afV~f~   48 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCY------VDRNKRTAFVTLL   48 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEE------EEGGGTEEEECCS
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeee------eeccCCceEEEEC
Confidence            45899999999999999999999999 33333      3456899999995

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.76  E-value=4.2e-09  Score=77.14  Aligned_cols=46  Identities=11%  Similarity=-0.003  Sum_probs=40.8

Q ss_pred             CCceEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLK-ATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ..++|||+|||.. +|+++|..+|++||.|.+|.++.+      +|+|||+|.
T Consensus         7 ~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~   53 (89)
T d1x4da1           7 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMA   53 (89)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEES
T ss_pred             CCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEc
Confidence            3459999999986 789999999999999999999876      479999995

>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=98.72  E-value=7.1e-07  Score=82.04  Aligned_cols=221  Identities=10%  Similarity=-0.002  Sum_probs=134.1

Q ss_pred             CChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcc---------hhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcc-
Q 013489           37 GDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLK---------VGNVVRDVYSRATKNCPWVGELWVRSLLSLERSR-  106 (442)
Q Consensus        37 g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~---------~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~-  106 (442)
                      ...+.+..+|+++|..+|.+..+|..-..++.....         ..+.+...|+++++..|.+..+|......+.... 
T Consensus        43 ~~~~~al~~~~~~l~~~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~pk~~~~~~~~~~~~~~~~~  122 (334)
T d1dcea1          43 ELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPE  122 (334)
T ss_dssp             CCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCSS
T ss_pred             cccHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhCCCcHHHHHHhhHHHHHhcc
Confidence            345799999999999999999999765555443221         2345888999999999999999998776554433 


Q ss_pred             CCHHHHHHHHHHHHhCChhhHHHHH-HHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhhHHHH
Q 013489          107 ASEEEISTVFEKSLLCAFSTFEEYL-DLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGLLRLY  185 (442)
Q Consensus       107 ~~~~~~~~i~~~al~~~~~~~~~~~-~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~  185 (442)
                      .+.+.+...+++++...+....... ..+..+.                     ....++.|+.++..++...+.....|
T Consensus       123 ~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~---------------------~~~~~~~Al~~~~~~i~~~p~~~~a~  181 (334)
T d1dcea1         123 PNWARELELCARFLEADERNFHCWDYRRFVAAQ---------------------AAVAPAEELAFTDSLITRNFSNYSSW  181 (334)
T ss_dssp             CCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH---------------------TCCCHHHHHHHHHTTTTTTCCCHHHH
T ss_pred             ccHHHHHHHHHHHHhhCchhhhhhhhHHHHHHH---------------------hccccHHHHHHHHHHHHcCCCCHHHH
Confidence            3467889999999987665433321 2221110                     01223445555555555555555666


Q ss_pred             HHHHHHHHHcCCCHHHH------------------------------HHHHHHHHHhchhHHHHHHHHHHHHHhcccHHH
Q 013489          186 AYWAHLEQSMGKDMVSA------------------------------RGVWERLLKISGAMLEAWQSYISMEIELDHINE  235 (442)
Q Consensus       186 ~~~a~~e~~~~~~~~~a------------------------------r~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~  235 (442)
                      ...+.+....| +++.|                              ...|.+++...|.....|...+......|+...
T Consensus       182 ~~l~~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~a~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~  260 (334)
T d1dcea1         182 HYRSCLLPQLH-PQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEPLFRCELSVEKSTVLQSELE  260 (334)
T ss_dssp             HHHHHHHHHHS-CCCCSSSCCSSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCCCCSSSCCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhc-CHHHHHHHHHHhHHhHHHHHHHHHHHHHhcchhHHHHHHHHHHHhCcchhhHHHHHHHHHHHHhhHHH
Confidence            66666665555 43333                              333333333333333222223333344567788


Q ss_pred             HHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCCHhhHHHHHHhhchhHH
Q 013489          236 ARSIYKRCYSKRFTGTGSEDICHAWLRFEREYGTLEDFDHSVQKVTPRLE  285 (442)
Q Consensus       236 ar~i~~ral~~~~~~~~~~~i~~~~~~fE~~~G~~~~~~~~~~~~~~~~~  285 (442)
                      |...|..++..     .| .....|...-..+-..+.+++|++-+...+.
T Consensus       261 a~~~~~~~~~~-----~p-~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~  304 (334)
T d1dcea1         261 SCKELQELEPE-----NK-WCLLTIILLMRALDPLLYEKETLQYFSTLKA  304 (334)
T ss_dssp             HHHHHHHHCTT-----CH-HHHHHHHHHHHHHCTGGGHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhh-----Cc-hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            88888888752     23 3345666666666666666666665554444

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.66  E-value=9e-09  Score=77.20  Aligned_cols=44  Identities=9%  Similarity=0.125  Sum_probs=39.0

Q ss_pred             ceEEE--cCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          392 CTAFL--SNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v--~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++||  ||||+++|+++|+.+|++||.|.+|+++.+      +|||||+|.
T Consensus        19 ~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~   64 (101)
T d2cq2a1          19 QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYR   64 (101)
T ss_dssp             SEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEES
T ss_pred             ceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEEC
Confidence            47788  559999999999999999999999988765      589999995

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.45  E-value=6.1e-09  Score=78.58  Aligned_cols=48  Identities=6%  Similarity=-0.054  Sum_probs=45.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          393 TAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       393 ~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      .++|++++..+++++|+++|++||.|.+|+|+.+ .+|+++|||||+|.
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~   76 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFR   76 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEES
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEe
Confidence            6889999999999999999999999999999988 69999999999995

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.44  E-value=6.8e-08  Score=68.86  Aligned_cols=45  Identities=11%  Similarity=0.009  Sum_probs=37.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          390 DECTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       390 ~~~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      +.+.|+|+++|++.+++.| .+|++||.|.++++..      ++|||||+|.
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~   47 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQ   47 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEES
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEc
Confidence            3568999999999887655 5799999999997643      4699999996

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.44  E-value=5.3e-08  Score=73.24  Aligned_cols=47  Identities=6%  Similarity=0.025  Sum_probs=39.2

Q ss_pred             CCCceEEEcCCCCCC-CH----HHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNINLKA-TY----EDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl~~~~-~~----~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ....+|||+||+.++ ++    ++|+.+|+.||.|.+++++.      ++|||||+|.
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~   54 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFS   54 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECS
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEEC
Confidence            345699999999986 33    56999999999999998874      4789999995

>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=98.36  E-value=8.5e-06  Score=62.33  Aligned_cols=100  Identities=17%  Similarity=0.044  Sum_probs=83.9

Q ss_pred             HHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcc
Q 013489           27 MIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLERSR  106 (442)
Q Consensus        27 ~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~~  106 (442)
                      ..=+......|+++.|..+|+++|..+|.++.+|...+..+... ++.+.+...|.+|+...|.....|......+.. .
T Consensus         7 ~~~g~~~~~~g~~~eAi~~~~~al~~~p~~~~~~~~~a~~~~~~-~~~~~A~~~~~~al~~~p~~~~~~~~~g~~~~~-~   84 (117)
T d1elwa_           7 KEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKK-GDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEF-L   84 (117)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-T
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhcCCcchhhhhccccccccc-ccccccchhhhhHHHhccchhhHHHHHHHHHHH-c
Confidence            33444456789999999999999999999999999999877654 566789999999999999999999988775554 7


Q ss_pred             CCHHHHHHHHHHHHhCChhhHH
Q 013489          107 ASEEEISTVFEKSLLCAFSTFE  128 (442)
Q Consensus       107 ~~~~~~~~i~~~al~~~~~~~~  128 (442)
                      +..+.+...|++++...|....
T Consensus        85 ~~~~~A~~~~~~a~~~~p~~~~  106 (117)
T d1elwa_          85 NRFEEAKRTYEEGLKHEANNPQ  106 (117)
T ss_dssp             TCHHHHHHHHHHHHTTCTTCHH
T ss_pred             cCHHHHHHHHHHHHHhCCCCHH
Confidence            8899999999999988776533

>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=98.21  E-value=8.4e-06  Score=62.36  Aligned_cols=93  Identities=13%  Similarity=-0.054  Sum_probs=82.1

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      +|-..|..+|..+|.    +...|...+......|+++.+...|+++|..+|.++..|...+..+. ..+..+.+...|+
T Consensus        21 eAi~~~~~al~~~p~----~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~g~~~~-~~~~~~~A~~~~~   95 (117)
T d1elwa_          21 DALQCYSEAIKLDPH----NHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALE-FLNRFEEAKRTYE   95 (117)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-HTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCc----chhhhhcccccccccccccccchhhhhHHHhccchhhHHHHHHHHHH-HccCHHHHHHHHH
Confidence            455689999988876    78899999999999999999999999999999999999999998666 4456788999999


Q ss_pred             HHHHcCCCcHHHHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLL  100 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~  100 (442)
                      +|+...|.+..+|..+..
T Consensus        96 ~a~~~~p~~~~~~~~l~~  113 (117)
T d1elwa_          96 EGLKHEANNPQLKEGLQN  113 (117)
T ss_dssp             HHHTTCTTCHHHHHHHHH
T ss_pred             HHHHhCCCCHHHHHHHHH
Confidence            999999999999988655

>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=98.20  E-value=0.00026  Score=63.63  Aligned_cols=63  Identities=16%  Similarity=0.105  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchh----HHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA----MLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~----~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ..++...+.+....+ +++.|...+++++...+.    ....|...+......|+++.|..+|++++.
T Consensus       213 ~~~~~~~~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  279 (366)
T d1hz4a_         213 SNANKVRVIYWQMTG-DKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNE  279 (366)
T ss_dssp             HHHHHHHHHHHHHTT-CHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcc-cHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            345555566666666 788888888777766332    233455556666677788888888887764

>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=98.20  E-value=4.7e-05  Score=61.37  Aligned_cols=102  Identities=11%  Similarity=-0.082  Sum_probs=85.8

Q ss_pred             HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHH
Q 013489           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER  104 (442)
Q Consensus        25 ~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~  104 (442)
                      ....-+....+.|+++.|...|+++|..+|.+...|..++..+... +..+.+...|++|+...|.....|..++..+..
T Consensus        12 ~l~~~gn~~~~~~~y~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~-~~~~~A~~~~~kal~~~p~~~~a~~~~g~~~~~   90 (159)
T d1a17a_          12 ELKTQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRT-ECYGYALGDATRAIELDKKYIKGYYRRAASNMA   90 (159)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHhhhccccchhhhhhhhhhHHHHHhc-cccchHHHHHHHHHHHcccchHHHHHHHHHHHH
Confidence            3444555556789999999999999999999999999999877654 567889999999999999999999998875554


Q ss_pred             ccCCHHHHHHHHHHHHhCChhhHH
Q 013489          105 SRASEEEISTVFEKSLLCAFSTFE  128 (442)
Q Consensus       105 ~~~~~~~~~~i~~~al~~~~~~~~  128 (442)
                       .++.+++...|++++...+....
T Consensus        91 -~g~~~eA~~~~~~a~~~~p~~~~  113 (159)
T d1a17a_          91 -LGKFRAALRDYETVVKVKPHDKD  113 (159)
T ss_dssp             -TTCHHHHHHHHHHHHHHSTTCHH
T ss_pred             -cCCHHHHHHHHHHHHHcCCCCHH
Confidence             78899999999999987766433

>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=98.11  E-value=1.6e-05  Score=60.22  Aligned_cols=94  Identities=10%  Similarity=-0.029  Sum_probs=78.5

Q ss_pred             HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHH
Q 013489           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER  104 (442)
Q Consensus        25 ~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~  104 (442)
                      .+..........|++..+...|+++|..+|.++..|...+..+.. .+..+.+...|++|++..|.....|......+. 
T Consensus        18 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~-~~~~~~A~~~~~~al~~~p~~~~a~~~la~~y~-   95 (112)
T d1hxia_          18 NPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAE-NEKDGLAIIALNHARMLDPKDIAVHAALAVSHT-   95 (112)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHhhhcccccccchhhhhhhhhhhh-hhhHHHhhcccccccccccccccchHHHHHHHH-
Confidence            345555556778999999999999999999999999999987764 456678999999999999999999999776444 


Q ss_pred             ccCCHHHHHHHHHHHH
Q 013489          105 SRASEEEISTVFEKSL  120 (442)
Q Consensus       105 ~~~~~~~~~~i~~~al  120 (442)
                      ..+..+++...|++.|
T Consensus        96 ~~g~~~~A~~~l~~~l  111 (112)
T d1hxia_          96 NEHNANAALASLRAWL  111 (112)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHh
Confidence            4677888888888865

>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=98.03  E-value=3.5e-05  Score=62.18  Aligned_cols=93  Identities=13%  Similarity=-0.146  Sum_probs=81.9

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      +|...|+.+|..+|.    +...|..++......|+++.|...|+++|..+|.+...|..++..+.. .++.+.+...|+
T Consensus        28 ~A~~~~~~al~~~p~----~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~~~~a~~~~g~~~~~-~g~~~eA~~~~~  102 (159)
T d1a17a_          28 NAIKFYSQAIELNPS----NAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMA-LGKFRAALRDYE  102 (159)
T ss_dssp             HHHHHHHHHHHHSTT----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHH
T ss_pred             HHHHHhhhccccchh----hhhhhhhhHHHHHhccccchHHHHHHHHHHHcccchHHHHHHHHHHHH-cCCHHHHHHHHH
Confidence            467889999988876    788999999999999999999999999999999999999999887764 456678999999


Q ss_pred             HHHHcCCCcHHHHHHHHH
Q 013489           83 RATKNCPWVGELWVRSLL  100 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~  100 (442)
                      +++...|....++..+..
T Consensus       103 ~a~~~~p~~~~~~~~l~~  120 (159)
T d1a17a_         103 TVVKVKPHDKDAKMKYQE  120 (159)
T ss_dssp             HHHHHSTTCHHHHHHHHH
T ss_pred             HHHHcCCCCHHHHHHHHH
Confidence            999999999888777544

>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=97.99  E-value=1.5e-05  Score=60.31  Aligned_cols=79  Identities=5%  Similarity=-0.107  Sum_probs=57.0

Q ss_pred             HHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHH
Q 013489          165 QRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCY  244 (442)
Q Consensus       165 ~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral  244 (442)
                      ..|+.++..++...|.....|...+.+....+ +++.|...|+++++.+|+...+|...+......|+.+.|...|++.|
T Consensus        33 ~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~-~~~~A~~~~~~al~~~p~~~~a~~~la~~y~~~g~~~~A~~~l~~~l  111 (112)
T d1hxia_          33 AEAALAFEAVCQKEPEREEAWRSLGLTQAENE-KDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWL  111 (112)
T ss_dssp             HHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhcccccccchhhhhhhhhhhhhh-hHHHhhcccccccccccccccchHHHHHHHHHCCCHHHHHHHHHHHh
Confidence            44444444444434555667777777777777 78888888888888888888888888888877888888888887765

>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=97.98  E-value=3e-05  Score=64.73  Aligned_cols=98  Identities=12%  Similarity=-0.081  Sum_probs=82.6

Q ss_pred             HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHH
Q 013489           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSLER  104 (442)
Q Consensus        25 ~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~  104 (442)
                      ....-.+.....|+++.|+..|++||..+|.++.+|...+..+.. .++.+.+...|++|+...|.....|......+..
T Consensus         6 ~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~p~~~~~~~~lg~~y~~-~~~~~~Ai~~~~~al~l~p~~~~a~~~lg~~~~~   84 (201)
T d2c2la1           6 ELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLK-MQQPEQALADCRRALELDGQSVKAHFFLGQCQLE   84 (201)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHH-TTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHhh-hhhhhhhhHHHHHHHHhCCCcHHHHHHHHHHHHH
Confidence            344555556678999999999999999999999999999887664 4567889999999999999999999998775554


Q ss_pred             ccCCHHHHHHHHHHHHhCCh
Q 013489          105 SRASEEEISTVFEKSLLCAF  124 (442)
Q Consensus       105 ~~~~~~~~~~i~~~al~~~~  124 (442)
                       .+..+.+...|++|+...+
T Consensus        85 -l~~~~~A~~~~~~al~l~p  103 (201)
T d2c2la1          85 -MESYDEAIANLQRAYSLAK  103 (201)
T ss_dssp             -TTCHHHHHHHHHHHHHHHH
T ss_pred             -CCCHHHHHHHHHHHHHhCc
Confidence             7889999999999997543

>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=97.93  E-value=0.00059  Score=60.51  Aligned_cols=120  Identities=12%  Similarity=0.161  Sum_probs=73.6

Q ss_pred             hHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhH-------HHHHHHHHHHHH
Q 013489          156 DYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAM-------LEAWQSYISMEI  228 (442)
Q Consensus       156 ~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~-------~~~w~~~~~~e~  228 (442)
                      ++......|.+|+.+.... ........++...+.+....| +++.|..+|++++...+..       ..++...+....
T Consensus       133 ~~~~A~~~~~~A~~l~~~~-~~~~~~~~~~~~la~~~~~~g-~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  210 (290)
T d1qqea_         133 DYAKAIDCYELAGEWYAQD-QSVALSNKCFIKCADLKALDG-QYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQL  210 (290)
T ss_dssp             CHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhc-CchhhhhhHHHHHHHHHHHcC-hHHHHHHHHHHHHHhCccchhhhhhHHHHHHHHHHHHH
Confidence            3444445566666554322 111223457777888989999 9999999999999875432       235556666666


Q ss_pred             hcccHHHHHHHHHHHHhcccCCCCh----HHHHHHHHHHHHHhCCHhhHHHHHHhh
Q 013489          229 ELDHINEARSIYKRCYSKRFTGTGS----EDICHAWLRFEREYGTLEDFDHSVQKV  280 (442)
Q Consensus       229 ~~g~~~~ar~i~~ral~~~~~~~~~----~~i~~~~~~fE~~~G~~~~~~~~~~~~  280 (442)
                      ..|++..|...|++++..  .+..+    ..+....+.. -..|+++.+..++...
T Consensus       211 ~~~d~~~A~~~~~~~~~~--~~~~~~sre~~~l~~l~~a-~~~~d~e~~~eai~~y  263 (290)
T d1qqea_         211 AATDAVAAARTLQEGQSE--DPNFADSRESNFLKSLIDA-VNEGDSEQLSEHCKEF  263 (290)
T ss_dssp             HTTCHHHHHHHHHGGGCC-----------HHHHHHHHHH-HHTTCTTTHHHHHHHH
T ss_pred             HhccHHHHHHHHHHHHHh--CCCccchHHHHHHHHHHHH-HHhcCHHHHHHHHHHH
Confidence            789999999999999863  21111    1233332222 2236777777776643

>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=97.81  E-value=1e-05  Score=59.80  Aligned_cols=49  Identities=20%  Similarity=0.276  Sum_probs=38.6

Q ss_pred             CCCceEEEcCC--CCCCC---------HHHHHHHhccCCCeeEEEEeeCCCCCCCcceEEEEee
Q 013489          389 TDECTAFLSNI--NLKAT---------YEDLRRFFSDVGGVSSIRILHDKFTGKSRVVQSDIYT  441 (442)
Q Consensus       389 ~~~~~v~v~nl--~~~~~---------~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~  441 (442)
                      ...++|+|.|+  |.++.         .++|+..|+.||.|..|.++.+    .++|||||+|.
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~   65 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFR   65 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECS
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEEC
Confidence            44569999998  54321         2678999999999999988665    36799999996

>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=97.79  E-value=4e-05  Score=58.92  Aligned_cols=92  Identities=10%  Similarity=-0.108  Sum_probs=73.3

Q ss_pred             HhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc--chhhHHHHHHHHHHHcCCCcH--HHHHHHHHHHHHccCCH
Q 013489           34 QSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL--KVGNVVRDVYSRATKNCPWVG--ELWVRSLLSLERSRASE  109 (442)
Q Consensus        34 ~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~--~~~~~~~~v~erAl~~~p~s~--~lW~~y~~~le~~~~~~  109 (442)
                      ...++++++...|+++|..+|.++.+..+|+..+....  ++...+..+|++++..-|...  ..|.... ......++.
T Consensus        10 ~~~~~l~~Ae~~Y~~aL~~~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg-~~y~~~g~~   88 (122)
T d1nzna_          10 VSVEDLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLA-VGNYRLKEY   88 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHH-HHHHHTTCH
T ss_pred             cCHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHH-HHHHHHhhh
Confidence            34557889999999999999999999999999886432  344568999999999777543  3665544 355567999


Q ss_pred             HHHHHHHHHHHhCChhh
Q 013489          110 EEISTVFEKSLLCAFST  126 (442)
Q Consensus       110 ~~~~~i~~~al~~~~~~  126 (442)
                      +.+...|++++...|.+
T Consensus        89 ~~A~~~~~~aL~~~P~~  105 (122)
T d1nzna_          89 EKALKYVRGLLQTEPQN  105 (122)
T ss_dssp             HHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHhCcCC
Confidence            99999999999987764

>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=97.75  E-value=4.3e-05  Score=63.77  Aligned_cols=82  Identities=18%  Similarity=0.195  Sum_probs=71.4

Q ss_pred             HHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHH
Q 013489          163 TFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKR  242 (442)
Q Consensus       163 ~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~r  242 (442)
                      -|+.|+.++..++...|....+|...+.+....| +++.|...|+++++.+|+++..|...+......|+++.|...|++
T Consensus        19 ~~~~Ai~~~~kal~~~p~~~~~~~~lg~~y~~~~-~~~~Ai~~~~~al~l~p~~~~a~~~lg~~~~~l~~~~~A~~~~~~   97 (201)
T d2c2la1          19 KYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQ-QPEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQR   97 (201)
T ss_dssp             CHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCCCHHHHHhHHHHHhhhh-hhhhhhHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            3455666555555546667789999999999999 999999999999999999999999999999999999999999999


Q ss_pred             HHh
Q 013489          243 CYS  245 (442)
Q Consensus       243 al~  245 (442)
                      |+.
T Consensus        98 al~  100 (201)
T d2c2la1          98 AYS  100 (201)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            996

>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=97.64  E-value=0.00094  Score=55.32  Aligned_cols=148  Identities=7%  Similarity=-0.045  Sum_probs=102.3

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~  101 (442)
                      -+..|.. .......|+++.+...|+++   .|.++.+|........ ..++.+.+...|++|++..|.....|......
T Consensus         5 ~~~l~~~-g~~~~~~~d~~~Al~~~~~i---~~~~~~~~~nlG~~~~-~~g~~~~A~~~~~kAl~ldp~~~~a~~~~g~~   79 (192)
T d1hh8a_           5 AISLWNE-GVLAADKKDWKGALDAFSAV---QDPHSRICFNIGCMYT-ILKNMTEAEKAFTRSINRDKHLAVAYFQRGML   79 (192)
T ss_dssp             HHHHHHH-HHHHHHTTCHHHHHHHHHTS---SSCCHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHH-HHHHHHCCCHHHHHHHHHhc---CCCCHHHHHHHHHHHH-HcCCchhHHHHHHHHHHHhhhhhhhHHHHHHH
Confidence            4556765 44456789999999999864   4567889988777655 45677889999999999999999999997764


Q ss_pred             HHHccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhh
Q 013489          102 LERSRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGL  181 (442)
Q Consensus       102 le~~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~  181 (442)
                      + ...++.+++...|++|+.....+..                          .++             ......-....
T Consensus        80 ~-~~~g~~~~A~~~~~kAl~~~~~n~~--------------------------~~~-------------~~~~~~~~~~~  119 (192)
T d1hh8a_          80 Y-YQTEKYDLAIKDLKEALIQLRGNQL--------------------------IDY-------------KILGLQFKLFA  119 (192)
T ss_dssp             H-HHTTCHHHHHHHHHHHHHTTTTCSE--------------------------EEC-------------GGGTBCCEEEH
T ss_pred             H-HhhccHHHHHHHHHHHHHhCccCch--------------------------HHH-------------HHhhhhcccch
Confidence            4 4478899999999999864322100                          000             00000000011


Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchh
Q 013489          182 LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA  215 (442)
Q Consensus       182 ~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~  215 (442)
                      .+++...+.++...+ +++.|.+.+.+++...|.
T Consensus       120 ~e~~~n~a~~~~~~~-~~~~A~~~l~~A~~~~~~  152 (192)
T d1hh8a_         120 CEVLYNIAFMYAKKE-EWKKAEEQLALATSMKSE  152 (192)
T ss_dssp             HHHHHHHHHHHHHTT-CHHHHHHHHHHHHTTCCS
T ss_pred             HHHHHHHHHHHHHCC-CHHHHHHHHHHHHhcCCC
Confidence            234555666777788 899999999999988664

>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=97.57  E-value=0.00052  Score=56.94  Aligned_cols=118  Identities=3%  Similarity=-0.113  Sum_probs=87.6

Q ss_pred             HHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHH
Q 013489            6 AHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRAT   85 (442)
Q Consensus         6 ~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl   85 (442)
                      ..|+.+|.......+.+..+|.+........|+++.|...|++||..+|.++..|......... .++.+.+...|++|+
T Consensus        19 ~d~~~Al~~~~~i~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~~~~a~~~~g~~~~~-~g~~~~A~~~~~kAl   97 (192)
T d1hh8a_          19 KDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQ-TEKYDLAIKDLKEAL   97 (192)
T ss_dssp             TCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhhhhhHHHHHHHHHh-hccHHHHHHHHHHHH
Confidence            3455665432111122567899988888999999999999999999999999999999887654 456678999999999


Q ss_pred             HcCCCc----------------HHHHHHHHHHHHHccCCHHHHHHHHHHHHhCChh
Q 013489           86 KNCPWV----------------GELWVRSLLSLERSRASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus        86 ~~~p~s----------------~~lW~~y~~~le~~~~~~~~~~~i~~~al~~~~~  125 (442)
                      ...|..                ..+|..... +....+..+.+...|.+|+...+.
T Consensus        98 ~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~-~~~~~~~~~~A~~~l~~A~~~~~~  152 (192)
T d1hh8a_          98 IQLRGNQLIDYKILGLQFKLFACEVLYNIAF-MYAKKEEWKKAEEQLALATSMKSE  152 (192)
T ss_dssp             HTTTTCSEEECGGGTBCCEEEHHHHHHHHHH-HHHHTTCHHHHHHHHHHHHTTCCS
T ss_pred             HhCccCchHHHHHhhhhcccchHHHHHHHHH-HHHHCCCHHHHHHHHHHHHhcCCC
Confidence            865431                355656555 334478888999999999876543

>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=97.51  E-value=0.0012  Score=53.44  Aligned_cols=97  Identities=5%  Similarity=-0.095  Sum_probs=74.2

Q ss_pred             hhhHHHHHHhhcCCCCC----h-------HhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc
Q 013489            3 NARAHLEEQISRQDLSD----S-------EKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL   71 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~----~-------~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~   71 (442)
                      .|...|+.+|...+...    .       -....|.+.+....+.|+++.+...++++|..+|.++..|..-+..+. ..
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            46778888887654221    0       012345556666678899999999999999999999999988887665 44


Q ss_pred             chhhHHHHHHHHHHHcCCCcHHHHHHHHH
Q 013489           72 KVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (442)
Q Consensus        72 ~~~~~~~~v~erAl~~~p~s~~lW~~y~~  100 (442)
                      +..+.+...|++|+..-|....+...+..
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            56788999999999999998887766554

>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=97.49  E-value=0.021  Score=50.24  Aligned_cols=204  Identities=12%  Similarity=0.037  Sum_probs=119.9

Q ss_pred             HHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHH-----HHHHHHHHHHHhcchhhHHHHHHHHHHHcCCC---cH-HHHH
Q 013489           26 YMIYLKYEQSSGDPGRVQLLYERAITDFPVSSD-----LWLDYTQYLDKTLKVGNVVRDVYSRATKNCPW---VG-ELWV   96 (442)
Q Consensus        26 w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~-----lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~---s~-~lW~   96 (442)
                      ..-.+......|+++.+..+|+++|...|.+..     .+........ ..++.+.+...|++++...|.   .. .++.
T Consensus        15 ~~lrA~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~-~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~   93 (366)
T d1hz4a_          15 NALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLH-CKGELTRSLALMQQTEQMARQHDVWHYALWS   93 (366)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHH-HHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHH-HCCCHHHHHHHHHHHHHHHHhhcchHHHHHH
Confidence            333455557789999999999999999988654     2333333233 335667899999999985532   11 1222


Q ss_pred             HHH-HHHHHccCCHHHHHHHHHHHHhCChh------hHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHH
Q 013489           97 RSL-LSLERSRASEEEISTVFEKSLLCAFS------TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASD  169 (442)
Q Consensus        97 ~y~-~~le~~~~~~~~~~~i~~~al~~~~~------~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~  169 (442)
                      .+. .......++...+...+.+++.....      .........+..   +...         ..++......+..+..
T Consensus        94 ~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~---~~~~---------~~~~~~a~~~~~~~~~  161 (366)
T d1hz4a_          94 LIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQ---LLWA---------WARLDEAEASARSGIE  161 (366)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHH---HHHH---------TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHH---HHHH---------hcchhhhHHHHHHHHH
Confidence            111 12233457778888888887743111      011111111111   0000         0233344455555555


Q ss_pred             HHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-------hhHHHHHHHHHHHHHhcccHHHHHHHHHH
Q 013489          170 YLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKIS-------GAMLEAWQSYISMEIELDHINEARSIYKR  242 (442)
Q Consensus       170 ~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~-------~~~~~~w~~~~~~e~~~g~~~~ar~i~~r  242 (442)
                      ......  .......+...+......+ +...+...+..++...       +....++.....+....|+.+.|...+.+
T Consensus       162 ~~~~~~--~~~~~~~~~~~~~~~~~~~-~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~  238 (366)
T d1hz4a_         162 VLSSYQ--PQQQLQCLAMLIQCSLARG-DLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRH  238 (366)
T ss_dssp             HTTTSC--GGGGHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             Hhhhhh--hhhHHHHHHHHHHHHHhhh-hHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHH
Confidence            432211  1222334445566666677 8899999998888762       22345777778888888999999999999


Q ss_pred             HHh
Q 013489          243 CYS  245 (442)
Q Consensus       243 al~  245 (442)
                      ++.
T Consensus       239 ~~~  241 (366)
T d1hz4a_         239 TAK  241 (366)
T ss_dssp             SCC
T ss_pred             HHH
Confidence            886

>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=97.48  E-value=0.0003  Score=55.59  Aligned_cols=89  Identities=9%  Similarity=-0.029  Sum_probs=48.1

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhc----------CChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc-
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSS----------GDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL-   71 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~----------g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~-   71 (442)
                      +|+..||.+|..+|.    +.++|..+.......          +.++.++..|++||..+|.++..|......+...+ 
T Consensus        15 ~A~~~~e~al~~~P~----~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~P~~~~a~~~lG~~y~~~g~   90 (145)
T d1zu2a1          15 QIRQDAENTYKSNPL----DADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYTSFAF   90 (145)
T ss_dssp             HHHHHHHHHHHHCTT----CHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhCCc----chHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhcchhhHHHhhHHHHHHHccc
Confidence            355666666666654    555555555443221          23355666677777777777766665554433221 


Q ss_pred             ---------chhhHHHHHHHHHHHcCCCcHHHH
Q 013489           72 ---------KVGNVVRDVYSRATKNCPWVGELW   95 (442)
Q Consensus        72 ---------~~~~~~~~v~erAl~~~p~s~~lW   95 (442)
                               +..+.+...|++|+..-|.....|
T Consensus        91 ~~~~~~~~~~~~~~A~~~~~kal~l~P~~~~~~  123 (145)
T d1zu2a1          91 LTPDETEAKHNFDLATQFFQQAVDEQPDNTHYL  123 (145)
T ss_dssp             HCCCHHHHHHHHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             chhhHHHHHHhHHHhhhhhhcccccCCCHHHHH
Confidence                     112345566666666666554433

>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=97.41  E-value=0.00016  Score=69.81  Aligned_cols=62  Identities=5%  Similarity=0.015  Sum_probs=56.4

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ..+...+.+....+ +++.|+..|.+++...|++...|...+.+....|+...|...|.||+.
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            46667788888888 999999999999999999999999999999999999999999999995

>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=97.41  E-value=5.1e-05  Score=56.42  Aligned_cols=51  Identities=24%  Similarity=0.018  Sum_probs=39.7

Q ss_pred             CceEEEcCC--CCCCC--------HHHHHHHhccCCCeeEEEEeeCCCCC--CCcceEEEEee
Q 013489          391 ECTAFLSNI--NLKAT--------YEDLRRFFSDVGGVSSIRILHDKFTG--KSRVVQSDIYT  441 (442)
Q Consensus       391 ~~~v~v~nl--~~~~~--------~~~l~~~f~~~G~i~~~~~~~~~~~g--~~~g~~fv~f~  441 (442)
                      ++.|.+.|+  |....        .++|+..|++||.|.+|.|++++.++  ...|++||+|.
T Consensus         4 s~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~   66 (104)
T d1o0pa_           4 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFT   66 (104)
T ss_dssp             CSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEES
T ss_pred             CcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEEC
Confidence            348999998  44432        35789999999999999998876543  45699999996

>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=97.37  E-value=0.0033  Score=50.64  Aligned_cols=96  Identities=8%  Similarity=0.070  Sum_probs=72.5

Q ss_pred             hhHHHHHHHHHHHHHHHhhhhcCch--------hhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHH
Q 013489          155 LDYSLIRETFQRASDYLSEQMKNTD--------GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISM  226 (442)
Q Consensus       155 ~~~~~~r~~~~~a~~~l~~~~~~~~--------~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~  226 (442)
                      .++......|.+|+.++.......+        -...++...+..+...+ +++.|...++++|..+|+++..|...+..
T Consensus        27 ~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~-~~~~A~~~~~~al~~~p~~~~a~~~~g~~  105 (170)
T d1p5qa1          27 GKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQ-AFSAAIESCNKALELDSNNEKGLSRRGEA  105 (170)
T ss_dssp             TCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhh-hcccccchhhhhhhccccchhhhHHHHHH
Confidence            3455555667777766543222111        11245556777888888 99999999999999999999999999999


Q ss_pred             HHhcccHHHHHHHHHHHHhcccCCCCh
Q 013489          227 EIELDHINEARSIYKRCYSKRFTGTGS  253 (442)
Q Consensus       227 e~~~g~~~~ar~i~~ral~~~~~~~~~  253 (442)
                      ....|+++.|...|++|+.  +.++.+
T Consensus       106 ~~~~g~~~~A~~~~~~al~--l~P~n~  130 (170)
T d1p5qa1         106 HLAVNDFELARADFQKVLQ--LYPNNK  130 (170)
T ss_dssp             HHHTTCHHHHHHHHHHHHH--HCSSCH
T ss_pred             HHHhhhHHHHHHHHHHHHH--hCCCCH
Confidence            9999999999999999997  344444

>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=97.35  E-value=0.003  Score=50.81  Aligned_cols=95  Identities=9%  Similarity=0.117  Sum_probs=71.0

Q ss_pred             hHHHHHHHHHHHHHHHhhhhcCc--------hhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHH
Q 013489          156 DYSLIRETFQRASDYLSEQMKNT--------DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISME  227 (442)
Q Consensus       156 ~~~~~r~~~~~a~~~l~~~~~~~--------~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e  227 (442)
                      ++......|.+|+.++.......        +-...++...+..+..++ ++..|...+++++..+|++...|...+...
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            34444455666666554332211        112245556777788888 999999999999999999999999999999


Q ss_pred             HhcccHHHHHHHHHHHHhcccCCCCh
Q 013489          228 IELDHINEARSIYKRCYSKRFTGTGS  253 (442)
Q Consensus       228 ~~~g~~~~ar~i~~ral~~~~~~~~~  253 (442)
                      ...|+++.|...|.+++.  +.++.+
T Consensus       109 ~~l~~~~~A~~~~~~al~--l~P~n~  132 (168)
T d1kt1a1         109 LLMNEFESAKGDFEKVLE--VNPQNK  132 (168)
T ss_dssp             HHTTCHHHHHHHHHHHHH--SCTTCH
T ss_pred             HHcCCHHHHHHHHHHHHH--hCCCCH
Confidence            999999999999999997  444544

>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=97.33  E-value=0.00094  Score=52.54  Aligned_cols=89  Identities=9%  Similarity=-0.097  Sum_probs=65.9

Q ss_pred             CChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc---------chhhHHHHHHHHHHHcCCCcHHHHHHHHHHHHHc--
Q 013489           37 GDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL---------KVGNVVRDVYSRATKNCPWVGELWVRSLLSLERS--  105 (442)
Q Consensus        37 g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~---------~~~~~~~~v~erAl~~~p~s~~lW~~y~~~le~~--  105 (442)
                      +.++.++..|+++|..+|.+++.|..+...+....         +..+.+...|++|+...|.....|......+...  
T Consensus        11 ~~fe~A~~~~e~al~~~P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~P~~~~a~~~lG~~y~~~g~   90 (145)
T d1zu2a1          11 LLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYTSFAF   90 (145)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhcchhhHHHhhHHHHHHHccc
Confidence            34678999999999999999999999987665321         2235688999999999999999887755433221  


Q ss_pred             -c-------CCHHHHHHHHHHHHhCChh
Q 013489          106 -R-------ASEEEISTVFEKSLLCAFS  125 (442)
Q Consensus       106 -~-------~~~~~~~~i~~~al~~~~~  125 (442)
                       .       ..++.+...|++|+...|.
T Consensus        91 ~~~~~~~~~~~~~~A~~~~~kal~l~P~  118 (145)
T d1zu2a1          91 LTPDETEAKHNFDLATQFFQQAVDEQPD  118 (145)
T ss_dssp             HCCCHHHHHHHHHHHHHHHHHHHHHCTT
T ss_pred             chhhHHHHHHhHHHhhhhhhcccccCCC
Confidence             1       1245677778888876665

>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=97.25  E-value=0.00078  Score=51.72  Aligned_cols=98  Identities=11%  Similarity=-0.054  Sum_probs=74.9

Q ss_pred             HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH---
Q 013489           25 QYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS---  101 (442)
Q Consensus        25 ~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~---  101 (442)
                      .+.+-.+.....|+++.++..|+++|..+|.+..+|......+... ++.+.+...|++|+...|.....|..+...   
T Consensus         6 ~~k~~G~~~~~~~~y~~Ai~~y~~al~~~p~~~~~~~~~a~~~~~~-~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~   84 (128)
T d1elra_           6 KEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEK-GDYNKCRELCEKAIEVGRENREDYRQIAKAYAR   84 (128)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHhHHHHHHHc-CchHHHHHHHHHHHHhCcccHHHHHHHHHHHHH
Confidence            4555555566789999999999999999999999999998877644 566889999999999877665555544332   


Q ss_pred             ---HHHccCCHHHHHHHHHHHHhCC
Q 013489          102 ---LERSRASEEEISTVFEKSLLCA  123 (442)
Q Consensus       102 ---le~~~~~~~~~~~i~~~al~~~  123 (442)
                         .....+.++++...|++++...
T Consensus        85 lg~~~~~~~~~~~A~~~~~kal~~~  109 (128)
T d1elra_          85 IGNSYFKEEKYKDAIHFYNKSLAEH  109 (128)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHhcC
Confidence               2223567788888888888654

>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=97.21  E-value=0.0023  Score=51.51  Aligned_cols=65  Identities=15%  Similarity=-0.014  Sum_probs=59.5

Q ss_pred             hhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          180 GLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       180 ~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ....++...+.....++ +++.|...|+++|+.+|+++..|...+......|+++.|...|++|+.
T Consensus        75 ~~~~~~~nla~~~~~~~-~~~~Ai~~~~~al~~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~  139 (169)
T d1ihga1          75 VALSCVLNIGACKLKMS-DWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQE  139 (169)
T ss_dssp             HHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhhc-ccchhhhhhhhhhhhhhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHH
Confidence            34567777888888888 999999999999999999999999999999999999999999999997

>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=97.21  E-value=0.0018  Score=49.24  Aligned_cols=89  Identities=9%  Similarity=-0.065  Sum_probs=69.8

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcC---ChhhHHHHHHHHHhcCCCC--HHHHHHHHHHHHHhcchhhHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSG---DPGRVQLLYERAITDFPVS--SDLWLDYTQYLDKTLKVGNVV   77 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g---~~~~~~~lyERal~~~p~~--~~lW~~Y~~~l~~~~~~~~~~   77 (442)
                      +|.+.|+.+|...|.    +.+++.+|+......+   +...++.+|+++|...|.+  .+.|...+.... ..++.+.+
T Consensus        17 ~Ae~~Y~~aL~~~p~----~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y~-~~g~~~~A   91 (122)
T d1nzna_          17 KFEKKFQSEKAAGSV----SKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNY-RLKEYEKA   91 (122)
T ss_dssp             HHHHHHHHHHHHSCC----CHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHH-HTTCHHHH
T ss_pred             HHHHHHHHHHhhCCC----CHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHHH-HHhhhHHH
Confidence            578899999999887    7889999999887544   5567999999999987654  346765554444 45677889


Q ss_pred             HHHHHHHHHcCCCcHHHHH
Q 013489           78 RDVYSRATKNCPWVGELWV   96 (442)
Q Consensus        78 ~~v~erAl~~~p~s~~lW~   96 (442)
                      ...|++++..-|.......
T Consensus        92 ~~~~~~aL~~~P~~~~A~~  110 (122)
T d1nzna_          92 LKYVRGLLQTEPQNNQAKE  110 (122)
T ss_dssp             HHHHHHHHHHCTTCHHHHH
T ss_pred             HHHHHHHHHhCcCCHHHHH
Confidence            9999999999998866443

>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=97.20  E-value=0.0043  Score=48.94  Aligned_cols=68  Identities=15%  Similarity=0.048  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCCh
Q 013489          183 RLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGS  253 (442)
Q Consensus       183 ~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~  253 (442)
                      .++...+.....++ +++.|...++++|..+|+++..|...+......|+++.|...|++++.  +.++.+
T Consensus        68 ~~~~Nla~~~~~l~-~~~~Al~~~~~al~~~p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~--l~P~n~  135 (153)
T d2fbna1          68 SCNLNLATCYNKNK-DYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAAS--LNPNNL  135 (153)
T ss_dssp             HHHHHHHHHHHHTT-CHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH--HSTTCH
T ss_pred             HHHhhHHHHHHHhc-ccchhhhhhhccccccchhhhhhHHhHHHHHHcCCHHHHHHHHHHHHH--hCCCCH
Confidence            45666777788888 999999999999999999999999999999999999999999999997  344444

>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=97.14  E-value=0.004  Score=49.97  Aligned_cols=97  Identities=4%  Similarity=-0.028  Sum_probs=71.7

Q ss_pred             hhhHHHHHHhhcCCCC---ChH--------hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhc
Q 013489            3 NARAHLEEQISRQDLS---DSE--------KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTL   71 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~---~~~--------~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~   71 (442)
                      +|...|..+|...+..   ...        ....+.+.+....+.|++..++..|+++|..+|.++..|...+..+.. .
T Consensus        33 ~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~~~~~~~-l  111 (168)
T d1kt1a1          33 QAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQLL-M  111 (168)
T ss_dssp             HHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH-T
T ss_pred             HHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcccchHHHHHHHHHHHHH-c
Confidence            3566788877543211   111        122344455555678999999999999999999999999999886664 4


Q ss_pred             chhhHHHHHHHHHHHcCCCcHHHHHHHHH
Q 013489           72 KVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (442)
Q Consensus        72 ~~~~~~~~v~erAl~~~p~s~~lW~~y~~  100 (442)
                      +..+.+...|++|+...|.+..++..+..
T Consensus       112 ~~~~~A~~~~~~al~l~P~n~~~~~~l~~  140 (168)
T d1kt1a1         112 NEFESAKGDFEKVLEVNPQNKAARLQIFM  140 (168)
T ss_dssp             TCHHHHHHHHHHHHHSCTTCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            56788999999999999999888877654

>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=97.08  E-value=0.0052  Score=48.43  Aligned_cols=97  Identities=6%  Similarity=-0.117  Sum_probs=69.5

Q ss_pred             hhhHHHHHHhhcCCCCC---hH---------hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh
Q 013489            3 NARAHLEEQISRQDLSD---SE---------KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKT   70 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~---~~---------~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~   70 (442)
                      +|-..|..+|...+...   ..         ....|.+.+....+.|++..++..|+++|..+|.++..|..-+..+...
T Consensus        35 ~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~p~~~ka~~~~g~~~~~l  114 (153)
T d2fbna1          35 EAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYF  114 (153)
T ss_dssp             HHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhccccccchhhhhhHHhHHHHHHc
Confidence            35567777775543211   00         1234555566566778899999999999999999999888888766643


Q ss_pred             cchhhHHHHHHHHHHHcCCCcHHHHHHHHH
Q 013489           71 LKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (442)
Q Consensus        71 ~~~~~~~~~v~erAl~~~p~s~~lW~~y~~  100 (442)
                       ++.+.+...|++|+...|....++..+..
T Consensus       115 -g~~~~A~~~~~~al~l~P~n~~~~~~l~~  143 (153)
T d2fbna1         115 -GFLEEAKENLYKAASLNPNNLDIRNSYEL  143 (153)
T ss_dssp             -TCHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             -CCHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence             46677889999999999988888776543

>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=97.05  E-value=0.0026  Score=48.64  Aligned_cols=81  Identities=14%  Similarity=0.153  Sum_probs=60.0

Q ss_pred             HHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHH-------HHHHHHHHHHhcccHHHH
Q 013489          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLE-------AWQSYISMEIELDHINEA  236 (442)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~-------~w~~~~~~e~~~g~~~~a  236 (442)
                      |++|+.++..++...|....++...+.+....| +++.|...|+++|..+|++..       ++..........++++.|
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            455555555555445666678888899999999 999999999999998776544       444455555666788888


Q ss_pred             HHHHHHHHh
Q 013489          237 RSIYKRCYS  245 (442)
Q Consensus       237 r~i~~ral~  245 (442)
                      ...|++++.
T Consensus        99 ~~~~~kal~  107 (128)
T d1elra_          99 IHFYNKSLA  107 (128)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            888888886

>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=96.75  E-value=0.0036  Score=50.30  Aligned_cols=77  Identities=12%  Similarity=-0.077  Sum_probs=49.2

Q ss_pred             hHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHH
Q 013489           22 KFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSL   99 (442)
Q Consensus        22 ~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~   99 (442)
                      ....|.+.+....+.|+++.|+..|+++|..+|.++..|..-+..+.. .+..+.+...|++|+..-|....++..+.
T Consensus        76 ~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~p~~~~a~~~~g~~~~~-l~~~~~A~~~~~~al~l~p~n~~~~~~l~  152 (169)
T d1ihga1          76 ALSCVLNIGACKLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQG-LKEYDQALADLKKAQEIAPEDKAIQAELL  152 (169)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhhcccchhhhhhhhhhhhhhhhhhHHHhHHHHHHH-ccCHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence            444555555555666777777777777777777777777666655543 34455677777777777776666655543

>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=96.68  E-value=0.16  Score=43.85  Aligned_cols=167  Identities=10%  Similarity=-0.025  Sum_probs=97.0

Q ss_pred             HccCCHHHHHHHHHHHHhCChh--hHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcCchhh
Q 013489          104 RSRASEEEISTVFEKSLLCAFS--TFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKNTDGL  181 (442)
Q Consensus       104 ~~~~~~~~~~~i~~~al~~~~~--~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~~~~~  181 (442)
                      ...++.+++...|++|+.+...  ........+.... .+-++.         .++......+++++.+.... ......
T Consensus        48 ~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g-~~y~~~---------~~~~~A~~~~~~a~~~~~~~-~~~~~~  116 (290)
T d1qqea_          48 RLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAY-KCFKSG---------GNSVNAVDSLENAIQIFTHR-GQFRRG  116 (290)
T ss_dssp             HHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHHHHT---------TCHHHHHHHHHHHHHHHHHT-TCHHHH
T ss_pred             HHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHH-HHHHHh---------CCcHHHHHHHHHhhHHhhhc-ccchhH
Confidence            3456777888888888754211  1111112221111 111111         34445556777777765432 222233


Q ss_pred             HHHHHHHHHHHHH-cCCCHHHHHHHHHHHHHhch------hHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCCh-
Q 013489          182 LRLYAYWAHLEQS-MGKDMVSARGVWERLLKISG------AMLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGS-  253 (442)
Q Consensus       182 ~~l~~~~a~~e~~-~~~~~~~ar~i~~~~l~~~~------~~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~-  253 (442)
                      ..++...+.+... .+ +++.|.+.|++++...+      ....++...+.+....|+++.|..+|++++......... 
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            4556666665544 56 99999999999997732      124578889999999999999999999999742111110 


Q ss_pred             ---HHHHHHHHHHHHHhCCHhhHHHHHHhhch
Q 013489          254 ---EDICHAWLRFEREYGTLEDFDHSVQKVTP  282 (442)
Q Consensus       254 ---~~i~~~~~~fE~~~G~~~~~~~~~~~~~~  282 (442)
                         ..++..-.......|+.+....+++++..
T Consensus       196 ~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~  227 (290)
T d1qqea_         196 WSLKDYFLKKGLCQLAATDAVAAARTLQEGQS  227 (290)
T ss_dssp             GGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGC
T ss_pred             hhHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence               11222222233346787777777766544

>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=96.65  E-value=0.014  Score=47.26  Aligned_cols=100  Identities=9%  Similarity=0.027  Sum_probs=76.3

Q ss_pred             ChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCH----------------------HHHHHHHHHHHHhcchhhH
Q 013489           19 DSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSS----------------------DLWLDYTQYLDKTLKVGNV   76 (442)
Q Consensus        19 ~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~----------------------~lW~~Y~~~l~~~~~~~~~   76 (442)
                      |...+..+..-..-....|+++.+...|.+||..++...                      ..|...+..+.. .++.+.
T Consensus         7 D~~~f~~~~~~g~~~~~~g~~e~A~~~~~~AL~l~rG~~l~~~~~~~w~~~~r~~l~~~~~~a~~~la~~~~~-~g~~~~   85 (179)
T d2ff4a2           7 DLGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIA-CGRASA   85 (179)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHH-TTCHHH
T ss_pred             cHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCchH
Confidence            344566666666666788999999999999999766432                      244444444443 356678


Q ss_pred             HHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCHHHHHHHHHHHH
Q 013489           77 VRDVYSRATKNCPWVGELWVRSLLSLERSRASEEEISTVFEKSL  120 (442)
Q Consensus        77 ~~~v~erAl~~~p~s~~lW~~y~~~le~~~~~~~~~~~i~~~al  120 (442)
                      +...+++++...|.+..+|...+..+.. .+...++...|+++.
T Consensus        86 Al~~~~~al~~~P~~e~~~~~l~~al~~-~Gr~~eAl~~y~~~~  128 (179)
T d2ff4a2          86 VIAELEALTFEHPYREPLWTQLITAYYL-SDRQSDALGAYRRVK  128 (179)
T ss_dssp             HHHHHHHHHHHSTTCHHHHHHHHHHHHT-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCccHHHHHHHHHHHHH-hcCHHHHHHHHHHHH
Confidence            9999999999999999999999986665 688888999999874

>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=96.61  E-value=0.0072  Score=43.27  Aligned_cols=74  Identities=19%  Similarity=0.103  Sum_probs=56.5

Q ss_pred             hhHHHHHHHHHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHh
Q 013489          155 LDYSLIRETFQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE  229 (442)
Q Consensus       155 ~~~~~~r~~~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~  229 (442)
                      .++.....-|++|+...............++...+......| ++++|...|+++|+.+|++..++.....++..
T Consensus        19 g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g-~~~~A~~~y~~aL~l~P~~~~a~~Nl~~~~~~   92 (95)
T d1tjca_          19 ADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQG-DLDKALLLTKKLLELDPEHQRANGNLKYFEYI   92 (95)
T ss_dssp             TCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcC-ChHHHHHHHHHHHHhCcCCHHHHHHHHHHHHH
Confidence            456666677788877665443333445677888888889999 99999999999999999999988777666643

>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=96.54  E-value=0.019  Score=49.73  Aligned_cols=66  Identities=15%  Similarity=-0.024  Sum_probs=55.3

Q ss_pred             hcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHH
Q 013489           35 SSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLS  101 (442)
Q Consensus        35 ~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~  101 (442)
                      ..|+++.+...|+++|..+|.+...|..++..+... ++.+.+...|++++...|.....|..|...
T Consensus         8 ~~G~l~eAl~~l~~al~~~P~d~~ar~~La~lL~~~-G~~e~A~~~l~~a~~l~P~~~~~~~~l~~l   73 (264)
T d1zbpa1           8 SEGQLQQALELLIEAIKASPKDASLRSSFIELLCID-GDFERADEQLMQSIKLFPEYLPGASQLRHL   73 (264)
T ss_dssp             TTTCHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHCGGGHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHhCCCcHHHHHHHHHH
Confidence            468899999999999999999999999999888755 456778899999999999888888777653

>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=96.36  E-value=0.0029  Score=55.11  Aligned_cols=115  Identities=15%  Similarity=0.014  Sum_probs=81.9

Q ss_pred             hhhHHHHHHhhcCCCCChHhHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Q 013489            3 NARAHLEEQISRQDLSDSEKFQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYS   82 (442)
Q Consensus         3 ~~r~~yE~~l~~~~~~~~~~~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~e   82 (442)
                      ++...|+.+|+.+|.    +...+..++.+....|+.+++...|++++..+|.+...|..|...+.... ....+...+.
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            577889999999987    88899999999999999999999999999999999999999988765322 1111111111


Q ss_pred             HHHHcCCCcHHHHHHHHH--HHHHccCCHHHHHHHHHHHHhCCh
Q 013489           83 RATKNCPWVGELWVRSLL--SLERSRASEEEISTVFEKSLLCAF  124 (442)
Q Consensus        83 rAl~~~p~s~~lW~~y~~--~le~~~~~~~~~~~i~~~al~~~~  124 (442)
                      ++  ..+....-|..++.  .+....++.+++..+++++....+
T Consensus        89 ~~--~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~~p  130 (264)
T d1zbpa1          89 TA--KVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELRQ  130 (264)
T ss_dssp             CE--ECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCC
T ss_pred             hh--hcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCC
Confidence            11  12222344444432  123346888999999999886543

>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=95.93  E-value=0.057  Score=43.43  Aligned_cols=87  Identities=13%  Similarity=0.082  Sum_probs=66.3

Q ss_pred             HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHcCCCcHHHHHHHHHHH
Q 013489           23 FQQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKTLKVGNVVRDVYSRATKNCPWVGELWVRSLLSL  102 (442)
Q Consensus        23 ~~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~~~~~~~~~~v~erAl~~~p~s~~lW~~y~~~l  102 (442)
                      ...|...++.....|+++.+...++++|..+|.+..+|...+..+... +....+..+|+++.+.+.            -
T Consensus        67 ~~a~~~la~~~~~~g~~~~Al~~~~~al~~~P~~e~~~~~l~~al~~~-Gr~~eAl~~y~~~~~~L~------------~  133 (179)
T d2ff4a2          67 VLAHTAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLS-DRQSDALGAYRRVKTTLA------------D  133 (179)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHH------------H
T ss_pred             HHHHHHHHHHHHHCCCchHHHHHHHHHHHhCCccHHHHHHHHHHHHHh-cCHHHHHHHHHHHHHHHH------------H
Confidence            467888888888899999999999999999999999999999988754 456779999999866311            1


Q ss_pred             HHccCCHHHHHHHHHHHHhC
Q 013489          103 ERSRASEEEISTVFEKSLLC  122 (442)
Q Consensus       103 e~~~~~~~~~~~i~~~al~~  122 (442)
                      +.-..+..++..++++.+..
T Consensus       134 eLG~~P~~~l~~l~~~il~~  153 (179)
T d2ff4a2         134 DLGIDPGPTLRALNERILRQ  153 (179)
T ss_dssp             HHSCCCCHHHHHHHHHHHTT
T ss_pred             HhCCCcCHHHHHHHHHHHhC
Confidence            22233445566666666643

>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=95.72  E-value=0.058  Score=38.19  Aligned_cols=73  Identities=10%  Similarity=0.034  Sum_probs=54.7

Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhchh-------HHHHHHHHHHHHHhcccHHHHHHHHHHHHhcccCCCChHHHHHHH
Q 013489          188 WAHLEQSMGKDMVSARGVWERLLKISGA-------MLEAWQSYISMEIELDHINEARSIYKRCYSKRFTGTGSEDICHAW  260 (442)
Q Consensus       188 ~a~~e~~~~~~~~~ar~i~~~~l~~~~~-------~~~~w~~~~~~e~~~g~~~~ar~i~~ral~~~~~~~~~~~i~~~~  260 (442)
                      .+......| ++..|...|+++++..|.       ...++..........|++++|...|++||.  +.++.+. ++...
T Consensus        11 lG~~~~~~g-~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~--l~P~~~~-a~~Nl   86 (95)
T d1tjca_          11 LGKVAYTEA-DYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE--LDPEHQR-ANGNL   86 (95)
T ss_dssp             HHHHHHHTT-CHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTTCHH-HHHHH
T ss_pred             HHHHHHHCC-CHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHH--hCcCCHH-HHHHH
Confidence            345556778 999999999999988543       356777888888899999999999999997  4555553 44333


Q ss_pred             HHHH
Q 013489          261 LRFE  264 (442)
Q Consensus       261 ~~fE  264 (442)
                      ..+|
T Consensus        87 ~~~~   90 (95)
T d1tjca_          87 KYFE   90 (95)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            3333

>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=95.59  E-value=0.023  Score=54.05  Aligned_cols=63  Identities=16%  Similarity=0.074  Sum_probs=46.8

Q ss_pred             HHHHHHHHhhhhcCchhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHH
Q 013489          164 FQRASDYLSEQMKNTDGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEAWQSYISME  227 (442)
Q Consensus       164 ~~~a~~~l~~~~~~~~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e  227 (442)
                      ++.|+.++.+++...|.....|...+.+....| +...|...|.+++...|.....+.....+.
T Consensus       168 ~~~A~~~y~~A~~l~P~~~~~~~~Lg~~~~~~~-~~~~A~~~y~ral~~~~~~~~a~~nL~~~~  230 (497)
T d1ya0a1         168 TSQAESYYRHAAQLVPSNGQPYNQLAILASSKG-DHLTTIFYYCRSIAVKFPFPAASTNLQKAL  230 (497)
T ss_dssp             HHHHHHHHHHHHHHCTTBSHHHHHHHHHHHHTT-CHHHHHHHHHHHHSSSBCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCchHHHHHHHHHHHHcC-CHHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Confidence            445555555555445666678888999988889 999999999999998777777666665543

>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=92.47  E-value=0.86  Score=34.84  Aligned_cols=89  Identities=15%  Similarity=-0.029  Sum_probs=61.5

Q ss_pred             hHHHHHHHHHHHHHHHhhhhcCc-----hhhHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchh-----------HHHH
Q 013489          156 DYSLIRETFQRASDYLSEQMKNT-----DGLLRLYAYWAHLEQSMGKDMVSARGVWERLLKISGA-----------MLEA  219 (442)
Q Consensus       156 ~~~~~r~~~~~a~~~l~~~~~~~-----~~~~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~-----------~~~~  219 (442)
                      ++......|++|+.+........     .....+|...+.....+| +++.|...+++++..++.           ...+
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            34444566666666543322110     112346777788888899 999999999999987543           2235


Q ss_pred             HHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          220 WQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       220 w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      +..........|+++.|...|++|+.
T Consensus       103 ~~~~g~~~~~lg~~eeA~~~~~~Al~  128 (156)
T d2hr2a1         103 VYSRALALDGLGRGAEAMPEFKKVVE  128 (156)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            56667777788999999999999985

>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=92.26  E-value=2.6  Score=34.87  Aligned_cols=225  Identities=9%  Similarity=-0.022  Sum_probs=119.0

Q ss_pred             HHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHh---cchhhHHHHHHHHHHHcCCCcHHHHHHHHH
Q 013489           24 QQYMIYLKYEQSSGDPGRVQLLYERAITDFPVSSDLWLDYTQYLDKT---LKVGNVVRDVYSRATKNCPWVGELWVRSLL  100 (442)
Q Consensus        24 ~~w~~y~~~e~~~g~~~~~~~lyERal~~~p~~~~lW~~Y~~~l~~~---~~~~~~~~~v~erAl~~~p~s~~lW~~y~~  100 (442)
                      +.|..........+|...|...|++|...  .+...+.....+...-   .++...+...++++...-.  ...+.....
T Consensus         3 ~~~~~lG~~~~~~~d~~~A~~~~~kAa~~--g~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~~--~~a~~~l~~   78 (265)
T d1ouva_           3 KELVGLGAKSYKEKDFTQAKKYFEKACDL--KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNY--SNGCHLLGN   78 (265)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC--HHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHC--CCHHHHHHHHHHHHcCCCcchhHHHHHHhhcccccccc--cchhhcccc
Confidence            46777777777789999999999999875  5677777666655431   2455678888999887442  222322222


Q ss_pred             HHHH---ccCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHHhhccCccchhhhHHHHHHHHHHHHHHHhhhhcC
Q 013489          101 SLER---SRASEEEISTVFEKSLLCAFSTFEEYLDLFLTRIDGLRRRILFSGEVEGVLDYSLIRETFQRASDYLSEQMKN  177 (442)
Q Consensus       101 ~le~---~~~~~~~~~~i~~~al~~~~~~~~~~~~~~~~~~~~l~rr~~~~~~~~~~~~~~~~r~~~~~a~~~l~~~~~~  177 (442)
                      ....   .....+.+...|+++...+.......+...  +..       .... .  .+.       ..+...+......
T Consensus        79 ~~~~~~~~~~~~~~a~~~~~~a~~~g~~~a~~~l~~~--~~~-------~~~~-~--~~~-------~~a~~~~~~~~~~  139 (265)
T d1ouva_          79 LYYSGQGVSQNTNKALQYYSKACDLKYAEGCASLGGI--YHD-------GKVV-T--RDF-------KKAVEYFTKACDL  139 (265)
T ss_dssp             HHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHH--HHH-------CSSS-C--CCH-------HHHHHHHHHHHHT
T ss_pred             ccccccccchhhHHHHHHHhhhhhhhhhhHHHhhccc--ccC-------CCcc-c--chh-------HHHHHHhhhhhcc
Confidence            2221   123456778888888876554222111111  110       0000 0  111       1122222221111


Q ss_pred             chhhHHHHHHHHHHHHH---cCCCHHHHHHHHHHHHHhchhHHHHHHHHHHHHHh----cccHHHHHHHHHHHHhcccCC
Q 013489          178 TDGLLRLYAYWAHLEQS---MGKDMVSARGVWERLLKISGAMLEAWQSYISMEIE----LDHINEARSIYKRCYSKRFTG  250 (442)
Q Consensus       178 ~~~~~~l~~~~a~~e~~---~~~~~~~ar~i~~~~l~~~~~~~~~w~~~~~~e~~----~g~~~~ar~i~~ral~~~~~~  250 (442)
                      .  ....+..++.+...   ...+...+...++.+....  +...+..+..+...    ..+++.|...|.+|...    
T Consensus       140 ~--~~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~a~~~g--~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~----  211 (265)
T d1ouva_         140 N--DGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLK--DSPGCFNAGNMYHHGEGATKNFKEALARYSKACEL----  211 (265)
T ss_dssp             T--CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT--CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHT----
T ss_pred             c--ccchhhhhhhhhccCCCcccccccchhhhhcccccc--ccccccchhhhcccCcccccchhhhhhhHhhhhcc----
Confidence            1  12234444444443   2236778888888887652  22333333333322    34899999999999863    


Q ss_pred             CChHHHHHHHHHHHHHhCCHhhHHHHHHh
Q 013489          251 TGSEDICHAWLRFEREYGTLEDFDHSVQK  279 (442)
Q Consensus       251 ~~~~~i~~~~~~fE~~~G~~~~~~~~~~~  279 (442)
                      ..+...+.-=.-+++-.|...+...|++-
T Consensus       212 g~~~a~~~LG~~y~~G~g~~~n~~~A~~~  240 (265)
T d1ouva_         212 ENGGGCFNLGAMQYNGEGVTRNEKQAIEN  240 (265)
T ss_dssp             TCHHHHHHHHHHHHTTSSSSCCSTTHHHH
T ss_pred             cCHHHHHHHHHHHHcCCCCccCHHHHHHH
Confidence            34554444333344445544444444443

>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=90.59  E-value=1.3  Score=33.79  Aligned_cols=56  Identities=18%  Similarity=0.132  Sum_probs=44.1

Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHhchhH------------HHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          189 AHLEQSMGKDMVSARGVWERLLKISGAM------------LEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       189 a~~e~~~~~~~~~ar~i~~~~l~~~~~~------------~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      +......| +++.|.+.|+++|..+|+.            ..+|..........|+++.|...|++++.
T Consensus        16 g~~~~~~g-~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~   83 (156)
T d2hr2a1          16 AQRQLVAG-EYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALH   83 (156)
T ss_dssp             HHHHHHHT-CHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHcC-CHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhh
Confidence            33445667 8999999999999885532            34677777778888999999999999985

>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=90.42  E-value=0.38  Score=33.36  Aligned_cols=50  Identities=6%  Similarity=0.020  Sum_probs=40.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCCC--cceEEEEee
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHDKFTGKS--RVVQSDIYT  441 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~--~g~~fv~f~  441 (442)
                      ++|-|.+||++.|++++.+.++..|.+.-...+..+.+.+.  -.-|||.|.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~   53 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFK   53 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEES
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeC
Confidence            37899999999999999999999999888877776555442  256788875

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.54  E-value=0.57  Score=34.57  Aligned_cols=48  Identities=10%  Similarity=0.003  Sum_probs=27.7

Q ss_pred             CHHHHHHHHHHHHHhchhH-HHHHHHHHHHHHhcccHHHHHHHHHHHHh
Q 013489          198 DMVSARGVWERLLKISGAM-LEAWQSYISMEIELDHINEARSIYKRCYS  245 (442)
Q Consensus       198 ~~~~ar~i~~~~l~~~~~~-~~~w~~~~~~e~~~g~~~~ar~i~~ral~  245 (442)
                      ++.++..+++.+++.+|.. .+.|...+--....|++++|+..++++|.
T Consensus        53 d~~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~  101 (124)
T d2pqrb1          53 DERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE  101 (124)
T ss_dssp             HHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHc
Confidence            4556666666666655533 34554444444456666666666666665

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.99  E-value=0.71  Score=34.01  Aligned_cols=57  Identities=11%  Similarity=0.073  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHhhhhcCchhh-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhHHHH
Q 013489          162 ETFQRASDYLSEQMKNTDGL-LRLYAYWAHLEQSMGKDMVSARGVWERLLKISGAMLEA  219 (442)
Q Consensus       162 ~~~~~a~~~l~~~~~~~~~~-~~l~~~~a~~e~~~~~~~~~ar~i~~~~l~~~~~~~~~  219 (442)
                      ..+++++.+|...+...+.. .+.|-+.+-...++| ++++|+..++++|+..|++...
T Consensus        52 ~d~~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklg-dy~~A~~~~~~~L~ieP~n~qA  109 (124)
T d2pqrb1          52 NDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLG-EYSMAKRYVDTLFEHERNNKQV  109 (124)
T ss_dssp             HHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHCTTCHHH
T ss_pred             HHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHh-hHHHHHHHHHHHHccCCCcHHH
Confidence            45678999988877654433 456666676777888 9999999999999999987764

>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=87.40  E-value=0.82  Score=31.83  Aligned_cols=34  Identities=21%  Similarity=0.294  Sum_probs=29.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeeC
Q 013489          392 CTAFLSNINLKATYEDLRRFFSDVGGVSSIRILHD  426 (442)
Q Consensus       392 ~~v~v~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~  426 (442)
                      ..||.-..|......+|.++|++||.| .|.++.|
T Consensus        16 dHVf~~tFP~~Wk~~dI~~lFSpfG~V-~VswIdd   49 (100)
T d1whva_          16 DHVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDD   49 (100)
T ss_dssp             CSEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEET
T ss_pred             ceeEEEeCCcccchhHHHHHhcCCCce-EEEEecC
Confidence            389999999999999999999999986 4556655