Citrus Sinensis ID: 040394

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-
Protein Sequence
MKLISLLQRHVSRTKKPKLQLRFFSYTNQQTPTQHELDQTFASFHSLPSIPCLNLLGLCKSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLVDLDIANDFSFSRVVSLA
Secondary Structure (PSIPRED)
ccHHHHHHHHccccccHHHHHHHHHHcccccccHHHHHHHHHcccccccccHHHHHHHcccccHHHHHHHHHHHHccccHHHHHHHHHHHHccccHHHHHHHHcccccccHHHHHHHHHHHHHccccHHHHHHHHHHHHccccccccHHHHHHHHHccccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHcccHHHHHHHHcccccccccHHHHHHHHHHccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccHHHHHHHHHccccccEEHHHHHHHHHHHcccccHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHccccHHHHHHHHccccccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccEEEHHHHHHHHHccccHHHHHHHHccccccccccHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHcccHHHHHHHHHHHHHcHHccccccccccHHHHHHHHcccccHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccHHHHHHHHHHHccccHHHHHHHHHHHHccccccccccEEEEccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHcccHHHHHHHHHHHccccHHHHHHHHHHHccccccccHHHHHHHHHHcHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccHHHHHHHHHHccccccEHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccHHHHHHHHHHccccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccHHHHHHHHHHcccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHcHcHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHcccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHcHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccHHHHHHHHHHcccccEEEHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHcccHHHHHHHHHHccccccEHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccEEEEEEEccccccccHHHcc
Coil and Loop (DISEMBL)
MKLISLLqrhvsrtkkpklQLRFFsytnqqtptqheldqtfasfhslpsipclnllglckstgsLKAFHALLIVDGLTNDKCNTKLVSMygsfghvkyarsvfdsmpnpdfysFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCElrdidegmKVHCEIVkvggpdsfvLTGLVDMYAKcrdigssrqvfDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMRegfvegnqITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYtqsgypdkalklftdkkwadffpnhVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFettsekdviAWNSIisglddnvspdAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIggygmqgdgggsLALFSDmlneevqpneVIFTTILSAcshtgmvgegWKCFYSMCrdfkfvpsmkHYVCMVDLLARAGRLEEALEFmenmpiepdvslFGAFlhgcglysrfdLGEVMIKKMLELHPDKACYYVLVSNLyasdgrwiRVNQVRELMKqrglskspgcslvdldiandfsFSRVVSLA
Flexible Loop (DISEMBL)
mklisllqrhvsrtkkpklqlRFFSYTNQQTPTQHELDQTFASFHSLPSIPCLNLLGLCKSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQrglskspgcslvdldiandfSFSRVVSLA
Low Complexity Region (SEG)
MKLISLLQRHVSRTKKPKLQLRFFSYTNQQTPTQHELDQTFASFHSLPSIPCLNLLGLCKSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIggygmqgdgggSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDllaragrleealeFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLVDLDIANDFSFSRVVSLA
Disordered region (IsUnstruct)
*******************QLRFFSYTN*******ELDQTFASFHSLPSIPCLNLLGLCKSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLVDLDIANDFSFSR*****
Disordered Region (DISOPRED)
********RHV***KKPKLQLRFFS******************FHSLPSIPCLNLLGLCKSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLVDLDIANDFSFSR**S**
Disordered Region (DISEMBL)
MKLISLLQRHVSRTKKPKLQLRFFSYTNQQTPTQHELDQTFASFHSLPSIPCLNLLGLCKSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELM********PGCSLVDLDIANDFSFSRVVSLA
Disordered Region (DISPRO)
MKLISLLQRHVSRTKKPKLQLRFFSYTNQQTPTQHELDQTFASFHSLPSIPCLNLLGLCKSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLVDLDIAND**********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKLISLLQRHVSRTKKPKLQLRFFSYTNQQTPTQHELDQTFASFHSLPSIPCLNLLGLCKSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCxxxxxxxxxxxxxxxxxxxxxPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLVDLDIANDFSFSRVVSLA
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	691	2.2.26 [Sep-21-2011]
Q9ZQ74	689	Pentatricopeptide repeat-	yes	no	0.960	0.963	0.571	0.0
Q3E6Q1	809	Pentatricopeptide repeat-	no	no	0.903	0.771	0.366	1e-120
O81767	823	Pentatricopeptide repeat-	no	no	0.890	0.747	0.357	1e-114
Q9SN39	871	Pentatricopeptide repeat-	no	no	0.904	0.717	0.358	1e-111
Q9FLZ9	677	Pentatricopeptide repeat-	no	no	0.901	0.920	0.338	1e-108
Q9SS97	660	Putative pentatricopeptid	no	no	0.835	0.874	0.339	1e-106
Q9LUJ2	842	Pentatricopeptide repeat-	no	no	0.888	0.729	0.349	1e-106
Q9LFL5	850	Pentatricopeptide repeat-	no	no	0.892	0.725	0.335	1e-105
Q9SS60	882	Pentatricopeptide repeat-	no	no	0.852	0.667	0.349	1e-104
Q9SVA5	834	Pentatricopeptide repeat-	no	no	0.878	0.727	0.332	1e-103

>sp|Q9ZQ74|PP146_ARATH Pentatricopeptide repeat-containing protein At2g03380, mitochondrial OS=Arabidopsis thaliana GN=PCMP-E47 PE=3 SV=1

 Score =  772 bits (1994), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 391/684 (57%), Positives = 489/684 (71%), Gaps = 20/684 (2%)

Query: 11  VSRTKKPKLQLRFFSYTNQQTPTQHELDQTFASFHSLPSIPCLNLLGLCKSTGSLKAFHA 70
           +S T++     R  S+T  +     E +   +S H   S PC  LL  C +  SL+  H 
Sbjct: 7   LSPTRRFGFPPRCVSFTTIKELILTE-ENDGSSLHYAASSPCFLLLSKCTNIDSLRQSHG 65

Query: 71  LLIVDGLTND-KCNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKD 129
           +L  +GL  D    TKLVS+YG FG+ K AR VFD +P PDFY ++VM+R Y LN    +
Sbjct: 66  VLTGNGLMGDISIATKLVSLYGFFGYTKDARLVFDQIPEPDFYLWKVMLRCYCLNKESVE 125

Query: 130 IVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDM 189
           +V+ Y  + K    +D+ VFSK LKAC EL+D+D G K+HC++VKV   D+ VLTGL+DM
Sbjct: 126 VVKLYDLLMKHGFRYDDIVFSKALKACTELQDLDNGKKIHCQLVKVPSFDNVVLTGLLDM 185

Query: 190 YAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITL 249
           YAKC +I S+ +VF++   +NVV WTSMIAGYV+ND  +EGLVLFNRMRE  V GN+ T 
Sbjct: 186 YAKCGEIKSAHKVFNDITLRNVVCWTSMIAGYVKNDLCEEGLVLFNRMRENNVLGNEYTY 245

Query: 250 GSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCS 309
           G+L+ AC KL ALHQGKW HG ++K GIE++S LVT+LLDMYVKCG+I +AR VF+E   
Sbjct: 246 GTLIMACTKLSALHQGKWFHGCLVKSGIELSSCLVTSLLDMYVKCGDISNARRVFNEHSH 305

Query: 310 IDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMV 369
           +DLV WTAMIVGYT +G  ++AL LF   K  +  PN VTIASVLS    + NL +GR V
Sbjct: 306 VDLVMWTAMIVGYTHNGSVNEALSLFQKMKGVEIKPNCVTIASVLSGCGLIENLELGRSV 365

Query: 370 HSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDN---- 425
           H L I++G+ D  V NALV MYAKC+   DA+Y+FE  SEKD++AWNSIISG   N    
Sbjct: 366 HGLSIKVGIWDTNVANALVHMYAKCYQNRDAKYVFEMESEKDIVAWNSIISGFSQNGSIH 425

Query: 426 -------------VSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLL-SSNVYVGTA 471
                        V+P+ VT+ S+ SACASLG++ VGSSLHAYS K G L SS+V+VGTA
Sbjct: 426 EALFLFHRMNSESVTPNGVTVASLFSACASLGSLAVGSSLHAYSVKLGFLASSSVHVGTA 485

Query: 472 LLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPN 531
           LL+FYAKCGD QSAR++FD + EKNT+TWSAMIGGYG QGD  GSL LF +ML ++ +PN
Sbjct: 486 LLDFYAKCGDPQSARLIFDTIEEKNTITWSAMIGGYGKQGDTIGSLELFEEMLKKQQKPN 545

Query: 532 EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFM 591
           E  FT+ILSAC HTGMV EG K F SM +D+ F PS KHY CMVD+LARAG LE+AL+ +
Sbjct: 546 ESTFTSILSACGHTGMVNEGKKYFSSMYKDYNFTPSTKHYTCMVDMLARAGELEQALDII 605

Query: 592 ENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWI 651
           E MPI+PDV  FGAFLHGCG++SRFDLGE++IKKML+LHPD A YYVLVSNLYASDGRW 
Sbjct: 606 EKMPIQPDVRCFGAFLHGCGMHSRFDLGEIVIKKMLDLHPDDASYYVLVSNLYASDGRWN 665

Query: 652 RVNQVRELMKQRGLSKSPGCSLVD 675
           +  +VR LMKQRGLSK  G S ++
Sbjct: 666 QAKEVRNLMKQRGLSKIAGHSTME 689

Arabidopsis thaliana (taxid: 3702)

>sp|Q3E6Q1|PPR32_ARATH Pentatricopeptide repeat-containing protein At1g11290 OS=Arabidopsis thaliana GN=PCMP-H40 PE=2 SV=1

 Score =  434 bits (1116), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 237/647 (36%), Positives = 372/647 (57%), Gaps = 23/647 (3%)

Query: 51  PCLNLLGLCKSTGSLKAFHALLIVDGLTNDKC-NTKLVSMYGSFGHVKYARSVFDSMPNP 109
           P   LL  C S   L+    L+  +GL  +    TKLVS++  +G V  A  VF+ + + 
Sbjct: 39  PAALLLERCSSLKELRQILPLVFKNGLYQEHFFQTKLVSLFCRYGSVDEAARVFEPIDSK 98

Query: 110 DFYSFQVMIRWYF-LNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKV 168
               +  M++ +  ++DL K + +F+  MR    E   + F+ +LK C +  ++  G ++
Sbjct: 99  LNVLYHTMLKGFAKVSDLDKAL-QFFVRMRYDDVEPVVYNFTYLLKVCGDEAELRVGKEI 157

Query: 169 HCEIVKVG-GPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCA 227
           H  +VK G   D F +TGL +MYAKCR +  +R+VFD   ++++VSW +++AGY QN  A
Sbjct: 158 HGLLVKSGFSLDLFAMTGLENMYAKCRQVNEARKVFDRMPERDLVSWNTIVAGYSQNGMA 217

Query: 228 QEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTAL 287
           +  L +   M E  ++ + IT+ S++ A + LR +  GK +HGY ++ G +   ++ TAL
Sbjct: 218 RMALEMVKSMCEENLKPSFITIVSVLPAVSALRLISVGKEIHGYAMRSGFDSLVNISTAL 277

Query: 288 LDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNH 347
           +DMY KCG++  AR +FD +   ++VSW +MI  Y Q+  P +A+ +F         P  
Sbjct: 278 VDMYAKCGSLETARQLFDGMLERNVVSWNSMIDAYVQNENPKEAMLIFQKMLDEGVKPTD 337

Query: 348 VTIASVLSASAQLGNLNMGRMVHSLGIRLGLE-DYTVINALVDMYAKCHVIADARYIFET 406
           V++   L A A LG+L  GR +H L + LGL+ + +V+N+L+ MY KC  +  A  +F  
Sbjct: 338 VSVMGALHACADLGDLERGRFIHKLSVELGLDRNVSVVNSLISMYCKCKEVDTAASMFGK 397

Query: 407 TSEKDVIAWNSIISGLDDN-----------------VSPDAVTLVSVISACASLGAVQVG 449
              + +++WN++I G   N                 V PD  T VSVI+A A L      
Sbjct: 398 LQSRTLVSWNAMILGFAQNGRPIDALNYFSQMRSRTVKPDTFTYVSVITAIAELSITHHA 457

Query: 450 SSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGM 509
             +H    +   L  NV+V TAL++ YAKCG    AR++FD M E++  TW+AMI GYG 
Sbjct: 458 KWIHGVVMR-SCLDKNVFVTTALVDMYAKCGAIMIARLIFDMMSERHVTTWNAMIDGYGT 516

Query: 510 QGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMK 569
            G G  +L LF +M    ++PN V F +++SACSH+G+V  G KCFY M  ++    SM 
Sbjct: 517 HGFGKAALELFEEMQKGTIKPNGVTFLSVISACSHSGLVEAGLKCFYMMKENYSIELSMD 576

Query: 570 HYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLEL 629
           HY  MVDLL RAGRL EA +F+  MP++P V+++GA L  C ++   +  E   +++ EL
Sbjct: 577 HYGAMVDLLGRAGRLNEAWDFIMQMPVKPAVNVYGAMLGACQIHKNVNFAEKAAERLFEL 636

Query: 630 HPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLVDL 676
           +PD   Y+VL++N+Y +   W +V QVR  M ++GL K+PGCS+V++
Sbjct: 637 NPDDGGYHVLLANIYRAASMWEKVGQVRVSMLRQGLRKTPGCSMVEI 683

Arabidopsis thaliana (taxid: 3702)

>sp|O81767|PP348_ARATH Pentatricopeptide repeat-containing protein At4g33990 OS=Arabidopsis thaliana GN=EMB2758 PE=3 SV=2

 Score =  411 bits (1057), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 231/646 (35%), Positives = 370/646 (57%), Gaps = 31/646 (4%)

Query: 55  LLGLCKSTGSLKAFHALLIVDGLTNDKC-NTKLVSMYGSFGHVKYARSVFDSMPNPDFYS 113
           L   C +  S K  HA L+V     + C + KLV++Y   G+V  AR  FD + N D Y+
Sbjct: 60  LFRYCTNLQSAKCLHARLVVSKQIQNVCISAKLVNLYCYLGNVALARHTFDHIQNRDVYA 119

Query: 114 FQVMIRWYFLNDLYKDIVE-FYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEI 172
           + +MI  Y       +++  F   M       D   F  VLKAC   R + +G K+HC  
Sbjct: 120 WNLMISGYGRAGNSSEVIRCFSLFMLSSGLTPDYRTFPSVLKAC---RTVIDGNKIHCLA 176

Query: 173 VKVGGP-DSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGL 231
           +K G   D +V   L+ +Y++ + +G++R +FDE   +++ SW +MI+GY Q+  A+E L
Sbjct: 177 LKFGFMWDVYVAASLIHLYSRYKAVGNARILFDEMPVRDMGSWNAMISGYCQSGNAKEAL 236

Query: 232 VLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMY 291
            L N +R      + +T+ SL++AC +    ++G  +H Y +K G+E    +   L+D+Y
Sbjct: 237 TLSNGLRAM----DSVTVVSLLSACTEAGDFNRGVTIHSYSIKHGLESELFVSNKLIDLY 292

Query: 292 VKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIA 351
            + G +RD + VFD +   DL+SW ++I  Y  +  P +A+ LF + + +   P+ +T+ 
Sbjct: 293 AEFGRLRDCQKVFDRMYVRDLISWNSIIKAYELNEQPLRAISLFQEMRLSRIQPDCLTLI 352

Query: 352 SVLSASAQLGNLNMGRMVHSLGIRLG--LEDYTVINALVDMYAKCHVIADARYIFETTSE 409
           S+ S  +QLG++   R V    +R G  LED T+ NA+V MYAK  ++  AR +F     
Sbjct: 353 SLASILSQLGDIRACRSVQGFTLRKGWFLEDITIGNAVVVMYAKLGLVDSARAVFNWLPN 412

Query: 410 KDVIAWNSIISGLDDN------------------VSPDAVTLVSVISACASLGAVQVGSS 451
            DVI+WN+IISG   N                  ++ +  T VSV+ AC+  GA++ G  
Sbjct: 413 TDVISWNTIISGYAQNGFASEAIEMYNIMEEEGEIAANQGTWVSVLPACSQAGALRQGMK 472

Query: 452 LHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQG 511
           LH    K GL   +V+V T+L + Y KCG  + A  +F  +   N+V W+ +I  +G  G
Sbjct: 473 LHGRLLKNGLYL-DVFVVTSLADMYGKCGRLEDALSLFYQIPRVNSVPWNTLIACHGFHG 531

Query: 512 DGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHY 571
            G  ++ LF +ML+E V+P+ + F T+LSACSH+G+V EG  CF  M  D+   PS+KHY
Sbjct: 532 HGEKAVMLFKEMLDEGVKPDHITFVTLLSACSHSGLVDEGQWCFEMMQTDYGITPSLKHY 591

Query: 572 VCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHP 631
            CMVD+  RAG+LE AL+F+++M ++PD S++GA L  C ++   DLG++  + + E+ P
Sbjct: 592 GCMVDMYGRAGQLETALKFIKSMSLQPDASIWGALLSACRVHGNVDLGKIASEHLFEVEP 651

Query: 632 DKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLVDLD 677
           +   Y+VL+SN+YAS G+W  V+++R +   +GL K+PG S +++D
Sbjct: 652 EHVGYHVLLSNMYASAGKWEGVDEIRSIAHGKGLRKTPGWSSMEVD 697

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SN39|PP320_ARATH Pentatricopeptide repeat-containing protein At4g18750, chloroplastic OS=Arabidopsis thaliana GN=PCMP-H45 PE=2 SV=1

 Score =  404 bits (1038), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 235/655 (35%), Positives = 364/655 (55%), Gaps = 30/655 (4%)

Query: 48  PSIPCLNLLGLCKSTGSLK---AFHALLIVDGLTND-KCNTKLVSMYGSFGHVKYARSVF 103
           P   C ++L LC  + SLK        +  +G   D    +KL  MY + G +K A  VF
Sbjct: 94  PRTLC-SVLQLCADSKSLKDGKEVDNFIRGNGFVIDSNLGSKLSLMYTNCGDLKEASRVF 152

Query: 104 DSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDID 163
           D +       + +++     +  +   +  +K M     E D++ FS V K+   LR + 
Sbjct: 153 DEVKIEKALFWNILMNELAKSGDFSGSIGLFKKMMSSGVEMDSYTFSCVSKSFSSLRSVH 212

Query: 164 EGMKVHCEIVKVG-GPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYV 222
            G ++H  I+K G G  + V   LV  Y K + + S+R+VFDE  +++V+SW S+I GYV
Sbjct: 213 GGEQLHGFILKSGFGERNSVGNSLVAFYLKNQRVDSARKVFDEMTERDVISWNSIINGYV 272

Query: 223 QNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSH 282
            N  A++GL +F +M    +E +  T+ S+   CA  R +  G+ +H   +K        
Sbjct: 273 SNGLAEKGLSVFVQMLVSGIEIDLATIVSVFAGCADSRLISLGRAVHSIGVKACFSREDR 332

Query: 283 LVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWAD 342
               LLDMY KCG++  A++VF E+    +VS+T+MI GY + G   +A+KLF + +   
Sbjct: 333 FCNTLLDMYSKCGDLDSAKAVFREMSDRSVVSYTSMIAGYAREGLAGEAVKLFEEMEEEG 392

Query: 343 FFPNHVTIASVLSASAQLGNLNMGRMVHSLGIR---LGLEDYTVINALVDMYAKCHVIAD 399
             P+  T+ +VL+  A+   L+ G+ VH   I+   LG  D  V NAL+DMYAKC  + +
Sbjct: 393 ISPDVYTVTAVLNCCARYRLLDEGKRVHEW-IKENDLGF-DIFVSNALMDMYAKCGSMQE 450

Query: 400 ARYIFETTSEKDVIAWNSIISGLDDNV------------------SPDAVTLVSVISACA 441
           A  +F     KD+I+WN+II G   N                   SPD  T+  V+ ACA
Sbjct: 451 AELVFSEMRVKDIISWNTIIGGYSKNCYANEALSLFNLLLEEKRFSPDERTVACVLPACA 510

Query: 442 SLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWS 501
           SL A   G  +H Y  + G  S   +V  +L++ YAKCG    A M+FD +  K+ V+W+
Sbjct: 511 SLSAFDKGREIHGYIMRNGYFSDR-HVANSLVDMYAKCGALLLAHMLFDDIASKDLVSWT 569

Query: 502 AMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRD 561
            MI GYGM G G  ++ALF+ M    ++ +E+ F ++L ACSH+G+V EGW+ F  M  +
Sbjct: 570 VMIAGYGMHGFGKEAIALFNQMRQAGIEADEISFVSLLYACSHSGLVDEGWRFFNIMRHE 629

Query: 562 FKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEV 621
            K  P+++HY C+VD+LAR G L +A  F+ENMPI PD +++GA L GC ++    L E 
Sbjct: 630 CKIEPTVEHYACIVDMLARTGDLIKAYRFIENMPIPPDATIWGALLCGCRIHHDVKLAEK 689

Query: 622 MIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLVDL 676
           + +K+ EL P+   YYVL++N+YA   +W +V ++R+ + QRGL K+PGCS +++
Sbjct: 690 VAEKVFELEPENTGYYVLMANIYAEAEKWEQVKRLRKRIGQRGLRKNPGCSWIEI 744

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FLZ9|PP405_ARATH Pentatricopeptide repeat-containing protein At5g39350 OS=Arabidopsis thaliana GN=PCMP-E16 PE=2 SV=1

 Score =  392 bits (1007), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 220/649 (33%), Positives = 352/649 (54%), Gaps = 26/649 (4%)

Query: 53  LNLLGLCKSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPNPDFY 112
           LN     +S    KA H  +I  G  +    + L   Y   GH+ YAR +F+ MP     
Sbjct: 22  LNHFAATQSISKTKALHCHVITGGRVSGHILSTLSVTYALCGHITYARKLFEEMPQSSLL 81

Query: 113 SFQVMIRWYFLNDLYKDIVE-FYKCMRKRLK-EHDNFVFSKVLKACCELRDIDEGMKVHC 170
           S+ ++IR Y    LY D +  F + + + +K   D + +  V KA  EL+ +  G+ VH 
Sbjct: 82  SYNIVIRMYVREGLYHDAISVFIRMVSEGVKCVPDGYTYPFVAKAAGELKSMKLGLVVHG 141

Query: 171 EIVKVG-GPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQE 229
            I++   G D +V   L+ MY     +  +R VFD   +++V+SW +MI+GY +N    +
Sbjct: 142 RILRSWFGRDKYVQNALLAMYMNFGKVEMARDVFDVMKNRDVISWNTMISGYYRNGYMND 201

Query: 230 GLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLD 289
            L++F+ M    V+ +  T+ S++  C  L+ L  G+ +H  + +  +     +  AL++
Sbjct: 202 ALMMFDWMVNESVDLDHATIVSMLPVCGHLKDLEMGRNVHKLVEEKRLGDKIEVKNALVN 261

Query: 290 MYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVT 349
           MY+KCG + +AR VFD +   D+++WT MI GYT+ G  + AL+L    ++    PN VT
Sbjct: 262 MYLKCGRMDEARFVFDRMERRDVITWTCMINGYTEDGDVENALELCRLMQFEGVRPNAVT 321

Query: 350 IASVLSASAQLGNLNMGRMVHSLGIRLGL-EDYTVINALVDMYAKCHVIADARYIFETTS 408
           IAS++S       +N G+ +H   +R  +  D  +  +L+ MYAKC  +     +F   S
Sbjct: 322 IASLVSVCGDALKVNDGKCLHGWAVRQQVYSDIIIETSLISMYAKCKRVDLCFRVFSGAS 381

Query: 409 EKDVIAWNSIISGLDDN-----------------VSPDAVTLVSVISACASLGAVQVGSS 451
           +     W++II+G   N                 V P+  TL S++ A A+L  ++   +
Sbjct: 382 KYHTGPWSAIIAGCVQNELVSDALGLFKRMRREDVEPNIATLNSLLPAYAALADLRQAMN 441

Query: 452 LHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK----NTVTWSAMIGGY 507
           +H Y TK G +SS +   T L++ Y+KCG  +SA  +F+ ++EK    + V W A+I GY
Sbjct: 442 IHCYLTKTGFMSS-LDAATGLVHVYSKCGTLESAHKIFNGIQEKHKSKDVVLWGALISGY 500

Query: 508 GMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS 567
           GM GDG  +L +F +M+   V PNE+ FT+ L+ACSH+G+V EG   F  M   +K +  
Sbjct: 501 GMHGDGHNALQVFMEMVRSGVTPNEITFTSALNACSHSGLVEEGLTLFRFMLEHYKTLAR 560

Query: 568 MKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKML 627
             HY C+VDLL RAGRL+EA   +  +P EP  +++GA L  C  +    LGE+   K+ 
Sbjct: 561 SNHYTCIVDLLGRAGRLDEAYNLITTIPFEPTSTVWGALLAACVTHENVQLGEMAANKLF 620

Query: 628 ELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLVDL 676
           EL P+    YVL++N+YA+ GRW  + +VR +M+  GL K PG S +++
Sbjct: 621 ELEPENTGNYVLLANIYAALGRWKDMEKVRSMMENVGLRKKPGHSTIEI 669

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SS97|PP205_ARATH Putative pentatricopeptide repeat-containing protein At3g01580 OS=Arabidopsis thaliana GN=PCMP-E87 PE=3 SV=2

 Score =  386 bits (991), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 204/601 (33%), Positives = 335/601 (55%), Gaps = 24/601 (3%)

Query: 99  ARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCE 158
           AR +F  M     Y +  +++       +++++  +  M +  ++ DNF     LKAC E
Sbjct: 13  ARQMFGEMTKRSLYQWNTLLKSLSREKQWEEVLYHFSHMFRDEEKPDNFTLPVALKACGE 72

Query: 159 LRDIDEGMKVHCEIVK--VGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTS 216
           LR+++ G  +H  + K    G D +V + L+ MY KC  +  + ++FDE    ++V+W+S
Sbjct: 73  LREVNYGEMIHGFVKKDVTLGSDLYVGSSLIYMYIKCGRMIEALRMFDELEKPDIVTWSS 132

Query: 217 MIAGYVQNDCAQEGLVLFNRM-REGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKI 275
           M++G+ +N    + +  F RM     V  +++TL +LV+AC KL     G+ +HG++++ 
Sbjct: 133 MVSGFEKNGSPYQAVEFFRRMVMASDVTPDRVTLITLVSACTKLSNSRLGRCVHGFVIRR 192

Query: 276 GIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLF 335
           G   +  LV +LL+ Y K    ++A ++F  +   D++SW+ +I  Y Q+G   +AL +F
Sbjct: 193 GFSNDLSLVNSLLNCYAKSRAFKEAVNLFKMIAEKDVISWSTVIACYVQNGAAAEALLVF 252

Query: 336 TDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLE-DYTVINALVDMYAKC 394
            D       PN  T+  VL A A   +L  GR  H L IR GLE +  V  ALVDMY KC
Sbjct: 253 NDMMDDGTEPNVATVLCVLQACAAAHDLEQGRKTHELAIRKGLETEVKVSTALVDMYMKC 312

Query: 395 HVIADARYIFETTSEKDVIAWNSIISG------------------LDDNVSPDAVTLVSV 436
               +A  +F     KDV++W ++ISG                  L++N  PDA+ +V V
Sbjct: 313 FSPEEAYAVFSRIPRKDVVSWVALISGFTLNGMAHRSIEEFSIMLLENNTRPDAILMVKV 372

Query: 437 ISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKN 496
           + +C+ LG ++     H+Y  K G   SN ++G +L+  Y++CG   +A  VF+ +  K+
Sbjct: 373 LGSCSELGFLEQAKCFHSYVIKYGF-DSNPFIGASLVELYSRCGSLGNASKVFNGIALKD 431

Query: 497 TVTWSAMIGGYGMQGDGGGSLALFSDML-NEEVQPNEVIFTTILSACSHTGMVGEGWKCF 555
           TV W+++I GYG+ G G  +L  F+ M+ + EV+PNEV F +ILSACSH G++ EG + F
Sbjct: 432 TVVWTSLITGYGIHGKGTKALETFNHMVKSSEVKPNEVTFLSILSACSHAGLIHEGLRIF 491

Query: 556 YSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSR 615
             M  D++  P+++HY  +VDLL R G L+ A+E  + MP  P   + G  L  C ++  
Sbjct: 492 KLMVNDYRLAPNLEHYAVLVDLLGRVGDLDTAIEITKRMPFSPTPQILGTLLGACRIHQN 551

Query: 616 FDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLVD 675
            ++ E + KK+ EL  + A YY+L+SN+Y   G W  V ++R  +KQRG+ K    SL++
Sbjct: 552 GEMAETVAKKLFELESNHAGYYMLMSNVYGVKGEWENVEKLRNSVKQRGIKKGLAESLIE 611

Query: 676 L 676
           +
Sbjct: 612 I 612

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LUJ2|PP249_ARATH Pentatricopeptide repeat-containing protein At3g22690 OS=Arabidopsis thaliana GN=PCMP-H56 PE=2 SV=1

 Score =  385 bits (988), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 237/678 (34%), Positives = 373/678 (55%), Gaps = 64/678 (9%)

Query: 59  CKSTGSLKAFHALLIVDGLTNDKCN-TKLVSMYGSFG---HVKYARSVFDSMPNPDFYS- 113
           CK+   LK FH  L   GL ND    TKLV+     G    + +A+ VF+   N + Y  
Sbjct: 42  CKTIDELKMFHRSLTKQGLDNDVSTITKLVARSCELGTRESLSFAKEVFE---NSESYGT 98

Query: 114 ---FQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHC 170
              +  +IR Y  + L  + +  +  M       D + F   L AC + R    G+++H 
Sbjct: 99  CFMYNSLIRGYASSGLCNEAILLFLRMMNSGISPDKYTFPFGLSACAKSRAKGNGIQIHG 158

Query: 171 EIVKVG-GPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQE 229
            IVK+G   D FV   LV  YA+C ++ S+R+VFDE  ++NVVSWTSMI GY + D A++
Sbjct: 159 LIVKMGYAKDLFVQNSLVHFYAECGELDSARKVFDEMSERNVVSWTSMICGYARRDFAKD 218

Query: 230 GLVLFNRM-REGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALL 288
            + LF RM R+  V  N +T+  +++ACAKL  L  G+ ++ +I   GIE+N  +V+AL+
Sbjct: 219 AVDLFFRMVRDEEVTPNSVTMVCVISACAKLEDLETGEKVYAFIRNSGIEVNDLMVSALV 278

Query: 289 DMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHV 348
           DMY+KC  I  A+ +FDE  + +L    AM   Y + G   +AL +F     +   P+ +
Sbjct: 279 DMYMKCNAIDVAKRLFDEYGASNLDLCNAMASNYVRQGLTREALGVFNLMMDSGVRPDRI 338

Query: 349 TIASVLSASAQLGNLNMGRMVHSLGIRLGLEDY-TVINALVDMYAKCH------------ 395
           ++ S +S+ +QL N+  G+  H   +R G E +  + NAL+DMY KCH            
Sbjct: 339 SMLSAISSCSQLRNILWGKSCHGYVLRNGFESWDNICNALIDMYMKCHRQDTAFRIFDRM 398

Query: 396 ----------VIA--------DARY-IFETTSEKDVIAWNSIISGL-------------- 422
                     ++A        DA +  FET  EK++++WN+IISGL              
Sbjct: 399 SNKTVVTWNSIVAGYVENGEVDAAWETFETMPEKNIVSWNTIISGLVQGSLFEEAIEVFC 458

Query: 423 ----DDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAK 478
                + V+ D VT++S+ SAC  LGA+ +   ++ Y  K G +  +V +GT L++ +++
Sbjct: 459 SMQSQEGVNADGVTMMSIASACGHLGALDLAKWIYYYIEKNG-IQLDVRLGTTLVDMFSR 517

Query: 479 CGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTI 538
           CGD +SA  +F+++  ++   W+A IG   M G+   ++ LF DM+ + ++P+ V F   
Sbjct: 518 CGDPESAMSIFNSLTNRDVSAWTAAIGAMAMAGNAERAIELFDDMIEQGLKPDGVAFVGA 577

Query: 539 LSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEP 598
           L+ACSH G+V +G + FYSM +     P   HY CMVDLL RAG LEEA++ +E+MP+EP
Sbjct: 578 LTACSHGGLVQQGKEIFYSMLKLHGVSPEDVHYGCMVDLLGRAGLLEEAVQLIEDMPMEP 637

Query: 599 DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRE 658
           +  ++ + L  C +    ++     +K+  L P++   YVL+SN+YAS GRW  + +VR 
Sbjct: 638 NDVIWNSLLAACRVQGNVEMAAYAAEKIQVLAPERTGSYVLLSNVYASAGRWNDMAKVRL 697

Query: 659 LMKQRGLSKSPGCSLVDL 676
            MK++GL K PG S + +
Sbjct: 698 SMKEKGLRKPPGTSSIQI 715

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LFL5|PP390_ARATH Pentatricopeptide repeat-containing protein At5g16860 OS=Arabidopsis thaliana GN=PCMP-H92 PE=2 SV=1

 Score =  381 bits (979), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 230/685 (33%), Positives = 346/685 (50%), Gaps = 68/685 (9%)

Query: 59  CKSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPNPD--FYSFQV 116
           CK+   +K  H  L+  G+      + L+S Y S G + +A S+    P  D   Y +  
Sbjct: 38  CKTISQVKLIHQKLLSFGILTLNLTSHLISTYISVGCLSHAVSLLRRFPPSDAGVYHWNS 97

Query: 117 MIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVG 176
           +IR Y  N      +  +  M       DN+ F  V KAC E+  +  G   H   +  G
Sbjct: 98  LIRSYGDNGCANKCLYLFGLMHSLSWTPDNYTFPFVFKACGEISSVRCGESAHALSLVTG 157

Query: 177 G-PDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFN 235
              + FV   LV MY++CR +  +R+VFDE    +VVSW S+I  Y +    +  L +F+
Sbjct: 158 FISNVFVGNALVAMYSRCRSLSDARKVFDEMSVWDVVSWNSIIESYAKLGKPKVALEMFS 217

Query: 236 RMREGF-VEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKC 294
           RM   F    + ITL +++  CA L     GK LH + +   +  N  +   L+DMY KC
Sbjct: 218 RMTNEFGCRPDNITLVNVLPPCASLGTHSLGKQLHCFAVTSEMIQNMFVGNCLVDMYAKC 277

Query: 295 GNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKK----------WADFF 344
           G + +A +VF  +   D+VSW AM+ GY+Q G  + A++LF   +          W+   
Sbjct: 278 GMMDEANTVFSNMSVKDVVSWNAMVAGYSQIGRFEDAVRLFEKMQEEKIKMDVVTWSAAI 337

Query: 345 -------------------------PNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLE 379
                                    PN VT+ SVLS  A +G L  G+ +H   I+  ++
Sbjct: 338 SGYAQRGLGYEALGVCRQMLSSGIKPNEVTLISVLSGCASVGALMHGKEIHCYAIKYPID 397

Query: 380 --------DYTVINALVDMYAKCHVIADARYIFETTS--EKDVIAWNSIISGL------- 422
                   +  VIN L+DMYAKC  +  AR +F++ S  E+DV+ W  +I G        
Sbjct: 398 LRKNGHGDENMVINQLIDMYAKCKKVDTARAMFDSLSPKERDVVTWTVMIGGYSQHGDAN 457

Query: 423 ------------DDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGT 470
                       D    P+A T+   + ACASL A+++G  +HAY+ +    +  ++V  
Sbjct: 458 KALELLSEMFEEDCQTRPNAFTISCALVACASLAALRIGKQIHAYALRNQQNAVPLFVSN 517

Query: 471 ALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQP 530
            L++ YAKCG    AR+VFD M  KN VTW++++ GYGM G G  +L +F +M     + 
Sbjct: 518 CLIDMYAKCGSISDARLVFDNMMAKNEVTWTSLMTGYGMHGYGEEALGIFDEMRRIGFKL 577

Query: 531 NEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEF 590
           + V    +L ACSH+GM+ +G + F  M   F   P  +HY C+VDLL RAGRL  AL  
Sbjct: 578 DGVTLLVVLYACSHSGMIDQGMEYFNRMKTVFGVSPGPEHYACLVDLLGRAGRLNAALRL 637

Query: 591 MENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRW 650
           +E MP+EP   ++ AFL  C ++ + +LGE   +K+ EL  +    Y L+SNLYA+ GRW
Sbjct: 638 IEEMPMEPPPVVWVAFLSCCRIHGKVELGEYAAEKITELASNHDGSYTLLSNLYANAGRW 697

Query: 651 IRVNQVRELMKQRGLSKSPGCSLVD 675
             V ++R LM+ +G+ K PGCS V+
Sbjct: 698 KDVTRIRSLMRHKGVKKRPGCSWVE 722

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SS60|PP210_ARATH Pentatricopeptide repeat-containing protein At3g03580 OS=Arabidopsis thaliana GN=PCMP-H23 PE=2 SV=1

 Score =  378 bits (971), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 213/610 (34%), Positives = 345/610 (56%), Gaps = 21/610 (3%)

Query: 86  LVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHD 145
           LV MY   G +  AR VFD MP  D  S+  +I  Y  +  Y++ +E Y  ++      D
Sbjct: 147 LVDMYSRMGLLTRARQVFDEMPVRDLVSWNSLISGYSSHGYYEEALEIYHELKNSWIVPD 206

Query: 146 NFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTG-LVDMYAKCRDIGSSRQVFD 204
           +F  S VL A   L  + +G  +H   +K G     V+   LV MY K R    +R+VFD
Sbjct: 207 SFTVSSVLPAFGNLLVVKQGQGLHGFALKSGVNSVVVVNNGLVAMYLKFRRPTDARRVFD 266

Query: 205 ETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQ 264
           E   ++ VS+ +MI GY++ +  +E + +F    + F + + +T+ S++ AC  LR L  
Sbjct: 267 EMDVRDSVSYNTMICGYLKLEMVEESVRMFLENLDQF-KPDLLTVSSVLRACGHLRDLSL 325

Query: 265 GKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQ 324
            K+++ Y+LK G  + S +   L+D+Y KCG++  AR VF+ +   D VSW ++I GY Q
Sbjct: 326 AKYIYNYMLKAGFVLESTVRNILIDVYAKCGDMITARDVFNSMECKDTVSWNSIISGYIQ 385

Query: 325 SGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGL-EDYTV 383
           SG   +A+KLF      +   +H+T   ++S S +L +L  G+ +HS GI+ G+  D +V
Sbjct: 386 SGDLMEAMKLFKMMMIMEEQADHITYLMLISVSTRLADLKFGKGLHSNGIKSGICIDLSV 445

Query: 384 INALVDMYAKCHVIADARYIFETTSEKDVIAWNSIIS----------GLD-------DNV 426
            NAL+DMYAKC  + D+  IF +    D + WN++IS          GL          V
Sbjct: 446 SNALIDMYAKCGEVGDSLKIFSSMGTGDTVTWNTVISACVRFGDFATGLQVTTQMRKSEV 505

Query: 427 SPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSAR 486
            PD  T +  +  CASL A ++G  +H    + G   S + +G AL+  Y+KCG  +++ 
Sbjct: 506 VPDMATFLVTLPMCASLAAKRLGKEIHCCLLRFGY-ESELQIGNALIEMYSKCGCLENSS 564

Query: 487 MVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTG 546
            VF+ M  ++ VTW+ MI  YGM G+G  +L  F+DM    + P+ V+F  I+ ACSH+G
Sbjct: 565 RVFERMSRRDVVTWTGMIYAYGMYGEGEKALETFADMEKSGIVPDSVVFIAIIYACSHSG 624

Query: 547 MVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAF 606
           +V EG  CF  M   +K  P ++HY C+VDLL+R+ ++ +A EF++ MPI+PD S++ + 
Sbjct: 625 LVDEGLACFEKMKTHYKIDPMIEHYACVVDLLSRSQKISKAEEFIQAMPIKPDASIWASV 684

Query: 607 LHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLS 666
           L  C      +  E + ++++EL+PD   Y +L SN YA+  +W +V+ +R+ +K + ++
Sbjct: 685 LRACRTSGDMETAERVSRRIIELNPDDPGYSILASNAYAALRKWDKVSLIRKSLKDKHIT 744

Query: 667 KSPGCSLVDL 676
           K+PG S +++
Sbjct: 745 KNPGYSWIEV 754

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SVA5|PP357_ARATH Pentatricopeptide repeat-containing protein At4g39530 OS=Arabidopsis thaliana GN=PCMP-E52 PE=1 SV=1

 Score =  377 bits (968), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 211/634 (33%), Positives = 347/634 (54%), Gaps = 27/634 (4%)

Query: 68  FHALLIVDGLTND-KCNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYF-LND 125
             + L+  G   D    T L+  Y   G++ YAR VFD++P     ++  MI     +  
Sbjct: 170 LQSFLVKSGFDRDVYVGTLLIDFYLKDGNIDYARLVFDALPEKSTVTWTTMISGCVKMGR 229

Query: 126 LYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGP-DSFVLT 184
            Y  +  FY+ M   +   D ++ S VL AC  L  ++ G ++H  I++ G   D+ ++ 
Sbjct: 230 SYVSLQLFYQLMEDNVVP-DGYILSTVLSACSILPFLEGGKQIHAHILRYGLEMDASLMN 288

Query: 185 GLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEG 244
            L+D Y KC  + ++ ++F+   +KN++SWT++++GY QN   +E + LF  M +  ++ 
Sbjct: 289 VLIDSYVKCGRVIAAHKLFNGMPNKNIISWTTLLSGYKQNALHKEAMELFTSMSKFGLKP 348

Query: 245 NQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVF 304
           +     S++T+CA L AL  G  +H Y +K  +  +S++  +L+DMY KC  + DAR VF
Sbjct: 349 DMYACSSILTSCASLHALGFGTQVHAYTIKANLGNDSYVTNSLIDMYAKCDCLTDARKVF 408

Query: 305 DELCSIDLVSWTAMIVGYTQSGYP---DKALKLFTDKKWADFFPNHVTIASVLSASAQLG 361
           D   + D+V + AMI GY++ G      +AL +F D ++    P+ +T  S+L ASA L 
Sbjct: 409 DIFAAADVVLFNAMIEGYSRLGTQWELHEALNIFRDMRFRLIRPSLLTFVSLLRASASLT 468

Query: 362 NLNMGRMVHSLGIRLGLE-DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIIS 420
           +L + + +H L  + GL  D    +AL+D+Y+ C+ + D+R +F+    KD++ WNS+ +
Sbjct: 469 SLGLSKQIHGLMFKYGLNLDIFAGSALIDVYSNCYCLKDSRLVFDEMKVKDLVIWNSMFA 528

Query: 421 G--------------LDDNVS---PDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLS 463
           G              L+  +S   PD  T  ++++A  +L +VQ+G   H    K+GL  
Sbjct: 529 GYVQQSENEEALNLFLELQLSRERPDEFTFANMVTAAGNLASVQLGQEFHCQLLKRGL-E 587

Query: 464 SNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDM 523
            N Y+  ALL+ YAKCG  + A   FD+   ++ V W+++I  Y   G+G  +L +   M
Sbjct: 588 CNPYITNALLDMYAKCGSPEDAHKAFDSAASRDVVCWNSVISSYANHGEGKKALQMLEKM 647

Query: 524 LNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGR 583
           ++E ++PN + F  +LSACSH G+V +G K F  M R F   P  +HYVCMV LL RAGR
Sbjct: 648 MSEGIEPNYITFVGVLSACSHAGLVEDGLKQFELMLR-FGIEPETEHYVCMVSLLGRAGR 706

Query: 584 LEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNL 643
           L +A E +E MP +P   ++ + L GC      +L E   +  +   P  +  + ++SN+
Sbjct: 707 LNKARELIEKMPTKPAAIVWRSLLSGCAKAGNVELAEHAAEMAILSDPKDSGSFTMLSNI 766

Query: 644 YASDGRWIRVNQVRELMKQRGLSKSPGCSLVDLD 677
           YAS G W    +VRE MK  G+ K PG S + ++
Sbjct: 767 YASKGMWTEAKKVRERMKVEGVVKEPGRSWIGIN 800

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	691
225423551	700	PREDICTED: pentatricopeptide repeat-cont	0.972	0.96	0.689	0.0
224112156	665	predicted protein [Populus trichocarpa]	0.933	0.969	0.664	0.0
357474955	871	Pentatricopeptide repeat-containing prot	0.913	0.724	0.600	0.0
449464466	1830	PREDICTED: LOW QUALITY PROTEIN: uncharac	0.853	0.322	0.615	0.0
356521639	699	PREDICTED: pentatricopeptide repeat-cont	0.962	0.951	0.570	0.0
297814636	708	predicted protein [Arabidopsis lyrata su	0.949	0.926	0.578	0.0
15227623	689	pentatricopeptide repeat-containing prot	0.960	0.963	0.571	0.0
326495056	673	predicted protein [Hordeum vulgare subsp	0.918	0.943	0.503	0.0
242092246	683	hypothetical protein SORBIDRAFT_10g00580	0.895	0.906	0.508	0.0
357118484	678	PREDICTED: pentatricopeptide repeat-cont	0.940	0.958	0.483	0.0

>gi|225423551|ref|XP_002274884.1| PREDICTED: pentatricopeptide repeat-containing protein At2g03380, mitochondrial [Vitis vinifera] gi|147818711|emb|CAN65040.1| hypothetical protein VITISV_009460 [Vitis vinifera]

 Score =  991 bits (2561), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 485/703 (68%), Positives = 567/703 (80%), Gaps = 31/703 (4%)

Query: 1   MKLISLLQRHVSRTKKPKLQLRFFSYTN-QQTPTQHELDQTFASFHSLPSIPCLNLLGLC 59
           MK ISLL RH        LQ R  + T  Q+TP   E+D+T AS  S+ S PC +LLG+C
Sbjct: 1   MKRISLLHRH--------LQWRNLTVTALQRTP---EIDRTIASIQSISSNPCFSLLGIC 49

Query: 60  KSTGSLKAFHALLIVDGLTNDK-CNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMI 118
           K+  SL+  HALL+V GL+ D  C TKLVS+YGSFGHV+ AR +FD + NPD YS++VMI
Sbjct: 50  KTVSSLRKIHALLVVHGLSEDLLCETKLVSLYGSFGHVECARLMFDRIRNPDLYSWKVMI 109

Query: 119 RWYFLNDLYKDIVEFYKC-MRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGG 177
           RWYFLND Y +IV+FY   +RK L E+DN VFS VLKAC ELR+ DEG K+HC+IVKVG 
Sbjct: 110 RWYFLNDSYSEIVQFYNTRLRKCLNEYDNVVFSIVLKACSELRETDEGRKLHCQIVKVGS 169

Query: 178 PDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRM 237
           PDSFVLTGLVDMYAKCR++  SR+VFDE LD+NVV WTSMI GYVQNDC +EGLVLFNRM
Sbjct: 170 PDSFVLTGLVDMYAKCREVEDSRRVFDEILDRNVVCWTSMIVGYVQNDCLKEGLVLFNRM 229

Query: 238 REGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNI 297
           REG VEGNQ TLGSLVTAC KL ALHQGKW+HGY++K G ++NS LVT LLD+Y KCG+I
Sbjct: 230 REGLVEGNQYTLGSLVTACTKLGALHQGKWVHGYVIKSGFDLNSFLVTPLLDLYFKCGDI 289

Query: 298 RDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSAS 357
           RDA SVFDEL +IDLVSWTAMIVGY Q GYP +ALKLFTD++W D  PN VT +SVLSA 
Sbjct: 290 RDAFSVFDELSTIDLVSWTAMIVGYAQRGYPREALKLFTDERWKDLLPNTVTTSSVLSAC 349

Query: 358 AQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNS 417
           AQ G+LNMGR VH LGI+LG ED T  NALVDMYAKCH+I DARY+FET  +KDVIAWNS
Sbjct: 350 AQTGSLNMGRSVHCLGIKLGSEDATFENALVDMYAKCHMIGDARYVFETVFDKDVIAWNS 409

Query: 418 IISGL-----------------DDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQG 460
           IISG                   D+V PDA+TLVSV+SACAS+GA +VGSSLH Y+ K G
Sbjct: 410 IISGYTQNGYAYEALELFDQMRSDSVYPDAITLVSVLSACASVGAYRVGSSLHGYAIKAG 469

Query: 461 LLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALF 520
           LLS +VYVGTALLNFYAKCGDA+SAR++FD M EKNT+TWSAMIGGYG+QGD   SL LF
Sbjct: 470 LLSGSVYVGTALLNFYAKCGDAESARVIFDEMGEKNTITWSAMIGGYGIQGDCSRSLELF 529

Query: 521 SDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLAR 580
            DML E+++PNEVIFTTILSACSH+GM+GEGW+ F +MC+ + FVPSMKHY CMVDLLAR
Sbjct: 530 GDMLKEKLEPNEVIFTTILSACSHSGMLGEGWRYFNTMCQVYNFVPSMKHYACMVDLLAR 589

Query: 581 AGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLV 640
           AGRLEEAL+F+E +PI+PDVSL GAFLHGC L+SRFDLGEV +++MLELHPDKACYYVL+
Sbjct: 590 AGRLEEALDFIEKIPIQPDVSLLGAFLHGCRLHSRFDLGEVAVRRMLELHPDKACYYVLM 649

Query: 641 SNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLVDLDIANDFS 683
           SNLYAS+GRW + NQV ELMKQRGL+K PG SLVD++ +NDFS
Sbjct: 650 SNLYASEGRWSQANQVMELMKQRGLAKLPGWSLVDIETSNDFS 692

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224112156|ref|XP_002316102.1| predicted protein [Populus trichocarpa] gi|222865142|gb|EEF02273.1| predicted protein [Populus trichocarpa]

 Score =  914 bits (2361), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 442/665 (66%), Positives = 526/665 (79%), Gaps = 20/665 (3%)

Query: 47  LPSIPCLN--LLGLCKSTGSLKAFHALLIVDGLTND-KCNTKLVSMYGSFGHVKYARSVF 103
           +P  P L+     LC +  +L   HA L+V GLT D  C+TKLVS+YGSFG +  AR VF
Sbjct: 1   MPLPPILHNFFYSLCDNINTLMEMHAYLVVQGLTRDLSCSTKLVSLYGSFGRLDLARLVF 60

Query: 104 DSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDID 163
           D++P+PDF S++V+IRWYFLN  ++DIV FY  MR  LKE DN VFS VLKAC E R+ D
Sbjct: 61  DTIPHPDFLSWKVIIRWYFLNSEFRDIVGFYNRMRVCLKECDNVVFSHVLKACSESRNFD 120

Query: 164 EGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQ 223
           EG KVHC+IVK G PDSFV TGLVDMYAKC +I  SR VFDE LD+NV SW+SMIAGYVQ
Sbjct: 121 EGRKVHCQIVKFGNPDSFVFTGLVDMYAKCGEIECSRSVFDENLDRNVFSWSSMIAGYVQ 180

Query: 224 NDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHL 283
           N+ AQ+GLVLFNRMRE  +E NQITLG LV AC KL ALHQGKWLHGY++K GIE+ S+L
Sbjct: 181 NNLAQDGLVLFNRMREELIEANQITLGILVHACKKLGALHQGKWLHGYLIKCGIELGSYL 240

Query: 284 VTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADF 343
           VTALLD+Y KCG +RDARSVFDEL  ID+VSWTAMIVGYTQ+G P++ALKLF  K+    
Sbjct: 241 VTALLDLYAKCGVVRDARSVFDELHGIDIVSWTAMIVGYTQNGCPEEALKLFLQKEQVAV 300

Query: 344 FPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYI 403
            PN VTIASV S+ +QL NLN+GR +H L I+LG  D  V N+LVD YAKC +  DARY+
Sbjct: 301 LPNDVTIASVFSSCSQLLNLNLGRSIHGLSIKLGSRDPIVTNSLVDFYAKCQMNRDARYV 360

Query: 404 FETTSEKDVIAWNSIISGLDDN-----------------VSPDAVTLVSVISACASLGAV 446
           FET S++DV+AWNSIIS    N                 V PDAVTLVSV+SACASL A+
Sbjct: 361 FETISDRDVVAWNSIISAFSQNGSAYEALELFHQMRMGSVLPDAVTLVSVLSACASLNAL 420

Query: 447 QVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGG 506
           QVGSS HAY+ K+GLLSSNVYVGTALL FYAKCGDA+SAR++FD M +K+TVTWSAMI G
Sbjct: 421 QVGSSFHAYAVKRGLLSSNVYVGTALLTFYAKCGDAESARVIFDGMDQKSTVTWSAMISG 480

Query: 507 YGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVP 566
           YG+QG+G GSL++F DML  E++PNE IFT+ILSACSHTGM+GEGW+ F  +C+D+  VP
Sbjct: 481 YGIQGNGRGSLSIFGDMLKAELKPNEEIFTSILSACSHTGMIGEGWRLFTMICQDYNLVP 540

Query: 567 SMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKM 626
           S KHY CMVDLLARAGRL+EAL+F++ MP++PDVSLFGAFLHGCGL+SRFDLGE+ IK+M
Sbjct: 541 STKHYTCMVDLLARAGRLKEALDFIQKMPVQPDVSLFGAFLHGCGLHSRFDLGELAIKRM 600

Query: 627 LELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLVDLDIANDFSFSR 686
           LELHP  ACYYVL+ NLYASD RW +V QVRELMKQRGL K+PGCSL+++D+ +DFSFSR
Sbjct: 601 LELHPGDACYYVLMCNLYASDARWSKVKQVRELMKQRGLMKTPGCSLMEMDVDHDFSFSR 660

Query: 687 VVSLA 691
             SLA
Sbjct: 661 AASLA 665

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357474955|ref|XP_003607763.1| Pentatricopeptide repeat-containing protein [Medicago truncatula] gi|355508818|gb|AES89960.1| Pentatricopeptide repeat-containing protein [Medicago truncatula]

 Score =  817 bits (2111), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 395/658 (60%), Positives = 499/658 (75%), Gaps = 27/658 (4%)

Query: 47  LPSIPCLNLLGLCKSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSM 106
           +P  P ++L  +CK   ++K  HA LI+ G   D   T L+S+Y SFG +++AR++F  +
Sbjct: 38  VPLPPTIHLSRICKHPTTVKTLHASLIISGHPPD---TTLISLYASFGFLRHARTLFHRL 94

Query: 107 PNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKE-HDNFVFSKVLKACCELRDIDEG 165
           P+P  +SF+++IRW+FLND++  +V FY   R  L   +D  VFS +LK   +LRDI   
Sbjct: 95  PSPTHHSFKLIIRWHFLNDVHSHVVSFYNLARTTLGSFNDLVVFSILLKTASQLRDIVLT 154

Query: 166 MKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQND 225
            K+HC I+K    DSFVLT LVD Y+KC  +  +R+VFDE  D++VVSWTSMI  YVQN+
Sbjct: 155 TKLHCNILKSNAADSFVLTSLVDAYSKCGKLRDARKVFDEIPDRSVVSWTSMIVAYVQNE 214

Query: 226 CAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVT 285
           CA+EGL+LFNRMREGF++GN  T+GSLVTAC KL  LHQGKW+HGY++K GIEINS+L T
Sbjct: 215 CAEEGLMLFNRMREGFLDGNVFTVGSLVTACTKLGCLHQGKWVHGYVIKNGIEINSYLAT 274

Query: 286 ALLDMYVKCGNIRDARSVFDELC------SIDLVSWTAMIVGYTQSGYPDKALKLFTDKK 339
           +LL+MYVKCG+I DARSVFDE          DLV WTAMIVGYTQ GYP  AL+LFTDKK
Sbjct: 275 SLLNMYVKCGDIGDARSVFDEFSVSTCGGGDDLVFWTAMIVGYTQRGYPQAALELFTDKK 334

Query: 340 WADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIAD 399
           W    PN VT+AS+LSA AQL N+ MG+++H L ++ GL+D ++ N+LVDMYAKC +I D
Sbjct: 335 WYRILPNSVTLASLLSACAQLENIVMGKLLHVLVVKYGLDDTSLRNSLVDMYAKCGLIPD 394

Query: 400 ARYIFETTSEKDVIAWNSIISGLDDNVS-----------------PDAVTLVSVISACAS 442
           A Y+F TT +KDV++WNS+ISG   + S                 PDAVT+V V+SACAS
Sbjct: 395 AHYVFATTVDKDVVSWNSVISGYAQSGSAYEALDLFNRMRMESFLPDAVTVVGVLSACAS 454

Query: 443 LGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSA 502
           +GA Q+G SLH ++ K GL+SS++YVGTALLNFYAKCGDA SARMVFD M EKN VTW+A
Sbjct: 455 VGAHQIGLSLHGFALKYGLVSSSIYVGTALLNFYAKCGDATSARMVFDGMGEKNAVTWAA 514

Query: 503 MIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDF 562
           MIGG GMQGDG GSLALF DML EE+ PNEV+FTT+L+ACSH+GMV EG   F  MC++ 
Sbjct: 515 MIGGCGMQGDGVGSLALFRDMLKEELVPNEVVFTTLLAACSHSGMVEEGLMIFDFMCKEL 574

Query: 563 KFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVM 622
            FVPSMKHY CMVDLLARAG L+EAL+F++ MP++P V +FGAFLHGCGL+S FD GEV 
Sbjct: 575 NFVPSMKHYACMVDLLARAGNLQEALDFIDKMPVQPGVGVFGAFLHGCGLHSNFDFGEVA 634

Query: 623 IKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLVDLDIAN 680
           I++MLELHPD+ACYYVL+SNLYASDGRW  V +VRE++KQRGL+K PG SLV++D+ N
Sbjct: 635 IRRMLELHPDQACYYVLISNLYASDGRWGMVKEVREMIKQRGLNKVPGVSLVEMDVNN 692

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449464466|ref|XP_004149950.1| PREDICTED: LOW QUALITY PROTEIN: uncharacterized protein LOC101216349 [Cucumis sativus]

 Score =  809 bits (2090), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 389/632 (61%), Positives = 482/632 (76%), Gaps = 42/632 (6%)

Query: 64   SLKAFHALLIVDGLT-NDKCNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYF 122
            +L  FH LLIV GL  N  C+TKLV +YG+ G V+ AR VFD MPNPDFY+++VMIRWYF
Sbjct: 1135 TLIKFHGLLIVHGLIGNLLCDTKLVGVYGALGDVRSARMVFDQMPNPDFYAWKVMIRWYF 1194

Query: 123  LNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFV 182
            LNDL+ D++ FY  MR   +E DN +FS +LKAC ELR+I EG KVHC+IVKVGGPDSFV
Sbjct: 1195 LNDLFVDVIPFYNRMRMSFRECDNIIFSIILKACSELREIVEGRKVHCQIVKVGGPDSFV 1254

Query: 183  LTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFV 242
            +TGL+DMY KC  +  S  VF+E +DKNVVSWTSMIAGYVQN+CA+EGLVLFNRMR+  V
Sbjct: 1255 MTGLIDMYGKCGQVECSSAVFEEIMDKNVVSWTSMIAGYVQNNCAEEGLVLFNRMRDALV 1314

Query: 243  EGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARS 302
            E N  TLGS++ A  KLRALHQGKW+HGY +K   E++S L T  LDMYVKCG  RDAR 
Sbjct: 1315 ESNPFTLGSIINAFTKLRALHQGKWVHGYAIKNIAELSSFLATTFLDMYVKCGQTRDARM 1374

Query: 303  VFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGN 362
            ++DEL +IDLVSWT MIVGYTQ+  P+  L+LF D+  +D  PN                
Sbjct: 1375 IYDELPTIDLVSWTVMIVGYTQARQPNDGLRLFADEIRSDLLPN---------------- 1418

Query: 363  LNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGL 422
                    S  +++  +    +NAL+DMYAKCH I+DA  IF    EKDVI WNS+ISG 
Sbjct: 1419 --------SALLQVFFQRVRFLNALIDMYAKCHTISDAYAIFHGVLEKDVITWNSMISGY 1470

Query: 423  DDN-----------------VSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSN 465
              N                 ++PDA+TLVS +SA A+LGA+QVGSSLHAYS K GL SSN
Sbjct: 1471 AQNGSAYDALRLFNQMRSYSLAPDAITLVSTLSASATLGAIQVGSSLHAYSVKGGLFSSN 1530

Query: 466  VYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLN 525
            +Y+GTALLNFYAKCGDA+SARMVFD+M  KN +TWSAMIGGYG+QGDG GSL++FS+ML 
Sbjct: 1531 LYIGTALLNFYAKCGDARSARMVFDSMGVKNIITWSAMIGGYGVQGDGSGSLSIFSNMLK 1590

Query: 526  EEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLE 585
            E+++PNEVIFTT+LSACS++GMV EG + F SM +D+ FVPSMKHY CMVDLLAR+G+L+
Sbjct: 1591 EDLKPNEVIFTTVLSACSYSGMVEEGGRYFKSMIQDYNFVPSMKHYACMVDLLARSGKLD 1650

Query: 586  EALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYA 645
            EAL+F++ MP++ DVSL+GAFLHGCGLYSRFDLGEV++++ML+LH ++ACYYVLVSNLYA
Sbjct: 1651 EALDFIKKMPVQRDVSLYGAFLHGCGLYSRFDLGEVVVREMLQLHRNEACYYVLVSNLYA 1710

Query: 646  SDGRWIRVNQVRELMKQRGLSKSPGCSLVDLD 677
            SDG+W +VN+VR+LM QRGL+K PG SLV+ +
Sbjct: 1711 SDGKWGQVNEVRDLMLQRGLNKVPGYSLVETN 1742

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356521639|ref|XP_003529461.1| PREDICTED: pentatricopeptide repeat-containing protein At2g03380, mitochondrial-like [Glycine max]

 Score =  790 bits (2039), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 404/708 (57%), Positives = 502/708 (70%), Gaps = 43/708 (6%)

Query: 7   LQRHVSRTKKPKLQLR--FFSYTNQQTPTQHELDQTFASFHSLPSIPCLNLLGLCKSTGS 64
           + R +  T KP+L     +  +  +Q P               PS P   L  LC +  S
Sbjct: 4   ISRVLRVTTKPRLHWNSLYHHHGQKQQP---------------PSPPTFYLSRLCTNLPS 48

Query: 65  LKAFHALLIVDGLTNDKCNTKLVSM-YGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFL 123
           LK  HA  ++ GLTND   +  +   Y SFG +++AR +F+ +P  D Y F+VMIR YFL
Sbjct: 49  LKTLHASFLIHGLTNDLLLSTKLLSLYASFGQLRHARKIFNHLPTRDLYCFKVMIRAYFL 108

Query: 124 NDLYKDIVEFYKCMRKRLKE--HDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSF 181
           ND    +V  Y+ MR  L    HD  +FS V K+C E RD       HC  VK    DSF
Sbjct: 109 NDTPSGVVSLYRLMRLSLHPTPHDYVLFSIVFKSCAESRDFQTLTITHCHFVKSLPSDSF 168

Query: 182 VLTGLVDMYAKCRDIGSSRQVFDETLDKN-VVSWTSMIAGYVQNDCAQEGLVLFNRMREG 240
           VLT LVD YAK   +  + + FDE  + + VVSWTSMI  YVQNDCA+EGL LFNRMRE 
Sbjct: 169 VLTCLVDAYAKFARVDEATRAFDEIHENDDVVSWTSMIVAYVQNDCAREGLTLFNRMREA 228

Query: 241 FVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDA 300
           FV+GN+ T+GSLV+AC KL  LHQGKW+HG+++K GI +NS+L T+LL+MYVKCGNI+DA
Sbjct: 229 FVDGNEFTVGSLVSACTKLNWLHQGKWVHGFVIKNGICVNSYLTTSLLNMYVKCGNIQDA 288

Query: 301 RSVFDELCSI----DLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSA 356
             VFDE  S     DLVSWTAMIVGY+Q GYP  AL+LF DKKW+   PN VT++S+LS+
Sbjct: 289 CKVFDESSSSSYDRDLVSWTAMIVGYSQRGYPHLALELFKDKKWSGILPNSVTVSSLLSS 348

Query: 357 SAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWN 416
            AQLGN  MG+++H L ++ GL+D+ V NALVDMYAKC V++DAR +FE   EKDV++WN
Sbjct: 349 CAQLGNSVMGKLLHGLAVKCGLDDHPVRNALVDMYAKCGVVSDARCVFEAMLEKDVVSWN 408

Query: 417 SIISGLDDN-----------------VSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQ 459
           SIISG   +                  SPDAVT+V ++SACASLG + +G S+H  + K 
Sbjct: 409 SIISGFVQSGEAYEALNLFRRMGLELFSPDAVTVVGILSACASLGMLHLGCSVHGLALKD 468

Query: 460 GLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLAL 519
           GL+ S++YVGTALLNFYAKCGDA++ARMVFD+M EKN VTW AMIGGYGMQGDG GSL L
Sbjct: 469 GLVVSSIYVGTALLNFYAKCGDARAARMVFDSMGEKNAVTWGAMIGGYGMQGDGNGSLTL 528

Query: 520 FSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLA 579
           F DML E V+PNEV+FTTIL+ACSH+GMVGEG + F  MC +  FVPSMKHY CMVD+LA
Sbjct: 529 FRDMLEELVEPNEVVFTTILAACSHSGMVGEGSRLFNLMCGELNFVPSMKHYACMVDMLA 588

Query: 580 RAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVL 639
           RAG LEEAL+F+E MP++P VS+FGAFLHGCGL+SRF+LG   IKKMLELHPD+ACYYVL
Sbjct: 589 RAGNLEEALDFIERMPVQPSVSVFGAFLHGCGLHSRFELGGAAIKKMLELHPDEACYYVL 648

Query: 640 VSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLVDLDIANDFSFSRV 687
           VSNLYASDGRW  V QVRE++KQRGL+K PGCS V++D+ ND S+++V
Sbjct: 649 VSNLYASDGRWGMVKQVREMIKQRGLNKVPGCSSVEMDLQND-SYAKV 695

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297814636|ref|XP_002875201.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297814638|ref|XP_002875202.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297321039|gb|EFH51460.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297321040|gb|EFH51461.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  782 bits (2019), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 391/676 (57%), Positives = 493/676 (72%), Gaps = 20/676 (2%)

Query: 19  LQLRFFSYTNQQTPTQHELDQTFASFHSLPSIPCLNLLGLCKSTGSLKAFHALLIVDGLT 78
           +++R F++T  Q     E D   +S +   S PC  LL  C +  SL+  H +L  +GL 
Sbjct: 27  MRMRCFTFTTIQELNLPE-DNDESSLNYAASRPCFLLLSKCTNIDSLRQAHGVLTGNGLM 85

Query: 79  ND-KCNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCM 137
            D    TKLVS+YGSFG+ K AR VFD +P PDFY ++V++R Y LN+   ++++FY  +
Sbjct: 86  GDISIATKLVSLYGSFGYTKDARLVFDQIPEPDFYLWKVILRCYCLNNESFEVIKFYDLL 145

Query: 138 RKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIG 197
            K    +D+ VFSK LKAC E++D+D G K+HC+IVKV   D+ VLTGL+DMYAKC +I 
Sbjct: 146 MKHGFGYDDIVFSKALKACTEVQDLDNGKKIHCQIVKVPSFDNVVLTGLLDMYAKCGEIK 205

Query: 198 SSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACA 257
           SS +VF++   +NVV WTSMIAGYV+ND  +EGLVLFNRMRE  V GN+ T G+LV AC 
Sbjct: 206 SSYKVFEDITLRNVVCWTSMIAGYVKNDLYEEGLVLFNRMRENSVLGNEYTYGTLVMACT 265

Query: 258 KLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTA 317
           KLRALHQGKW HG ++K GIE++S LVT+LLDMYVKCG+I +AR VF+E   +DLV WTA
Sbjct: 266 KLRALHQGKWFHGCLIKSGIELSSCLVTSLLDMYVKCGDISNARRVFNEHSHVDLVMWTA 325

Query: 318 MIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLG 377
           MIVGYT +G  ++AL LF         PN VTIASVLS    +GNL +GR +H L I++G
Sbjct: 326 MIVGYTHNGSVNEALSLFQKMSGVGIKPNCVTIASVLSGCGLVGNLELGRSIHGLSIKVG 385

Query: 378 LEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDN------------ 425
           + D  V NALV MYAKC+   DA+Y+FE  SEKD++AWNSIISG   N            
Sbjct: 386 IWDTNVANALVHMYAKCYQNRDAKYVFEMESEKDIVAWNSIISGFSQNGSIHEALFLFHR 445

Query: 426 -----VSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLL-SSNVYVGTALLNFYAKC 479
                V P+ VT+ S+ SACASLG++ +GSSLHAYS K G L SS+V+VGTALL+FYAKC
Sbjct: 446 MNTESVMPNGVTVASLFSACASLGSLAIGSSLHAYSVKLGFLASSSVHVGTALLDFYAKC 505

Query: 480 GDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTIL 539
           GDA+SAR++FD + EKNT+TWSAMIGGYG QGD  GSL LF +ML ++ +PNE  FT++L
Sbjct: 506 GDAESARLIFDTIEEKNTITWSAMIGGYGKQGDTKGSLELFEEMLKKQQKPNESTFTSVL 565

Query: 540 SACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPD 599
           SACSHTGMV EG K F SM +D+ F PS KHY CMVD+LARAG LE+AL+ +E MPI+PD
Sbjct: 566 SACSHTGMVNEGKKYFSSMYKDYNFTPSTKHYTCMVDMLARAGELEQALDIIEKMPIQPD 625

Query: 600 VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVREL 659
           V  FGAFLHGCG++SRFDLGE++IKKML+LHPD A YYVLVSNLYASDGRW +  +VR L
Sbjct: 626 VRCFGAFLHGCGMHSRFDLGEIVIKKMLDLHPDDASYYVLVSNLYASDGRWSQAKEVRNL 685

Query: 660 MKQRGLSKSPGCSLVD 675
           MKQRGLSK  G S+++
Sbjct: 686 MKQRGLSKIAGHSIME 701

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15227623|ref|NP_178437.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana] gi|75216181|sp|Q9ZQ74.1|PP146_ARATH RecName: Full=Pentatricopeptide repeat-containing protein At2g03380, mitochondrial; Flags: Precursor gi|4335760|gb|AAD17437.1| unknown protein [Arabidopsis thaliana] gi|330250600|gb|AEC05694.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana]

 Score =  772 bits (1994), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 391/684 (57%), Positives = 489/684 (71%), Gaps = 20/684 (2%)

Query: 11  VSRTKKPKLQLRFFSYTNQQTPTQHELDQTFASFHSLPSIPCLNLLGLCKSTGSLKAFHA 70
           +S T++     R  S+T  +     E +   +S H   S PC  LL  C +  SL+  H 
Sbjct: 7   LSPTRRFGFPPRCVSFTTIKELILTE-ENDGSSLHYAASSPCFLLLSKCTNIDSLRQSHG 65

Query: 71  LLIVDGLTND-KCNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKD 129
           +L  +GL  D    TKLVS+YG FG+ K AR VFD +P PDFY ++VM+R Y LN    +
Sbjct: 66  VLTGNGLMGDISIATKLVSLYGFFGYTKDARLVFDQIPEPDFYLWKVMLRCYCLNKESVE 125

Query: 130 IVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDM 189
           +V+ Y  + K    +D+ VFSK LKAC EL+D+D G K+HC++VKV   D+ VLTGL+DM
Sbjct: 126 VVKLYDLLMKHGFRYDDIVFSKALKACTELQDLDNGKKIHCQLVKVPSFDNVVLTGLLDM 185

Query: 190 YAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITL 249
           YAKC +I S+ +VF++   +NVV WTSMIAGYV+ND  +EGLVLFNRMRE  V GN+ T 
Sbjct: 186 YAKCGEIKSAHKVFNDITLRNVVCWTSMIAGYVKNDLCEEGLVLFNRMRENNVLGNEYTY 245

Query: 250 GSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCS 309
           G+L+ AC KL ALHQGKW HG ++K GIE++S LVT+LLDMYVKCG+I +AR VF+E   
Sbjct: 246 GTLIMACTKLSALHQGKWFHGCLVKSGIELSSCLVTSLLDMYVKCGDISNARRVFNEHSH 305

Query: 310 IDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMV 369
           +DLV WTAMIVGYT +G  ++AL LF   K  +  PN VTIASVLS    + NL +GR V
Sbjct: 306 VDLVMWTAMIVGYTHNGSVNEALSLFQKMKGVEIKPNCVTIASVLSGCGLIENLELGRSV 365

Query: 370 HSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDN---- 425
           H L I++G+ D  V NALV MYAKC+   DA+Y+FE  SEKD++AWNSIISG   N    
Sbjct: 366 HGLSIKVGIWDTNVANALVHMYAKCYQNRDAKYVFEMESEKDIVAWNSIISGFSQNGSIH 425

Query: 426 -------------VSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLL-SSNVYVGTA 471
                        V+P+ VT+ S+ SACASLG++ VGSSLHAYS K G L SS+V+VGTA
Sbjct: 426 EALFLFHRMNSESVTPNGVTVASLFSACASLGSLAVGSSLHAYSVKLGFLASSSVHVGTA 485

Query: 472 LLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPN 531
           LL+FYAKCGD QSAR++FD + EKNT+TWSAMIGGYG QGD  GSL LF +ML ++ +PN
Sbjct: 486 LLDFYAKCGDPQSARLIFDTIEEKNTITWSAMIGGYGKQGDTIGSLELFEEMLKKQQKPN 545

Query: 532 EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFM 591
           E  FT+ILSAC HTGMV EG K F SM +D+ F PS KHY CMVD+LARAG LE+AL+ +
Sbjct: 546 ESTFTSILSACGHTGMVNEGKKYFSSMYKDYNFTPSTKHYTCMVDMLARAGELEQALDII 605

Query: 592 ENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWI 651
           E MPI+PDV  FGAFLHGCG++SRFDLGE++IKKML+LHPD A YYVLVSNLYASDGRW 
Sbjct: 606 EKMPIQPDVRCFGAFLHGCGMHSRFDLGEIVIKKMLDLHPDDASYYVLVSNLYASDGRWN 665

Query: 652 RVNQVRELMKQRGLSKSPGCSLVD 675
           +  +VR LMKQRGLSK  G S ++
Sbjct: 666 QAKEVRNLMKQRGLSKIAGHSTME 689

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326495056|dbj|BAJ85624.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  659 bits (1701), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 333/662 (50%), Positives = 440/662 (66%), Gaps = 27/662 (4%)

Query: 42  ASFHSLPSIP-----CLNLLGLCKSTGSLKAFHALLIVDGLTND-KCNTKLVSMYGSFGH 95
           A  HS+  +P        LL  C +  SL+A HA L+  GL    +  TKL+S Y + G 
Sbjct: 11  ADAHSVEHLPHGGALLHRLLPACATLPSLRALHARLLAHGLLRALRARTKLLSCYAALGD 70

Query: 96  VKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKE-HDNFVF-SKVL 153
           +  AR V D  P PD Y+++V + W+     + D +  ++ MR+R  E HD+ V  S  L
Sbjct: 71  LASARRVLDETPRPDPYTYRVALGWHAAAGRHADALALHRGMRRRCPEAHDDVVLLSLAL 130

Query: 154 KACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVS 213
           KA     D   G ++HC  VK GG D FV+  LVDMYAK  D+ ++R+VFD  L +NVVS
Sbjct: 131 KASVRSADFRYGRRLHCNAVKAGGADGFVMNCLVDMYAKAGDLENARKVFDRILGRNVVS 190

Query: 214 WTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYIL 273
           WTSM++G +QN  A+EGL LFN MRE  V  ++ T+ S++ AC  L +LHQG+W+HG ++
Sbjct: 191 WTSMLSGCLQNGFAEEGLALFNEMREERVLPSEYTMASVLMACTMLGSLHQGRWVHGSVI 250

Query: 274 KIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALK 333
           K G+  N  +  A+LDMYVKCG + DAR +FDEL  +DLV WT MIVGYTQ+G P  AL 
Sbjct: 251 KHGMVFNPFITAAVLDMYVKCGEVEDARRLFDELGFVDLVLWTTMIVGYTQNGSPLDALL 310

Query: 334 LFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRL-GLEDYTVINALVDMYA 392
           LF+DKK+    PN VTIA+VLSASAQL NL++GR++H++ ++L  +E+  V+NALVDMYA
Sbjct: 311 LFSDKKFVHIVPNSVTIATVLSASAQLRNLSLGRLIHAMSVKLLVIENDVVMNALVDMYA 370

Query: 393 KCHVIADARYIFETTSEKDVIAWNSIISGLDDN-----------------VSPDAVTLVS 435
           KC  +++A  IF   S KDV+ WNS+I+G  +N                  SPDA+++V+
Sbjct: 371 KCKALSEANGIFGRISNKDVVTWNSLIAGYVENDMGNEALMLFSQMRVQGSSPDAISIVN 430

Query: 436 VISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK 495
            +SAC  LG + +G   H Y+ K+  LS NVYV TALLN Y KC D  SA+ VF  M E+
Sbjct: 431 ALSACVCLGDLLIGKCFHTYAVKRAFLS-NVYVNTALLNLYNKCADLPSAQRVFSEMSER 489

Query: 496 NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCF 555
           N+VTW AMIGGYGMQGD  GS+ L + ML + +QPNEV+FT+ILS CSHTGMV  G  CF
Sbjct: 490 NSVTWGAMIGGYGMQGDSAGSIDLLNKMLKDNIQPNEVVFTSILSTCSHTGMVSVGKMCF 549

Query: 556 YSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSR 615
            SM + F   PSMKHY CMVD+LARAG LEEALEF++ MP+  D+S++GAFLHGC L+SR
Sbjct: 550 DSMAQYFNITPSMKHYACMVDVLARAGNLEEALEFIQKMPMPADISIWGAFLHGCKLHSR 609

Query: 616 FDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLVD 675
            + GE  I +M+ LHPDK  +YVL+SNLY S GRW +   +R LM++RGL K PGCS V 
Sbjct: 610 LEFGEEAINRMMVLHPDKPDFYVLMSNLYTSYGRWDKSLAIRRLMQERGLVKLPGCSSVG 669

Query: 676 LD 677
           L+
Sbjct: 670 LE 671

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242092246|ref|XP_002436613.1| hypothetical protein SORBIDRAFT_10g005800 [Sorghum bicolor] gi|241914836|gb|EER87980.1| hypothetical protein SORBIDRAFT_10g005800 [Sorghum bicolor]

 Score =  654 bits (1686), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 328/645 (50%), Positives = 435/645 (67%), Gaps = 26/645 (4%)

Query: 53  LNLLGLCKSTGSLKAFHALLIVDG----LTNDKCNTKLVSMYGSFGHVKYARSVFDSMPN 108
           L LL  C +  SL+  HA L+       L + +  TKL+S Y + G +  AR VFD  P 
Sbjct: 33  LRLLPSCGTLPSLRVLHARLLTHTQGLLLGSLRARTKLLSCYAALGDLASARMVFDGTPR 92

Query: 109 PDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRL---KEHDNFVFSKVLKACCELRDIDEG 165
           PD YS+ VM+      + + + V  ++ MR+R    +  D+FV S  LKAC    D   G
Sbjct: 93  PDAYSYGVMLWCLVQAERHAEAVALHQDMRRRRPCPEAQDDFVLSLALKACIRSADYGYG 152

Query: 166 MKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQND 225
            ++HC+ VKVGG D FV+  LVDMYAK  D+  +R+VF+    +NVVSWTSM++G VQN 
Sbjct: 153 TRLHCDAVKVGGADGFVMNSLVDMYAKAGDLECARKVFERIPGRNVVSWTSMLSGCVQNG 212

Query: 226 CAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVT 285
            A +GL+LFN+MR+  V  ++ T+ +++TAC+ L  LHQG+W+HG ++K G+  NS +  
Sbjct: 213 FAADGLLLFNKMRQDNVPPSEYTIATVITACSALIGLHQGRWMHGSVIKQGLMSNSFISA 272

Query: 286 ALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFP 345
           ALLDMYVKCG + DA+ VFDEL  IDLV WT MIVGYTQ+G P  AL+LF DKK+A+  P
Sbjct: 273 ALLDMYVKCGELEDAQCVFDELSYIDLVLWTTMIVGYTQNGNPLDALRLFLDKKFANIVP 332

Query: 346 NHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYT-VINALVDMYAKCHVIADARYIF 404
           N VTIA+VLSASAQL +L++GR +H + ++LGL +YT V+NALVDMYAKC  +++A  IF
Sbjct: 333 NSVTIATVLSASAQLRDLSLGRSIHGIAVKLGLVEYTVVVNALVDMYAKCQAVSEANRIF 392

Query: 405 ETTSEKDVIAWNSIISGLDDN-----------------VSPDAVTLVSVISACASLGAVQ 447
            + S KDV+AWNS++SG  +N                  SPDA+++V  +SA   LG + 
Sbjct: 393 GSISNKDVVAWNSMLSGYAENNMCNDALMLFKQMSLKGPSPDAISVVHALSASVCLGDLL 452

Query: 448 VGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGY 507
           +G S H Y+ K   L SN+YV TALLN Y KCGD  SAR VFD M ++N+VTW AMIGGY
Sbjct: 453 IGKSFHGYAVKHAFL-SNIYVSTALLNLYNKCGDLPSARRVFDEMNDRNSVTWCAMIGGY 511

Query: 508 GMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS 567
           GMQGD  GS+ LF +ML + V PN+V FT+ILS CSHTGMV    + F SM + F   PS
Sbjct: 512 GMQGDSAGSIDLFGEMLKDGVHPNDVAFTSILSTCSHTGMVTAAKRYFDSMAQHFNITPS 571

Query: 568 MKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKML 627
           MKHY CMVD+LARAG LEEALEF++NMP++ D S++GAFLHGC L+SR   GE  IK+M+
Sbjct: 572 MKHYACMVDVLARAGNLEEALEFIDNMPMQADTSVWGAFLHGCELHSRLQFGEEAIKRMM 631

Query: 628 ELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCS 672
            LHP++   YVL+SNLY S+G W +   +R  M+++GL K PG S
Sbjct: 632 VLHPERPDLYVLISNLYTSNGMWEKSQAIRRWMQEKGLVKLPGYS 676

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357118484|ref|XP_003560984.1| PREDICTED: pentatricopeptide repeat-containing protein At2g03380, mitochondrial-like [Brachypodium distachyon]

 Score =  646 bits (1667), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 326/674 (48%), Positives = 440/674 (65%), Gaps = 24/674 (3%)

Query: 26  YTNQQTPTQHELDQTFASFHSLPSIPCLN-LLGLCKSTGSLKAFHALLIVDGLTND-KCN 83
           +    TP  H +D       S  + P L+ LL  C +  SL+A HA L+  GL    + +
Sbjct: 5   FRPSATPDAHSVDH-LPRASSPDANPLLHRLLPACTTLPSLRALHARLLAHGLLRGLRAH 63

Query: 84  TKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKR--L 141
           TKL+S Y + G +  AR V D  P+PD Y+++V + W+     + + V  ++ MR+R   
Sbjct: 64  TKLLSCYAALGDLASARRVLDETPHPDAYTYKVALGWHAAAGRHAEAVAVHRDMRRRCPA 123

Query: 142 KEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQ 201
           ++ D  V S  LKA     D   G ++HC++VK GG D FV+  LVDMYAK  D+ ++R+
Sbjct: 124 EQEDVVVLSLALKAAVRSADFGYGRRLHCDVVKAGGGDLFVMNNLVDMYAKGGDLKNARK 183

Query: 202 VFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRA 261
           VFD   D+NVVSWTSM++G +QN  A+EGLVLFN MR+  +  ++ T+ S++ AC  L +
Sbjct: 184 VFDRIPDRNVVSWTSMLSGCLQNGLAKEGLVLFNEMRQESILPSEYTMASVLMACTMLGS 243

Query: 262 LHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVG 321
           LHQG+ +HG ++K G+  N  +  A+LDMYVKCG   DAR VFDEL  +DLV WT MIVG
Sbjct: 244 LHQGRLIHGSVMKHGLVSNHFITAAMLDMYVKCGEAEDARQVFDELSFVDLVLWTTMIVG 303

Query: 322 YTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLG-LED 380
           YTQ+G P  AL LF D K+    PN VTIA+VLSASAQL NL++GR +H + ++LG +E+
Sbjct: 304 YTQNGSPLDALLLFVDDKFMRIVPNSVTIATVLSASAQLRNLSLGRSIHGISVKLGAVEN 363

Query: 381 YTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDN--------------- 425
             V+NALVDMYAKC  ++DA+ IF     KDV+ WNS+I+G  +N               
Sbjct: 364 DVVMNALVDMYAKCKALSDAKGIFGRVLNKDVVTWNSLIAGYAENDMGSDALMLFSHMRV 423

Query: 426 --VSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQ 483
               PDA+++V+ +SAC  LG + +G   H Y+ K   +S N+YV TALLN Y KC D  
Sbjct: 424 QGSLPDAISVVNALSACVCLGDLLIGKCFHTYAVKHAFMS-NIYVNTALLNLYNKCADLP 482

Query: 484 SARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACS 543
           SA+ VF  M ++NTVTW AMIGGYGMQGD  GS+ LF++ML + +QPNE +FT+ILS CS
Sbjct: 483 SAQRVFSEMNDRNTVTWGAMIGGYGMQGDSAGSIDLFNEMLKDNIQPNEAVFTSILSTCS 542

Query: 544 HTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLF 603
           HTGMV  G KCF SM   F   PSMKHY CMVD+LARAG LEEALEF++ MP++ D S++
Sbjct: 543 HTGMVTVGKKCFESMAHYFNITPSMKHYACMVDVLARAGNLEEALEFIQKMPMQADTSIW 602

Query: 604 GAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQR 663
            AFLHGC L+SR +  E  + +M+ LHPD   + V++SNLY S GRW +   +R+LMK+R
Sbjct: 603 QAFLHGCKLHSRLEFAEEAVNRMMVLHPDTPDFCVMMSNLYTSYGRWDKSLAIRKLMKER 662

Query: 664 GLSKSPGCSLVDLD 677
           GL K PGCS V L+
Sbjct: 663 GLVKLPGCSSVGLE 676

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	691
TAIR|locus:2063771	689	AT2G03380 [Arabidopsis thalian	0.630	0.632	0.513	2.1e-193
TAIR|locus:2202074	809	CRR22 "CHLORORESPIRATORY REDUC	0.528	0.451	0.373	3.3e-56
TAIR|locus:2096414	882	AT3G03580 [Arabidopsis thalian	0.525	0.411	0.338	3.7e-100
TAIR|locus:2118964	823	EMB2758 "embryo defective 2758	0.890	0.747	0.342	1.9e-99
TAIR|locus:2122551	834	AT4G39530 [Arabidopsis thalian	0.525	0.435	0.314	1.5e-98
TAIR|locus:2124137	871	DOT4 "DEFECTIVELY ORGANIZED TR	0.360	0.285	0.38	5.4e-98
TAIR|locus:2089333	654	AT3G16610 "AT3G16610" [Arabido	0.426	0.451	0.361	3.4e-94
TAIR|locus:2175653	677	AT5G39350 "AT5G39350" [Arabido	0.551	0.562	0.308	4.3e-92
TAIR|locus:2082886	850	EMB2261 "embryo defective 2261	0.425	0.345	0.346	7.3e-92
TAIR|locus:2060640	738	OTP81 "ORGANELLE TRANSCRIPT PR	0.369	0.345	0.375	4.8e-91

TAIR|locus:2063771 AT2G03380 [Arabidopsis thaliana (taxid:3702)]

 Score = 1088 (388.1 bits), Expect = 2.1e-193, Sum P(2) = 2.1e-193
 Identities = 226/440 (51%), Positives = 295/440 (67%)

Query:    42 ASFHSLPSIPCLNLLGLCKSTGSLKAFHALLIVDGLTND-KCNTKLVSMYGSFGHVKYAR 100
             +S H   S PC  LL  C +  SL+  H +L  +GL  D    TKLVS+YG FG+ K AR
Sbjct:    37 SSLHYAASSPCFLLLSKCTNIDSLRQSHGVLTGNGLMGDISIATKLVSLYGFFGYTKDAR 96

Query:   101 SVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELR 160
              VFD +P PDFY ++VM+R Y LN    ++V+ Y  + K    +D+ VFSK LKAC EL+
Sbjct:    97 LVFDQIPEPDFYLWKVMLRCYCLNKESVEVVKLYDLLMKHGFRYDDIVFSKALKACTELQ 156

Query:   161 DIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAG 220
             D+D G K+HC++VKV   D+ VLTGL+DMYAKC +I S+ +VF++   +NVV WTSMIAG
Sbjct:   157 DLDNGKKIHCQLVKVPSFDNVVLTGLLDMYAKCGEIKSAHKVFNDITLRNVVCWTSMIAG 216

Query:   221 YVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEIN 280
             YV+ND  +EGLVLFNRMRE  V GN+ T G+L+ AC KL ALHQGKW HG ++K GIE++
Sbjct:   217 YVKNDLCEEGLVLFNRMRENNVLGNEYTYGTLIMACTKLSALHQGKWFHGCLVKSGIELS 276

Query:   281 SHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKW 340
             S LVT+LLDMYVKCG+I +AR VF+E   +DLV WTAMIVGYT +G  ++AL LF   K 
Sbjct:   277 SCLVTSLLDMYVKCGDISNARRVFNEHSHVDLVMWTAMIVGYTHNGSVNEALSLFQKMKG 336

Query:   341 ADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADA 400
              +  PN VTIASVLS    + NL +GR VH L I++G+ D  V NALV MYAKC+   DA
Sbjct:   337 VEIKPNCVTIASVLSGCGLIENLELGRSVHGLSIKVGIWDTNVANALVHMYAKCYQNRDA 396

Query:   401 RYIFETTSEKDVIAWNSIISGLDDNVS-PDAVTLVSVI-SACASLGAVQVGSSLHAYSTK 458
             +Y+FE  SEKD++AWNSIISG   N S  +A+ L   + S   +   V V S   A ++ 
Sbjct:   397 KYVFEMESEKDIVAWNSIISGFSQNGSIHEALFLFHRMNSESVTPNGVTVASLFSACASL 456

Query:   459 QGL-LSSNVYVGTALLNFYA 477
               L + S+++  +  L F A
Sbjct:   457 GSLAVGSSLHAYSVKLGFLA 476

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2202074 CRR22 "CHLORORESPIRATORY REDUCTION22" [Arabidopsis thaliana (taxid:3702)]

 Score = 579 (208.9 bits), Expect = 3.3e-56, P = 3.3e-56
 Identities = 140/375 (37%), Positives = 209/375 (55%)

Query:    55 LLGLCKSTGSL---KAFHALLIVDGLTNDK-CNTKLVSMYGSFGHVKYARSVFDSMPNPD 110
             LL +C     L   K  H LL+  G + D    T L +MY     V  AR VFD MP  D
Sbjct:   141 LLKVCGDEAELRVGKEIHGLLVKSGFSLDLFAMTGLENMYAKCRQVNEARKVFDRMPERD 200

Query:   111 FYSFQVMIRWYFLNDLYKDIVEFYKCM-RKRLKEHDNFVFSKVLKACCELRDIDEGMKVH 169
               S+  ++  Y  N + +  +E  K M  + LK     + S VL A   LR I  G ++H
Sbjct:   201 LVSWNTIVAGYSQNGMARMALEMVKSMCEENLKPSFITIVS-VLPAVSALRLISVGKEIH 259

Query:   170 CEIVKVGGPDSFV--LTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCA 227
                ++  G DS V   T LVDMYAKC  + ++RQ+FD  L++NVVSW SMI  YVQN+  
Sbjct:   260 GYAMR-SGFDSLVNISTALVDMYAKCGSLETARQLFDGMLERNVVSWNSMIDAYVQNENP 318

Query:   228 QEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTAL 287
             +E +++F +M +  V+   +++   + ACA L  L +G+++H   +++G++ N  +V +L
Sbjct:   319 KEAMLIFQKMLDEGVKPTDVSVMGALHACADLGDLERGRFIHKLSVELGLDRNVSVVNSL 378

Query:   288 LDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNH 347
             + MY KC  +  A S+F +L S  LVSW AMI+G+ Q+G P  AL  F+  +     P+ 
Sbjct:   379 ISMYCKCKEVDTAASMFGKLQSRTLVSWNAMILGFAQNGRPIDALNYFSQMRSRTVKPDT 438

Query:   348 VTIASVLSASAQLGNLNMGRMVHSLGIRLGLE-DYTVINALVDMYAKCHVIADARYIFET 406
              T  SV++A A+L   +  + +H + +R  L+ +  V  ALVDMYAKC  I  AR IF+ 
Sbjct:   439 FTYVSVITAIAELSITHHAKWIHGVVMRSCLDKNVFVTTALVDMYAKCGAIMIARLIFDM 498

Query:   407 TSEKDVIAWNSIISG 421
              SE+ V  WN++I G
Sbjct:   499 MSERHVTTWNAMIDG 513

GO:0005739 "mitochondrion" evidence=ISM

GO:0004519 "endonuclease activity" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0016556 "mRNA modification" evidence=RCA;IMP

TAIR|locus:2096414 AT3G03580 [Arabidopsis thaliana (taxid:3702)]

 Score = 522 (188.8 bits), Expect = 3.7e-100, Sum P(2) = 3.7e-100
 Identities = 126/372 (33%), Positives = 211/372 (56%)

Query:    56 LGLCKSTGSLKAFHALLIVDGL-TNDKCNTKLVSMYGSFGHVKYARSVFDSM-PNPDFYS 113
             L    +   L+  HAL+I  GL ++D  + KL+  Y  F     + SVF  + P  + Y 
Sbjct:    14 LSSSSNLNELRRIHALVISLGLDSSDFFSGKLIDKYSHFREPASSLSVFRRVSPAKNVYL 73

Query:   114 FQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIV 173
             +  +IR +  N L+ + +EFY  +R+     D + F  V+KAC  L D + G  V+ +I+
Sbjct:    74 WNSIIRAFSKNGLFPEALEFYGKLRESKVSPDKYTFPSVIKACAGLFDAEMGDLVYEQIL 133

Query:   174 KVG-GPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLV 232
              +G   D FV   LVDMY++   +  +RQVFDE   +++VSW S+I+GY  +   +E L 
Sbjct:   134 DMGFESDLFVGNALVDMYSRMGLLTRARQVFDEMPVRDLVSWNSLISGYSSHGYYEEALE 193

Query:   233 LFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVT--ALLDM 290
             +++ ++  ++  +  T+ S++ A   L  + QG+ LHG+ LK G+  NS +V    L+ M
Sbjct:   194 IYHELKNSWIVPDSFTVSSVLPAFGNLLVVKQGQGLHGFALKSGV--NSVVVVNNGLVAM 251

Query:   291 YVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTI 350
             Y+K     DAR VFDE+   D VS+  MI GY +    ++++++F +     F P+ +T+
Sbjct:   252 YLKFRRPTDARRVFDEMDVRDSVSYNTMICGYLKLEMVEESVRMFLENL-DQFKPDLLTV 310

Query:   351 ASVLSASAQLGNLNMGRMVHSLGIRLGLE-DYTVINALVDMYAKCHVIADARYIFETTSE 409
             +SVL A   L +L++ + +++  ++ G   + TV N L+D+YAKC  +  AR +F +   
Sbjct:   311 SSVLRACGHLRDLSLAKYIYNYMLKAGFVLESTVRNILIDVYAKCGDMITARDVFNSMEC 370

Query:   410 KDVIAWNSIISG 421
             KD ++WNSIISG
Sbjct:   371 KDTVSWNSIISG 382

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2118964 EMB2758 "embryo defective 2758" [Arabidopsis thaliana (taxid:3702)]

 Score = 987 (352.5 bits), Expect = 1.9e-99, P = 1.9e-99
 Identities = 221/646 (34%), Positives = 357/646 (55%)

Query:    55 LLGLCKSTGSLKAFHALLIVDGLTNDKC-NTKLVSMYGSFGHVKYARSVFDSMPNPDFYS 113
             L   C +  S K  HA L+V     + C + KLV++Y   G+V  AR  FD + N D Y+
Sbjct:    60 LFRYCTNLQSAKCLHARLVVSKQIQNVCISAKLVNLYCYLGNVALARHTFDHIQNRDVYA 119

Query:   114 FQVMIRWYFLNDLYKDIVEFYKC-MRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEI 172
             + +MI  Y       +++  +   M       D   F  VLKAC   R + +G K+HC  
Sbjct:   120 WNLMISGYGRAGNSSEVIRCFSLFMLSSGLTPDYRTFPSVLKAC---RTVIDGNKIHCLA 176

Query:   173 VKVGGP-DSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGL 231
             +K G   D +V   L+ +Y++ + +G++R +FDE   +++ SW +MI+GY Q+  A+E L
Sbjct:   177 LKFGFMWDVYVAASLIHLYSRYKAVGNARILFDEMPVRDMGSWNAMISGYCQSGNAKEAL 236

Query:   232 VLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMY 291
              L N +R      + +T+ SL++AC +    ++G  +H Y +K G+E    +   L+D+Y
Sbjct:   237 TLSNGLRAM----DSVTVVSLLSACTEAGDFNRGVTIHSYSIKHGLESELFVSNKLIDLY 292

Query:   292 VKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIA 351
              + G +RD + VFD +   DL+SW ++I  Y  +  P +A+ LF + + +   P+ +T+ 
Sbjct:   293 AEFGRLRDCQKVFDRMYVRDLISWNSIIKAYELNEQPLRAISLFQEMRLSRIQPDCLTLI 352

Query:   352 SVLSASAQLGNLNMGRMVHSLGIRLG--LEDYTVINALVDMYAKCHVIADARYIFETTSE 409
             S+ S  +QLG++   R V    +R G  LED T+ NA+V MYAK  ++  AR +F     
Sbjct:   353 SLASILSQLGDIRACRSVQGFTLRKGWFLEDITIGNAVVVMYAKLGLVDSARAVFNWLPN 412

Query:   410 KDVIAWNSIISGLDDN-VSPDAV-----------------TLVSVISACASLGAVQVGSS 451
              DVI+WN+IISG   N  + +A+                 T VSV+ AC+  GA++ G  
Sbjct:   413 TDVISWNTIISGYAQNGFASEAIEMYNIMEEEGEIAANQGTWVSVLPACSQAGALRQGMK 472

Query:   452 LHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIXXXXXXX 511
             LH    K GL   +V+V T+L + Y KCG  + A  +F  +   N+V W+ +I       
Sbjct:   473 LHGRLLKNGLYL-DVFVVTSLADMYGKCGRLEDALSLFYQIPRVNSVPWNTLIACHGFHG 531

Query:   512 XXXXSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHY 571
                 ++ LF +ML+E V+P+ + F T+LSACSH+G+V EG  CF  M  D+   PS+KHY
Sbjct:   532 HGEKAVMLFKEMLDEGVKPDHITFVTLLSACSHSGLVDEGQWCFEMMQTDYGITPSLKHY 591

Query:   572 VCMVDXXXXXXXXXXXXXFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHP 631
              CMVD             F+++M ++PD S++GA L  C ++   DLG++  + + E+ P
Sbjct:   592 GCMVDMYGRAGQLETALKFIKSMSLQPDASIWGALLSACRVHGNVDLGKIASEHLFEVEP 651

Query:   632 DKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLVDLD 677
             +   Y+VL+SN+YAS G+W  V+++R +   +GL K+PG S +++D
Sbjct:   652 EHVGYHVLLSNMYASAGKWEGVDEIRSIAHGKGLRKTPGWSSMEVD 697

GO:0005739 "mitochondrion" evidence=ISM

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

TAIR|locus:2122551 AT4G39530 [Arabidopsis thaliana (taxid:3702)]

 Score = 543 (196.2 bits), Expect = 1.5e-98, Sum P(2) = 1.5e-98
 Identities = 117/372 (31%), Positives = 208/372 (55%)

Query:    70 ALLIVDGLTNDK-CNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYF-LNDLY 127
             + L+  G   D    T L+  Y   G++ YAR VFD++P     ++  MI     +   Y
Sbjct:   172 SFLVKSGFDRDVYVGTLLIDFYLKDGNIDYARLVFDALPEKSTVTWTTMISGCVKMGRSY 231

Query:   128 KDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVG-GPDSFVLTGL 186
               +  FY+ M   +   D ++ S VL AC  L  ++ G ++H  I++ G   D+ ++  L
Sbjct:   232 VSLQLFYQLMEDNVVP-DGYILSTVLSACSILPFLEGGKQIHAHILRYGLEMDASLMNVL 290

Query:   187 VDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQ 246
             +D Y KC  + ++ ++F+   +KN++SWT++++GY QN   +E + LF  M +  ++ + 
Sbjct:   291 IDSYVKCGRVIAAHKLFNGMPNKNIISWTTLLSGYKQNALHKEAMELFTSMSKFGLKPDM 350

Query:   247 ITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDE 306
                 S++T+CA L AL  G  +H Y +K  +  +S++  +L+DMY KC  + DAR VFD 
Sbjct:   351 YACSSILTSCASLHALGFGTQVHAYTIKANLGNDSYVTNSLIDMYAKCDCLTDARKVFDI 410

Query:   307 LCSIDLVSWTAMIVGYTQSGYP---DKALKLFTDKKWADFFPNHVTIASVLSASAQLGNL 363
               + D+V + AMI GY++ G      +AL +F D ++    P+ +T  S+L ASA L +L
Sbjct:   411 FAAADVVLFNAMIEGYSRLGTQWELHEALNIFRDMRFRLIRPSLLTFVSLLRASASLTSL 470

Query:   364 NMGRMVHSLGIRLGLE-DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISG- 421
              + + +H L  + GL  D    +AL+D+Y+ C+ + D+R +F+    KD++ WNS+ +G 
Sbjct:   471 GLSKQIHGLMFKYGLNLDIFAGSALIDVYSNCYCLKDSRLVFDEMKVKDLVIWNSMFAGY 530

Query:   422 LDDNVSPDAVTL 433
             +  + + +A+ L
Sbjct:   531 VQQSENEEALNL 542

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2124137 DOT4 "DEFECTIVELY ORGANIZED TRIBUTARIES 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 506 (183.2 bits), Expect = 5.4e-98, Sum P(2) = 5.4e-98
 Identities = 95/250 (38%), Positives = 148/250 (59%)

Query:   427 SPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSAR 486
             SPD  T+  V+ ACASL A   G  +H Y  + G  S   +V  +L++ YAKCG    A 
Sbjct:   496 SPDERTVACVLPACASLSAFDKGREIHGYIMRNGYFSDR-HVANSLVDMYAKCGALLLAH 554

Query:   487 MVFDAMREKNTVTWSAMIXXXXXXXXXXXSLALFSDMLNEEVQPNEVIFTTILSACSHTG 546
             M+FD +  K+ V+W+ MI           ++ALF+ M    ++ +E+ F ++L ACSH+G
Sbjct:   555 MLFDDIASKDLVSWTVMIAGYGMHGFGKEAIALFNQMRQAGIEADEISFVSLLYACSHSG 614

Query:   547 MVGEGWKCFYSMCRDFKFVPSMKHYVCMVDXXXXXXXXXXXXXFMENMPIEPDVSLFGAF 606
             +V EGW+ F  M  + K  P+++HY C+VD             F+ENMPI PD +++GA 
Sbjct:   615 LVDEGWRFFNIMRHECKIEPTVEHYACIVDMLARTGDLIKAYRFIENMPIPPDATIWGAL 674

Query:   607 LHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLS 666
             L GC ++    L E + +K+ EL P+   YYVL++N+YA   +W +V ++R+ + QRGL 
Sbjct:   675 LCGCRIHHDVKLAEKVAEKVFELEPENTGYYVLMANIYAEAEKWEQVKRLRKRIGQRGLR 734

Query:   667 KSPGCSLVDL 676
             K+PGCS +++
Sbjct:   735 KNPGCSWIEI 744

GO:0009507 "chloroplast" evidence=ISM

GO:0010087 "phloem or xylem histogenesis" evidence=IMP

GO:0010305 "leaf vascular tissue pattern formation" evidence=IMP

GO:0010588 "cotyledon vascular tissue pattern formation" evidence=IMP

GO:0048366 "leaf development" evidence=IMP

TAIR|locus:2089333 AT3G16610 "AT3G16610" [Arabidopsis thaliana (taxid:3702)]

 Score = 490 (177.5 bits), Expect = 3.4e-94, Sum P(2) = 3.4e-94
 Identities = 114/315 (36%), Positives = 161/315 (51%)

Query:   380 DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDN-------------- 425
             D TV N ++  YAK   + DA   F     KDVI++NS+I+G   N              
Sbjct:   342 DLTVQNTIISFYAKYGSLCDAFRQFSEIGLKDVISYNSLITGCVVNCRPEESFRLFHEMR 401

Query:   426 ---VSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDA 482
                + PD  TL+ V++AC+ L A+  GSS H Y    G  + N  +  AL++ Y KCG  
Sbjct:   402 TSGIRPDITTLLGVLTACSHLAALGHGSSCHGYCVVHGY-AVNTSICNALMDMYTKCGKL 460

Query:   483 QSARMVFDAMREKNTVTWSAMIXXXXXXXXXXXSLALFSDMLNEEVQPNEVIFTTILSAC 542
               A+ VFD M +++ V+W+ M+           +L+LF+ M    V P+EV    ILSAC
Sbjct:   461 DVAKRVFDTMHKRDIVSWNTMLFGFGIHGLGKEALSLFNSMQETGVNPDEVTLLAILSAC 520

Query:   543 SHTGMVGEGWKCFYSMCR-DFKFVPSMKHYVCMVDXXXXXXXXXXXXXFMENMPIEPDVS 601
             SH+G+V EG + F SM R DF  +P + HY CM D             F+  MP EPD+ 
Sbjct:   521 SHSGLVDEGKQLFNSMSRGDFNVIPRIDHYNCMTDLLARAGYLDEAYDFVNKMPFEPDIR 580

Query:   602 LFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMK 661
             + G  L  C  Y   +LG  + KKM  L        VL+SN Y++  RW    ++R + K
Sbjct:   581 VLGTLLSACWTYKNAELGNEVSKKMQSLGETTESL-VLLSNTYSAAERWEDAARIRMIQK 639

Query:   662 QRGLSKSPGCSLVDL 676
             +RGL K+PG S VD+
Sbjct:   640 KRGLLKTPGYSWVDV 654

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0006302 "double-strand break repair" evidence=RCA

GO:0006312 "mitotic recombination" evidence=RCA

GO:0007062 "sister chromatid cohesion" evidence=RCA

GO:0007129 "synapsis" evidence=RCA

GO:0007131 "reciprocal meiotic recombination" evidence=RCA

GO:0042138 "meiotic DNA double-strand break formation" evidence=RCA

GO:0045132 "meiotic chromosome segregation" evidence=RCA

TAIR|locus:2175653 AT5G39350 "AT5G39350" [Arabidopsis thaliana (taxid:3702)]

 Score = 503 (182.1 bits), Expect = 4.3e-92, Sum P(2) = 4.3e-92
 Identities = 119/386 (30%), Positives = 200/386 (51%)

Query:    53 LNLLGLCKSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPNPDFY 112
             LN     +S    KA H  +I  G  +    + L   Y   GH+ YAR +F+ MP     
Sbjct:    22 LNHFAATQSISKTKALHCHVITGGRVSGHILSTLSVTYALCGHITYARKLFEEMPQSSLL 81

Query:   113 SFQVMIRWYFLNDLYKDIVE-FYKCMRKRLK-EHDNFVFSKVLKACCELRDIDEGMKVHC 170
             S+ ++IR Y    LY D +  F + + + +K   D + +  V KA  EL+ +  G+ VH 
Sbjct:    82 SYNIVIRMYVREGLYHDAISVFIRMVSEGVKCVPDGYTYPFVAKAAGELKSMKLGLVVHG 141

Query:   171 EIVKVG-GPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQE 229
              I++   G D +V   L+ MY     +  +R VFD   +++V+SW +MI+GY +N    +
Sbjct:   142 RILRSWFGRDKYVQNALLAMYMNFGKVEMARDVFDVMKNRDVISWNTMISGYYRNGYMND 201

Query:   230 GLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLD 289
              L++F+ M    V+ +  T+ S++  C  L+ L  G+ +H  + +  +     +  AL++
Sbjct:   202 ALMMFDWMVNESVDLDHATIVSMLPVCGHLKDLEMGRNVHKLVEEKRLGDKIEVKNALVN 261

Query:   290 MYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVT 349
             MY+KCG + +AR VFD +   D+++WT MI GYT+ G  + AL+L    ++    PN VT
Sbjct:   262 MYLKCGRMDEARFVFDRMERRDVITWTCMINGYTEDGDVENALELCRLMQFEGVRPNAVT 321

Query:   350 IASVLSASAQLGNLNMGRMVHSLGIRLGL-EDYTVINALVDMYAKCHVIADARYIFETTS 408
             IAS++S       +N G+ +H   +R  +  D  +  +L+ MYAKC  +     +F   S
Sbjct:   322 IASLVSVCGDALKVNDGKCLHGWAVRQQVYSDIIIETSLISMYAKCKRVDLCFRVFSGAS 381

Query:   409 EKDVIAWNSIISGLDDN-VSPDAVTL 433
             +     W++II+G   N +  DA+ L
Sbjct:   382 KYHTGPWSAIIAGCVQNELVSDALGL 407

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2082886 EMB2261 "embryo defective 2261" [Arabidopsis thaliana (taxid:3702)]

 Score = 531 (192.0 bits), Expect = 7.3e-92, Sum P(2) = 7.3e-92
 Identities = 108/312 (34%), Positives = 175/312 (56%)

Query:   382 TVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPD------------ 429
             +V N+++ M+ K   + DA+  FE+ SEK+++++N+ + G   N++ +            
Sbjct:   409 SVANSVISMFVKSDRMEDAQRAFESLSEKNLVSYNTFLDGTCRNLNFEQAFKLLSEITER 468

Query:   430 -----AVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQS 484
                  A T  S++S  A++G+++ G  +H+   K GL S N  V  AL++ Y+KCG   +
Sbjct:   469 ELGVSAFTFASLLSGVANVGSIRKGEQIHSQVVKLGL-SCNQPVCNALISMYSKCGSIDT 527

Query:   485 ARMVFDAMREKNTVTWSAMIXXXXXXXXXXXSLALFSDMLNEEVQPNEVIFTTILSACSH 544
             A  VF+ M  +N ++W++MI            L  F+ M+ E V+PNEV +  ILSACSH
Sbjct:   528 ASRVFNFMENRNVISWTSMITGFAKHGFAIRVLETFNQMIEEGVKPNEVTYVAILSACSH 587

Query:   545 TGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDXXXXXXXXXXXXXFMENMPIEPDVSLFG 604
              G+V EGW+ F SM  D K  P M+HY CMVD             F+  MP + DV ++ 
Sbjct:   588 VGLVSEGWRHFNSMYEDHKIKPKMEHYACMVDLLCRAGLLTDAFEFINTMPFQADVLVWR 647

Query:   605 AFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRG 664
              FL  C ++S  +LG++  +K+LEL P++   Y+ +SN+YA  G+W    ++R  MK+R 
Sbjct:   648 TFLGACRVHSNTELGKLAARKILELDPNEPAAYIQLSNIYACAGKWEESTEMRRKMKERN 707

Query:   665 LSKSPGCSLVDL 676
             L K  GCS +++
Sbjct:   708 LVKEGGCSWIEV 719

GO:0009507 "chloroplast" evidence=ISM

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

TAIR|locus:2060640 OTP81 "ORGANELLE TRANSCRIPT PROCESSING 81" [Arabidopsis thaliana (taxid:3702)]

 Score = 504 (182.5 bits), Expect = 4.8e-91, Sum P(2) = 4.8e-91
 Identities = 96/256 (37%), Positives = 152/256 (59%)

Query:   422 LDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGD 481
             L  N+  + +TLVS +SACA +GA+++G  +H+Y  K G+   N +V +AL++ Y+KCGD
Sbjct:   357 LQKNMKLNQITLVSTLSACAQVGALELGRWIHSYIKKHGI-RMNFHVTSALIHMYSKCGD 415

Query:   482 AQSARMVFDAMREKNTVTWSAMIXXXXXXXXXXXSLALFSDMLNEEVQPNEVIFTTILSA 541
              + +R VF+++ +++   WSAMI           ++ +F  M    V+PN V FT +  A
Sbjct:   416 LEKSREVFNSVEKRDVFVWSAMIGGLAMHGCGNEAVDMFYKMQEANVKPNGVTFTNVFCA 475

Query:   542 CSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDXXXXXXXXXXXXXFMENMPIEPDVS 601
             CSHTG+V E    F+ M  ++  VP  KHY C+VD             F+E MPI P  S
Sbjct:   476 CSHTGLVDEAESLFHQMESNYGIVPEEKHYACIVDVLGRSGYLEKAVKFIEAMPIPPSTS 535

Query:   602 LFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMK 661
             ++GA L  C +++  +L E+   ++LEL P     +VL+SN+YA  G+W  V+++R+ M+
Sbjct:   536 VWGALLGACKIHANLNLAEMACTRLLELEPRNDGAHVLLSNIYAKLGKWENVSELRKHMR 595

Query:   662 QRGLSKSPGCSLVDLD 677
               GL K PGCS +++D
Sbjct:   596 VTGLKKEPGCSSIEID 611

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0031425 "chloroplast RNA processing" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9ZQ74	PP146_ARATH	No assigned EC number	0.5716	0.9609	0.9637	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00030081001 SubName- Full=Putative uncharacterized protein (Chromosome chr1 scaffold_5, whole genome shotgun sequence); (700 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	691
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-167
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	1e-99
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	4e-72
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-56
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-53
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	2e-49
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	1e-21
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	9e-11
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	2e-09
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-07
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	4e-06
pfam13041	50	pfam13041, PPR_2, PPR repeat family	4e-05
pfam13041	50	pfam13041, PPR_2, PPR repeat family	4e-04
pfam13041	50	pfam13041, PPR_2, PPR repeat family	5e-04
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	0.002
pfam01535	31	pfam01535, PPR, PPR repeat	0.002

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score =  500 bits (1289), Expect = e-167
 Identities = 232/609 (38%), Positives = 363/609 (59%), Gaps = 20/609 (3%)

Query: 86  LVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHD 145
           ++SM+  FG + +A  VF  MP  D +S+ V++  Y     + + +  Y  M       D
Sbjct: 127 MLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPD 186

Query: 146 NFVFSKVLKACCELRDIDEGMKVHCEIVKVG-GPDSFVLTGLVDMYAKCRDIGSSRQVFD 204
            + F  VL+ C  + D+  G +VH  +V+ G   D  V+  L+ MY KC D+ S+R VFD
Sbjct: 187 VYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFD 246

Query: 205 ETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQ 264
               ++ +SW +MI+GY +N    EGL LF  MRE  V+ + +T+ S+++AC  L     
Sbjct: 247 RMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERL 306

Query: 265 GKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQ 324
           G+ +HGY++K G  ++  +  +L+ MY+  G+  +A  VF  + + D VSWTAMI GY +
Sbjct: 307 GREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEK 366

Query: 325 SGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVI 384
           +G PDKAL+ +   +  +  P+ +TIASVLSA A LG+L++G  +H L  R GL  Y V+
Sbjct: 367 NGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVV 426

Query: 385 -NALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDN----------------VS 427
            NAL++MY+KC  I  A  +F    EKDVI+W SII+GL  N                + 
Sbjct: 427 ANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTLK 486

Query: 428 PDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARM 487
           P++VTL++ +SACA +GA+  G  +HA+  + G+   + ++  ALL+ Y +CG    A  
Sbjct: 487 PNSVTLIAALSACARIGALMCGKEIHAHVLRTGI-GFDGFLPNALLDLYVRCGRMNYAWN 545

Query: 488 VFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGM 547
            F++  EK+ V+W+ ++ GY   G G  ++ LF+ M+   V P+EV F ++L ACS +GM
Sbjct: 546 QFNS-HEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGM 604

Query: 548 VGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFL 607
           V +G + F+SM   +   P++KHY C+VDLL RAG+L EA  F+  MPI PD +++GA L
Sbjct: 605 VTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALL 664

Query: 608 HGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSK 667
           + C ++   +LGE+  + + EL P+   YY+L+ NLYA  G+W  V +VR+ M++ GL+ 
Sbjct: 665 NACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTV 724

Query: 668 SPGCSLVDL 676
            PGCS V++
Sbjct: 725 DPGCSWVEV 733

Length = 857

>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing protein; Provisional

 Score =  320 bits (822), Expect = e-99
 Identities = 161/482 (33%), Positives = 253/482 (52%), Gaps = 33/482 (6%)

Query: 226 CAQ-EGLVLFNRMREGF--VEGNQI---------TLGSLVTACAKLRALHQGKWLHGYIL 273
           C+Q E LV   R RE     E  +          T  +LV AC  L+++   K ++ ++ 
Sbjct: 91  CSQIEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVE 150

Query: 274 KIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALK 333
             G E + +++  +L M+VKCG + DAR +FDE+   +L SW  +I G   +G   +A  
Sbjct: 151 SSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFA 210

Query: 334 LFTDKKWADFF-PNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGL-EDYTVINALVDMY 391
           LF +  W D       T   +L ASA LG+   G+ +H   ++ G+  D  V  AL+DMY
Sbjct: 211 LFREM-WEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMY 269

Query: 392 AKCHVIADARYIFETTSEKDVIAWNSIISGL-----------------DDNVSPDAVTLV 434
           +KC  I DAR +F+   EK  +AWNS+++G                  D  VS D  T  
Sbjct: 270 SKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFS 329

Query: 435 SVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE 494
            +I   + L  ++     HA   + G    ++   TAL++ Y+K G  + AR VFD M  
Sbjct: 330 IMIRIFSRLALLEHAKQAHAGLIRTGF-PLDIVANTALVDLYSKWGRMEDARNVFDRMPR 388

Query: 495 KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKC 554
           KN ++W+A+I GYG  G G  ++ +F  M+ E V PN V F  +LSAC ++G+  +GW+ 
Sbjct: 389 KNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEI 448

Query: 555 FYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYS 614
           F SM  + +  P   HY CM++LL R G L+EA   +   P +P V+++ A L  C ++ 
Sbjct: 449 FQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHK 508

Query: 615 RFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLV 674
             +LG +  +K+  + P+K   YV++ NLY S GR     +V E +K++GLS  P C+ +
Sbjct: 509 NLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWI 568

Query: 675 DL 676
           ++
Sbjct: 569 EV 570

Length = 697

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score =  250 bits (639), Expect = 4e-72
 Identities = 151/525 (28%), Positives = 259/525 (49%), Gaps = 42/525 (8%)

Query: 145 DNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVL-TGLVDMYAKCRDIGSSRQVF 203
           D   +  + + C   R ++EG +V    +         L   ++ M+ +  ++  +  VF
Sbjct: 85  DEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMFVRFGELVHAWYVF 144

Query: 204 DETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALH 263
            +  ++++ SW  ++ GY +     E L L++RM    V  +  T   ++  C  +  L 
Sbjct: 145 GKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLA 204

Query: 264 QGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYT 323
           +G+ +H ++++ G E++  +V AL+ MYVKCG++  AR VFD +   D +SW AMI GY 
Sbjct: 205 RGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYF 264

Query: 324 QSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLE-DYT 382
           ++G   + L+LF   +     P+ +TI SV+SA   LG+  +GR +H   ++ G   D +
Sbjct: 265 ENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVS 324

Query: 383 VINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDN----------------- 425
           V N+L+ MY       +A  +F     KD ++W ++ISG + N                 
Sbjct: 325 VCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDN 384

Query: 426 VSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSA 485
           VSPD +T+ SV+SACA LG + VG  LH  + ++GL+S  V V  AL+  Y+KC     A
Sbjct: 385 VSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISY-VVVANALIEMYSKCKCIDKA 443

Query: 486 RMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHT 545
             VF  + EK+ ++W+++I G  +      +L  F  ML   ++PN V     LSAC+  
Sbjct: 444 LEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLL-TLKPNSVTLIAALSACARI 502

Query: 546 GMVGEGWKCFYSMCRDF----KFVPSMKHYVCMVDLLARAGRLEEAL-EFMENMPIEPDV 600
           G +  G +    + R       F+P+      ++DL  R GR+  A  +F  +   E DV
Sbjct: 503 GALMCGKEIHAHVLRTGIGFDGFLPN-----ALLDLYVRCGRMNYAWNQFNSH---EKDV 554

Query: 601 SLFGAFLHGCGLYSRFDLGEVMI---KKMLE--LHPDKACYYVLV 640
             +   L G   Y     G + +    +M+E  ++PD+  +  L+
Sbjct: 555 VSWNILLTG---YVAHGKGSMAVELFNRMVESGVNPDEVTFISLL 596

Length = 857

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score =  206 bits (526), Expect = 1e-56
 Identities = 120/391 (30%), Positives = 194/391 (49%), Gaps = 21/391 (5%)

Query: 228 QEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTAL 287
           ++ L L   M+E  V  ++    +L   C   RA+ +G  +    L     +   L  A+
Sbjct: 68  EQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAM 127

Query: 288 LDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNH 347
           L M+V+ G +  A  VF ++   DL SW  ++ GY ++GY D+AL L+    WA   P+ 
Sbjct: 128 LSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDV 187

Query: 348 VTIASVLSASAQLGNLNMGRMVHSLGIRLGLE-DYTVINALVDMYAKCHVIADARYIFET 406
            T   VL     + +L  GR VH+  +R G E D  V+NAL+ MY KC  +  AR +F+ 
Sbjct: 188 YTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDR 247

Query: 407 TSEKDVIAWNSIISG-----------------LDDNVSPDAVTLVSVISACASLGAVQVG 449
              +D I+WN++ISG                  + +V PD +T+ SVISAC  LG  ++G
Sbjct: 248 MPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLG 307

Query: 450 SSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGM 509
             +H Y  K G  + +V V  +L+  Y   G    A  VF  M  K+ V+W+AMI GY  
Sbjct: 308 REMHGYVVKTG-FAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEK 366

Query: 510 QGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMK 569
            G    +L  ++ M  + V P+E+   ++LSAC+  G +  G K  + +      +  + 
Sbjct: 367 NGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVK-LHELAERKGLISYVV 425

Query: 570 HYVCMVDLLARAGRLEEALEFMENMPIEPDV 600
               ++++ ++   +++ALE   N+P E DV
Sbjct: 426 VANALIEMYSKCKCIDKALEVFHNIP-EKDV 455

Length = 857

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score =  197 bits (502), Expect = 2e-53
 Identities = 128/439 (29%), Positives = 203/439 (46%), Gaps = 35/439 (7%)

Query: 66  KAFHALLIVDGLTNDK--CNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFL 123
           +  H  ++  G   D   CN+ L+ MY S G    A  VF  M   D  S+  MI  Y  
Sbjct: 308 REMHGYVVKTGFAVDVSVCNS-LIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEK 366

Query: 124 NDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVL 183
           N L    +E Y  M +     D    + VL AC  L D+D G+K+H E+ +  G  S+V+
Sbjct: 367 NGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLH-ELAERKGLISYVV 425

Query: 184 TG--LVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGF 241
               L++MY+KC+ I  + +VF    +K+V+SWTS+IAG   N+   E L+ F +M    
Sbjct: 426 VANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQML-LT 484

Query: 242 VEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDAR 301
           ++ N +TL + ++ACA++ AL  GK +H ++L+ GI  +  L  ALLD+YV+CG +  A 
Sbjct: 485 LKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAW 544

Query: 302 SVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLG 361
           + F+     D+VSW  ++ GY   G    A++LF     +   P+ VT  S+L A ++ G
Sbjct: 545 NQFN-SHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSG 603

Query: 362 NLNMG-----RMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWN 416
            +  G      M     I   L+ Y     +VD+  +   + +A                
Sbjct: 604 MVTQGLEYFHSMEEKYSITPNLKHYA---CVVDLLGRAGKLTEAYNFINKMP-------- 652

Query: 417 SIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFY 476
                    ++PD     ++++AC     V++G     +  +    S   Y+   L N Y
Sbjct: 653 ---------ITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYI--LLCNLY 701

Query: 477 AKCGDAQSARMVFDAMREK 495
           A  G       V   MRE 
Sbjct: 702 ADAGKWDEVARVRKTMREN 720

Length = 857

>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing protein; Provisional

 Score =  184 bits (468), Expect = 2e-49
 Identities = 97/304 (31%), Positives = 157/304 (51%), Gaps = 2/304 (0%)

Query: 60  KSTGSLKAFHALLIVDGLTNDK-CNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMI 118
           KS   +KA +  +   G   D+    +++ M+   G +  AR +FD MP  +  S+  +I
Sbjct: 137 KSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTII 196

Query: 119 RWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVG-G 177
                   Y++    ++ M +   + +   F  +L+A   L     G ++HC ++K G  
Sbjct: 197 GGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVV 256

Query: 178 PDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRM 237
            D+FV   L+DMY+KC DI  +R VFD   +K  V+W SM+AGY  +  ++E L L+  M
Sbjct: 257 GDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEM 316

Query: 238 REGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNI 297
           R+  V  +Q T   ++   ++L  L   K  H  +++ G  ++    TAL+D+Y K G +
Sbjct: 317 RDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRM 376

Query: 298 RDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSAS 357
            DAR+VFD +   +L+SW A+I GY   G   KA+++F         PNHVT  +VLSA 
Sbjct: 377 EDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSAC 436

Query: 358 AQLG 361
              G
Sbjct: 437 RYSG 440

Length = 697

>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing protein; Provisional

 Score = 99.6 bits (248), Expect = 1e-21
 Identities = 81/326 (24%), Positives = 136/326 (41%), Gaps = 34/326 (10%)

Query: 86  LVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHD 145
           L+ MY   G ++ AR VFD MP     ++  M+  Y L+   ++ +  Y  MR      D
Sbjct: 265 LIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSID 324

Query: 146 NFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVL-TGLVDMYAKCRDIGSSRQVFD 204
            F FS +++    L  ++   + H  +++ G P   V  T LVD+Y+K   +  +R VFD
Sbjct: 325 QFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFD 384

Query: 205 ETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQ 264
               KN++SW ++IAGY  +    + + +F RM    V  N +T  ++++AC       Q
Sbjct: 385 RMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQ 444

Query: 265 GKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQ 324
           G        +I   ++ +       M+  C                       MI    +
Sbjct: 445 GW-------EIFQSMSENHRIKPRAMHYAC-----------------------MIELLGR 474

Query: 325 SGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVI 384
            G  D+A  +      A F P     A++L+A     NL +GR+       +G E     
Sbjct: 475 EGLLDEAYAMIRR---APFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNY 531

Query: 385 NALVDMYAKCHVIADARYIFETTSEK 410
             L+++Y      A+A  + ET   K
Sbjct: 532 VVLLNLYNSSGRQAEAAKVVETLKRK 557

Length = 697

>gnl|CDD|215636 PLN03218, PLN03218, maturation of RBCL 1; Provisional

 Score = 65.3 bits (159), Expect = 9e-11
 Identities = 47/194 (24%), Positives = 86/194 (44%), Gaps = 15/194 (7%)

Query: 425 NVSPDAVTLVSVISACASLGAVQ----VGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCG 480
           NV PD V   ++ISAC   GAV     V + + A +    +   ++ VG AL+   A  G
Sbjct: 537 NVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHP--IDPDHITVG-ALMKACANAG 593

Query: 481 DAQSARMVFDAMREKNT----VTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFT 536
               A+ V+  + E N       ++  +     +GD   +L+++ DM  + V+P+EV F+
Sbjct: 594 QVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFS 653

Query: 537 TILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMEN--- 593
            ++    H G + + ++      R          Y  ++   + A   ++ALE  E+   
Sbjct: 654 ALVDVAGHAGDLDKAFEILQDA-RKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKS 712

Query: 594 MPIEPDVSLFGAFL 607
           + + P VS   A +
Sbjct: 713 IKLRPTVSTMNALI 726

Length = 1060

>gnl|CDD|215636 PLN03218, PLN03218, maturation of RBCL 1; Provisional

 Score = 60.7 bits (147), Expect = 2e-09
 Identities = 108/489 (22%), Positives = 199/489 (40%), Gaps = 96/489 (19%)

Query: 128 KDIVEFYKCMRKR-LKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGL 186
           KD ++  + M KR L + D    +K  KAC + R + E  +   ++++     +F    L
Sbjct: 387 KDCIDLLEDMEKRGLLDMDKIYHAKFFKACKKQRAVKEAFRF-AKLIRNPTLSTF--NML 443

Query: 187 VDMYAKCRDIGSSRQVF----DETLDKNVVSWTSMIAGYVQNDCAQEGLV-----LFNRM 237
           + + A  +DI  + +V     +  L  +   +T++I+      CA+ G V     +F+ M
Sbjct: 444 MSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLIST-----CAKSGKVDAMFEVFHEM 498

Query: 238 REGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNI 297
               VE N  T G+L+  CA  RA    K    Y    GI  +               N+
Sbjct: 499 VNAGVEANVHTFGALIDGCA--RAGQVAKAFGAY----GIMRSK--------------NV 538

Query: 298 RDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWAD---FFPNHVTIASVL 354
           +  R VF+           A+I    QSG  D+A  +  + K A+     P+H+T+ +++
Sbjct: 539 KPDRVVFN-----------ALISACGQSGAVDRAFDVLAEMK-AETHPIDPDHITVGALM 586

Query: 355 SASAQLGNLNMGR----MVHSLGIRLGLEDYT-VINALVDMYAKCHVIAD---ARYIFET 406
            A A  G ++  +    M+H   I+   E YT  +N+       C    D   A  I++ 
Sbjct: 587 KACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNS-------CSQKGDWDFALSIYDD 639

Query: 407 TSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGL-LSSN 465
             +K               V PD V   +++      G +     +   + KQG+ L + 
Sbjct: 640 MKKKG--------------VKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTV 685

Query: 466 VYVGTALLNFYAKCGDAQSARMVFD---AMREKNTV-TWSAMIGGY--GMQGDGGGSLAL 519
            Y  ++L+   +   + + A  +++   +++ + TV T +A+I     G Q     +L +
Sbjct: 686 SY--SSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLP--KALEV 741

Query: 520 FSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLA 579
            S+M    + PN + ++ +L A         G     S  ++    P++    C+  L  
Sbjct: 742 LSEMKRLGLCPNTITYSILLVASERKDDADVGLD-LLSQAKEDGIKPNLVMCRCITGLCL 800

Query: 580 RAGRLEEAL 588
           R  R E+A 
Sbjct: 801 R--RFEKAC 807

Length = 1060

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 47.4 bits (114), Expect = 2e-07
 Identities = 12/50 (24%), Positives = 26/50 (52%)

Query: 495 KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSH 544
            + VT++ +I GY  +G    +L LF++M    ++PN   ++ ++     
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|215636 PLN03218, PLN03218, maturation of RBCL 1; Provisional

 Score = 49.9 bits (119), Expect = 4e-06
 Identities = 32/130 (24%), Positives = 57/130 (43%), Gaps = 5/130 (3%)

Query: 470 TALLNFYAKCGDAQSARMVFDAMR----EKNTVTWSAMIGGYGMQGDGGGSLALFSDMLN 525
           T L++  AK G   +   VF  M     E N  T+ A+I G    G    +   +  M +
Sbjct: 476 TTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRS 535

Query: 526 EEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFV-PSMKHYVCMVDLLARAGRL 584
           + V+P+ V+F  ++SAC  +G V   +     M  +   + P       ++   A AG++
Sbjct: 536 KNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQV 595

Query: 585 EEALEFMENM 594
           + A E  + +
Sbjct: 596 DRAKEVYQMI 605

Length = 1060

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 41.2 bits (98), Expect = 4e-05
 Identities = 15/50 (30%), Positives = 27/50 (54%)

Query: 209 KNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAK 258
            +VV++ ++I GY +    +E L LFN M++  ++ N  T   L+    K
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 38.2 bits (90), Expect = 4e-04
 Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 2/47 (4%)

Query: 311 DLVSWTAMIVGYTQSGYPDKALKLFTD-KKWADFFPNHVTIASVLSA 356
           D+V++  +I GY + G  ++ALKLF + KK     PN  T + ++  
Sbjct: 2   DVVTYNTLIDGYCKKGKVEEALKLFNEMKKR-GIKPNVYTYSILIDG 47

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 37.8 bits (89), Expect = 5e-04
 Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 4/47 (8%)

Query: 465 NVYVGTALLNFYAKCGDAQSARMVFDAMREK----NTVTWSAMIGGY 507
           +V     L++ Y K G  + A  +F+ M+++    N  T+S +I G 
Sbjct: 2   DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGL 48

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|215636 PLN03218, PLN03218, maturation of RBCL 1; Provisional

 Score = 41.0 bits (96), Expect = 0.002
 Identities = 32/146 (21%), Positives = 69/146 (47%), Gaps = 9/146 (6%)

Query: 533 VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEAL---E 589
            ++TT++S C+ +G V   ++ F+ M  +     ++  +  ++D  ARAG++ +A     
Sbjct: 473 KLYTTLISTCAKSGKVDAMFEVFHEM-VNAGVEANVHTFGALIDGCARAGQVAKAFGAYG 531

Query: 590 FMENMPIEPDVSLFGAFLHGCG----LYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYA 645
            M +  ++PD  +F A +  CG    +   FD+   M  +   + PD      L+    A
Sbjct: 532 IMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKAC-A 590

Query: 646 SDGRWIRVNQVRELMKQRGLSKSPGC 671
           + G+  R  +V +++ +  +  +P  
Sbjct: 591 NAGQVDRAKEVYQMIHEYNIKGTPEV 616

Length = 1060

>gnl|CDD|144943 pfam01535, PPR, PPR repeat

 Score = 35.9 bits (84), Expect = 0.002
 Identities = 11/28 (39%), Positives = 18/28 (64%)

Query: 212 VSWTSMIAGYVQNDCAQEGLVLFNRMRE 239
           V++ S+I+GY +    +E L LF  M+E
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKE 28

This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR. Length = 31

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	691
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	100.0
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	100.0
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.98
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.97
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.96
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.94
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.91
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.9
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.88
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.88
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.87
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.86
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.85
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.84
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.84
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.84
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.83
PRK14574	822	hmsH outer membrane protein; Provisional	99.83
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.82
KOG2076	895	consensus RNA polymerase III transcription factor	99.82
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.8
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.8
KOG2076	895	consensus RNA polymerase III transcription factor	99.8
PRK14574	822	hmsH outer membrane protein; Provisional	99.79
KOG2003	840	consensus TPR repeat-containing protein [General f	99.76
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.73
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.73
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.7
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.66
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.66
KOG2003	840	consensus TPR repeat-containing protein [General f	99.61
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.58
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.58
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.58
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.57
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.56
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.55
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.54
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.51
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.51
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.5
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.5
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.5
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.49
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.48
KOG1126	638	consensus DNA-binding cell division cycle control	99.47
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.47
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	99.42
KOG3785	557	consensus Uncharacterized conserved protein [Funct	99.42
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.41
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.41
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.41
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.4
KOG2376	652	consensus Signal recognition particle, subunit Srp	99.36
KOG1126	638	consensus DNA-binding cell division cycle control	99.36
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.36
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.34
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.33
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	99.32
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.31
PF13041	50	PPR_2: PPR repeat family	99.29
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.29
KOG3616	1636	consensus Selective LIM binding factor [Transcript	99.27
KOG3616	1636	consensus Selective LIM binding factor [Transcript	99.26
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	99.25
PF13041	50	PPR_2: PPR repeat family	99.24
KOG3785	557	consensus Uncharacterized conserved protein [Funct	99.22
PRK12370	553	invasion protein regulator; Provisional	99.19
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	99.18
KOG1129	478	consensus TPR repeat-containing protein [General f	99.18
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.18
PRK12370	553	invasion protein regulator; Provisional	99.16
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.16
KOG2376	652	consensus Signal recognition particle, subunit Srp	99.16
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.15
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	99.13
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.13
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	99.11
KOG1129	478	consensus TPR repeat-containing protein [General f	99.09
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.06
PRK11189	296	lipoprotein NlpI; Provisional	99.05
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	99.04
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.03
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.02
KOG4340	459	consensus Uncharacterized conserved protein [Funct	99.0
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	99.0
PRK11189	296	lipoprotein NlpI; Provisional	99.0
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	98.99
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	98.91
KOG1125	579	consensus TPR repeat-containing protein [General f	98.9
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.88
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.86
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.84
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.84
KOG4340	459	consensus Uncharacterized conserved protein [Funct	98.78
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	98.77
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	98.74
PRK04841	903	transcriptional regulator MalT; Provisional	98.74
PRK04841	903	transcriptional regulator MalT; Provisional	98.67
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.66
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.64
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.59
PF12854	34	PPR_1: PPR repeat	98.59
KOG1125	579	consensus TPR repeat-containing protein [General f	98.58
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	98.55
PRK15359	144	type III secretion system chaperone protein SscB;	98.54
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.51
PF12854	34	PPR_1: PPR repeat	98.51
PRK15359	144	type III secretion system chaperone protein SscB;	98.48
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.47
PLN02789	320	farnesyltranstransferase	98.46
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.38
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.37
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.36
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.36
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.35
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.35
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	98.34
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.33
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.31
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.28
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.27
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.24
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.21
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.21
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	98.2
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.16
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.16
PLN02789	320	farnesyltranstransferase	98.16
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.15
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.11
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.09
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.09
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.07
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	98.03
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.03
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.0
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.0
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.96
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.95
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.95
PF13812	34	PPR_3: Pentatricopeptide repeat domain	97.95
PF13812	34	PPR_3: Pentatricopeptide repeat domain	97.92
KOG3060	289	consensus Uncharacterized conserved protein [Funct	97.92
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.9
COG3898	531	Uncharacterized membrane-bound protein [Function u	97.87
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	97.84
KOG0553	304	consensus TPR repeat-containing protein [General f	97.83
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.82
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.81
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.71
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.67
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.66
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.65
PF13371	73	TPR_9: Tetratricopeptide repeat	97.61
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.61
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.61
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.58
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.55
KOG0553	304	consensus TPR repeat-containing protein [General f	97.51
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.51
COG4700	251	Uncharacterized protein conserved in bacteria cont	97.51
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	97.48
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.47
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.47
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	97.46
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	97.45
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.44
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.43
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.4
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.37
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.33
PRK15331	165	chaperone protein SicA; Provisional	97.32
PF12688	120	TPR_5: Tetratrico peptide repeat	97.32
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.3
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	97.3
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.3
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	97.29
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	97.28
PRK10803	263	tol-pal system protein YbgF; Provisional	97.26
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	97.25
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.24
PF13431	34	TPR_17: Tetratricopeptide repeat	97.23
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.21
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.19
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.16
PF12688	120	TPR_5: Tetratrico peptide repeat	97.16
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	97.13
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.12
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.09
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.08
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.06
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.03
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	97.0
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.98
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	96.98
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	96.97
PF13428	44	TPR_14: Tetratricopeptide repeat	96.96
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	96.93
COG4700	251	Uncharacterized protein conserved in bacteria cont	96.9
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	96.87
KOG2796	366	consensus Uncharacterized conserved protein [Funct	96.85
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	96.83
PRK10803	263	tol-pal system protein YbgF; Provisional	96.83
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.8
PF13371	73	TPR_9: Tetratricopeptide repeat	96.76
KOG1258	577	consensus mRNA processing protein [RNA processing	96.76
KOG2041	1189	consensus WD40 repeat protein [General function pr	96.55
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	96.54
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	96.52
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	96.47
PF13512	142	TPR_18: Tetratricopeptide repeat	96.44
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	96.34
COG3898	531	Uncharacterized membrane-bound protein [Function u	96.33
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	96.29
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	96.26
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	96.25
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.22
KOG1585	308	consensus Protein required for fusion of vesicles	96.22
KOG2796	366	consensus Uncharacterized conserved protein [Funct	96.2
PRK11906	458	transcriptional regulator; Provisional	96.17
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	96.07
KOG1258	577	consensus mRNA processing protein [RNA processing	95.97
PF03704	146	BTAD: Bacterial transcriptional activator domain;	95.93
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	95.92
COG0457	291	NrfG FOG: TPR repeat [General function prediction	95.91
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	95.89
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	95.8
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	95.77
KOG2041	1189	consensus WD40 repeat protein [General function pr	95.76
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	95.55
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	95.54
KOG4555	175	consensus TPR repeat-containing protein [Function	95.49
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	95.27
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	95.26
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	95.21
KOG3941	406	consensus Intermediate in Toll signal transduction	95.09
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.03
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	95.02
KOG3941	406	consensus Intermediate in Toll signal transduction	95.01
PF03704	146	BTAD: Bacterial transcriptional activator domain;	94.96
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	94.9
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	94.74
PF13512	142	TPR_18: Tetratricopeptide repeat	94.72
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	94.7
COG4105	254	ComL DNA uptake lipoprotein [General function pred	94.63
smart00299	140	CLH Clathrin heavy chain repeat homology.	94.36
COG3118	304	Thioredoxin domain-containing protein [Posttransla	94.32
PRK11619	644	lytic murein transglycosylase; Provisional	94.28
COG3118	304	Thioredoxin domain-containing protein [Posttransla	94.28
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	94.26
PRK15331	165	chaperone protein SicA; Provisional	94.22
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	94.21
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	94.13
PF13428	44	TPR_14: Tetratricopeptide repeat	93.97
KOG2610	491	consensus Uncharacterized conserved protein [Funct	93.94
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	93.93
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	93.78
KOG1941	518	consensus Acetylcholine receptor-associated protei	93.7
PRK11906	458	transcriptional regulator; Provisional	93.58
KOG4234	271	consensus TPR repeat-containing protein [General f	93.54
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	93.53
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	93.35
KOG2610	491	consensus Uncharacterized conserved protein [Funct	93.27
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	93.27
KOG2396	568	consensus HAT (Half-A-TPR) repeat-containing prote	93.18
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	93.13
KOG4555	175	consensus TPR repeat-containing protein [Function	93.08
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	92.38
COG3629	280	DnrI DNA-binding transcriptional activator of the	92.26
COG4105	254	ComL DNA uptake lipoprotein [General function pred	92.14
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	92.04
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	91.83
PF13431	34	TPR_17: Tetratricopeptide repeat	91.79
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	91.61
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	91.59
KOG1585	308	consensus Protein required for fusion of vesicles	91.5
KOG1941	518	consensus Acetylcholine receptor-associated protei	91.05
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	90.8
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	90.56
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	90.27
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	90.07
KOG4648	536	consensus Uncharacterized conserved protein, conta	89.9
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	89.82
KOG1550	552	consensus Extracellular protein SEL-1 and related	89.75
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	89.31
COG3629	280	DnrI DNA-binding transcriptional activator of the	89.14
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	89.14
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	89.13
KOG0403	645	consensus Neoplastic transformation suppressor Pdc	89.1
KOG0403	645	consensus Neoplastic transformation suppressor Pdc	88.9
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	88.77
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	88.75
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	88.69
KOG4570	418	consensus Uncharacterized conserved protein [Funct	88.65
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	88.0
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	87.92
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	87.6
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	87.53
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	87.0
PRK09687	280	putative lyase; Provisional	86.92
PRK09687	280	putative lyase; Provisional	86.88
PF09986	214	DUF2225: Uncharacterized protein conserved in bact	86.84
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	86.46
PF14853	53	Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repe	86.42
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	86.28
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	86.18
COG2976	207	Uncharacterized protein conserved in bacteria [Fun	86.0
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	85.97
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	85.56
KOG4648	536	consensus Uncharacterized conserved protein, conta	85.54
COG0457	291	NrfG FOG: TPR repeat [General function prediction	85.3
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	85.29
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	85.25
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	85.11
COG2976	207	Uncharacterized protein conserved in bacteria [Fun	85.01
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	84.61
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	84.5
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	84.13
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	84.03
KOG4570	418	consensus Uncharacterized conserved protein [Funct	83.92
COG4455	273	ImpE Protein of avirulence locus involved in tempe	83.22
KOG1586	288	consensus Protein required for fusion of vesicles	83.14
KOG1586	288	consensus Protein required for fusion of vesicles	83.03
PF06552	186	TOM20_plant: Plant specific mitochondrial import r	83.01
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	82.78
KOG4642	284	consensus Chaperone-dependent E3 ubiquitin protein	82.75
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	82.64
KOG4234	271	consensus TPR repeat-containing protein [General f	82.55
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	82.44
COG4455	273	ImpE Protein of avirulence locus involved in tempe	82.27
smart00028	34	TPR Tetratricopeptide repeats. Repeats present in	82.1
COG3947	361	Response regulator containing CheY-like receiver a	81.95
PRK11619	644	lytic murein transglycosylase; Provisional	81.6
KOG1464	440	consensus COP9 signalosome, subunit CSN2 [Posttran	81.15
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	81.1
PF14561	90	TPR_20: Tetratricopeptide repeat; PDB: 3QOU_A 2R5S	80.41
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	80.14

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=5.8e-95  Score=810.24  Aligned_cols=655  Identities=36%  Similarity=0.671  Sum_probs=638.2

Q ss_pred             CCCChHHHHhhhcC-------CCchhHHHHHhhc---cCchhHHHHHHHHHHhCCCCch-hhhHHHHHHhcCCChHHHHH
Q 040394           33 TQHELDQTFASFHS-------LPSIPCLNLLGLC---KSTGSLKAFHALLIVDGLTNDK-CNTKLVSMYGSFGHVKYARS  101 (691)
Q Consensus        33 ~~~~~~~a~~~~~~-------~~~~~~~~ll~~~---~~~~~a~~~~~~~~~~~~~~~~-~~~~l~~~~~~~g~~~~A~~  101 (691)
                      ..+.+++|..+|..       |+..++..++..|   +.+..+..++..+.+.++.++. +++.++..|++.|+++.|.+
T Consensus        63 ~~g~~~~A~~l~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~n~li~~~~~~g~~~~A~~  142 (857)
T PLN03077         63 SHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMFVRFGELVHAWY  142 (857)
T ss_pred             hCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHHHhhCCCHHHHHHHHHHHHHcCCCCCchHHHHHHHHHHhCCChHHHHH
Confidence            56788888888876       6667788888888   6788899999999999988888 99999999999999999999


Q ss_pred             HhccCCCCCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCC-Ch
Q 040394          102 VFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGP-DS  180 (691)
Q Consensus       102 ~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~  180 (691)
                      +|++|++||..+||.++.+|++.|++++|+++|++|...|+.||..||+.++++|++.++++.+.+++..+.+.|.+ |.
T Consensus       143 ~f~~m~~~d~~~~n~li~~~~~~g~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~  222 (857)
T PLN03077        143 VFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDV  222 (857)
T ss_pred             HHhcCCCCCeeEHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHhCCccchhhHHHHHHHHHHcCCCccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999976 99


Q ss_pred             hHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccC
Q 040394          181 FVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLR  260 (691)
Q Consensus       181 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~  260 (691)
                      .+++.|+.+|+++|++++|.++|++|.+||..+||++|.+|++.|++++|+++|++|.+.|+.||..||+.++.+|++.|
T Consensus       223 ~~~n~Li~~y~k~g~~~~A~~lf~~m~~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g  302 (857)
T PLN03077        223 DVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLG  302 (857)
T ss_pred             chHhHHHHHHhcCCCHHHHHHHHhcCCCCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhH
Q 040394          261 ALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKW  340 (691)
Q Consensus       261 ~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  340 (691)
                      +++.+.+++..|.+.|+.||..+|+.||.+|++.|++++|.++|++|..||..+||++|.+|++.|++++|+++|++|.+
T Consensus       303 ~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~  382 (857)
T PLN03077        303 DERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQ  382 (857)
T ss_pred             ChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCC-chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHH
Q 040394          341 ADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLE-DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSII  419 (691)
Q Consensus       341 ~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li  419 (691)
                      .|+.||..||+.++.+|++.|+++.|.++++.+.+.|.. +..+++.++++|++.|++++|.++|++|.++|+++||++|
T Consensus       383 ~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~vs~~~mi  462 (857)
T PLN03077        383 DNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSII  462 (857)
T ss_pred             hCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCeeeHHHHH
Confidence            999999999999999999999999999999999999999 9999999999999999999999999999999999999999


Q ss_pred             HhhhC----------------CCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHH
Q 040394          420 SGLDD----------------NVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQ  483 (691)
Q Consensus       420 ~~~~~----------------~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  483 (691)
                      .++.+                ++.||..||+.++.+|++.|+++.+.+++..+.+.|+ .++..++++++++|+++|+++
T Consensus       463 ~~~~~~g~~~eA~~lf~~m~~~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~-~~~~~~~naLi~~y~k~G~~~  541 (857)
T PLN03077        463 AGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGI-GFDGFLPNALLDLYVRCGRMN  541 (857)
T ss_pred             HHHHHCCCHHHHHHHHHHHHhCCCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCC-CccceechHHHHHHHHcCCHH
Confidence            99865                6899999999999999999999999999999999998 999999999999999999999


Q ss_pred             HHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcC
Q 040394          484 SARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFK  563 (691)
Q Consensus       484 ~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~  563 (691)
                      +|.++|+.+ .+|..+||+||.+|+++|+.++|+++|++|.+.|+.||..||+.++.+|++.|++++|.++|+.|.+.+|
T Consensus       542 ~A~~~f~~~-~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~g  620 (857)
T PLN03077        542 YAWNQFNSH-EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYS  620 (857)
T ss_pred             HHHHHHHhc-CCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHHHhC
Confidence            999999999 8999999999999999999999999999999999999999999999999999999999999999976889


Q ss_pred             CCCChhHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHH
Q 040394          564 FVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNL  643 (691)
Q Consensus       564 ~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~  643 (691)
                      +.|+..+|++++++|++.|++++|.+++++|+.+||..+|++|+.+|..+|+.+.++...+++++++|+++.+|..++++
T Consensus       621 i~P~~~~y~~lv~~l~r~G~~~eA~~~~~~m~~~pd~~~~~aLl~ac~~~~~~e~~e~~a~~l~~l~p~~~~~y~ll~n~  700 (857)
T PLN03077        621 ITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNL  700 (857)
T ss_pred             CCCchHHHHHHHHHHHhCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhhCCCCcchHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhCCCcHHHHHHHHHHHhCCCccCCCeeEEEeCCeeeEEeeeccc
Q 040394          644 YASDGRWIRVNQVRELMKQRGLSKSPGCSLVDLDIANDFSFSRVVS  689 (691)
Q Consensus       644 ~~~~g~~~~A~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~  689 (691)
                      |...|+|++|.++.+.|++.|++++||++|++++++.|.|..|+.+
T Consensus       701 ya~~g~~~~a~~vr~~M~~~g~~k~~g~s~ie~~~~~~~f~~~d~~  746 (857)
T PLN03077        701 YADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDES  746 (857)
T ss_pred             HHHCCChHHHHHHHHHHHHcCCCCCCCccEEEECCEEEEEecCCCC
Confidence            9999999999999999999999999999999999999999999865

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=1e-74  Score=647.37  Aligned_cols=556  Identities=26%  Similarity=0.460  Sum_probs=531.7

Q ss_pred             CCCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCC-ChhHHHHH
Q 040394          108 NPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGP-DSFVLTGL  186 (691)
Q Consensus       108 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l  186 (691)
                      .++..++|.++.+|++.|++++|..+|++|.+.|++|+..+|..++++|.+.+..+.+..++..+.+.++. +...++.|
T Consensus        48 ~~~~~~~n~~i~~l~~~g~~~~A~~l~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~n~l  127 (857)
T PLN03077         48 SSSTHDSNSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAM  127 (857)
T ss_pred             ccchhhHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHHHhhCCCHHHHHHHHHHHHHcCCCCCchHHHHH
Confidence            46778899999999999999999999999999999999999999999999999999999999999999976 99999999


Q ss_pred             HHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHH
Q 040394          187 VDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGK  266 (691)
Q Consensus       187 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~  266 (691)
                      +.+|++.|+++.|.++|++|.+||..+||.+|.+|++.|++++|+++|++|...|+.||..||+.++++|+..+++..+.
T Consensus       128 i~~~~~~g~~~~A~~~f~~m~~~d~~~~n~li~~~~~~g~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~~~~~~~~~~~  207 (857)
T PLN03077        128 LSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGR  207 (857)
T ss_pred             HHHHHhCCChHHHHHHHhcCCCCCeeEHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHhCCccchhhHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCc
Q 040394          267 WLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPN  346 (691)
Q Consensus       267 ~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  346 (691)
                      +++..|.+.|+.||..+++.||.+|+++|++++|.++|++|..+|.++||++|.+|++.|++++|+++|++|...|+.||
T Consensus       208 ~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd  287 (857)
T PLN03077        208 EVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPD  287 (857)
T ss_pred             HHHHHHHHcCCCcccchHhHHHHHHhcCCCHHHHHHHHhcCCCCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCC-chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhC-
Q 040394          347 HVTIASVLSASAQLGNLNMGRMVHSLGIRLGLE-DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDD-  424 (691)
Q Consensus       347 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~-  424 (691)
                      ..||+.++.+|+..|+++.|.+++..+.+.|.. +..+|+.++.+|++.|++++|.++|++|..+|.++||++|.+|.+ 
T Consensus       288 ~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~  367 (857)
T PLN03077        288 LMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKN  367 (857)
T ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhC
Confidence            999999999999999999999999999999998 999999999999999999999999999999999999999999977 


Q ss_pred             ----------------CCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHH
Q 040394          425 ----------------NVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMV  488 (691)
Q Consensus       425 ----------------~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  488 (691)
                                      |+.||..||+.++.+|++.|+++.|.++++.+.+.|. .++..+++.|+++|++.|++++|.++
T Consensus       368 g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~-~~~~~~~n~Li~~y~k~g~~~~A~~v  446 (857)
T PLN03077        368 GLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGL-ISYVVVANALIEMYSKCKCIDKALEV  446 (857)
T ss_pred             CCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCC-CcchHHHHHHHHHHHHcCCHHHHHHH
Confidence                            8999999999999999999999999999999999998 99999999999999999999999999


Q ss_pred             HHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCCh
Q 040394          489 FDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSM  568 (691)
Q Consensus       489 ~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~  568 (691)
                      |++|.++|..+|+++|.+|++.|+.++|+.+|++|.. ++.||..||+.++.+|++.|+++.+.+++..+ .+.|+.+|.
T Consensus       447 f~~m~~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~-~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~-~~~g~~~~~  524 (857)
T PLN03077        447 FHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLL-TLKPNSVTLIAALSACARIGALMCGKEIHAHV-LRTGIGFDG  524 (857)
T ss_pred             HHhCCCCCeeeHHHHHHHHHHCCCHHHHHHHHHHHHh-CCCCCHhHHHHHHHHHhhhchHHHhHHHHHHH-HHhCCCccc
Confidence            9999999999999999999999999999999999986 59999999999999999999999999999999 556999999


Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh--cCCCCchhHHHHHHHHHh
Q 040394          569 KHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLE--LHPDKACYYVLVSNLYAS  646 (691)
Q Consensus       569 ~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~p~~~~~~~~l~~~~~~  646 (691)
                      .++++|+++|+++|++++|.++|+.+  .||..+|++++.+|.+.|+.++|.++|++|.+  ..|+ ..+|..+..+|.+
T Consensus       525 ~~~naLi~~y~k~G~~~~A~~~f~~~--~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd-~~T~~~ll~a~~~  601 (857)
T PLN03077        525 FLPNALLDLYVRCGRMNYAWNQFNSH--EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPD-EVTFISLLCACSR  601 (857)
T ss_pred             eechHHHHHHHHcCCHHHHHHHHHhc--CCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC-cccHHHHHHHHhh
Confidence            99999999999999999999999888  78889999999999999999999999998887  5666 6677777788899


Q ss_pred             CCCcHHHHHHHHHHH-hCCCccCC
Q 040394          647 DGRWIRVNQVRELMK-QRGLSKSP  669 (691)
Q Consensus       647 ~g~~~~A~~~~~~~~-~~g~~~~~  669 (691)
                      .|++++|.++|+.|. +.|+.|+.
T Consensus       602 ~g~v~ea~~~f~~M~~~~gi~P~~  625 (857)
T PLN03077        602 SGMVTQGLEYFHSMEEKYSITPNL  625 (857)
T ss_pred             cChHHHHHHHHHHHHHHhCCCCch
Confidence            999999999999998 67887654

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

Probab=100.00  E-value=6.9e-74  Score=625.30  Aligned_cols=498  Identities=30%  Similarity=0.555  Sum_probs=474.5

Q ss_pred             CCCcchHHHHHHHHHhCCChhHHHHHHHHHHHcC-CCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCC-ChhHHHH
Q 040394          108 NPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRL-KEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGP-DSFVLTG  185 (691)
Q Consensus       108 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~-~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~  185 (691)
                      .++..+|+.++.++.+.|++++|+++|+.|...+ +.||..+|+.++.+|++.++.+.+.+++..|.+.|.. |..+|+.
T Consensus        84 ~~~~~~~~~~i~~l~~~g~~~~Al~~f~~m~~~~~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n~  163 (697)
T PLN03081         84 RKSGVSLCSQIEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNR  163 (697)
T ss_pred             CCCceeHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHHH
Confidence            3577799999999999999999999999999864 7899999999999999999999999999999999965 9999999


Q ss_pred             HHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhH
Q 040394          186 LVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQG  265 (691)
Q Consensus       186 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a  265 (691)
                      |+.+|++.|++++|.++|++|.+||..+||++|.+|++.|++++|+++|++|.+.|+.||..||+.++.+|++.|+.+.+
T Consensus       164 Li~~y~k~g~~~~A~~lf~~m~~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~~  243 (697)
T PLN03081        164 VLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAG  243 (697)
T ss_pred             HHHHHhcCCCHHHHHHHHhcCCCCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCCcHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCC
Q 040394          266 KWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFP  345 (691)
Q Consensus       266 ~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  345 (691)
                      .+++..+.+.|+.||..+|+.||++|+++|++++|.++|++|.++|+++||+||.+|++.|++++|+++|++|...|+.|
T Consensus       244 ~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~p  323 (697)
T PLN03081        244 QQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSI  323 (697)
T ss_pred             HHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999886655


Q ss_pred             cHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCC
Q 040394          346 NHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDN  425 (691)
Q Consensus       346 ~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~  425 (691)
                      |..||                                                                           
T Consensus       324 d~~t~---------------------------------------------------------------------------  328 (697)
T PLN03081        324 DQFTF---------------------------------------------------------------------------  328 (697)
T ss_pred             CHHHH---------------------------------------------------------------------------
Confidence            55555                                                                           


Q ss_pred             CCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHH
Q 040394          426 VSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIG  505 (691)
Q Consensus       426 ~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~  505 (691)
                              +.++.+|++.|+++.|.+++..|.+.|+ +++..++++|+++|+++|++++|.++|++|.++|+.+||+||.
T Consensus       329 --------~~ll~a~~~~g~~~~a~~i~~~m~~~g~-~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~d~~t~n~lI~  399 (697)
T PLN03081        329 --------SIMIRIFSRLALLEHAKQAHAGLIRTGF-PLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIA  399 (697)
T ss_pred             --------HHHHHHHHhccchHHHHHHHHHHHHhCC-CCCeeehHHHHHHHHHCCCHHHHHHHHHhCCCCCeeeHHHHHH
Confidence                    5555555666666667777777777887 8999999999999999999999999999999999999999999


Q ss_pred             HHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChH
Q 040394          506 GYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLE  585 (691)
Q Consensus       506 ~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~  585 (691)
                      +|+++|+.++|+++|++|.+.|+.||..||+.++.+|++.|++++|.++|+.|.++.|+.|+..+|+.++++|++.|+++
T Consensus       400 ~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~~  479 (697)
T PLN03081        400 GYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLD  479 (697)
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHHHhcCCHH
Confidence            99999999999999999999999999999999999999999999999999999878899999999999999999999999


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          586 EALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       586 ~A~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      +|.+++++|+.+|+..+|++|+.+|..+|+++.|..+++++.+..|++...|..++++|.+.|+|++|.++++.|.+.|+
T Consensus       480 eA~~~~~~~~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~~~p~~~~~y~~L~~~y~~~G~~~~A~~v~~~m~~~g~  559 (697)
T PLN03081        480 EAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGL  559 (697)
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHhCCCCCCCcchHHHHHHHHhCCCHHHHHHHHHHHHHcCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCeeEEEeCCeeeEEeeeccc
Q 040394          666 SKSPGCSLVDLDIANDFSFSRVVS  689 (691)
Q Consensus       666 ~~~~~~~~~~~~~~~~~~~~~~~~  689 (691)
                      .+.||++|++++++.|+|+.|+.+
T Consensus       560 ~k~~g~s~i~~~~~~~~f~~~d~~  583 (697)
T PLN03081        560 SMHPACTWIEVKKQDHSFFSGDRL  583 (697)
T ss_pred             ccCCCeeEEEECCeEEEEccCCCC
Confidence            999999999999999999999764

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=4.8e-67  Score=572.02  Aligned_cols=528  Identities=16%  Similarity=0.187  Sum_probs=486.1

Q ss_pred             CCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCC-C-ChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHH
Q 040394          142 KEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGG-P-DSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIA  219 (691)
Q Consensus       142 ~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~  219 (691)
                      ..++...|..++..+++.|++++|.++|++|.+.|. + +..+++.++..|.+.|.+++|..+|+.|..||..+|+.+|.
T Consensus       366 ~~~~~~~~~~~y~~l~r~G~l~eAl~Lfd~M~~~gvv~~~~v~~~~li~~~~~~g~~~eAl~lf~~M~~pd~~Tyn~LL~  445 (1060)
T PLN03218        366 GKRKSPEYIDAYNRLLRDGRIKDCIDLLEDMEKRGLLDMDKIYHAKFFKACKKQRAVKEAFRFAKLIRNPTLSTFNMLMS  445 (1060)
T ss_pred             CCCCchHHHHHHHHHHHCcCHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            456778899999999999999999999999999984 3 88888999999999999999999999999999999999999


Q ss_pred             HHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHH
Q 040394          220 GYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRD  299 (691)
Q Consensus       220 ~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~  299 (691)
                      +|++.|++++|.++|++|.+.|+.||..+|+.+|.+|++.|++++|.++|++|.+.|+.||..+|+.||.+|++.|++++
T Consensus       446 a~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~ee  525 (1060)
T PLN03218        446 VCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAK  525 (1060)
T ss_pred             HHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhc----CCCChhHHHHHHHHHHhcCCchhHHHHHHHhhH--CCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHH
Q 040394          300 ARSVFDEL----CSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKW--ADFFPNHVTIASVLSASAQLGNLNMGRMVHSLG  373 (691)
Q Consensus       300 A~~~~~~~----~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~  373 (691)
                      |.++|++|    ..||..+|+.||.+|++.|++++|.++|++|..  .|+.||..||+.+|.+|++.|++++|.++++.|
T Consensus       526 Al~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M  605 (1060)
T PLN03218        526 AFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMI  605 (1060)
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            99999999    568999999999999999999999999999986  689999999999999999999999999999999


Q ss_pred             HHhCCC-chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHH
Q 040394          374 IRLGLE-DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSL  452 (691)
Q Consensus       374 ~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~  452 (691)
                      .+.++. +..+|+.++.+|++.|++++|.++|++|.+.              |+.||..||+.++.+|++.|++++|.++
T Consensus       606 ~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~--------------Gv~PD~~TynsLI~a~~k~G~~eeA~~l  671 (1060)
T PLN03218        606 HEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKK--------------GVKPDEVFFSALVDVAGHAGDLDKAFEI  671 (1060)
T ss_pred             HHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHc--------------CCCCCHHHHHHHHHHHHhCCCHHHHHHH
Confidence            999988 9999999999999999999999999999988              8999999999999999999999999999


Q ss_pred             HHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcc----cCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCC
Q 040394          453 HAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMR----EKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEV  528 (691)
Q Consensus       453 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~  528 (691)
                      ++.|.+.|+ +|+..+|+.++.+|++.|++++|.++|++|.    .||..+|++||.+|++.|++++|.++|++|.+.|+
T Consensus       672 ~~eM~k~G~-~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi  750 (1060)
T PLN03218        672 LQDARKQGI-KLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGL  750 (1060)
T ss_pred             HHHHHHcCC-CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCC
Confidence            999999998 9999999999999999999999999999996    58999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHh----c-------------------CChH
Q 040394          529 QPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLAR----A-------------------GRLE  585 (691)
Q Consensus       529 ~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~----~-------------------g~~~  585 (691)
                      .||..||+.++.+|++.|++++|.+++++| .+.|+.||..+|++++..|.+    +                   +..+
T Consensus       751 ~Pd~~Ty~sLL~a~~k~G~le~A~~l~~~M-~k~Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g~~~~~n~w~~  829 (1060)
T PLN03218        751 CPNTITYSILLVASERKDDADVGLDLLSQA-KEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQIENKWTS  829 (1060)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHH-HHcCCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccccccccchHH
Confidence            999999999999999999999999999999 666999999999999876432    2                   2346


Q ss_pred             HHHHHHHhC---CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-cCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHH
Q 040394          586 EALEFMENM---PIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLE-LHPDKACYYVLVSNLYASDGRWIRVNQVRELMK  661 (691)
Q Consensus       586 ~A~~~~~~~---~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  661 (691)
                      +|+.+|++|   ++.||..+|+.++.+++..++.+.+..+++.+.. -.+.+..+|..+...+.+  ..++|..++++|.
T Consensus       830 ~Al~lf~eM~~~Gi~Pd~~T~~~vL~cl~~~~~~~~~~~m~~~m~~~~~~~~~~~y~~Li~g~~~--~~~~A~~l~~em~  907 (1060)
T PLN03218        830 WALMVYRETISAGTLPTMEVLSQVLGCLQLPHDATLRNRLIENLGISADSQKQSNLSTLVDGFGE--YDPRAFSLLEEAA  907 (1060)
T ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHhcccccHHHHHHHHHHhccCCCCcchhhhHHHHHhhcc--ChHHHHHHHHHHH
Confidence            799999999   8999999999999888888999998888887654 344557788888887732  2368999999999


Q ss_pred             hCCCccCCCeeEEEeCCeeeEEeeec
Q 040394          662 QRGLSKSPGCSLVDLDIANDFSFSRV  687 (691)
Q Consensus       662 ~~g~~~~~~~~~~~~~~~~~~~~~~~  687 (691)
                      +.|+.|+....-.....+++++..|.
T Consensus       908 ~~Gi~p~~~~~~~~~~~d~~~~~~~a  933 (1060)
T PLN03218        908 SLGVVPSVSFKKSPIVIDAEELPVFA  933 (1060)
T ss_pred             HcCCCCCcccccCceEEEcccCcchh
Confidence            99998877532225556666666653

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=7.5e-67  Score=570.48  Aligned_cols=526  Identities=14%  Similarity=0.188  Sum_probs=448.7

Q ss_pred             hhHHHHHhhc---cCchhHHHHHHHHHHhCC-CCch-hhhHHHHHHhcCCChHHHHHHhccCCCCCcchHHHHHHHHHhC
Q 040394           50 IPCLNLLGLC---KSTGSLKAFHALLIVDGL-TNDK-CNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLN  124 (691)
Q Consensus        50 ~~~~~ll~~~---~~~~~a~~~~~~~~~~~~-~~~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~ll~~~~~~  124 (691)
                      ..+..++..+   |+++.|..+++.|...+. +++. .++.++..|.+.|.+++|..+|+.|+.||..+|+.++.+|++.
T Consensus       371 ~~~~~~y~~l~r~G~l~eAl~Lfd~M~~~gvv~~~~v~~~~li~~~~~~g~~~eAl~lf~~M~~pd~~Tyn~LL~a~~k~  450 (1060)
T PLN03218        371 PEYIDAYNRLLRDGRIKDCIDLLEDMEKRGLLDMDKIYHAKFFKACKKQRAVKEAFRFAKLIRNPTLSTFNMLMSVCASS  450 (1060)
T ss_pred             hHHHHHHHHHHHCcCHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHhC
Confidence            3344444444   888899999999988885 4455 6778889999999999999999999889999999999999999


Q ss_pred             CChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCC-ChhHHHHHHHHhHhcCChHHHHHHH
Q 040394          125 DLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGP-DSFVLTGLVDMYAKCRDIGSSRQVF  203 (691)
Q Consensus       125 ~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~  203 (691)
                      |+++.|.++|++|.+.|+.||..+|+.+|.+|++.|++++|.++|++|.+.|.. |..+|+.++.+|++.|++++|.++|
T Consensus       451 g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf  530 (1060)
T PLN03218        451 QDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAY  530 (1060)
T ss_pred             cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999998865 9999999999999999999999999


Q ss_pred             hccC----CCChhhHHHHHHHHHhCCChhHHHHHHHHHHh--CCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCC
Q 040394          204 DETL----DKNVVSWTSMIAGYVQNDCAQEGLVLFNRMRE--GFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGI  277 (691)
Q Consensus       204 ~~~~----~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~  277 (691)
                      ++|.    .||..+|+.||.+|++.|++++|.++|++|..  .|+.||..||+++|.+|++.|++++|.++|+.|.+.|+
T Consensus       531 ~~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        531 GIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNI  610 (1060)
T ss_pred             HHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCC
Confidence            8883    47889999999999999999999999999976  67889999999999999999999999999999999999


Q ss_pred             CCchHHHHHHHHHHHhcCCHHHHHHHHHhc----CCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHH
Q 040394          278 EINSHLVTALLDMYVKCGNIRDARSVFDEL----CSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASV  353 (691)
Q Consensus       278 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~~----~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l  353 (691)
                      .|+..+|+.+|.+|++.|++++|.++|++|    ..||..+|+.+|.+|++.|++++|.+++++|.+.|+.||..+|+.+
T Consensus       611 ~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tynsL  690 (1060)
T PLN03218        611 KGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSL  690 (1060)
T ss_pred             CCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            999999999999999999999999999998    4578889999999999999999999999999999999999999999


Q ss_pred             HHHHhcCCChhhHHHHHHHHHHhCCC-chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHH
Q 040394          354 LSASAQLGNLNMGRMVHSLGIRLGLE-DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVT  432 (691)
Q Consensus       354 l~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~  432 (691)
                      |.+|++.|++++|.++|+.|.+.|.. +..+|+.+|.+|++.|++++|.++|++|...              |+.||..|
T Consensus       691 I~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~--------------Gi~Pd~~T  756 (1060)
T PLN03218        691 MGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRL--------------GLCPNTIT  756 (1060)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHc--------------CCCCCHHH
Confidence            99999999999999999999888877 8888999999999999999999999998877              78899999


Q ss_pred             HHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCC
Q 040394          433 LVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGD  512 (691)
Q Consensus       433 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~  512 (691)
                      |+.++.+|++.|+++.|.+++.+|.+.|+ .|+..+|+.++..|.  +++++|..+.+.+..     |+. .......+.
T Consensus       757 y~sLL~a~~k~G~le~A~~l~~~M~k~Gi-~pd~~tynsLIglc~--~~y~ka~~l~~~v~~-----f~~-g~~~~~n~w  827 (1060)
T PLN03218        757 YSILLVASERKDDADVGLDLLSQAKEDGI-KPNLVMCRCITGLCL--RRFEKACALGEPVVS-----FDS-GRPQIENKW  827 (1060)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHH--HHHHHHhhhhhhhhh-----hhc-cccccccch
Confidence            99999999999999999999999999998 899999999886543  245555554433321     110 111112234


Q ss_pred             hHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHH
Q 040394          513 GGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFME  592 (691)
Q Consensus       513 ~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~  592 (691)
                      .+.|..+|++|.+.|+.||..||+.++.+++..+..+.+..+++.| ...+..|+..+|++||+++++.  .++|..+++
T Consensus       828 ~~~Al~lf~eM~~~Gi~Pd~~T~~~vL~cl~~~~~~~~~~~m~~~m-~~~~~~~~~~~y~~Li~g~~~~--~~~A~~l~~  904 (1060)
T PLN03218        828 TSWALMVYRETISAGTLPTMEVLSQVLGCLQLPHDATLRNRLIENL-GISADSQKQSNLSTLVDGFGEY--DPRAFSLLE  904 (1060)
T ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccccHHHHHHHHHHh-ccCCCCcchhhhHHHHHhhccC--hHHHHHHHH
Confidence            4679999999999999999999999998888899999999999888 5557788899999999988432  468999999


Q ss_pred             hC---CCCCCHH
Q 040394          593 NM---PIEPDVS  601 (691)
Q Consensus       593 ~~---~~~p~~~  601 (691)
                      +|   |+.|+..
T Consensus       905 em~~~Gi~p~~~  916 (1060)
T PLN03218        905 EAASLGVVPSVS  916 (1060)
T ss_pred             HHHHcCCCCCcc
Confidence            99   7777764

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

Probab=100.00  E-value=2.8e-63  Score=541.98  Aligned_cols=482  Identities=25%  Similarity=0.411  Sum_probs=439.0

Q ss_pred             CCCChHHHHhhhcC--------CCchhHHHHHhhc---cCchhHHHHHHHHHHhCCCCch-hhhHHHHHHhcCCChHHHH
Q 040394           33 TQHELDQTFASFHS--------LPSIPCLNLLGLC---KSTGSLKAFHALLIVDGLTNDK-CNTKLVSMYGSFGHVKYAR  100 (691)
Q Consensus        33 ~~~~~~~a~~~~~~--------~~~~~~~~ll~~~---~~~~~a~~~~~~~~~~~~~~~~-~~~~l~~~~~~~g~~~~A~  100 (691)
                      ..+++++|+.+|+.        |+..++..++.+|   +..+.+..++..+.+.|+.++. +++.++++|++.|++++|.
T Consensus        99 ~~g~~~~Al~~f~~m~~~~~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n~Li~~y~k~g~~~~A~  178 (697)
T PLN03081         99 ACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDAR  178 (697)
T ss_pred             cCCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHhcCCCHHHHH
Confidence            34555666655543        5677888888888   7788899999999999999999 9999999999999999999


Q ss_pred             HHhccCCCCCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCC-C
Q 040394          101 SVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGP-D  179 (691)
Q Consensus       101 ~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~  179 (691)
                      ++|++|++||..+||+++.+|++.|++++|+++|++|.+.|+.|+..+|+.++.+|++.|+.+.+.+++..+.+.|.. |
T Consensus       179 ~lf~~m~~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d  258 (697)
T PLN03081        179 RLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGD  258 (697)
T ss_pred             HHHhcCCCCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCCCcc
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999966 9


Q ss_pred             hhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHcc
Q 040394          180 SFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKL  259 (691)
Q Consensus       180 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~  259 (691)
                      ..+|++|+++|+++|++++|.++|++|.++|+++||+||.+|++.|++++|+++|++|.+.|+.||..||++++.+|++.
T Consensus       259 ~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~  338 (697)
T PLN03081        259 TFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRL  338 (697)
T ss_pred             ceeHHHHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhh
Q 040394          260 RALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKK  339 (691)
Q Consensus       260 ~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  339 (691)
                      |++++|.+++..|.+.|+.||..+|++||++|+++|++++|.++|++|.++|+.+||+||.+|++.|+.++|+++|++|.
T Consensus       339 g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~  418 (697)
T PLN03081        339 ALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMI  418 (697)
T ss_pred             cchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHH-hCCC-chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHH
Q 040394          340 WADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIR-LGLE-DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNS  417 (691)
Q Consensus       340 ~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~-~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  417 (691)
                      +.|+.||..||+.++.+|++.|.+++|.++|+.|.+ .|.. +..+|+.++++|++.|++++|.+++++|.         
T Consensus       419 ~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~~eA~~~~~~~~---------  489 (697)
T PLN03081        419 AEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAP---------  489 (697)
T ss_pred             HhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHHHhcCCHHHHHHHHHHCC---------
Confidence            999999999999999999999999999999999986 5776 88999999999999999999999999884         


Q ss_pred             HHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCH
Q 040394          418 IISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNT  497 (691)
Q Consensus       418 li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  497 (691)
                              +.|+..+|++++.+|+..|+++.|..+++++.+.+  |.+..+|..++++|++.|++++|.++++.|.+.+.
T Consensus       490 --------~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~~~--p~~~~~y~~L~~~y~~~G~~~~A~~v~~~m~~~g~  559 (697)
T PLN03081        490 --------FKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMG--PEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGL  559 (697)
T ss_pred             --------CCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHhCCC--CCCCcchHHHHHHHHhCCCHHHHHHHHHHHHHcCC
Confidence                    67999999999999999999999999999997666  66788999999999999999999999999986432


Q ss_pred             -----hHHHH-------HHHHHhcCCC----hHHHHHHHHHHHHCCCCCCHH
Q 040394          498 -----VTWSA-------MIGGYGMQGD----GGGSLALFSDMLNEEVQPNEV  533 (691)
Q Consensus       498 -----~~~~~-------li~~~~~~~~----~~~A~~~~~~m~~~g~~p~~~  533 (691)
                           .+|..       ++.+-..+.+    ++...++..+|.+.|..||..
T Consensus       560 ~k~~g~s~i~~~~~~~~f~~~d~~h~~~~~i~~~l~~l~~~~~~~gy~~~~~  611 (697)
T PLN03081        560 SMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEEN  611 (697)
T ss_pred             ccCCCeeEEEECCeEEEEccCCCCCccHHHHHHHHHHHHHHHHHcCCCCCcc
Confidence                 22311       1111111111    234556777888888888754

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

Probab=100.00  E-value=3.2e-37  Score=354.72  Aligned_cols=577  Identities=12%  Similarity=0.046  Sum_probs=342.4

Q ss_pred             cCchhHHHHHHHHHHhCCCCchhhhHHHHHHhcCCChHHHHHHhccCCC---CCcchHHHHHHHHHhCCChhHHHHHHHH
Q 040394           60 KSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPN---PDFYSFQVMIRWYFLNDLYKDIVEFYKC  136 (691)
Q Consensus        60 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~ll~~~~~~~~~~~a~~~~~~  136 (691)
                      ++.+.|...++.++...+.....+..+...+.+.|++++|...+..+..   .+...+..+...+.+.|++++|.++|++
T Consensus       309 g~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  388 (899)
T TIGR02917       309 GNLEQAYQYLNQILKYAPNSHQARRLLASIQLRLGRVDEAIATLSPALGLDPDDPAALSLLGEAYLALGDFEKAAEYLAK  388 (899)
T ss_pred             CCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            4455555555555444332222444555555555555555555554432   2333455555555555555555555555


Q ss_pred             HHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCC---CChhh
Q 040394          137 MRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLD---KNVVS  213 (691)
Q Consensus       137 m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~  213 (691)
                      +.+.. +.+...+..+...+...|+.++|.+.++.+.+..+........++..+.+.|++++|..+++++..   ++..+
T Consensus       389 ~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~  467 (899)
T TIGR02917       389 ATELD-PENAAARTQLGISKLSQGDPSEAIADLETAAQLDPELGRADLLLILSYLRSGQFDKALAAAKKLEKKQPDNASL  467 (899)
T ss_pred             HHhcC-CCCHHHHHHHHHHHHhCCChHHHHHHHHHHHhhCCcchhhHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCCcHH
Confidence            55432 223334444445555555555555555555555444444455555555555666666555555432   24445


Q ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHh
Q 040394          214 WTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVK  293 (691)
Q Consensus       214 ~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~  293 (691)
                      |..+...+...|++++|.+.|+++.+... .+...+..+...+...|++++|.++++.+.+.+ +.+..++..+...+.+
T Consensus       468 ~~~l~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~  545 (899)
T TIGR02917       468 HNLLGAIYLGKGDLAKAREAFEKALSIEP-DFFPAAANLARIDIQEGNPDDAIQRFEKVLTID-PKNLRAILALAGLYLR  545 (899)
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHhhCC-CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHH
Confidence            55566666666666666666666554321 233344455555556666666666666665543 2244555556666666


Q ss_pred             cCCHHHHHHHHHhc---CCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHH
Q 040394          294 CGNIRDARSVFDEL---CSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVH  370 (691)
Q Consensus       294 ~g~~~~A~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~  370 (691)
                      .|+.++|..+|+++   ...+...+..++..+.+.|++++|.++++.+... .+.+..+|..+..++...|++++|...+
T Consensus       546 ~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~A~~~~  624 (899)
T TIGR02917       546 TGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAADA-APDSPEAWLMLGRAQLAAGDLNKAVSSF  624 (899)
T ss_pred             cCCHHHHHHHHHHHHHhCccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHc-CCCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            66666666666555   2223345555566666666666666666665543 2334455556666666666666666666


Q ss_pred             HHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHH
Q 040394          371 SLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGS  450 (691)
Q Consensus       371 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~  450 (691)
                      +.+.+..+.+...+..+...+.+.|++++|...|+++.+.               .+.+..++..+...+...|+++.|.
T Consensus       625 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~---------------~~~~~~~~~~l~~~~~~~~~~~~A~  689 (899)
T TIGR02917       625 KKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRALEL---------------KPDNTEAQIGLAQLLLAAKRTESAK  689 (899)
T ss_pred             HHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhc---------------CCCCHHHHHHHHHHHHHcCCHHHHH
Confidence            6666655555555666666666666666666666655433               2334566666677777777777777


Q ss_pred             HHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCC
Q 040394          451 SLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEV  528 (691)
Q Consensus       451 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~  528 (691)
                      .+++.+.+..  +.+...+..+...+.+.|++++|...|+.+..  |+..++..++..+.+.|++++|.+.++++.+.. 
T Consensus       690 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~-  766 (899)
T TIGR02917       690 KIAKSLQKQH--PKAALGFELEGDLYLRQKDYPAAIQAYRKALKRAPSSQNAIKLHRALLASGNTAEAVKTLEAWLKTH-  766 (899)
T ss_pred             HHHHHHHhhC--cCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-
Confidence            7777776665  55666666677777777777777777776653  444556666777777777777777777776642 


Q ss_pred             CCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHH
Q 040394          529 QPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAF  606 (691)
Q Consensus       529 ~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l  606 (691)
                      +.+...+..+...|...|++++|.+.|+++.+.  .+++...++.+...+...|+ .+|++.++++ ...| +..++..+
T Consensus       767 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~~l~~~~~~~~~-~~A~~~~~~~~~~~~~~~~~~~~~  843 (899)
T TIGR02917       767 PNDAVLRTALAELYLAQKDYDKAIKHYRTVVKK--APDNAVVLNNLAWLYLELKD-PRALEYAEKALKLAPNIPAILDTL  843 (899)
T ss_pred             CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHhcCc-HHHHHHHHHHHhhCCCCcHHHHHH
Confidence            445556666666777777777777777766433  12335666677777777777 6677777766 3333 34456666


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHH
Q 040394          607 LHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMK  661 (691)
Q Consensus       607 ~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  661 (691)
                      ...+...|++++|...++++++..|.++.++..++.++.+.|++++|.+++++|+
T Consensus       844 ~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  898 (899)
T TIGR02917       844 GWLLVEKGEADRALPLLRKAVNIAPEAAAIRYHLALALLATGRKAEARKELDKLL  898 (899)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            6667777777777777777777777777777777777777777777777777765

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.

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

Probab=100.00  E-value=1.1e-36  Score=350.14  Aligned_cols=581  Identities=11%  Similarity=0.023  Sum_probs=408.0

Q ss_pred             cCchhHHHHHHHHHHhCCCCchhhhHHHHHHhcCCChHHHHHHhccCCC---CCcchHHHHHHHHHhCCChhHHHHHHHH
Q 040394           60 KSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPN---PDFYSFQVMIRWYFLNDLYKDIVEFYKC  136 (691)
Q Consensus        60 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~ll~~~~~~~~~~~a~~~~~~  136 (691)
                      ++.+.|...++.+++..+.....+..+...+...|++++|...|+++.+   .+...+..+...+.+.|++++|...++.
T Consensus       275 ~~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~  354 (899)
T TIGR02917       275 KNYEDARETLQDALKSAPEYLPALLLAGASEYQLGNLEQAYQYLNQILKYAPNSHQARRLLASIQLRLGRVDEAIATLSP  354 (899)
T ss_pred             cCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            4444444444444444332222333344445555555555555554431   2233445555555666666666666666


Q ss_pred             HHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCC---Chhh
Q 040394          137 MRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDK---NVVS  213 (691)
Q Consensus       137 m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~  213 (691)
                      +.+.. +.+...+..+...+.+.|++++|...|+.+.+..+.+...+..+...+...|++++|.+.|++..+.   +...
T Consensus       355 ~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~  433 (899)
T TIGR02917       355 ALGLD-PDDPAALSLLGEAYLALGDFEKAAEYLAKATELDPENAAARTQLGISKLSQGDPSEAIADLETAAQLDPELGRA  433 (899)
T ss_pred             HHhcC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhCCChHHHHHHHHHHHhhCCcchhh
Confidence            55442 3344455555566666666666666666666555555556666666666666666666666554321   2334


Q ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHh
Q 040394          214 WTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVK  293 (691)
Q Consensus       214 ~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~  293 (691)
                      +..++..+.+.|++++|.++++++... .+++..++..+...+...|+.++|.+.|+++.+.. +.+...+..+...+..
T Consensus       434 ~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~  511 (899)
T TIGR02917       434 DLLLILSYLRSGQFDKALAAAKKLEKK-QPDNASLHNLLGAIYLGKGDLAKAREAFEKALSIE-PDFFPAAANLARIDIQ  511 (899)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHh-CCCCcHHHHHHHHHHHhCCCHHHHHHHHHHHHhhC-CCcHHHHHHHHHHHHH
Confidence            445556666666666666666666543 23355566666667777777777777777766543 2244555666666777


Q ss_pred             cCCHHHHHHHHHhcC---CCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHH
Q 040394          294 CGNIRDARSVFDELC---SIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVH  370 (691)
Q Consensus       294 ~g~~~~A~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~  370 (691)
                      .|++++|.+.|+++.   +.+..++..+...+.+.|+.++|..+++++...+ +.+...+..+...+...|++++|..++
T Consensus       512 ~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~  590 (899)
T TIGR02917       512 EGNPDDAIQRFEKVLTIDPKNLRAILALAGLYLRTGNEEEAVAWLEKAAELN-PQEIEPALALAQYYLGKGQLKKALAIL  590 (899)
T ss_pred             CCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchhHHHHHHHHHHHCCCHHHHHHHH
Confidence            777777777776662   2345566666777777777777777777765542 234455566666777777777777777


Q ss_pred             HHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHH
Q 040394          371 SLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGS  450 (691)
Q Consensus       371 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~  450 (691)
                      +.+.+..+.+...+..+...|...|++++|...|+++.+.               .+.+...+..+...+...|++++|.
T Consensus       591 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~---------------~~~~~~~~~~l~~~~~~~~~~~~A~  655 (899)
T TIGR02917       591 NEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLAL---------------QPDSALALLLLADAYAVMKNYAKAI  655 (899)
T ss_pred             HHHHHcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---------------CCCChHHHHHHHHHHHHcCCHHHHH
Confidence            7777666666667777777777777777777777766543               2345667788888888999999999


Q ss_pred             HHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCC
Q 040394          451 SLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEE  527 (691)
Q Consensus       451 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g  527 (691)
                      .+++.+.+..  |.+...+..++..+...|++++|..+++.+.+   .+...+..+...+...|++++|...++++... 
T Consensus       656 ~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~-  732 (899)
T TIGR02917       656 TSLKRALELK--PDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKR-  732 (899)
T ss_pred             HHHHHHHhcC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhh-
Confidence            9999988876  67788888999999999999999999998875   35667888889999999999999999999885 


Q ss_pred             CCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC--CCCCCHHHHHH
Q 040394          528 VQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM--PIEPDVSLFGA  605 (691)
Q Consensus       528 ~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~--~~~p~~~~~~~  605 (691)
                       .|+..++..+..++.+.|++++|.+.++.+.+.  .+.+...+..+...|...|++++|.+.|+++  ..+++..+++.
T Consensus       733 -~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~--~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~  809 (899)
T TIGR02917       733 -APSSQNAIKLHRALLASGNTAEAVKTLEAWLKT--HPNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKAPDNAVVLNN  809 (899)
T ss_pred             -CCCchHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCHHHHHH
Confidence             466677778888999999999999999988544  3345778888999999999999999999998  34556778999


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCc
Q 040394          606 FLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLS  666 (691)
Q Consensus       606 l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~  666 (691)
                      +...+...|+ .+|+..++++.+..|+++.++..++.++...|++++|.++++++++.+..
T Consensus       810 l~~~~~~~~~-~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~  869 (899)
T TIGR02917       810 LAWLYLELKD-PRALEYAEKALKLAPNIPAILDTLGWLLVEKGEADRALPLLRKAVNIAPE  869 (899)
T ss_pred             HHHHHHhcCc-HHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            9999999999 88999999999999999999999999999999999999999999997753

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.

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.98  E-value=7.1e-27  Score=268.23  Aligned_cols=587  Identities=9%  Similarity=0.044  Sum_probs=376.9

Q ss_pred             cCchhHHHHHHHHHHhCCCCchhhhHHHHHHhcCCChHHHHHHhccCCC--CCcchH-----------------HHHHHH
Q 040394           60 KSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPN--PDFYSF-----------------QVMIRW  120 (691)
Q Consensus        60 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~~-----------------~~ll~~  120 (691)
                      ++.+.|+..++.+....+.+..++..++.++.+.|+.++|.+.+++..+  |+...+                 ..+.+.
T Consensus        42 ~~~d~a~~~l~kl~~~~p~~p~~~~~~~~~~l~~g~~~~A~~~l~~l~~~~P~~~~~~~~~~~~~~~~~~~~~~l~~A~l  121 (1157)
T PRK11447         42 HREDLVRQSLYRLELIDPNNPDVIAARFRLLLRQGDSDGAQKLLDRLSQLAPDSNAYRSSRTTMLLSTPEGRQALQQARL  121 (1157)
T ss_pred             CChHHHHHHHHHHHccCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhhCCCChHHHHHHHHHHhcCCchhhHHHHHHH
Confidence            8888999999988887665544888899999999999999999999864  443322                 233446


Q ss_pred             HHhCCChhHHHHHHHHHHHcCCCCCcch-HHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHH
Q 040394          121 YFLNDLYKDIVEFYKCMRKRLKEHDNFV-FSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSS  199 (691)
Q Consensus       121 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~-~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  199 (691)
                      +.+.|++++|+..|+++.+.+ +|+... ...........|+.++|...++++.+..|.+...+..+...+...|+.++|
T Consensus       122 l~~~g~~~eA~~~~~~~l~~~-p~~~~la~~y~~~~~~~~g~~~~A~~~L~~ll~~~P~~~~~~~~LA~ll~~~g~~~eA  200 (1157)
T PRK11447        122 LATTGRTEEALASYDKLFNGA-PPELDLAVEYWRLVAKLPAQRPEAINQLQRLNADYPGNTGLRNTLALLLFSSGRRDEG  200 (1157)
T ss_pred             HHhCCCHHHHHHHHHHHccCC-CCChHHHHHHHHHHhhCCccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHccCCHHHH
Confidence            788999999999999998763 344321 111122233569999999999999999888999999999999999999999


Q ss_pred             HHHHhccCCCCh------hhH-----------------HHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHH
Q 040394          200 RQVFDETLDKNV------VSW-----------------TSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTAC  256 (691)
Q Consensus       200 ~~~~~~~~~~~~------~~~-----------------~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~  256 (691)
                      +..++++...+.      ..|                 ...+..+-.......|...+.++......|+... ...-..+
T Consensus       201 l~~l~~~~~~~~~~~~aa~~~~~~l~~~~~~~~~~~~l~~~l~~~p~~~~~~~A~~~L~~~~~~~~dp~~~~-~~~G~~~  279 (1157)
T PRK11447        201 FAVLEQMAKSPAGRDAAAQLWYGQIKDMPVSDASVAALQKYLQVFSDGDSVAAARSQLAEQQKQLADPAFRA-RAQGLAA  279 (1157)
T ss_pred             HHHHHHHhhCCCchHHHHHHHHHHHhccCCChhhHHHHHHHHHHCCCchHHHHHHHHHHHHHHhccCcchHH-HHHHHHH
Confidence            999998744211      111                 1111111112223445555555544322333221 2234556


Q ss_pred             HccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCC--CCh---hHHHH------------HH
Q 040394          257 AKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCS--IDL---VSWTA------------MI  319 (691)
Q Consensus       257 ~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~--~~~---~~~~~------------li  319 (691)
                      ...|++++|...|++.++.. +.+..++..+...+.+.|++++|...|++...  |+.   ..|..            ..
T Consensus       280 ~~~g~~~~A~~~l~~aL~~~-P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g  358 (1157)
T PRK11447        280 VDSGQGGKAIPELQQAVRAN-PKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQG  358 (1157)
T ss_pred             HHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHH
Confidence            78899999999999999864 33678899999999999999999999998732  321   12222            23


Q ss_pred             HHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHH
Q 040394          320 VGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIAD  399 (691)
Q Consensus       320 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  399 (691)
                      ..+.+.|++++|.+.|++..... +.+...+..+...+...|++++|+..++.+.+..+.+...+..+...|. .++.++
T Consensus       359 ~~~~~~g~~~eA~~~~~~Al~~~-P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~~~~a~~~L~~l~~-~~~~~~  436 (1157)
T PRK11447        359 DAALKANNLAQAERLYQQARQVD-NTDSYAVLGLGDVAMARKDYAAAERYYQQALRMDPGNTNAVRGLANLYR-QQSPEK  436 (1157)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH-hcCHHH
Confidence            45778999999999999998863 2345667778889999999999999999999998887777888888875 467899


Q ss_pred             HHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhc
Q 040394          400 ARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKC  479 (691)
Q Consensus       400 a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  479 (691)
                      |..+++.+..............      .....+..+...+...|+.++|...+++..+..  |.++..+..+...|.+.
T Consensus       437 A~~~l~~l~~~~~~~~~~~~~~------l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~--P~~~~~~~~LA~~~~~~  508 (1157)
T PRK11447        437 ALAFIASLSASQRRSIDDIERS------LQNDRLAQQAEALENQGKWAQAAELQRQRLALD--PGSVWLTYRLAQDLRQA  508 (1157)
T ss_pred             HHHHHHhCCHHHHHHHHHHHHH------hhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHc
Confidence            9999988764321111000000      011234445556667777777777777777766  56666666777777777


Q ss_pred             CCHHHHHHHHHhccc--C-CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCC-----------------------------
Q 040394          480 GDAQSARMVFDAMRE--K-NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEE-----------------------------  527 (691)
Q Consensus       480 g~~~~A~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g-----------------------------  527 (691)
                      |++++|...++++.+  | +...+..+...+...++.++|+..++.+....                             
T Consensus       509 G~~~~A~~~l~~al~~~P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~  588 (1157)
T PRK11447        509 GQRSQADALMRRLAQQKPNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGK  588 (1157)
T ss_pred             CCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCC
Confidence            777777777776643  2 33333333334445555555555554432211                             


Q ss_pred             ----------CCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-C
Q 040394          528 ----------VQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-P  595 (691)
Q Consensus       528 ----------~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~  595 (691)
                                .+++...+..+...+.+.|++++|++.|++..+   ..|+ ...+..++..|...|++++|++.++.. .
T Consensus       589 ~~eA~~~l~~~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~---~~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~  665 (1157)
T PRK11447        589 EAEAEALLRQQPPSTRIDLTLADWAQQRGDYAAARAAYQRVLT---REPGNADARLGLIEVDIAQGDLAAARAQLAKLPA  665 (1157)
T ss_pred             HHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhc
Confidence                      122333344444455555555555555554432   2333 445555555555555555555555554 2


Q ss_pred             CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc------hhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          596 IEPD-VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKA------CYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       596 ~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~------~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      ..|+ ..++..+..++...|++++|.++++++++..|+++      ..+..++.++...|++++|.+.|++...
T Consensus       666 ~~p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A~~~y~~Al~  739 (1157)
T PRK11447        666 TANDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQALETYKDAMV  739 (1157)
T ss_pred             cCCCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            2222 23444445555555555555555555555444332      2334445555555555555555555544

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.97  E-value=4.4e-25  Score=253.51  Aligned_cols=542  Identities=9%  Similarity=0.007  Sum_probs=376.2

Q ss_pred             cCchhHHHHHHHHHHhCCCCchhh----------------hHHHHHHhcCCChHHHHHHhccCCC--CCcchHH--HHHH
Q 040394           60 KSTGSLKAFHALLIVDGLTNDKCN----------------TKLVSMYGSFGHVKYARSVFDSMPN--PDFYSFQ--VMIR  119 (691)
Q Consensus        60 ~~~~~a~~~~~~~~~~~~~~~~~~----------------~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~~~--~ll~  119 (691)
                      |+.+.|....+.+.+..+.+....                ..+.+.+.+.|++++|.+.|+++.+  |+.....  ....
T Consensus        76 g~~~~A~~~l~~l~~~~P~~~~~~~~~~~~~~~~~~~~~~l~~A~ll~~~g~~~eA~~~~~~~l~~~p~~~~la~~y~~~  155 (1157)
T PRK11447         76 GDSDGAQKLLDRLSQLAPDSNAYRSSRTTMLLSTPEGRQALQQARLLATTGRTEEALASYDKLFNGAPPELDLAVEYWRL  155 (1157)
T ss_pred             CCHHHHHHHHHHHHhhCCCChHHHHHHHHHHhcCCchhhHHHHHHHHHhCCCHHHHHHHHHHHccCCCCChHHHHHHHHH
Confidence            899999999999988876554422                3345678999999999999998764  2222211  1111


Q ss_pred             HHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCCh-------------------
Q 040394          120 WYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDS-------------------  180 (691)
Q Consensus       120 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~-------------------  180 (691)
                      .....|++++|++.|+++.+.. +-+...+..+...+...|+.++|...++++.+....+.                   
T Consensus       156 ~~~~~g~~~~A~~~L~~ll~~~-P~~~~~~~~LA~ll~~~g~~~eAl~~l~~~~~~~~~~~~aa~~~~~~l~~~~~~~~~  234 (1157)
T PRK11447        156 VAKLPAQRPEAINQLQRLNADY-PGNTGLRNTLALLLFSSGRRDEGFAVLEQMAKSPAGRDAAAQLWYGQIKDMPVSDAS  234 (1157)
T ss_pred             HhhCCccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHccCCHHHHHHHHHHHhhCCCchHHHHHHHHHHHhccCCChhh
Confidence            2234699999999999999873 44566777888889999999999999999876432111                   


Q ss_pred             -hHHHHHHHHhHhcCChHHHHHHHhccC----CCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHH
Q 040394          181 -FVLTGLVDMYAKCRDIGSSRQVFDETL----DKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTA  255 (691)
Q Consensus       181 -~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~  255 (691)
                       ..+...+..+-.....+.|...+++..    +|.. ........+...|++++|+..|++..+... .+...+..+..+
T Consensus       235 ~~~l~~~l~~~p~~~~~~~A~~~L~~~~~~~~dp~~-~~~~~G~~~~~~g~~~~A~~~l~~aL~~~P-~~~~a~~~Lg~~  312 (1157)
T PRK11447        235 VAALQKYLQVFSDGDSVAAARSQLAEQQKQLADPAF-RARAQGLAAVDSGQGGKAIPELQQAVRANP-KDSEALGALGQA  312 (1157)
T ss_pred             HHHHHHHHHHCCCchHHHHHHHHHHHHHHhccCcch-HHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHH
Confidence             111222222222223444555554331    1221 112335567788999999999999887532 266778888888


Q ss_pred             HHccCChhhHHHHHHHHHHHCCCCc-hHHH------------HHHHHHHHhcCCHHHHHHHHHhcC---CCChhHHHHHH
Q 040394          256 CAKLRALHQGKWLHGYILKIGIEIN-SHLV------------TALLDMYVKCGNIRDARSVFDELC---SIDLVSWTAMI  319 (691)
Q Consensus       256 ~~~~~~~~~a~~~~~~~~~~g~~~~-~~~~------------~~li~~~~~~g~~~~A~~~~~~~~---~~~~~~~~~li  319 (691)
                      +.+.|+.++|...|++..+...... ...+            ......+.+.|++++|...|+++.   ..+...+..+.
T Consensus       313 ~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g~~~~~~g~~~eA~~~~~~Al~~~P~~~~a~~~Lg  392 (1157)
T PRK11447        313 YSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQGDAALKANNLAQAERLYQQARQVDNTDSYAVLGLG  392 (1157)
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence            8999999999999999887643221 1111            122456778899999999998882   23556777788


Q ss_pred             HHHHhcCCchhHHHHHHHhhHCCCCCc-HHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCC---------chhHHHHHHH
Q 040394          320 VGYTQSGYPDKALKLFTDKKWADFFPN-HVTIASVLSASAQLGNLNMGRMVHSLGIRLGLE---------DYTVINALVD  389 (691)
Q Consensus       320 ~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~---------~~~~~~~l~~  389 (691)
                      ..+...|++++|++.|++..+.  .|+ ...+..+...+. .++.++|..+++.+......         ....+..+..
T Consensus       393 ~~~~~~g~~~eA~~~y~~aL~~--~p~~~~a~~~L~~l~~-~~~~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~  469 (1157)
T PRK11447        393 DVAMARKDYAAAERYYQQALRM--DPGNTNAVRGLANLYR-QQSPEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAE  469 (1157)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHH-hcCHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHH
Confidence            8899999999999999998875  343 445555555553 45678888777654332111         1234556777


Q ss_pred             HhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHH
Q 040394          390 MYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVG  469 (691)
Q Consensus       390 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  469 (691)
                      .+...|++++|...|++..+.+               +-+...+..+...+.+.|+.++|...++.+.+..  |.++..+
T Consensus       470 ~~~~~g~~~eA~~~~~~Al~~~---------------P~~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~~--P~~~~~~  532 (1157)
T PRK11447        470 ALENQGKWAQAAELQRQRLALD---------------PGSVWLTYRLAQDLRQAGQRSQADALMRRLAQQK--PNDPEQV  532 (1157)
T ss_pred             HHHHCCCHHHHHHHHHHHHHhC---------------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCCHHHH
Confidence            8888999999999998877542               2234566677778888888888888888887755  4444443


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhcc-------------------------------------------cCCHhHHHHHHHH
Q 040394          470 TALLNFYAKCGDAQSARMVFDAMR-------------------------------------------EKNTVTWSAMIGG  506 (691)
Q Consensus       470 ~~l~~~~~~~g~~~~A~~~~~~~~-------------------------------------------~~~~~~~~~li~~  506 (691)
                      ..+...+...++.++|...++.+.                                           ..+...+..+...
T Consensus       533 ~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~~~p~~~~~~~~La~~  612 (1157)
T PRK11447        533 YAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLRQQPPSTRIDLTLADW  612 (1157)
T ss_pred             HHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHHhCCCCchHHHHHHHH
Confidence            333333444444444444444332                                           1244456678888


Q ss_pred             HhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChH
Q 040394          507 YGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLE  585 (691)
Q Consensus       507 ~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~  585 (691)
                      +.+.|++++|+..|++..+.. +.+...+..+...+...|++++|.+.++...   ...|+ ...+..+..++...|+++
T Consensus       613 ~~~~g~~~~A~~~y~~al~~~-P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll---~~~p~~~~~~~~la~~~~~~g~~~  688 (1157)
T PRK11447        613 AQQRGDYAAARAAYQRVLTRE-PGNADARLGLIEVDIAQGDLAAARAQLAKLP---ATANDSLNTQRRVALAWAALGDTA  688 (1157)
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHh---ccCCCChHHHHHHHHHHHhCCCHH
Confidence            999999999999999999863 3456788888999999999999999999764   34555 556777888999999999


Q ss_pred             HHHHHHHhC-CCC----C---CHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040394          586 EALEFMENM-PIE----P---DVSLFGAFLHGCGLYSRFDLGEVMIKKMLE  628 (691)
Q Consensus       586 ~A~~~~~~~-~~~----p---~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  628 (691)
                      +|.++++++ ...    |   +...+..+...+...|+.++|+..|++++.
T Consensus       689 eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A~~~y~~Al~  739 (1157)
T PRK11447        689 AAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQALETYKDAMV  739 (1157)
T ss_pred             HHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            999999998 222    2   224566677888999999999999999986

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.96  E-value=4.9e-23  Score=225.33  Aligned_cols=579  Identities=11%  Similarity=0.018  Sum_probs=359.5

Q ss_pred             cCchhHHHHHHHHHHhCCCCchhhhHHHHHHhcCCChHHHHHHhccCCC--CCcchHHHHHHHHHhCCChhHHHHHHHHH
Q 040394           60 KSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPN--PDFYSFQVMIRWYFLNDLYKDIVEFYKCM  137 (691)
Q Consensus        60 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~~~~ll~~~~~~~~~~~a~~~~~~m  137 (691)
                      |+...|...++..++..+.+..++..+...|.+.|+.++|+..+++..+  |+...|..++..+   +++++|..+|+++
T Consensus        58 Gd~~~A~~~l~~Al~~dP~n~~~~~~LA~~yl~~g~~~~A~~~~~kAv~ldP~n~~~~~~La~i---~~~~kA~~~ye~l  134 (987)
T PRK09782         58 NDEATAIREFEYIHQQVPDNIPLTLYLAEAYRHFGHDDRARLLLEDQLKRHPGDARLERSLAAI---PVEVKSVTTVEEL  134 (987)
T ss_pred             CCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCcccHHHHHHHHHh---ccChhHHHHHHHH
Confidence            5666666666666666655533666666666666666666666666543  3323333333222   6666666666666


Q ss_pred             HHcCCCCCcchHHHHHHHH-----cccCChhHHHHHHHHHHHhCCC-Chh-HHHHHHHHhHhcCChHHHHHHHhccCCC-
Q 040394          138 RKRLKEHDNFVFSKVLKAC-----CELRDIDEGMKVHCEIVKVGGP-DSF-VLTGLVDMYAKCRDIGSSRQVFDETLDK-  209 (691)
Q Consensus       138 ~~~~~~~~~~~~~~ll~~~-----~~~~~~~~a~~~~~~~~~~~~~-~~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~~-  209 (691)
                      .... +-+..++..+....     ....+.++|.+.++ .....+. +.. ....+...|.+.|++++|++++.++.+. 
T Consensus       135 ~~~~-P~n~~~~~~la~~~~~~~~l~y~q~eqAl~AL~-lr~~~~~~~~~vL~L~~~rlY~~l~dw~~Ai~lL~~L~k~~  212 (987)
T PRK09782        135 LAQQ-KACDAVPTLRCRSEVGQNALRLAQLPVARAQLN-DATFAASPEGKTLRTDLLQRAIYLKQWSQADTLYNEARQQN  212 (987)
T ss_pred             HHhC-CCChhHHHHHHHHhhccchhhhhhHHHHHHHHH-HhhhCCCCCcHHHHHHHHHHHHHHhCHHHHHHHHHHHHhcC
Confidence            6542 21223333333320     11122244444444 2222221 222 2333355666666666666666555332 


Q ss_pred             --ChhhHHHHHHHHHh-CCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCC-CchH---
Q 040394          210 --NVVSWTSMIAGYVQ-NDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIE-INSH---  282 (691)
Q Consensus       210 --~~~~~~~li~~~~~-~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~-~~~~---  282 (691)
                        +......|...|.+ .++ +++..+++.    .++-+......+...+.+.|+.++|..++.++...-.. |...   
T Consensus       213 pl~~~~~~~L~~ay~q~l~~-~~a~al~~~----~lk~d~~l~~ala~~yi~~G~~~~A~~~L~~~~~~~~~~~~~~~~~  287 (987)
T PRK09782        213 TLSAAERRQWFDVLLAGQLD-DRLLALQSQ----GIFTDPQSRITYATALAYRGEKARLQHYLIENKPLFTTDAQEKSWL  287 (987)
T ss_pred             CCCHHHHHHHHHHHHHhhCH-HHHHHHhch----hcccCHHHHHHHHHHHHHCCCHHHHHHHHHhCcccccCCCccHHHH
Confidence              22223444444544 244 445444332    22235555555666666666666666555554332111 1111   


Q ss_pred             ---------------------------HHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHH--HHhcCCchhHHH
Q 040394          283 ---------------------------LVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVG--YTQSGYPDKALK  333 (691)
Q Consensus       283 ---------------------------~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~--~~~~g~~~~a~~  333 (691)
                                                 ..-.++..+.+.++++.+.++.. . .|....  ..+..  ....+...++.+
T Consensus       288 ~~l~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~--~~~r~~~~~~~~~~~~~~~  363 (987)
T PRK09782        288 YLLSKYSANPVQALANYTVQFADNRQYVVGATLPVLLKEGQYDAAQKLLA-T-LPANEM--LEERYAVSVATRNKAEALR  363 (987)
T ss_pred             HHHHhccCchhhhccchhhhhHHHHHHHHHHHHHHHHhccHHHHHHHHhc-C-CCcchH--HHHHHhhccccCchhHHHH
Confidence                                       11223566677777776766633 2 222222  12222  223356666766


Q ss_pred             HHHHhhHCCCCC-cHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCC---chhHHHHHHHHhHhcCC---hHHHHHHHHh
Q 040394          334 LFTDKKWADFFP-NHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLE---DYTVINALVDMYAKCHV---IADARYIFET  406 (691)
Q Consensus       334 ~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~l~~~~~~~g~---~~~a~~~~~~  406 (691)
                      .+..|...  .| +....-.+--...+.|+.++|..+++........   +....+.++..|.+.+.   ..++..+-..
T Consensus       364 ~~~~~y~~--~~~~~~~l~q~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~  441 (987)
T PRK09782        364 LARLLYQQ--EPANLTRLDQLTWQLMQNGQSREAADLLLQRYPFQGDARLSQTLMARLASLLESHPYLATPAKVAILSKP  441 (987)
T ss_pred             HHHHHHhc--CCCCHHHHHHHHHHHHHcccHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHhCCcccchHHHHHhccc
Confidence            67667665  22 3333334444566788899999998888774222   55666788889988887   4444444332


Q ss_pred             CCCCCc-----------hhHHHHHHhhhCCCCC--CHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHH
Q 040394          407 TSEKDV-----------IAWNSIISGLDDNVSP--DAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALL  473 (691)
Q Consensus       407 ~~~~~~-----------~~~~~li~~~~~~~~p--~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~  473 (691)
                      +...+.           ..+..++.++. ..++  +...+..+..++.. ++.++|...+.......  | +......+.
T Consensus       442 ~~~~~~~~~~~~~~~~~~~~~~~~~al~-~~p~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~~--P-d~~~~L~lA  516 (987)
T PRK09782        442 LPLAEQRQWQSQLPGIADNCPAIVRLLG-DMSPSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQRQ--P-DAWQHRAVA  516 (987)
T ss_pred             cccchhHHHHhhhhhhhhhHHHHHHhcc-cCCCCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHhC--C-chHHHHHHH
Confidence            322211           12233333332 1233  56677777777766 78888999888877665  3 333444455


Q ss_pred             HHHHhcCCHHHHHHHHHhccc--CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCH-HHHHHHHHHhcccCCHHH
Q 040394          474 NFYAKCGDAQSARMVFDAMRE--KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNE-VIFTTILSACSHTGMVGE  550 (691)
Q Consensus       474 ~~~~~~g~~~~A~~~~~~~~~--~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~-~~~~~ll~~~~~~g~~~~  550 (691)
                      ..+...|++++|...|+++..  ++...+..+...+.+.|+.++|...+++..+.+  |+. ..+..+.......|++++
T Consensus       517 ~al~~~Gr~eeAi~~~rka~~~~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~--P~~~~l~~~La~~l~~~Gr~~e  594 (987)
T PRK09782        517 YQAYQVEDYATALAAWQKISLHDMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRG--LGDNALYWWLHAQRYIPGQPEL  594 (987)
T ss_pred             HHHHHCCCHHHHHHHHHHHhccCCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CccHHHHHHHHHHHHhCCCHHH
Confidence            566789999999999998764  445567777888899999999999999999864  443 333334445556799999


Q ss_pred             HHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040394          551 GWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PIEPD-VSLFGAFLHGCGLYSRFDLGEVMIKKMLE  628 (691)
Q Consensus       551 A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  628 (691)
                      |...+++..   .+.|+...+..+..++.+.|++++|++.+++. ...|+ ...+..+...+...|++++|+..++++++
T Consensus       595 Al~~~~~AL---~l~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~  671 (987)
T PRK09782        595 ALNDLTRSL---NIAPSANAYVARATIYRQRHNVPAAVSDLRAALELEPNNSNYQAALGYALWDSGDIAQSREMLERAHK  671 (987)
T ss_pred             HHHHHHHHH---HhCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            999999774   46788888999999999999999999999998 55564 45778888889999999999999999999


Q ss_pred             cCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          629 LHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       629 ~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      ..|+++..+..++.++...|++++|...+++..+..
T Consensus       672 l~P~~~~a~~nLA~al~~lGd~~eA~~~l~~Al~l~  707 (987)
T PRK09782        672 GLPDDPALIRQLAYVNQRLDDMAATQHYARLVIDDI  707 (987)
T ss_pred             hCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence            999999999999999999999999999999998754

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.94  E-value=3.4e-21  Score=210.98  Aligned_cols=553  Identities=12%  Similarity=-0.006  Sum_probs=394.5

Q ss_pred             HHHhcCCChHHHHHHhccCCC--C-CcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhH
Q 040394           88 SMYGSFGHVKYARSVFDSMPN--P-DFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDE  164 (691)
Q Consensus        88 ~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~  164 (691)
                      ..+...|++++|...|+...+  | +..++..|...|...|++++|+..+++..+.  .|+...|..++..+   ++.++
T Consensus        52 ~~~~~~Gd~~~A~~~l~~Al~~dP~n~~~~~~LA~~yl~~g~~~~A~~~~~kAv~l--dP~n~~~~~~La~i---~~~~k  126 (987)
T PRK09782         52 LKAQKNNDEATAIREFEYIHQQVPDNIPLTLYLAEAYRHFGHDDRARLLLEDQLKR--HPGDARLERSLAAI---PVEVK  126 (987)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CcccHHHHHHHHHh---ccChh
Confidence            444455999999999998753  3 4567899999999999999999999999986  45555555545333   88999


Q ss_pred             HHHHHHHHHHhCCCChhHHHHHHHH--------hHhcCChHHHHHHHhccCCCC--hhhHHH-HHHHHHhCCChhHHHHH
Q 040394          165 GMKVHCEIVKVGGPDSFVLTGLVDM--------YAKCRDIGSSRQVFDETLDKN--VVSWTS-MIAGYVQNDCAQEGLVL  233 (691)
Q Consensus       165 a~~~~~~~~~~~~~~~~~~~~l~~~--------~~~~g~~~~A~~~~~~~~~~~--~~~~~~-li~~~~~~g~~~~A~~~  233 (691)
                      |..+++++.+..|.+..++..+...        |.+.+...++++  .+...|+  ..+... +...|.+.|++++|+++
T Consensus       127 A~~~ye~l~~~~P~n~~~~~~la~~~~~~~~l~y~q~eqAl~AL~--lr~~~~~~~~~vL~L~~~rlY~~l~dw~~Ai~l  204 (987)
T PRK09782        127 SVTTVEELLAQQKACDAVPTLRCRSEVGQNALRLAQLPVARAQLN--DATFAASPEGKTLRTDLLQRAIYLKQWSQADTL  204 (987)
T ss_pred             HHHHHHHHHHhCCCChhHHHHHHHHhhccchhhhhhHHHHHHHHH--HhhhCCCCCcHHHHHHHHHHHHHHhCHHHHHHH
Confidence            9999999999998888888888887        888877777777  3334443  443444 48999999999999999


Q ss_pred             HHHHHhCCCCCChhhHHHHHHHHHc-cCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCC---
Q 040394          234 FNRMREGFVEGNQITLGSLVTACAK-LRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCS---  309 (691)
Q Consensus       234 ~~~m~~~~~~p~~~t~~~li~~~~~-~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~---  309 (691)
                      ++++.+.+.. +..-...+-.++.. .++ +.+..+++.    .+.-+...+..+.+.|.+.|+.++|.++++++..   
T Consensus       205 L~~L~k~~pl-~~~~~~~L~~ay~q~l~~-~~a~al~~~----~lk~d~~l~~ala~~yi~~G~~~~A~~~L~~~~~~~~  278 (987)
T PRK09782        205 YNEARQQNTL-SAAERRQWFDVLLAGQLD-DRLLALQSQ----GIFTDPQSRITYATALAYRGEKARLQHYLIENKPLFT  278 (987)
T ss_pred             HHHHHhcCCC-CHHHHHHHHHHHHHhhCH-HHHHHHhch----hcccCHHHHHHHHHHHHHCCCHHHHHHHHHhCccccc
Confidence            9999997643 34445556667776 466 777777543    3346888999999999999999999999998822   


Q ss_pred             --CChhHHH------------------------------HHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHH
Q 040394          310 --IDLVSWT------------------------------AMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSAS  357 (691)
Q Consensus       310 --~~~~~~~------------------------------~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~  357 (691)
                        |+..+|-                              .++..+.+.++++-+.++.      .+.|.......-..+.
T Consensus       279 ~~~~~~~~~~~l~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~r~~~~  352 (987)
T PRK09782        279 TDAQEKSWLYLLSKYSANPVQALANYTVQFADNRQYVVGATLPVLLKEGQYDAAQKLL------ATLPANEMLEERYAVS  352 (987)
T ss_pred             CCCccHHHHHHHHhccCchhhhccchhhhhHHHHHHHHHHHHHHHHhccHHHHHHHHh------cCCCcchHHHHHHhhc
Confidence              2222211                              1244556666666555442      2445444322222233


Q ss_pred             hcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCC-C-c----hhHHHHHHhhhCCCCCCHH
Q 040394          358 AQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEK-D-V----IAWNSIISGLDDNVSPDAV  431 (691)
Q Consensus       358 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-~-~----~~~~~li~~~~~~~~p~~~  431 (691)
                      ...+...++...+..+.+..+.+.....-+.-...+.|+.++|..+|+..... . .    ..-+-++..+.....++..
T Consensus       353 ~~~~~~~~~~~~~~~~y~~~~~~~~~l~q~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~  432 (987)
T PRK09782        353 VATRNKAEALRLARLLYQQEPANLTRLDQLTWQLMQNGQSREAADLLLQRYPFQGDARLSQTLMARLASLLESHPYLATP  432 (987)
T ss_pred             cccCchhHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcccHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHhCCcccch
Confidence            34577888888888888887877777777888888999999999999987662 1 1    0112233333333222222


Q ss_pred             HHHHHH-H------HHhccCcHHHHHHHHHHHHHcC-CCCC--chhHHHHHHHHHHhcCCHHHHHHHHHhccc--CCHhH
Q 040394          432 TLVSVI-S------ACASLGAVQVGSSLHAYSTKQG-LLSS--NVYVGTALLNFYAKCGDAQSARMVFDAMRE--KNTVT  499 (691)
Q Consensus       432 ~~~~ll-~------~~~~~~~~~~a~~~~~~~~~~~-~~~~--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~  499 (691)
                      .-...+ .      -|.-.|+...+...+......- ..|+  +...+..+..++.. ++.++|...+.+...  |+...
T Consensus       433 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~~p~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~~Pd~~~  511 (987)
T PRK09782        433 AKVAILSKPLPLAEQRQWQSQLPGIADNCPAIVRLLGDMSPSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQRQPDAWQ  511 (987)
T ss_pred             HHHHHhccccccchhHHHHhhhhhhhhhHHHHHHhcccCCCCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHhCCchHH
Confidence            211111 0      0111233333333333332221 1144  67788888888877 889999998877664  44333


Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHH
Q 040394          500 WSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLL  578 (691)
Q Consensus       500 ~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~  578 (691)
                      ...+...+...|++++|...++++...  .|+...+..+..++.+.|+.++|.+.++...+   ..|+ ...+..+...+
T Consensus       512 ~L~lA~al~~~Gr~eeAi~~~rka~~~--~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~---l~P~~~~l~~~La~~l  586 (987)
T PRK09782        512 HRAVAYQAYQVEDYATALAAWQKISLH--DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQ---RGLGDNALYWWLHAQR  586 (987)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHh---cCCccHHHHHHHHHHH
Confidence            333445556899999999999998664  55556666677788899999999999998853   3454 33333344445


Q ss_pred             HhcCChHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHH
Q 040394          579 ARAGRLEEALEFMENM-PIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVR  657 (691)
Q Consensus       579 ~~~g~~~~A~~~~~~~-~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~  657 (691)
                      .+.|++++|+..+++. ...|+...+..+...+.+.|++++|+..++++++.+|+++..+..++.++...|++++|++.+
T Consensus       587 ~~~Gr~~eAl~~~~~AL~l~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~Pd~~~a~~nLG~aL~~~G~~eeAi~~l  666 (987)
T PRK09782        587 YIPGQPELALNDLTRSLNIAPSANAYVARATIYRQRHNVPAAVSDLRAALELEPNNSNYQAALGYALWDSGDIAQSREML  666 (987)
T ss_pred             HhCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            5669999999999998 677888899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCC
Q 040394          658 ELMKQRGL  665 (691)
Q Consensus       658 ~~~~~~g~  665 (691)
                      ++.++...
T Consensus       667 ~~AL~l~P  674 (987)
T PRK09782        667 ERAHKGLP  674 (987)
T ss_pred             HHHHHhCC
Confidence            99988543

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

Probab=99.91  E-value=1.6e-21  Score=188.91  Aligned_cols=434  Identities=12%  Similarity=0.105  Sum_probs=279.7

Q ss_pred             ccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCC---CChhhHHHHHHHHHhCCChhHHHHHH
Q 040394          158 ELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLD---KNVVSWTSMIAGYVQNDCAQEGLVLF  234 (691)
Q Consensus       158 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~A~~~~  234 (691)
                      +.|++.+|++.-...-..++.+....-.+-.++.+..+.+....--....+   ....+|..+...+-..|++++|+.+|
T Consensus        60 q~gd~~~a~~h~nmv~~~d~t~~~~llll~ai~~q~~r~d~s~a~~~~a~r~~~q~ae~ysn~aN~~kerg~~~~al~~y  139 (966)
T KOG4626|consen   60 QGGDYKQAEKHCNMVGQEDPTNTERLLLLSAIFFQGSRLDKSSAGSLLAIRKNPQGAEAYSNLANILKERGQLQDALALY  139 (966)
T ss_pred             hccCHHHHHHHHhHhhccCCCcccceeeehhhhhcccchhhhhhhhhhhhhccchHHHHHHHHHHHHHHhchHHHHHHHH
Confidence            445555555544433333333333333333444444444443322222211   13456777777777777777777777


Q ss_pred             HHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHH-HHHHHHHHhcCCHHHHHHHHHhcCC--CC
Q 040394          235 NRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLV-TALLDMYVKCGNIRDARSVFDELCS--ID  311 (691)
Q Consensus       235 ~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~-~~li~~~~~~g~~~~A~~~~~~~~~--~~  311 (691)
                      +.|.+...+ ....|..+..++...|+.+.|.+.|.+.++.  .|+.... +.+...+-..|++++|...+.+...  |.
T Consensus       140 ~~aiel~p~-fida~inla~al~~~~~~~~a~~~~~~alql--nP~l~ca~s~lgnLlka~Grl~ea~~cYlkAi~~qp~  216 (966)
T KOG4626|consen  140 RAAIELKPK-FIDAYINLAAALVTQGDLELAVQCFFEALQL--NPDLYCARSDLGNLLKAEGRLEEAKACYLKAIETQPC  216 (966)
T ss_pred             HHHHhcCch-hhHHHhhHHHHHHhcCCCcccHHHHHHHHhc--CcchhhhhcchhHHHHhhcccchhHHHHHHHHhhCCc
Confidence            777663221 3455666666666666666666666665543  3443322 2233333344556665555554422  22


Q ss_pred             -hhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHH
Q 040394          312 -LVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDM  390 (691)
Q Consensus       312 -~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  390 (691)
                       .++|+.|...+-..|+...|++.|++..                                   +..+.-..+|-.|...
T Consensus       217 fAiawsnLg~~f~~~Gei~~aiq~y~eAv-----------------------------------kldP~f~dAYiNLGnV  261 (966)
T KOG4626|consen  217 FAIAWSNLGCVFNAQGEIWLAIQHYEEAV-----------------------------------KLDPNFLDAYINLGNV  261 (966)
T ss_pred             eeeeehhcchHHhhcchHHHHHHHHHHhh-----------------------------------cCCCcchHHHhhHHHH
Confidence             2345555555555555555555555544                                   4444434444555555


Q ss_pred             hHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCC-HHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHH
Q 040394          391 YAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPD-AVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVG  469 (691)
Q Consensus       391 ~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  469 (691)
                      |...+.+++|...|.+...                ..|+ ...+..+...|-.+|+++.|...+++..+..  |.-+..|
T Consensus       262 ~ke~~~~d~Avs~Y~rAl~----------------lrpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~--P~F~~Ay  323 (966)
T KOG4626|consen  262 YKEARIFDRAVSCYLRALN----------------LRPNHAVAHGNLACIYYEQGLLDLAIDTYKRALELQ--PNFPDAY  323 (966)
T ss_pred             HHHHhcchHHHHHHHHHHh----------------cCCcchhhccceEEEEeccccHHHHHHHHHHHHhcC--CCchHHH
Confidence            5555666666555555442                2333 3345555555566666666666666666665  6667777


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhccc--C-CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCH-HHHHHHHHHhccc
Q 040394          470 TALLNFYAKCGDAQSARMVFDAMRE--K-NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNE-VIFTTILSACSHT  545 (691)
Q Consensus       470 ~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~-~~~~~ll~~~~~~  545 (691)
                      +.|..++-..|++.+|...+.+...  | ...+.+.|...|...|.+++|..+|....+  +.|.. ..++.+...|-+.
T Consensus       324 ~NlanALkd~G~V~ea~~cYnkaL~l~p~hadam~NLgni~~E~~~~e~A~~ly~~al~--v~p~~aaa~nNLa~i~kqq  401 (966)
T KOG4626|consen  324 NNLANALKDKGSVTEAVDCYNKALRLCPNHADAMNNLGNIYREQGKIEEATRLYLKALE--VFPEFAAAHNNLASIYKQQ  401 (966)
T ss_pred             hHHHHHHHhccchHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhccchHHHHHHHHHHh--hChhhhhhhhhHHHHHHhc
Confidence            7777777777777777777776653  2 345677777888888888888888887776  56665 4677888888999


Q ss_pred             CCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCH-HHHHHHHHHHHhcCCHHHHHHH
Q 040394          546 GMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEPDV-SLFGAFLHGCGLYSRFDLGEVM  622 (691)
Q Consensus       546 g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~-~~~~~l~~~~~~~g~~~~A~~~  622 (691)
                      |++++|+..|++..   .+.|+ ...|+.+...|-..|+.+.|+..+.+. .+.|.. ..++.|...|...|++.+|++-
T Consensus       402 gnl~~Ai~~Ykeal---rI~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~nPt~AeAhsNLasi~kDsGni~~AI~s  478 (966)
T KOG4626|consen  402 GNLDDAIMCYKEAL---RIKPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQINPTFAEAHSNLASIYKDSGNIPEAIQS  478 (966)
T ss_pred             ccHHHHHHHHHHHH---hcCchHHHHHHhcchHHHHhhhHHHHHHHHHHHHhcCcHHHHHHhhHHHHhhccCCcHHHHHH
Confidence            99999999998653   68888 778999999999999999999998887 777765 5889999999999999999999


Q ss_pred             HHHHHhcCCCCchhHHHHHHHHHhCCCcHH
Q 040394          623 IKKMLELHPDKACYYVLVSNLYASDGRWIR  652 (691)
Q Consensus       623 ~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  652 (691)
                      +++++++.|+.+..+-.++.++.--.+|.+
T Consensus       479 Y~~aLklkPDfpdA~cNllh~lq~vcdw~D  508 (966)
T KOG4626|consen  479 YRTALKLKPDFPDAYCNLLHCLQIVCDWTD  508 (966)
T ss_pred             HHHHHccCCCCchhhhHHHHHHHHHhcccc
Confidence            999999999999999888887766556555

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

Probab=99.90  E-value=2.3e-20  Score=180.96  Aligned_cols=424  Identities=11%  Similarity=0.074  Sum_probs=338.6

Q ss_pred             HHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhc
Q 040394          215 TSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKC  294 (691)
Q Consensus       215 ~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~  294 (691)
                      ..|..-..+.|++++|++.-...-..+.. +..+.-.+-..+.+..+.+.....-....+. .+.-..+|..+.+.+-..
T Consensus        52 l~lah~~yq~gd~~~a~~h~nmv~~~d~t-~~~~llll~ai~~q~~r~d~s~a~~~~a~r~-~~q~ae~ysn~aN~~ker  129 (966)
T KOG4626|consen   52 LELAHRLYQGGDYKQAEKHCNMVGQEDPT-NTERLLLLSAIFFQGSRLDKSSAGSLLAIRK-NPQGAEAYSNLANILKER  129 (966)
T ss_pred             HHHHHHHHhccCHHHHHHHHhHhhccCCC-cccceeeehhhhhcccchhhhhhhhhhhhhc-cchHHHHHHHHHHHHHHh
Confidence            33444455666666666654444322211 1111112222233333444333222222222 123457888888889899


Q ss_pred             CCHHHHHHHHHhcCC---CChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHH-HHhcCCChhhHHHHH
Q 040394          295 GNIRDARSVFDELCS---IDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLS-ASAQLGNLNMGRMVH  370 (691)
Q Consensus       295 g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~-~~~~~~~~~~a~~~~  370 (691)
                      |++++|+.+++.+.+   ..+..|..+..++...|+.+.|.+.|.+..+  +.|+.....+-+. .+...|++.+|...+
T Consensus       130 g~~~~al~~y~~aiel~p~fida~inla~al~~~~~~~~a~~~~~~alq--lnP~l~ca~s~lgnLlka~Grl~ea~~cY  207 (966)
T KOG4626|consen  130 GQLQDALALYRAAIELKPKFIDAYINLAAALVTQGDLELAVQCFFEALQ--LNPDLYCARSDLGNLLKAEGRLEEAKACY  207 (966)
T ss_pred             chHHHHHHHHHHHHhcCchhhHHHhhHHHHHHhcCCCcccHHHHHHHHh--cCcchhhhhcchhHHHHhhcccchhHHHH
Confidence            999999999988833   3566899999999999999999999988776  4777766555444 455679999999999


Q ss_pred             HHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCC-HHHHHHHHHHHhccCcHHHH
Q 040394          371 SLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPD-AVTLVSVISACASLGAVQVG  449 (691)
Q Consensus       371 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a  449 (691)
                      .++++..+.-..+|+.|...+-..|++..|+..|++..+-                .|+ ...|..|...|...+.++.|
T Consensus       208 lkAi~~qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkl----------------dP~f~dAYiNLGnV~ke~~~~d~A  271 (966)
T KOG4626|consen  208 LKAIETQPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKL----------------DPNFLDAYINLGNVYKEARIFDRA  271 (966)
T ss_pred             HHHHhhCCceeeeehhcchHHhhcchHHHHHHHHHHhhcC----------------CCcchHHHhhHHHHHHHHhcchHH
Confidence            9999888887778899999999999999999999998754                354 35788999999999999999


Q ss_pred             HHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--CC-HhHHHHHHHHHhcCCChHHHHHHHHHHHHC
Q 040394          450 SSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--KN-TVTWSAMIGGYGMQGDGGGSLALFSDMLNE  526 (691)
Q Consensus       450 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~-~~~~~~li~~~~~~~~~~~A~~~~~~m~~~  526 (691)
                      ...+.+.....  |.....+..+...|...|..+-|+..+++..+  |+ ...|+.|..++-..|++.+|...+.+....
T Consensus       272 vs~Y~rAl~lr--pn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l  349 (966)
T KOG4626|consen  272 VSCYLRALNLR--PNHAVAHGNLACIYYEQGLLDLAIDTYKRALELQPNFPDAYNNLANALKDKGSVTEAVDCYNKALRL  349 (966)
T ss_pred             HHHHHHHHhcC--CcchhhccceEEEEeccccHHHHHHHHHHHHhcCCCchHHHhHHHHHHHhccchHHHHHHHHHHHHh
Confidence            99999988876  77888888899999999999999999999875  43 568999999999999999999999999884


Q ss_pred             CCCCCH-HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCH-HH
Q 040394          527 EVQPNE-VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEPDV-SL  602 (691)
Q Consensus       527 g~~p~~-~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~-~~  602 (691)
                        .|+. ...+.+...+...|.+++|..+|...   +.+.|. ....+.|...|-.+|++++|+..+++. .++|+. ..
T Consensus       350 --~p~hadam~NLgni~~E~~~~e~A~~ly~~a---l~v~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI~P~fAda  424 (966)
T KOG4626|consen  350 --CPNHADAMNNLGNIYREQGKIEEATRLYLKA---LEVFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRIKPTFADA  424 (966)
T ss_pred             --CCccHHHHHHHHHHHHHhccchHHHHHHHHH---HhhChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhcCchHHHH
Confidence              5554 67888999999999999999999954   467888 678999999999999999999999998 889986 48


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          603 FGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       603 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      ++.+...|...|+...|.+.+.+++..+|.-...+..|+.+|..+|+..+|+.-+++.++...
T Consensus       425 ~~NmGnt~ke~g~v~~A~q~y~rAI~~nPt~AeAhsNLasi~kDsGni~~AI~sY~~aLklkP  487 (966)
T KOG4626|consen  425 LSNMGNTYKEMGDVSAAIQCYTRAIQINPTFAEAHSNLASIYKDSGNIPEAIQSYRTALKLKP  487 (966)
T ss_pred             HHhcchHHHHhhhHHHHHHHHHHHHhcCcHHHHHHhhHHHHhhccCCcHHHHHHHHHHHccCC
Confidence            999999999999999999999999999999999999999999999999999999999988543

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.88  E-value=6.6e-20  Score=188.32  Aligned_cols=303  Identities=13%  Similarity=0.089  Sum_probs=210.4

Q ss_pred             CCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCC---CHHHHHHH
Q 040394          360 LGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSP---DAVTLVSV  436 (691)
Q Consensus       360 ~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p---~~~~~~~l  436 (691)
                      .|++++|...+..+.+.++.+..++..+...+...|++++|..+++.+....              ..+   ...++..+
T Consensus        48 ~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~--------------~~~~~~~~~~~~~L  113 (389)
T PRK11788         48 NEQPDKAIDLFIEMLKVDPETVELHLALGNLFRRRGEVDRAIRIHQNLLSRP--------------DLTREQRLLALQEL  113 (389)
T ss_pred             cCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCC--------------CCCHHHHHHHHHHH
Confidence            3444444444444444444444444555555666666666666665554331              111   12345566


Q ss_pred             HHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCC--------HhHHHHHHHHHh
Q 040394          437 ISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKN--------TVTWSAMIGGYG  508 (691)
Q Consensus       437 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--------~~~~~~li~~~~  508 (691)
                      ...+...|+++.|..+|+.+.+..  +.+...+..++..+.+.|++++|.+.++.+.+.+        ...|..+...+.
T Consensus       114 a~~~~~~g~~~~A~~~~~~~l~~~--~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~  191 (389)
T PRK11788        114 GQDYLKAGLLDRAEELFLQLVDEG--DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQAL  191 (389)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHcCC--cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHH
Confidence            666666677777777776666554  5566667777777777777777777777765421        123456777788


Q ss_pred             cCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC--hhHHHHHHHHHHhcCChHH
Q 040394          509 MQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS--MKHYVCMVDLLARAGRLEE  586 (691)
Q Consensus       509 ~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~--~~~~~~li~~~~~~g~~~~  586 (691)
                      +.|++++|...++++.+.. +.+...+..+...+.+.|++++|.++++++...   .|+  ..++..++.+|.+.|++++
T Consensus       192 ~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~---~p~~~~~~~~~l~~~~~~~g~~~~  267 (389)
T PRK11788        192 ARGDLDAARALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQ---DPEYLSEVLPKLMECYQALGDEAE  267 (389)
T ss_pred             hCCCHHHHHHHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH---ChhhHHHHHHHHHHHHHHcCCHHH
Confidence            8899999999999888753 233456677778888899999999999988533   344  4567888999999999999


Q ss_pred             HHHHHHhC-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHh--CCCcHHHHHHHHHHHhC
Q 040394          587 ALEFMENM-PIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYAS--DGRWIRVNQVRELMKQR  663 (691)
Q Consensus       587 A~~~~~~~-~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~--~g~~~~A~~~~~~~~~~  663 (691)
                      |.+.++++ ...|+...+..++..+.+.|++++|..+++++.+..|++......+...+..  .|+.+++..++++|.+.
T Consensus       268 A~~~l~~~~~~~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~~  347 (389)
T PRK11788        268 GLEFLRRALEEYPGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSLRGFHRLLDYHLAEAEEGRAKESLLLLRDLVGE  347 (389)
T ss_pred             HHHHHHHHHHhCCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHhCcCHHHHHHHHHHhhhccCCccchhHHHHHHHHHHH
Confidence            99999998 5667777778899999999999999999999999999976554444333322  56999999999999999


Q ss_pred             CCccCCCeeEEEeCCeeeE
Q 040394          664 GLSKSPGCSLVDLDIANDF  682 (691)
Q Consensus       664 g~~~~~~~~~~~~~~~~~~  682 (691)
                      ++.++|.......+-....
T Consensus       348 ~~~~~p~~~c~~cg~~~~~  366 (389)
T PRK11788        348 QLKRKPRYRCRNCGFTART  366 (389)
T ss_pred             HHhCCCCEECCCCCCCCcc
Confidence            9999998776555544433

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

Probab=99.88  E-value=1.3e-17  Score=170.97  Aligned_cols=566  Identities=11%  Similarity=0.060  Sum_probs=245.1

Q ss_pred             cCchhHHHHHHHHHHhCCCCch-hhhHHHHHHhcCCChHHHHHHhccCCCCCcchHHHHHHHH---Hh---CCChhHHHH
Q 040394           60 KSTGSLKAFHALLIVDGLTNDK-CNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWY---FL---NDLYKDIVE  132 (691)
Q Consensus        60 ~~~~~a~~~~~~~~~~~~~~~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~ll~~~---~~---~~~~~~a~~  132 (691)
                      ++...+..+++.++...+...+ +.-.+..++.+.|+.+.|+..|.+..+-|+..-++++...   ..   ...+..++.
T Consensus       178 kdY~~al~yyk~al~inp~~~aD~rIgig~Cf~kl~~~~~a~~a~~ralqLdp~~v~alv~L~~~~l~~~d~~s~~~~~~  257 (1018)
T KOG2002|consen  178 KDYRGALKYYKKALRINPACKADVRIGIGHCFWKLGMSEKALLAFERALQLDPTCVSALVALGEVDLNFNDSDSYKKGVQ  257 (1018)
T ss_pred             ccHHHHHHHHHHHHhcCcccCCCccchhhhHHHhccchhhHHHHHHHHHhcChhhHHHHHHHHHHHHHccchHHHHHHHH
Confidence            4555555555555444333222 3334445555666666666666555443333222222211   11   122334444


Q ss_pred             HHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCC---ChhHHHHHHHHhHhcCChHHHHHHHhccCC-
Q 040394          133 FYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGP---DSFVLTGLVDMYAKCRDIGSSRQVFDETLD-  208 (691)
Q Consensus       133 ~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-  208 (691)
                      ++...-... +-++...+.|..-|.-.|+++.+..+...+...-..   -...|-.+..+|...|++++|...|.+... 
T Consensus       258 ll~~ay~~n-~~nP~~l~~LAn~fyfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~  336 (1018)
T KOG2002|consen  258 LLQRAYKEN-NENPVALNHLANHFYFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKA  336 (1018)
T ss_pred             HHHHHHhhc-CCCcHHHHHHHHHHhhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHcc
Confidence            444433331 334455555555555556666666666555554322   333455556666666666666665554422 


Q ss_pred             -CC--hhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccC----ChhhHHHHHHHHHHHCCCCch
Q 040394          209 -KN--VVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLR----ALHQGKWLHGYILKIGIEINS  281 (691)
Q Consensus       209 -~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~----~~~~a~~~~~~~~~~g~~~~~  281 (691)
                       ++  +..+--|...+.+.|+.+.+...|+...+.. +-+..|..++-..|...+    ..+.|..++....+.- +.|.
T Consensus       337 ~~d~~~l~~~GlgQm~i~~~dle~s~~~fEkv~k~~-p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~K~~~~~-~~d~  414 (1018)
T KOG2002|consen  337 DNDNFVLPLVGLGQMYIKRGDLEESKFCFEKVLKQL-PNNYETMKILGCLYAHSAKKQEKRDKASNVLGKVLEQT-PVDS  414 (1018)
T ss_pred             CCCCccccccchhHHHHHhchHHHHHHHHHHHHHhC-cchHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHHHhcc-cccH
Confidence             21  2233445555566666666666666555431 112333444434443332    2233333333333322 2234


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhc--------CCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHC---CCCCcH---
Q 040394          282 HLVTALLDMYVKCGNIRDARSVFDEL--------CSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWA---DFFPNH---  347 (691)
Q Consensus       282 ~~~~~li~~~~~~g~~~~A~~~~~~~--------~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~---g~~p~~---  347 (691)
                      ..|-.+...+... +...++.+|...        ....+...|.+...+...|++.+|...|......   ...+|.   
T Consensus       415 ~a~l~laql~e~~-d~~~sL~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~  493 (1018)
T KOG2002|consen  415 EAWLELAQLLEQT-DPWASLDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKS  493 (1018)
T ss_pred             HHHHHHHHHHHhc-ChHHHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCcccccc
Confidence            4444444433332 222223333221        2234445555555555566666666555554433   111222   


Q ss_pred             --HH-HHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhC
Q 040394          348 --VT-IASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDD  424 (691)
Q Consensus       348 --~t-~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~  424 (691)
                        .| --.+....-..++.+.|.+.+..+.+..|.-...|-.+..+....+...+|...++.....|             
T Consensus       494 ~~lt~~YNlarl~E~l~~~~~A~e~Yk~Ilkehp~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d-------------  560 (1018)
T KOG2002|consen  494 TNLTLKYNLARLLEELHDTEVAEEMYKSILKEHPGYIDAYLRLGCMARDKNNLYEASLLLKDALNID-------------  560 (1018)
T ss_pred             chhHHHHHHHHHHHhhhhhhHHHHHHHHHHHHCchhHHHHHHhhHHHHhccCcHHHHHHHHHHHhcc-------------
Confidence              11 11122233334455555555555555555444444444433333445555555555544332             


Q ss_pred             CCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHH
Q 040394          425 NVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMI  504 (691)
Q Consensus       425 ~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li  504 (691)
                        ..++..++.+...+.+...+..|..-|....+.-...+++...-+|.+.|...-            ..|..       
T Consensus       561 --~~np~arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l------------~~~~r-------  619 (1018)
T KOG2002|consen  561 --SSNPNARSLLGNLHLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGNVYIQAL------------HNPSR-------  619 (1018)
T ss_pred             --cCCcHHHHHHHHHHHhhhhhcccccHHHHHHhhhccCCchhHHHHhhHHHHHHh------------ccccc-------
Confidence              122222222333344444444444444433332221223333333333222110            00000       


Q ss_pred             HHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCCh
Q 040394          505 GGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRL  584 (691)
Q Consensus       505 ~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~  584 (691)
                      ..-...+..++|+++|.+.++.. +-|...-|-+--+++..|++.+|..+|.++.+..  .-...+|-.+.++|..+|++
T Consensus       620 n~ek~kk~~~KAlq~y~kvL~~d-pkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~--~~~~dv~lNlah~~~e~~qy  696 (1018)
T KOG2002|consen  620 NPEKEKKHQEKALQLYGKVLRND-PKNMYAANGIGIVLAEKGRFSEARDIFSQVREAT--SDFEDVWLNLAHCYVEQGQY  696 (1018)
T ss_pred             ChHHHHHHHHHHHHHHHHHHhcC-cchhhhccchhhhhhhccCchHHHHHHHHHHHHH--hhCCceeeeHHHHHHHHHHH
Confidence            00001122344444544444421 1222333333334444555555555555543221  11233444455555555555


Q ss_pred             HHHHHHHHhC----CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHH-----------------
Q 040394          585 EEALEFMENM----PIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNL-----------------  643 (691)
Q Consensus       585 ~~A~~~~~~~----~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~-----------------  643 (691)
                      -.|++.|+..    ..+.+......|..++.+.|++.+|.+.+..+..+.|.++.....++.+                 
T Consensus       697 ~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~~p~~~~v~FN~a~v~kkla~s~lr~~k~t~e  776 (1018)
T KOG2002|consen  697 RLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLKARHLAPSNTSVKFNLALVLKKLAESILRLEKRTLE  776 (1018)
T ss_pred             HHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCCccchHHhHHHHHHHHHHHHHHhcccccHH
Confidence            5555554443    2222334444455555555555555555555555555554443333332                 


Q ss_pred             --HHhCCCcHHHHHHHHHHHhCCCc
Q 040394          644 --YASDGRWIRVNQVRELMKQRGLS  666 (691)
Q Consensus       644 --~~~~g~~~~A~~~~~~~~~~g~~  666 (691)
                        ....+..+.|.++|..|...+-+
T Consensus       777 ev~~a~~~le~a~r~F~~ls~~~d~  801 (1018)
T KOG2002|consen  777 EVLEAVKELEEARRLFTELSKNGDK  801 (1018)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCC
Confidence              23334566777777777765543

>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=99.87  E-value=2.7e-18  Score=185.60  Aligned_cols=250  Identities=14%  Similarity=0.090  Sum_probs=168.2

Q ss_pred             cCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCC-CHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHH
Q 040394          394 CHVIADARYIFETTSEKDVIAWNSIISGLDDNVSP-DAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTAL  472 (691)
Q Consensus       394 ~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  472 (691)
                      .+++++|...|+.....+             ...| ....+..+...+...|++++|...++...+..  |.....+..+
T Consensus       307 ~~~y~~A~~~~~~al~~~-------------~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~--P~~~~~~~~l  371 (615)
T TIGR00990       307 DESYEEAARAFEKALDLG-------------KLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELD--PRVTQSYIKR  371 (615)
T ss_pred             hhhHHHHHHHHHHHHhcC-------------CCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCcHHHHHHH
Confidence            356667777776665431             1123 23455566666667777777777777777665  5556667777


Q ss_pred             HHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCC-HHHHHHHHHHhcccCCH
Q 040394          473 LNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPN-EVIFTTILSACSHTGMV  548 (691)
Q Consensus       473 ~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~-~~~~~~ll~~~~~~g~~  548 (691)
                      ...+...|++++|...|++..+   .+...|..+...+...|++++|+..|++..+.  .|+ ...+..+..++.+.|++
T Consensus       372 a~~~~~~g~~~eA~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l--~P~~~~~~~~la~~~~~~g~~  449 (615)
T TIGR00990       372 ASMNLELGDPDKAEEDFDKALKLNSEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDL--DPDFIFSHIQLGVTQYKEGSI  449 (615)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CccCHHHHHHHHHHHHHCCCH
Confidence            7777777777777777776653   24667777777777778888888888777764  343 44555566677777888


Q ss_pred             HHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCH-H-------HHHHHHHHHHhcCCHHH
Q 040394          549 GEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEPDV-S-------LFGAFLHGCGLYSRFDL  618 (691)
Q Consensus       549 ~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~-~-------~~~~l~~~~~~~g~~~~  618 (691)
                      ++|+..+++..+   ..|+ ...++.+..++...|++++|++.|++. ...|+. .       .++.....+...|++++
T Consensus       450 ~eA~~~~~~al~---~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~e  526 (615)
T TIGR00990       450 ASSMATFRRCKK---NFPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQDFIE  526 (615)
T ss_pred             HHHHHHHHHHHH---hCCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhhHHH
Confidence            888888876643   3444 567777777788888888888877775 333321 1       11122222334578888


Q ss_pred             HHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          619 GEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       619 A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      |..+++++++++|++...+..++.++.+.|++++|++.+++..+.
T Consensus       527 A~~~~~kAl~l~p~~~~a~~~la~~~~~~g~~~eAi~~~e~A~~l  571 (615)
T TIGR00990       527 AENLCEKALIIDPECDIAVATMAQLLLQQGDVDEALKLFERAAEL  571 (615)
T ss_pred             HHHHHHHHHhcCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            888888888888887777888888888888888888888777654

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

Probab=99.86  E-value=9.5e-17  Score=164.63  Aligned_cols=552  Identities=11%  Similarity=0.051  Sum_probs=395.3

Q ss_pred             ChHHHHHHhccCCCCCcc-hHHHHHHH--HHhCCChhHHHHHHHHHHHcC--CCCCcchHHHHHHHHcccCChhHHHHHH
Q 040394           95 HVKYARSVFDSMPNPDFY-SFQVMIRW--YFLNDLYKDIVEFYKCMRKRL--KEHDNFVFSKVLKACCELRDIDEGMKVH  169 (691)
Q Consensus        95 ~~~~A~~~~~~~~~~~~~-~~~~ll~~--~~~~~~~~~a~~~~~~m~~~~--~~~~~~~~~~ll~~~~~~~~~~~a~~~~  169 (691)
                      +++.|.+.|..+...+.. ....+.++  ....+++..|+.+|.......  .+||+.  ..+-.++.+.|+.+.|...|
T Consensus       145 ~~~~A~a~F~~Vl~~sp~Nil~LlGkA~i~ynkkdY~~al~yyk~al~inp~~~aD~r--Igig~Cf~kl~~~~~a~~a~  222 (1018)
T KOG2002|consen  145 SMDDADAQFHFVLKQSPDNILALLGKARIAYNKKDYRGALKYYKKALRINPACKADVR--IGIGHCFWKLGMSEKALLAF  222 (1018)
T ss_pred             cHHHHHHHHHHHHhhCCcchHHHHHHHHHHhccccHHHHHHHHHHHHhcCcccCCCcc--chhhhHHHhccchhhHHHHH
Confidence            368888888877542221 22233333  456789999999999976543  344543  23335667999999999999


Q ss_pred             HHHHHhCCCChhHHHHHHHHhHhcCChH---HHHHHHhcc---CCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCC
Q 040394          170 CEIVKVGGPDSFVLTGLVDMYAKCRDIG---SSRQVFDET---LDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVE  243 (691)
Q Consensus       170 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~---~A~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~  243 (691)
                      .+..+..|.++.++-.|.-.-....+.+   .+...+...   ...|++..+.|...|.-.|++..+..+...+......
T Consensus       223 ~ralqLdp~~v~alv~L~~~~l~~~d~~s~~~~~~ll~~ay~~n~~nP~~l~~LAn~fyfK~dy~~v~~la~~ai~~t~~  302 (1018)
T KOG2002|consen  223 ERALQLDPTCVSALVALGEVDLNFNDSDSYKKGVQLLQRAYKENNENPVALNHLANHFYFKKDYERVWHLAEHAIKNTEN  302 (1018)
T ss_pred             HHHHhcChhhHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhhcCCCcHHHHHHHHHHhhcccHHHHHHHHHHHHHhhhh
Confidence            9999999877777777766666555544   444444443   2358899999999999999999999999998765321


Q ss_pred             --CChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCch--HHHHHHHHHHHhcCCHHHHHHHHHhc---CCCChhHHH
Q 040394          244 --GNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINS--HLVTALLDMYVKCGNIRDARSVFDEL---CSIDLVSWT  316 (691)
Q Consensus       244 --p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~--~~~~~li~~~~~~g~~~~A~~~~~~~---~~~~~~~~~  316 (691)
                        .-...|-.+.+++-..|++++|..+|.+..+.  .++.  ..+--|...+.+.|+++.+...|+.+   .+.+..+..
T Consensus       303 ~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~--~~d~~~l~~~GlgQm~i~~~dle~s~~~fEkv~k~~p~~~etm~  380 (1018)
T KOG2002|consen  303 KSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKA--DNDNFVLPLVGLGQMYIKRGDLEESKFCFEKVLKQLPNNYETMK  380 (1018)
T ss_pred             hHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHcc--CCCCccccccchhHHHHHhchHHHHHHHHHHHHHhCcchHHHHH
Confidence              12345888999999999999999999887665  3444  34456788999999999999999998   233455666


Q ss_pred             HHHHHHHhcC----CchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHH----HHHhCCC-chhHHHHH
Q 040394          317 AMIVGYTQSG----YPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSL----GIRLGLE-DYTVINAL  387 (691)
Q Consensus       317 ~li~~~~~~g----~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~----~~~~~~~-~~~~~~~l  387 (691)
                      .|...|...+    ..+.|..++.+.... ..-|...|..+...+.+..-... ..++..    +...+.. .+.+.|.+
T Consensus       381 iLG~Lya~~~~~~~~~d~a~~~l~K~~~~-~~~d~~a~l~laql~e~~d~~~s-L~~~~~A~d~L~~~~~~ip~E~LNNv  458 (1018)
T KOG2002|consen  381 ILGCLYAHSAKKQEKRDKASNVLGKVLEQ-TPVDSEAWLELAQLLEQTDPWAS-LDAYGNALDILESKGKQIPPEVLNNV  458 (1018)
T ss_pred             HHHhHHHhhhhhhHHHHHHHHHHHHHHhc-ccccHHHHHHHHHHHHhcChHHH-HHHHHHHHHHHHHcCCCCCHHHHHhH
Confidence            6666676664    456677776665554 23456677666666665544333 544443    3455555 88999999


Q ss_pred             HHHhHhcCChHHHHHHHHhCCCC-CchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCch
Q 040394          388 VDMYAKCHVIADARYIFETTSEK-DVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNV  466 (691)
Q Consensus       388 ~~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  466 (691)
                      ...+...|++.+|...|+..... ... -|     ...|-.++..+--.+....-..++.+.|.+.|..+.+..  |.-.
T Consensus       459 aslhf~~g~~~~A~~~f~~A~~~~~~~-~n-----~de~~~~~lt~~YNlarl~E~l~~~~~A~e~Yk~Ilkeh--p~YI  530 (1018)
T KOG2002|consen  459 ASLHFRLGNIEKALEHFKSALGKLLEV-AN-----KDEGKSTNLTLKYNLARLLEELHDTEVAEEMYKSILKEH--PGYI  530 (1018)
T ss_pred             HHHHHHhcChHHHHHHHHHHhhhhhhh-cC-----ccccccchhHHHHHHHHHHHhhhhhhHHHHHHHHHHHHC--chhH
Confidence            99999999999999999987654 000 00     000112333333445556667789999999999999876  5555


Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCC-CCCCHHHHHHHHHHh
Q 040394          467 YVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEE-VQPNEVIFTTILSAC  542 (691)
Q Consensus       467 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g-~~p~~~~~~~ll~~~  542 (691)
                      ..|.-+..+....+...+|...+....+   .++..|+-+...+.+...+..|.+-|+...+.- ..+|..+...|-..|
T Consensus       531 d~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~~np~arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~  610 (1018)
T KOG2002|consen  531 DAYLRLGCMARDKNNLYEASLLLKDALNIDSSNPNARSLLGNLHLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGNVY  610 (1018)
T ss_pred             HHHHHhhHHHHhccCcHHHHHHHHHHHhcccCCcHHHHHHHHHHHhhhhhcccccHHHHHHhhhccCCchhHHHHhhHHH
Confidence            5555555444455788899999988774   467778888888888888888888777766532 224554444444433


Q ss_pred             cc------------cCCHHHHHHHHHHchhhcCCCC-ChhHHHHHHHHHHhcCChHHHHHHHHhC--CCCCCHHHHHHHH
Q 040394          543 SH------------TGMVGEGWKCFYSMCRDFKFVP-SMKHYVCMVDLLARAGRLEEALEFMENM--PIEPDVSLFGAFL  607 (691)
Q Consensus       543 ~~------------~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~~--~~~p~~~~~~~l~  607 (691)
                      ..            .+..+.|+++|.+.+   ...| |...-|-+.-+++..|++.+|.++|.+.  .......+|..+.
T Consensus       611 ~~~l~~~~rn~ek~kk~~~KAlq~y~kvL---~~dpkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~~~~dv~lNla  687 (1018)
T KOG2002|consen  611 IQALHNPSRNPEKEKKHQEKALQLYGKVL---RNDPKNMYAANGIGIVLAEKGRFSEARDIFSQVREATSDFEDVWLNLA  687 (1018)
T ss_pred             HHHhcccccChHHHHHHHHHHHHHHHHHH---hcCcchhhhccchhhhhhhccCchHHHHHHHHHHHHHhhCCceeeeHH
Confidence            21            345678888888664   3444 4777788888999999999999999998  2333556788899


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhc--CCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          608 HGCGLYSRFDLGEVMIKKMLEL--HPDKACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       608 ~~~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      .+|...|++..|+++|+...+.  ..+++.+...|+.++.+.|.+.+|.+.+......
T Consensus       688 h~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~  745 (1018)
T KOG2002|consen  688 HCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLKARHL  745 (1018)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            9999999999999999998873  3455788899999999999999999998777654

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.85  E-value=8.2e-17  Score=177.15  Aligned_cols=393  Identities=7%  Similarity=-0.035  Sum_probs=277.9

Q ss_pred             HHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhc---CCCChhHHHHHHHHHHhcCC
Q 040394          251 SLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDEL---CSIDLVSWTAMIVGYTQSGY  327 (691)
Q Consensus       251 ~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~---~~~~~~~~~~li~~~~~~g~  327 (691)
                      -.+......|+.++|.+++....... +.+...+..+...+.+.|++++|.++|++.   .+.+...+..+...+...|+
T Consensus        20 d~~~ia~~~g~~~~A~~~~~~~~~~~-~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~l~~~g~   98 (765)
T PRK10049         20 DWLQIALWAGQDAEVITVYNRYRVHM-QLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLEPQNDDYQRGLILTLADAGQ   98 (765)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCC
Confidence            34444555666666666666665422 334455677777777777777777777775   23345566677777788888


Q ss_pred             chhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhC
Q 040394          328 PDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETT  407 (691)
Q Consensus       328 ~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  407 (691)
                      +++|+..+++....  .|+...+..+..++...|+.++|...++.+.+..+.+..++..+..++...|..++|...++..
T Consensus        99 ~~eA~~~l~~~l~~--~P~~~~~~~la~~l~~~g~~~~Al~~l~~al~~~P~~~~~~~~la~~l~~~~~~e~Al~~l~~~  176 (765)
T PRK10049         99 YDEALVKAKQLVSG--APDKANLLALAYVYKRAGRHWDELRAMTQALPRAPQTQQYPTEYVQALRNNRLSAPALGAIDDA  176 (765)
T ss_pred             HHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCChHHHHHHHHhC
Confidence            88888888887765  3333226666667778888888888888888888887777777888888889999999888877


Q ss_pred             CCCCchhHHHHHHhhhCCCCCCH------HHHHHHHHHHh-----ccCcH---HHHHHHHHHHHHcCCCCCch-hHHH--
Q 040394          408 SEKDVIAWNSIISGLDDNVSPDA------VTLVSVISACA-----SLGAV---QVGSSLHAYSTKQGLLSSNV-YVGT--  470 (691)
Q Consensus       408 ~~~~~~~~~~li~~~~~~~~p~~------~~~~~ll~~~~-----~~~~~---~~a~~~~~~~~~~~~~~~~~-~~~~--  470 (691)
                      ...                 |+.      .....++....     ..+++   +.|...++.+.+.-...|.. ..+.  
T Consensus       177 ~~~-----------------p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a  239 (765)
T PRK10049        177 NLT-----------------PAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRA  239 (765)
T ss_pred             CCC-----------------HHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHH
Confidence            642                 221      01111222221     22233   67888888887642102221 1111  


Q ss_pred             --HHHHHHHhcCCHHHHHHHHHhcccCC--Hh--HHHHHHHHHhcCCChHHHHHHHHHHHHCCCCC---CHHHHHHHHHH
Q 040394          471 --ALLNFYAKCGDAQSARMVFDAMREKN--TV--TWSAMIGGYGMQGDGGGSLALFSDMLNEEVQP---NEVIFTTILSA  541 (691)
Q Consensus       471 --~l~~~~~~~g~~~~A~~~~~~~~~~~--~~--~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p---~~~~~~~ll~~  541 (691)
                        ..+..+...|++++|+..|+.+.+.+  ..  .-..+...|...|++++|+..|+++.+.....   .......+..+
T Consensus       240 ~~d~l~~Ll~~g~~~eA~~~~~~ll~~~~~~P~~a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a  319 (765)
T PRK10049        240 RIDRLGALLARDRYKDVISEYQRLKAEGQIIPPWAQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYS  319 (765)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHH
Confidence              11334567799999999999988632  11  22225778999999999999999988643111   12445566668


Q ss_pred             hcccCCHHHHHHHHHHchhhcC----------CCCC---hhHHHHHHHHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHH
Q 040394          542 CSHTGMVGEGWKCFYSMCRDFK----------FVPS---MKHYVCMVDLLARAGRLEEALEFMENM-P-IEPDVSLFGAF  606 (691)
Q Consensus       542 ~~~~g~~~~A~~~~~~m~~~~~----------~~p~---~~~~~~li~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l  606 (691)
                      +...|++++|.+.++.+.....          -.|+   ...+..+...+...|+.++|++.++++ . .+.+...+..+
T Consensus       320 ~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~n~~l~~~l  399 (765)
T PRK10049        320 LLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPGNQGLRIDY  399 (765)
T ss_pred             HHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence            8999999999999998854311          1123   224556778899999999999999998 3 34456788889


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          607 LHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       607 ~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      ...+...|++++|++.++++++++|++...+..++..+...|++++|...++.+++.
T Consensus       400 A~l~~~~g~~~~A~~~l~~al~l~Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~~  456 (765)
T PRK10049        400 ASVLQARGWPRAAENELKKAEVLEPRNINLEVEQAWTALDLQEWRQMDVLTDDVVAR  456 (765)
T ss_pred             HHHHHhcCCHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999999999999999999875

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.84  E-value=2.7e-18  Score=176.43  Aligned_cols=290  Identities=11%  Similarity=0.086  Sum_probs=155.0

Q ss_pred             cCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCC-C------hhhHHHHHHHHHhCCChhHHH
Q 040394          159 LRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDK-N------VVSWTSMIAGYVQNDCAQEGL  231 (691)
Q Consensus       159 ~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~------~~~~~~li~~~~~~g~~~~A~  231 (691)
                      .|++++|...|+++.+.++.+..++..+...+...|++++|..+++.+... +      ...+..+...|.+.|++++|.
T Consensus        48 ~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~~~~A~  127 (389)
T PRK11788         48 NEQPDKAIDLFIEMLKVDPETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGLLDRAE  127 (389)
T ss_pred             cCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCCHHHHH
Confidence            344444444444444443334444444444444444444444444433221 0      123444444555555555555


Q ss_pred             HHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCc----hHHHHHHHHHHHhcCCHHHHHHHHHhc
Q 040394          232 VLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEIN----SHLVTALLDMYVKCGNIRDARSVFDEL  307 (691)
Q Consensus       232 ~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~----~~~~~~li~~~~~~g~~~~A~~~~~~~  307 (691)
                      .+|+++.+.. +++..++..++..+.+.|++++|.+.++.+.+.+..+.    ...+..+...+.+.|++++|...|+++
T Consensus       128 ~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a  206 (389)
T PRK11788        128 ELFLQLVDEG-DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAARALLKKA  206 (389)
T ss_pred             HHHHHHHcCC-cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            5555554321 12334444555555555555555555555544332221    112344555555666666666666655


Q ss_pred             CC---CChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHH
Q 040394          308 CS---IDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVI  384 (691)
Q Consensus       308 ~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  384 (691)
                      .+   .+...+..+...+.+.|++++|.++++++...+......++..+..++...|++++|...++.+.+..+.. ..+
T Consensus       207 l~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~p~~-~~~  285 (389)
T PRK11788        207 LAADPQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEEYPGA-DLL  285 (389)
T ss_pred             HhHCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCc-hHH
Confidence            21   23345555666666666666666666666654322223445556666666666666666666666555443 233


Q ss_pred             HHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhc---cCcHHHHHHHHHHHHHcCC
Q 040394          385 NALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACAS---LGAVQVGSSLHAYSTKQGL  461 (691)
Q Consensus       385 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~---~~~~~~a~~~~~~~~~~~~  461 (691)
                      ..++..+.+.|++++|..+++++.+                ..|+..++..++..+..   .|+.+++..+++.+.+.++
T Consensus       286 ~~la~~~~~~g~~~~A~~~l~~~l~----------------~~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~~~~  349 (389)
T PRK11788        286 LALAQLLEEQEGPEAAQALLREQLR----------------RHPSLRGFHRLLDYHLAEAEEGRAKESLLLLRDLVGEQL  349 (389)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHH----------------hCcCHHHHHHHHHHhhhccCCccchhHHHHHHHHHHHHH
Confidence            6677777777888888887777654                34777777777766654   4477778888887777665


Q ss_pred             CCCchh
Q 040394          462 LSSNVY  467 (691)
Q Consensus       462 ~~~~~~  467 (691)
                       .+++.
T Consensus       350 -~~~p~  354 (389)
T PRK11788        350 -KRKPR  354 (389)
T ss_pred             -hCCCC
Confidence             44443

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.84  E-value=3e-17  Score=176.52  Aligned_cols=323  Identities=8%  Similarity=-0.044  Sum_probs=173.6

Q ss_pred             HHHHHHHhcCCHHHHHHHHHhc---CCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCc-HHHHHHHHHHHhcCC
Q 040394          286 ALLDMYVKCGNIRDARSVFDEL---CSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPN-HVTIASVLSASAQLG  361 (691)
Q Consensus       286 ~li~~~~~~g~~~~A~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~~~~~~  361 (691)
                      .++..+.+.|++++|..+++..   ...+...+..++.+....|++++|.+.++++...  .|+ ...+..+...+...|
T Consensus        47 ~~~~~~~~~g~~~~A~~l~~~~l~~~p~~~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~--~P~~~~a~~~la~~l~~~g  124 (656)
T PRK15174         47 LFAIACLRKDETDVGLTLLSDRVLTAKNGRDLLRRWVISPLASSQPDAVLQVVNKLLAV--NVCQPEDVLLVASVLLKSK  124 (656)
T ss_pred             HHHHHHHhcCCcchhHHHhHHHHHhCCCchhHHHHHhhhHhhcCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHcC
Confidence            3445555666666666666555   2223334444445555566666666666666554  332 334444555566666


Q ss_pred             ChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCH-HHHHHHHHHH
Q 040394          362 NLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDA-VTLVSVISAC  440 (691)
Q Consensus       362 ~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~-~~~~~ll~~~  440 (691)
                      ++++|...++.+.+..+.+...+..+...+...|++++|...++.+...                .|+. ..+..+ ..+
T Consensus       125 ~~~~Ai~~l~~Al~l~P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~----------------~P~~~~a~~~~-~~l  187 (656)
T PRK15174        125 QYATVADLAEQAWLAFSGNSQIFALHLRTLVLMDKELQAISLARTQAQE----------------VPPRGDMIATC-LSF  187 (656)
T ss_pred             CHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHh----------------CCCCHHHHHHH-HHH
Confidence            6666666666666665555556666666666666666666666554322                1222 222222 234


Q ss_pred             hccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHH--
Q 040394          441 ASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGG--  515 (691)
Q Consensus       441 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~--  515 (691)
                      ...|++++|...++.+.+... .++......+...+...|++++|...++...+   .+...+..+...+...|++++  
T Consensus       188 ~~~g~~~eA~~~~~~~l~~~~-~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~p~~~~~~~~Lg~~l~~~G~~~eA~  266 (656)
T PRK15174        188 LNKSRLPEDHDLARALLPFFA-LERQESAGLAVDTLCAVGKYQEAIQTGESALARGLDGAALRRSLGLAYYQSGRSREAK  266 (656)
T ss_pred             HHcCCHHHHHHHHHHHHhcCC-CcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhhH
Confidence            555666666666666555432 22233333444555566666666666665543   134455556666666666654  


Q ss_pred             --HHHHHHHHHHCCCCCC-HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHH
Q 040394          516 --SLALFSDMLNEEVQPN-EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFM  591 (691)
Q Consensus       516 --A~~~~~~m~~~g~~p~-~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~  591 (691)
                        |...+++..+.  .|+ ...+..+...+...|++++|...+++...   ..|+ ...+..+..+|.+.|++++|++.+
T Consensus       267 ~~A~~~~~~Al~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~---l~P~~~~a~~~La~~l~~~G~~~eA~~~l  341 (656)
T PRK15174        267 LQAAEHWRHALQF--NSDNVRIVTLYADALIRTGQNEKAIPLLQQSLA---THPDLPYVRAMYARALRQVGQYTAASDEF  341 (656)
T ss_pred             HHHHHHHHHHHhh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence              56666666553  333 34555555566666666666666665432   3344 344455556666666666666666


Q ss_pred             HhC-CCCCCHHH-HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC
Q 040394          592 ENM-PIEPDVSL-FGAFLHGCGLYSRFDLGEVMIKKMLELHPDK  633 (691)
Q Consensus       592 ~~~-~~~p~~~~-~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~  633 (691)
                      +++ ...|+... +..+..++...|+.++|...++++++..|++
T Consensus       342 ~~al~~~P~~~~~~~~~a~al~~~G~~deA~~~l~~al~~~P~~  385 (656)
T PRK15174        342 VQLAREKGVTSKWNRYAAAALLQAGKTSEAESVFEHYIQARASH  385 (656)
T ss_pred             HHHHHhCccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhChhh
Confidence            655 33444322 2223444555666666666666666666664

>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=99.84  E-value=3.5e-17  Score=176.89  Aligned_cols=91  Identities=10%  Similarity=0.077  Sum_probs=72.8

Q ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhc
Q 040394          114 FQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKC  193 (691)
Q Consensus       114 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~  193 (691)
                      +......+.+.|++++|+..|++.++.  .|+...|..+..++.+.|++++|...++..++..+.+..++..+..+|...
T Consensus       130 ~k~~G~~~~~~~~~~~Ai~~y~~al~~--~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~a~a~~~l  207 (615)
T TIGR00990       130 LKEKGNKAYRNKDFNKAIKLYSKAIEC--KPDPVYYSNRAACHNALGDWEKVVEDTTAALELDPDYSKALNRRANAYDGL  207 (615)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhc--CCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHc
Confidence            445667778888899999988888764  567777888888888888888888888888888777888888888888888


Q ss_pred             CChHHHHHHHhcc
Q 040394          194 RDIGSSRQVFDET  206 (691)
Q Consensus       194 g~~~~A~~~~~~~  206 (691)
                      |++++|..-|...
T Consensus       208 g~~~eA~~~~~~~  220 (615)
T TIGR00990       208 GKYADALLDLTAS  220 (615)
T ss_pred             CCHHHHHHHHHHH
Confidence            8888887766543

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

Probab=99.83  E-value=1.1e-13  Score=135.95  Aligned_cols=573  Identities=10%  Similarity=0.034  Sum_probs=450.4

Q ss_pred             cCchhHHHHHHHHHHhCCCCchhhhHHHHHHhcCCChHHHHHHhccCCC---CCcchHHHHH-------------H----
Q 040394           60 KSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPN---PDFYSFQVMI-------------R----  119 (691)
Q Consensus        60 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~ll-------------~----  119 (691)
                      +++..|+-+++.+.+..+.+.+-|-.-.+.-...|++..|+.+..+-.+   .+...|---+             +    
T Consensus       265 ~DikKaR~llKSvretnP~hp~gWIAsArLEEvagKl~~Ar~~I~~GCe~cprSeDvWLeaiRLhp~d~aK~vvA~Avr~  344 (913)
T KOG0495|consen  265 EDIKKARLLLKSVRETNPKHPPGWIASARLEEVAGKLSVARNLIMKGCEECPRSEDVWLEAIRLHPPDVAKTVVANAVRF  344 (913)
T ss_pred             HHHHHHHHHHHHHHhcCCCCCchHHHHHHHHHHhhHHHHHHHHHHHHHhhCCchHHHHHHHHhcCChHHHHHHHHHHHHh
Confidence            5566788888888888877666666666777778888888887764321   2222222111             1    


Q ss_pred             ------HHHhCC----ChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHH
Q 040394          120 ------WYFLND----LYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDM  189 (691)
Q Consensus       120 ------~~~~~~----~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  189 (691)
                            .++++-    +...=..++++..+. ++.++..|.    +.....+.+.|..++.+.++.-+.+...|.+    
T Consensus       345 ~P~Sv~lW~kA~dLE~~~~~K~RVlRKALe~-iP~sv~LWK----aAVelE~~~darilL~rAveccp~s~dLwlA----  415 (913)
T KOG0495|consen  345 LPTSVRLWLKAADLESDTKNKKRVLRKALEH-IPRSVRLWK----AAVELEEPEDARILLERAVECCPQSMDLWLA----  415 (913)
T ss_pred             CCCChhhhhhHHhhhhHHHHHHHHHHHHHHh-CCchHHHHH----HHHhccChHHHHHHHHHHHHhccchHHHHHH----
Confidence                  111111    112222334444443 233333333    3334556666888888888776666666654    


Q ss_pred             hHhcCChHHHHHHHhcc---CCCChhhHHHHHHHHHhCCChhHHHHHHHH----HHhCCCCCChhhHHHHHHHHHccCCh
Q 040394          190 YAKCRDIGSSRQVFDET---LDKNVVSWTSMIAGYVQNDCAQEGLVLFNR----MREGFVEGNQITLGSLVTACAKLRAL  262 (691)
Q Consensus       190 ~~~~g~~~~A~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~A~~~~~~----m~~~~~~p~~~t~~~li~~~~~~~~~  262 (691)
                      |.+..-++.|.++++..   ...+...|.+....--.+|+.+...+++++    +..+|+..+...|..=...|-..|..
T Consensus       416 larLetYenAkkvLNkaRe~iptd~~IWitaa~LEE~ngn~~mv~kii~rgl~~L~~ngv~i~rdqWl~eAe~~e~agsv  495 (913)
T KOG0495|consen  416 LARLETYENAKKVLNKAREIIPTDREIWITAAKLEEANGNVDMVEKIIDRGLSELQANGVEINRDQWLKEAEACEDAGSV  495 (913)
T ss_pred             HHHHHHHHHHHHHHHHHHhhCCCChhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhcceeecHHHHHHHHHHHhhcCCh
Confidence            45666788888888765   445778888877777889999988888765    45688999999998888899999999


Q ss_pred             hhHHHHHHHHHHHCCCCc--hHHHHHHHHHHHhcCCHHHHHHHHHhcC---CCChhHHHHHHHHHHhcCCchhHHHHHHH
Q 040394          263 HQGKWLHGYILKIGIEIN--SHLVTALLDMYVKCGNIRDARSVFDELC---SIDLVSWTAMIVGYTQSGYPDKALKLFTD  337 (691)
Q Consensus       263 ~~a~~~~~~~~~~g~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~  337 (691)
                      -....|....+..|+.-.  ..+|..-...|.+.+.++-|..+|....   ..+...|...+..--..|..++...+|++
T Consensus       496 ~TcQAIi~avigigvEeed~~~tw~~da~~~~k~~~~~carAVya~alqvfp~k~slWlra~~~ek~hgt~Esl~Allqk  575 (913)
T KOG0495|consen  496 ITCQAIIRAVIGIGVEEEDRKSTWLDDAQSCEKRPAIECARAVYAHALQVFPCKKSLWLRAAMFEKSHGTRESLEALLQK  575 (913)
T ss_pred             hhHHHHHHHHHhhccccchhHhHHhhhHHHHHhcchHHHHHHHHHHHHhhccchhHHHHHHHHHHHhcCcHHHHHHHHHH
Confidence            999999999998887643  4688888999999999999999998773   34667788887777788999999999999


Q ss_pred             hhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHH
Q 040394          338 KKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNS  417 (691)
Q Consensus       338 m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  417 (691)
                      .... ++-....|..........|++..|+.++..+.+..+.+...+-+-+........++.|..+|.+...        
T Consensus       576 av~~-~pkae~lwlM~ake~w~agdv~~ar~il~~af~~~pnseeiwlaavKle~en~e~eraR~llakar~--------  646 (913)
T KOG0495|consen  576 AVEQ-CPKAEILWLMYAKEKWKAGDVPAARVILDQAFEANPNSEEIWLAAVKLEFENDELERARDLLAKARS--------  646 (913)
T ss_pred             HHHh-CCcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHhhccccHHHHHHHHHHHhc--------
Confidence            8876 3344556666667888889999999999999999999999999999999999999999999999874        


Q ss_pred             HHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--C
Q 040394          418 IISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--K  495 (691)
Q Consensus       418 li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~  495 (691)
                              ..|+...|..-+..-.-.++.++|.+++++..+.-  |.-...|-.+.+.+-+.++++.|...|..-.+  |
T Consensus       647 --------~sgTeRv~mKs~~~er~ld~~eeA~rllEe~lk~f--p~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~cP  716 (913)
T KOG0495|consen  647 --------ISGTERVWMKSANLERYLDNVEEALRLLEEALKSF--PDFHKLWLMLGQIEEQMENIEMAREAYLQGTKKCP  716 (913)
T ss_pred             --------cCCcchhhHHHhHHHHHhhhHHHHHHHHHHHHHhC--CchHHHHHHHhHHHHHHHHHHHHHHHHHhccccCC
Confidence                    46888888877777778899999999999998876  78888999999999999999999999987765  3


Q ss_pred             -CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHH
Q 040394          496 -NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCM  574 (691)
Q Consensus       496 -~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~l  574 (691)
                       .+..|-.|...--+.|.+-.|..++++..-.+ +-|...|...|+.-.+.|+.+.|..++.+..++  ++.+...|..-
T Consensus       717 ~~ipLWllLakleEk~~~~~rAR~ildrarlkN-Pk~~~lwle~Ir~ElR~gn~~~a~~lmakALQe--cp~sg~LWaEa  793 (913)
T KOG0495|consen  717 NSIPLWLLLAKLEEKDGQLVRARSILDRARLKN-PKNALLWLESIRMELRAGNKEQAELLMAKALQE--CPSSGLLWAEA  793 (913)
T ss_pred             CCchHHHHHHHHHHHhcchhhHHHHHHHHHhcC-CCcchhHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCccchhHHHH
Confidence             56788888888888999999999999998764 456678888999999999999999998877555  44457778888


Q ss_pred             HHHHHhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHH
Q 040394          575 VDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVN  654 (691)
Q Consensus       575 i~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~  654 (691)
                      |....+.++-....+.+++..  .|......+...+....++++|...|+++...+|++..+|..+-..+...|.-++-.
T Consensus       794 I~le~~~~rkTks~DALkkce--~dphVllaia~lfw~e~k~~kar~Wf~Ravk~d~d~GD~wa~fykfel~hG~eed~k  871 (913)
T KOG0495|consen  794 IWLEPRPQRKTKSIDALKKCE--HDPHVLLAIAKLFWSEKKIEKAREWFERAVKKDPDNGDAWAWFYKFELRHGTEEDQK  871 (913)
T ss_pred             HHhccCcccchHHHHHHHhcc--CCchhHHHHHHHHHHHHHHHHHHHHHHHHHccCCccchHHHHHHHHHHHhCCHHHHH
Confidence            888888888888888888764  455666777888889999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhCCC
Q 040394          655 QVRELMKQRGL  665 (691)
Q Consensus       655 ~~~~~~~~~g~  665 (691)
                      +++.+......
T Consensus       872 ev~~~c~~~EP  882 (913)
T KOG0495|consen  872 EVLKKCETAEP  882 (913)
T ss_pred             HHHHHHhccCC
Confidence            99988877643

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.83  E-value=1.4e-15  Score=163.87  Aligned_cols=188  Identities=10%  Similarity=0.042  Sum_probs=104.4

Q ss_pred             HHHHHhcCCHHHHHHHHHhcccC----CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCC-----CCCCHHHHHHHHHHhc
Q 040394          473 LNFYAKCGDAQSARMVFDAMREK----NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEE-----VQPNEVIFTTILSACS  543 (691)
Q Consensus       473 ~~~~~~~g~~~~A~~~~~~~~~~----~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g-----~~p~~~~~~~ll~~~~  543 (691)
                      +.++.+.|++.++++.|+.+..+    ...+-..+..+|...+++++|+.+++++....     ..++......|.-++.
T Consensus       299 l~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~l  378 (822)
T PRK14574        299 LGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLN  378 (822)
T ss_pred             HHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHH
Confidence            34455566666666666666632    12233445666666666666666666665432     1122222345555666


Q ss_pred             ccCCHHHHHHHHHHchhhcC----------CCCC---hhHHHHHHHHHHhcCChHHHHHHHHhC--CCCCCHHHHHHHHH
Q 040394          544 HTGMVGEGWKCFYSMCRDFK----------FVPS---MKHYVCMVDLLARAGRLEEALEFMENM--PIEPDVSLFGAFLH  608 (691)
Q Consensus       544 ~~g~~~~A~~~~~~m~~~~~----------~~p~---~~~~~~li~~~~~~g~~~~A~~~~~~~--~~~p~~~~~~~l~~  608 (691)
                      ..+++++|..+++.+.+...          -.||   ...+..++..+...|++.+|++.++++  ..+-|......+..
T Consensus       379 d~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~Ae~~le~l~~~aP~n~~l~~~~A~  458 (822)
T PRK14574        379 ESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALNDLPTAQKKLEDLSSTAPANQNLRIALAS  458 (822)
T ss_pred             hcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            66666666666666633111          0122   223334455556666666666666666  22334555666666


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHH
Q 040394          609 GCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELM  660 (691)
Q Consensus       609 ~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  660 (691)
                      .+...|.+.+|++.++.+..++|++..+....+.++...|+|.+|..+.+.+
T Consensus       459 v~~~Rg~p~~A~~~~k~a~~l~P~~~~~~~~~~~~al~l~e~~~A~~~~~~l  510 (822)
T PRK14574        459 IYLARDLPRKAEQELKAVESLAPRSLILERAQAETAMALQEWHQMELLTDDV  510 (822)
T ss_pred             HHHhcCCHHHHHHHHHHHhhhCCccHHHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence            6666666666666666666666666666666666666666666665555444

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.82  E-value=1.8e-16  Score=170.67  Aligned_cols=348  Identities=9%  Similarity=-0.034  Sum_probs=259.5

Q ss_pred             cCCChHHHHHHhccCCC------CCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHH
Q 040394           92 SFGHVKYARSVFDSMPN------PDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEG  165 (691)
Q Consensus        92 ~~g~~~~A~~~~~~~~~------~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a  165 (691)
                      ++.+++.---+|...++      .+....-.++..+.+.|++++|..+++...... +-+...+..++.+....|+.++|
T Consensus        17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~l~~~~l~~~-p~~~~~l~~l~~~~l~~g~~~~A   95 (656)
T PRK15174         17 KQEDWEGLCLYFSQHPEKVRDSAGNEQNIILFAIACLRKDETDVGLTLLSDRVLTA-KNGRDLLRRWVISPLASSQPDAV   95 (656)
T ss_pred             hhhchhhHhHHhhcccHhhhhhcccccCHHHHHHHHHhcCCcchhHHHhHHHHHhC-CCchhHHHHHhhhHhhcCCHHHH
Confidence            44455555555554443      222344556667788899999999988888763 33344555556666778999999


Q ss_pred             HHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCC--C-ChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCC
Q 040394          166 MKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLD--K-NVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFV  242 (691)
Q Consensus       166 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~  242 (691)
                      ...++.+.+..|.+...+..+...+...|++++|...+++...  | +...+..+...+...|++++|...++++.....
T Consensus        96 ~~~l~~~l~~~P~~~~a~~~la~~l~~~g~~~~Ai~~l~~Al~l~P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P  175 (656)
T PRK15174         96 LQVVNKLLAVNVCQPEDVLLVASVLLKSKQYATVADLAEQAWLAFSGNSQIFALHLRTLVLMDKELQAISLARTQAQEVP  175 (656)
T ss_pred             HHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCC
Confidence            9999999988888888888889999999999999998888744  3 566788888888999999999998888866543


Q ss_pred             CCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcC---CCChhHHHHHH
Q 040394          243 EGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELC---SIDLVSWTAMI  319 (691)
Q Consensus       243 ~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~---~~~~~~~~~li  319 (691)
                      .+. ..+.. +..+...|++++|...++.+.+....++...+..+...+.+.|++++|...|++..   ..+...+..+.
T Consensus       176 ~~~-~a~~~-~~~l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~p~~~~~~~~Lg  253 (656)
T PRK15174        176 PRG-DMIAT-CLSFLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARGLDGAALRRSLG  253 (656)
T ss_pred             CCH-HHHHH-HHHHHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHH
Confidence            322 22322 23467888999999988888776544445555566777888899999998888872   23556777888


Q ss_pred             HHHHhcCCchh----HHHHHHHhhHCCCCC-cHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhc
Q 040394          320 VGYTQSGYPDK----ALKLFTDKKWADFFP-NHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKC  394 (691)
Q Consensus       320 ~~~~~~g~~~~----a~~~~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~  394 (691)
                      ..+...|++++    |...+++....  .| +...+..+...+...|++++|...++.+.+..+.+..++..+..+|.+.
T Consensus       254 ~~l~~~G~~~eA~~~A~~~~~~Al~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~~~~a~~~La~~l~~~  331 (656)
T PRK15174        254 LAYYQSGRSREAKLQAAEHWRHALQF--NSDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHPDLPYVRAMYARALRQV  331 (656)
T ss_pred             HHHHHcCCchhhHHHHHHHHHHHHhh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHC
Confidence            88888998885    78888887765  34 4567777788888889999999999998888888777888888899999


Q ss_pred             CChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHH-HHHHHHHHHhccCcHHHHHHHHHHHHHcC
Q 040394          395 HVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAV-TLVSVISACASLGAVQVGSSLHAYSTKQG  460 (691)
Q Consensus       395 g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~-~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  460 (691)
                      |++++|...|+++...                .|+.. .+..+..++...|+.++|...|+...+..
T Consensus       332 G~~~eA~~~l~~al~~----------------~P~~~~~~~~~a~al~~~G~~deA~~~l~~al~~~  382 (656)
T PRK15174        332 GQYTAASDEFVQLARE----------------KGVTSKWNRYAAAALLQAGKTSEAESVFEHYIQAR  382 (656)
T ss_pred             CCHHHHHHHHHHHHHh----------------CccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            9999999998887653                34433 33344567788899999999998887765

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

Probab=99.82  E-value=5.6e-15  Score=150.88  Aligned_cols=349  Identities=13%  Similarity=0.061  Sum_probs=199.9

Q ss_pred             ChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHH
Q 040394          311 DLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDM  390 (691)
Q Consensus       311 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  390 (691)
                      ++..|.-+..+|.+.|++.+|+.+|..+.....--+...|..+..++...|..++|.+.+..++...|.+..+.-.|...
T Consensus       413 ~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~~p~~~D~Ri~Lasl  492 (895)
T KOG2076|consen  413 DVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMELGEYEEAIEFYEKVLILAPDNLDARITLASL  492 (895)
T ss_pred             hHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHHhhHHHHHHHHHHHHhcCCCchhhhhhHHHH
Confidence            45578888899999999999999999988875555677888888999999999999999999999999988888999999


Q ss_pred             hHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCC---------
Q 040394          391 YAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGL---------  461 (691)
Q Consensus       391 ~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~---------  461 (691)
                      +.+.|+.++|.+.++.+...|..      .+-..+..|+..........+...|+.++-..+...|+....         
T Consensus       493 ~~~~g~~EkalEtL~~~~~~D~~------~~e~~a~~~e~ri~~~r~d~l~~~gk~E~fi~t~~~Lv~~~~~~~~~f~~~  566 (895)
T KOG2076|consen  493 YQQLGNHEKALETLEQIINPDGR------NAEACAWEPERRILAHRCDILFQVGKREEFINTASTLVDDFLKKRYIFPRN  566 (895)
T ss_pred             HHhcCCHHHHHHHHhcccCCCcc------chhhccccHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhcchH
Confidence            99999999999999997755421      001113445555555555566666666654444333332110         


Q ss_pred             ------------CCCchhHHHHHHHHHHhcCCHHHHHHHHHhcc--------cCCHh----HHHHHHHHHhcCCChHHHH
Q 040394          462 ------------LSSNVYVGTALLNFYAKCGDAQSARMVFDAMR--------EKNTV----TWSAMIGGYGMQGDGGGSL  517 (691)
Q Consensus       462 ------------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--------~~~~~----~~~~li~~~~~~~~~~~A~  517 (691)
                                  .+........++.+-.+.++.....+-...-.        .-+..    .+.-++.++++.+.+++|+
T Consensus       567 ~k~r~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~l~d~~~~~~~e~~~Lsiddwfel~~e~i~~L~k~~r~qeAl  646 (895)
T KOG2076|consen  567 KKKRRRAIAGTTSKRYSELLKQIIRAREKATDDNVMEKALSDGTEFRAVELRGLSIDDWFELFRELILSLAKLQRVQEAL  646 (895)
T ss_pred             HHHHHHhhccccccccchhHHHHHHHHhccCchHHhhhcccchhhhhhhhhccCcHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence                        00111111112222222222111111111000        00111    1223445555566666666


Q ss_pred             HHHHHHHHCCC--CCCH---HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC---hhHHHHHH--------------
Q 040394          518 ALFSDMLNEEV--QPNE---VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS---MKHYVCMV--------------  575 (691)
Q Consensus       518 ~~~~~m~~~g~--~p~~---~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~---~~~~~~li--------------  575 (691)
                      .+...+.....  .++.   ..-...+.++...+++..|...++.|....+...+   ...|+...              
T Consensus       647 ~vv~~a~~~~~f~~~~~~~k~l~~~~l~~s~~~~d~~~a~~~lR~~i~~~~~~~~~~q~~l~n~~~s~~~~~~q~v~~~R  726 (895)
T KOG2076|consen  647 SVVFTALEAYIFFQDSEIRKELQFLGLKASLYARDPGDAFSYLRSVITQFQFYLDVYQLNLWNLDFSYFSKYGQRVCYLR  726 (895)
T ss_pred             HHHHHHHhhhhhhccHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55555554321  1111   11122333445555566665555555444333222   12222111              


Q ss_pred             ---------------------HHHHhcCChHHHHHHHHhC-CCCCCHHHHHHHHH-HHH----------hcCCHHHHHHH
Q 040394          576 ---------------------DLLARAGRLEEALEFMENM-PIEPDVSLFGAFLH-GCG----------LYSRFDLGEVM  622 (691)
Q Consensus       576 ---------------------~~~~~~g~~~~A~~~~~~~-~~~p~~~~~~~l~~-~~~----------~~g~~~~A~~~  622 (691)
                                           +.+..++.+..|+..+-+. ...||....+.++. ++.          ++-..-++..+
T Consensus       727 ~~~~~~~~~~~~~~~l~~i~gh~~~~~~s~~~Al~~y~ra~~~~pd~Pl~nl~lglafih~a~qr~v~~Rh~~i~qG~af  806 (895)
T KOG2076|consen  727 LIMRLLVKNKDDTPPLALIYGHNLFVNASFKHALQEYMRAFRQNPDSPLINLCLGLAFIHLALQRRVSNRHAQIAQGFAF  806 (895)
T ss_pred             HHHHHhccCccCCcceeeeechhHhhccchHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence                                 2234455666665554443 33445333332222 221          22234556666


Q ss_pred             HHHHHhcCCC--CchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          623 IKKMLELHPD--KACYYVLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       623 ~~~~~~~~p~--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      +++..++.-.  ...+.+.++.+|-..|-..-|..+|++.++...
T Consensus       807 L~RY~~lR~~~~~QEa~YNigRayh~~gl~~LA~~YYekvL~~~p  851 (895)
T KOG2076|consen  807 LKRYKELRRCEEKQEAFYNIGRAYHQIGLVHLAVSYYEKVLEVSP  851 (895)
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHhCCCc
Confidence            6666664433  467888999999999999999999999998643

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.80  E-value=1.5e-15  Score=167.14  Aligned_cols=382  Identities=8%  Similarity=-0.062  Sum_probs=206.0

Q ss_pred             cCchhHHHHHHHHHHhCCCCchhhhHHHHHHhcCCChHHHHHHhccCC---CCCcchHHHHHHHHHhCCChhHHHHHHHH
Q 040394           60 KSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMP---NPDFYSFQVMIRWYFLNDLYKDIVEFYKC  136 (691)
Q Consensus        60 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~---~~~~~~~~~ll~~~~~~~~~~~a~~~~~~  136 (691)
                      |+.+.|..++.......+.+...+..+...+.+.|++++|..+|++..   ..+...+..+...+...|++++|+..+++
T Consensus        29 g~~~~A~~~~~~~~~~~~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~l~~~g~~~eA~~~l~~  108 (765)
T PRK10049         29 GQDAEVITVYNRYRVHMQLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLEPQNDDYQRGLILTLADAGQYDEALVKAKQ  108 (765)
T ss_pred             CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            666666666666655332222256667777777777777777777642   23344556666666777777777777777


Q ss_pred             HHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCC-CCh----
Q 040394          137 MRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLD-KNV----  211 (691)
Q Consensus       137 m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~~~----  211 (691)
                      ..+. .+.+.. +..+..++...|+.++|...++++.+..|.+...+..+...+...+..++|++.++.... |+.    
T Consensus       109 ~l~~-~P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~P~~~~~~~~la~~l~~~~~~e~Al~~l~~~~~~p~~~~~l  186 (765)
T PRK10049        109 LVSG-APDKAN-LLALAYVYKRAGRHWDELRAMTQALPRAPQTQQYPTEYVQALRNNRLSAPALGAIDDANLTPAEKRDL  186 (765)
T ss_pred             HHHh-CCCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCChHHHHHHHHhCCCCHHHHHHH
Confidence            7665 233334 666666666777777777777777777666666666666677677777777777766544 110    


Q ss_pred             --hhHHHHHHHHH-----hCCCh---hHHHHHHHHHHhC-CCCCChh-hHH----HHHHHHHccCChhhHHHHHHHHHHH
Q 040394          212 --VSWTSMIAGYV-----QNDCA---QEGLVLFNRMREG-FVEGNQI-TLG----SLVTACAKLRALHQGKWLHGYILKI  275 (691)
Q Consensus       212 --~~~~~li~~~~-----~~g~~---~~A~~~~~~m~~~-~~~p~~~-t~~----~li~~~~~~~~~~~a~~~~~~~~~~  275 (691)
                        .....++....     ..+++   ++|++.++.+.+. ...|+.. .+.    ..+.++...|+.++|...|+.+.+.
T Consensus       187 ~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll~~g~~~eA~~~~~~ll~~  266 (765)
T PRK10049        187 EADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLGALLARDRYKDVISEYQRLKAE  266 (765)
T ss_pred             HHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcc
Confidence              01111222221     11223   5566666666543 1222211 111    1123334556667777777776665


Q ss_pred             CCC-CchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCC-------hhHHHHHHHHHHhcCCchhHHHHHHHhhHCCC----
Q 040394          276 GIE-INSHLVTALLDMYVKCGNIRDARSVFDELCSID-------LVSWTAMIVGYTQSGYPDKALKLFTDKKWADF----  343 (691)
Q Consensus       276 g~~-~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~-------~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~----  343 (691)
                      +.. |+. ....+...|...|++++|+..|+++...+       ...+..+..++...|++++|.++++.+.....    
T Consensus       267 ~~~~P~~-a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~  345 (765)
T PRK10049        267 GQIIPPW-AQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENYPGALTVTAHTINNSPPFLR  345 (765)
T ss_pred             CCCCCHH-HHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEe
Confidence            422 221 11223556666677777777666652211       12344455556666777777766666655411    


Q ss_pred             -------CCcH---HHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCch
Q 040394          344 -------FPNH---VTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVI  413 (691)
Q Consensus       344 -------~p~~---~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  413 (691)
                             .|+.   ..+..+...+...|++++|...++.+....|.+...+..+...+...|++++|...+++....   
T Consensus       346 ~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l---  422 (765)
T PRK10049        346 LYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPGNQGLRIDYASVLQARGWPRAAENELKKAEVL---  422 (765)
T ss_pred             ecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhh---
Confidence                   1221   122333445555555666665555555555555555555555555555555555555555432   


Q ss_pred             hHHHHHHhhhCCCCCC-HHHHHHHHHHHhccCcHHHHHHHHHHHHHcC
Q 040394          414 AWNSIISGLDDNVSPD-AVTLVSVISACASLGAVQVGSSLHAYSTKQG  460 (691)
Q Consensus       414 ~~~~li~~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  460 (691)
                                   .|+ ...+......+...|+++.|+.+++.+.+..
T Consensus       423 -------------~Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~~~  457 (765)
T PRK10049        423 -------------EPRNINLEVEQAWTALDLQEWRQMDVLTDDVVARE  457 (765)
T ss_pred             -------------CCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC
Confidence                         233 2333333444455555555555555555543

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.80  E-value=6.4e-15  Score=137.47  Aligned_cols=320  Identities=18%  Similarity=0.197  Sum_probs=233.8

Q ss_pred             chHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHc--ccCChhHH-HHHHHHHHHhCCCChhHHHHHHH
Q 040394          112 YSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACC--ELRDIDEG-MKVHCEIVKVGGPDSFVLTGLVD  188 (691)
Q Consensus       112 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~--~~~~~~~a-~~~~~~~~~~~~~~~~~~~~l~~  188 (691)
                      .+=|.|+. +..+|.++++.-+|+.|.+.|+..+...-..+++..+  ...++--| ++.|-.|.+.|-.+..+|     
T Consensus       117 ~~E~nL~k-mIS~~EvKDs~ilY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sW-----  190 (625)
T KOG4422|consen  117 ETENNLLK-MISSREVKDSCILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSW-----  190 (625)
T ss_pred             cchhHHHH-HHhhcccchhHHHHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhcccccccccccc-----
Confidence            35566665 4567899999999999999998888877777765544  33333222 233334444443344454     


Q ss_pred             HhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHH
Q 040394          189 MYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWL  268 (691)
Q Consensus       189 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~  268 (691)
                         +.|++.+   ++-+.......+|.+||.++|+--..++|.++|++-.+...+.+..+||.+|.+-.-..+    .++
T Consensus       191 ---K~G~vAd---L~~E~~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~L  260 (625)
T KOG4422|consen  191 ---KSGAVAD---LLFETLPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKL  260 (625)
T ss_pred             ---ccccHHH---HHHhhcCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHH
Confidence               3455444   555555667789999999999999999999999999998899999999999988654333    789


Q ss_pred             HHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHH----Hhc----CCCChhHHHHHHHHHHhcCCchh-HHHHHHHhh
Q 040394          269 HGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVF----DEL----CSIDLVSWTAMIVGYTQSGYPDK-ALKLFTDKK  339 (691)
Q Consensus       269 ~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~----~~~----~~~~~~~~~~li~~~~~~g~~~~-a~~~~~~m~  339 (691)
                      ..+|....+.||..|+|+++.+..+.|+++.|...+    .+|    .+|...+|..+|..+++.++..+ +..++.+..
T Consensus       261 v~EMisqkm~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~  340 (625)
T KOG4422|consen  261 VAEMISQKMTPNLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQ  340 (625)
T ss_pred             HHHHHHhhcCCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHH
Confidence            999999999999999999999999999988765544    444    66888889888888888887754 344444433


Q ss_pred             ----HCCCCC----cHHHHHHHHHHHhcCCChhhHHHHHHHHHHh------CCC--chhHHHHHHHHhHhcCChHHHHHH
Q 040394          340 ----WADFFP----NHVTIASVLSASAQLGNLNMGRMVHSLGIRL------GLE--DYTVINALVDMYAKCHVIADARYI  403 (691)
Q Consensus       340 ----~~g~~p----~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~------~~~--~~~~~~~l~~~~~~~g~~~~a~~~  403 (691)
                          .+-++|    |...|...+..|....+.+.|.++.......      |+.  ...-|..+..+.++....+.-...
T Consensus       341 N~ltGK~fkp~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~  420 (625)
T KOG4422|consen  341 NSLTGKTFKPITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKW  420 (625)
T ss_pred             HhhccCcccCCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                222333    4456777778888888888888876655432      222  333456677777888888888888


Q ss_pred             HHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCC
Q 040394          404 FETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGL  461 (691)
Q Consensus       404 ~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  461 (691)
                      |+.|...              -+-|+..+...++++....+.++..-+++..++..|.
T Consensus       421 Y~~lVP~--------------~y~p~~~~m~~~lrA~~v~~~~e~ipRiw~D~~~~gh  464 (625)
T KOG4422|consen  421 YEDLVPS--------------AYFPHSQTMIHLLRALDVANRLEVIPRIWKDSKEYGH  464 (625)
T ss_pred             HHHhccc--------------eecCCchhHHHHHHHHhhcCcchhHHHHHHHHHHhhh
Confidence            8888766              4668888888888888888888888888888887774

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

Probab=99.80  E-value=3e-14  Score=145.61  Aligned_cols=592  Identities=12%  Similarity=0.096  Sum_probs=383.9

Q ss_pred             cCchhHHHHHHHHHHhCCCCchhhhHHHHHHhcCCChHHHHHHhccC---CCCCcchHHHHHHHHHhCCChhHHHHHHHH
Q 040394           60 KSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSM---PNPDFYSFQVMIRWYFLNDLYKDIVEFYKC  136 (691)
Q Consensus        60 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~---~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~  136 (691)
                      |+.+.|..+..++++..+.....|..|..+|...|+.+.+...+--.   ...|...|..+.....+.|++++|.-.|.+
T Consensus       153 g~~eeA~~i~~EvIkqdp~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~p~d~e~W~~ladls~~~~~i~qA~~cy~r  232 (895)
T KOG2076|consen  153 GDLEEAEEILMEVIKQDPRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLNPKDYELWKRLADLSEQLGNINQARYCYSR  232 (895)
T ss_pred             CCHHHHHHHHHHHHHhCccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHhcccHHHHHHHHHH
Confidence            99999999999999998877779999999999999999999877543   345667899999999999999999999999


Q ss_pred             HHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCC-ChhHHHHH----HHHhHhcCChHHHHHHHhccCC---
Q 040394          137 MRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGP-DSFVLTGL----VDMYAKCRDIGSSRQVFDETLD---  208 (691)
Q Consensus       137 m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l----~~~~~~~g~~~~A~~~~~~~~~---  208 (691)
                      .++.. +++...+-.-...|-+.|+...|..-|.++....+| |..-...+    +..+...++-+.|.+.++....   
T Consensus       233 AI~~~-p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~~~le~~~s~~~  311 (895)
T KOG2076|consen  233 AIQAN-PSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERAAKALEGALSKEK  311 (895)
T ss_pred             HHhcC-CcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhcc
Confidence            99873 455555555667788999999999999999998886 54444433    5556677888999988887644   


Q ss_pred             --CChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChh----------------------hHH----HHHHHHHccC
Q 040394          209 --KNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQI----------------------TLG----SLVTACAKLR  260 (691)
Q Consensus       209 --~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~----------------------t~~----~li~~~~~~~  260 (691)
                        -+...++.++..+.+...++.|......+......+|..                      .|.    -++-++.+.+
T Consensus       312 ~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v~rl~icL~~L~  391 (895)
T KOG2076|consen  312 DEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRVIRLMICLVHLK  391 (895)
T ss_pred             ccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchhHhHhhhhhccc
Confidence              245678999999999999999999988887622222221                      111    2333445666


Q ss_pred             ChhhHHHHHHHHHHHCCCC--chHHHHHHHHHHHhcCCHHHHHHHHHhcCC----CChhHHHHHHHHHHhcCCchhHHHH
Q 040394          261 ALHQGKWLHGYILKIGIEI--NSHLVTALLDMYVKCGNIRDARSVFDELCS----IDLVSWTAMIVGYTQSGYPDKALKL  334 (691)
Q Consensus       261 ~~~~a~~~~~~~~~~g~~~--~~~~~~~li~~~~~~g~~~~A~~~~~~~~~----~~~~~~~~li~~~~~~g~~~~a~~~  334 (691)
                      ..+....+.....+..+.|  +...|.-+.++|...|++.+|+++|..+..    .+...|--+...|...|.+++|.+.
T Consensus       392 ~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l~e~e~A~e~  471 (895)
T KOG2076|consen  392 ERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMELGEYEEAIEF  471 (895)
T ss_pred             ccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHHhhHHHHHHH
Confidence            6666777777777776444  567899999999999999999999999833    4677899999999999999999999


Q ss_pred             HHHhhHCCCCCcH-HHHHHHHHHHhcCCChhhHHHHHHHHHHhC--------CC-chhHHHHHHHHhHhcCChHHHHHHH
Q 040394          335 FTDKKWADFFPNH-VTIASVLSASAQLGNLNMGRMVHSLGIRLG--------LE-DYTVINALVDMYAKCHVIADARYIF  404 (691)
Q Consensus       335 ~~~m~~~g~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~--------~~-~~~~~~~l~~~~~~~g~~~~a~~~~  404 (691)
                      |+.....  .|+. ..-..|-..+.+.|+.++|.+.++.+...+        .. .........+.+.+.|+.++-..+-
T Consensus       472 y~kvl~~--~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~~~e~ri~~~r~d~l~~~gk~E~fi~t~  549 (895)
T KOG2076|consen  472 YEKVLIL--APDNLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAWEPERRILAHRCDILFQVGKREEFINTA  549 (895)
T ss_pred             HHHHHhc--CCCchhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhccccHHHHHHHHHHHHHHHhhhHHHHHHHH
Confidence            9998875  4544 344455667888999999999988855333        11 3444556677888888887754444


Q ss_pred             HhCCCCCchhHHHHH----------HhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHH------HHHHHcCCCCCch-h
Q 040394          405 ETTSEKDVIAWNSII----------SGLDDNVSPDAVTLVSVISACASLGAVQVGSSLH------AYSTKQGLLSSNV-Y  467 (691)
Q Consensus       405 ~~~~~~~~~~~~~li----------~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~------~~~~~~~~~~~~~-~  467 (691)
                      ..|....  ....++          .+...+..-...+....+.+-.+.++....++-.      .-....+....+. .
T Consensus       550 ~~Lv~~~--~~~~~~f~~~~k~r~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~l~d~~~~~~~e~~~Lsiddwfe  627 (895)
T KOG2076|consen  550 STLVDDF--LKKRYIFPRNKKKRRRAIAGTTSKRYSELLKQIIRAREKATDDNVMEKALSDGTEFRAVELRGLSIDDWFE  627 (895)
T ss_pred             HHHHHHH--HHHHHhcchHHHHHHHhhccccccccchhHHHHHHHHhccCchHHhhhcccchhhhhhhhhccCcHHHHHH
Confidence            3332210  000000          0000011122222223333333333221111111      1111122201111 2


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhcccC-----CHh----HHHHHHHHHhcCCChHHHHHHHHHHHHC-CC--CCCH-HH
Q 040394          468 VGTALLNFYAKCGDAQSARMVFDAMREK-----NTV----TWSAMIGGYGMQGDGGGSLALFSDMLNE-EV--QPNE-VI  534 (691)
Q Consensus       468 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~~~----~~~~li~~~~~~~~~~~A~~~~~~m~~~-g~--~p~~-~~  534 (691)
                      .+.-++..+++.+++++|+.+...+..-     +..    .-...+.+.+..+++..|...++.|+.. ++  .|.. ..
T Consensus       628 l~~e~i~~L~k~~r~qeAl~vv~~a~~~~~f~~~~~~~k~l~~~~l~~s~~~~d~~~a~~~lR~~i~~~~~~~~~~q~~l  707 (895)
T KOG2076|consen  628 LFRELILSLAKLQRVQEALSVVFTALEAYIFFQDSEIRKELQFLGLKASLYARDPGDAFSYLRSVITQFQFYLDVYQLNL  707 (895)
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHhhhhhhccHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhhhhhHHHHH
Confidence            3444555666666666666666655532     111    1223344555566666666666666543 10  1111 11


Q ss_pred             HHHHHHH-----------------------------------hcccCCHHHHHHHHHHchhhcCCCCChhHHHHHH-HHH
Q 040394          535 FTTILSA-----------------------------------CSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMV-DLL  578 (691)
Q Consensus       535 ~~~ll~~-----------------------------------~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li-~~~  578 (691)
                      |+..++.                                   ....+.+..|...+-..   +...|+....+.++ .++
T Consensus       708 ~n~~~s~~~~~~q~v~~~R~~~~~~~~~~~~~~~l~~i~gh~~~~~~s~~~Al~~y~ra---~~~~pd~Pl~nl~lglaf  784 (895)
T KOG2076|consen  708 WNLDFSYFSKYGQRVCYLRLIMRLLVKNKDDTPPLALIYGHNLFVNASFKHALQEYMRA---FRQNPDSPLINLCLGLAF  784 (895)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhccCccCCcceeeeechhHhhccchHHHHHHHHHH---HHhCCCCcHHHHHHHHHH
Confidence            2211111                                   12245566777765533   34567744444332 222


Q ss_pred             H----------hcCChHHHHHHHHhC---C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC-----------
Q 040394          579 A----------RAGRLEEALEFMENM---P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK-----------  633 (691)
Q Consensus       579 ~----------~~g~~~~A~~~~~~~---~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~-----------  633 (691)
                      .          |+-..-.+..++++.   . ......++-.+.++|-.-|=...|..+|++++++.|.+           
T Consensus       785 ih~a~qr~v~~Rh~~i~qG~afL~RY~~lR~~~~~QEa~YNigRayh~~gl~~LA~~YYekvL~~~p~~~~~~~~d~~dL  864 (895)
T KOG2076|consen  785 IHLALQRRVSNRHAQIAQGFAFLKRYKELRRCEEKQEAFYNIGRAYHQIGLVHLAVSYYEKVLEVSPKDVTDPKEDNYDL  864 (895)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHhCCCccccccccCCcccH
Confidence            1          122334556666555   1 11245577779999999999999999999999986543           


Q ss_pred             -chhHHHHHHHHHhCCCcHHHHHHHHH
Q 040394          634 -ACYYVLVSNLYASDGRWIRVNQVREL  659 (691)
Q Consensus       634 -~~~~~~l~~~~~~~g~~~~A~~~~~~  659 (691)
                       ..+-+.|.-+|..+|+.+.|..++++
T Consensus       865 rkeAA~NL~LIY~~SGn~~lArqil~k  891 (895)
T KOG2076|consen  865 RKEAAYNLHLIYKKSGNMQLARQILEK  891 (895)
T ss_pred             HHHHHhhhhhhhccCCcHHHHHHHHHh
Confidence             12345677889999999999998864

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.79  E-value=1.6e-14  Score=155.78  Aligned_cols=438  Identities=9%  Similarity=-0.000  Sum_probs=302.3

Q ss_pred             HcccCChhHHHHHHHHHHHhCCCCh-hHHHHHHHHhHhcCChHHHHHHHhccCCCChh-hHHHH--HHHHHhCCChhHHH
Q 040394          156 CCELRDIDEGMKVHCEIVKVGGPDS-FVLTGLVDMYAKCRDIGSSRQVFDETLDKNVV-SWTSM--IAGYVQNDCAQEGL  231 (691)
Q Consensus       156 ~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~l--i~~~~~~g~~~~A~  231 (691)
                      ..+.|+++.|...|++..+..+.+. .++ .++..+...|+.++|+..+++...|+.. .+..+  ...+...|++++|+
T Consensus        44 ~~r~Gd~~~Al~~L~qaL~~~P~~~~av~-dll~l~~~~G~~~~A~~~~eka~~p~n~~~~~llalA~ly~~~gdyd~Ai  122 (822)
T PRK14574         44 RARAGDTAPVLDYLQEESKAGPLQSGQVD-DWLQIAGWAGRDQEVIDVYERYQSSMNISSRGLASAARAYRNEKRWDQAL  122 (822)
T ss_pred             HHhCCCHHHHHHHHHHHHhhCccchhhHH-HHHHHHHHcCCcHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHH
Confidence            3478888999999999888887753 444 8888888889999999999988776443 33333  45777789999999


Q ss_pred             HHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcC--C
Q 040394          232 VLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELC--S  309 (691)
Q Consensus       232 ~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~--~  309 (691)
                      ++|+++.+.... +...+..++..+...++.++|.+.++.+...  .|+...+..++..+...++..+|++.++++.  .
T Consensus       123 ely~kaL~~dP~-n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~--dp~~~~~l~layL~~~~~~~~~AL~~~ekll~~~  199 (822)
T PRK14574        123 ALWQSSLKKDPT-NPDLISGMIMTQADAGRGGVVLKQATELAER--DPTVQNYMTLSYLNRATDRNYDALQASSEAVRLA  199 (822)
T ss_pred             HHHHHHHhhCCC-CHHHHHHHHHHHhhcCCHHHHHHHHHHhccc--CcchHHHHHHHHHHHhcchHHHHHHHHHHHHHhC
Confidence            999999876433 3455566677777888888888888887665  3455555444444444556656888888872  2


Q ss_pred             C-ChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHH
Q 040394          310 I-DLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALV  388 (691)
Q Consensus       310 ~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~  388 (691)
                      | +...+..++.++.+.|-...|.++..+-... +.|..  ...+-.        +.+.+    .++.+..         
T Consensus       200 P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~-f~~~~--~~~l~~--------~~~a~----~vr~a~~---------  255 (822)
T PRK14574        200 PTSEEVLKNHLEILQRNRIVEPALRLAKENPNL-VSAEH--YRQLER--------DAAAE----QVRMAVL---------  255 (822)
T ss_pred             CCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccc-cCHHH--HHHHHH--------HHHHH----HHhhccc---------
Confidence            3 4556677778888888888888776652211 11111  111100        00000    0110100         


Q ss_pred             HHhHhcC---ChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHH----HHHHHHHHHhccCcHHHHHHHHHHHHHcCC
Q 040394          389 DMYAKCH---VIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAV----TLVSVISACASLGAVQVGSSLHAYSTKQGL  461 (691)
Q Consensus       389 ~~~~~~g---~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~----~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  461 (691)
                      ..-...+   -.+.|+.-++.+...-           . ..++...    +..-.+-++...++..++.+.++.+...+.
T Consensus       256 ~~~~~~~r~~~~d~ala~~~~l~~~~-----------~-~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~  323 (822)
T PRK14574        256 PTRSETERFDIADKALADYQNLLTRW-----------G-KDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGY  323 (822)
T ss_pred             ccccchhhHHHHHHHHHHHHHHHhhc-----------c-CCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCC
Confidence            0000011   1233444444333210           0 1122222    223445677889999999999999999886


Q ss_pred             CCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC---------CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCC----
Q 040394          462 LSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK---------NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEV----  528 (691)
Q Consensus       462 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---------~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~----  528 (691)
                       +....+-..+.++|...+++++|+.+++.+..+         +......|..+|...+++++|..+++++.+.-.    
T Consensus       324 -~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~  402 (822)
T PRK14574        324 -KMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVG  402 (822)
T ss_pred             -CCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEe
Confidence             666778889999999999999999999998542         233357789999999999999999999998311    


Q ss_pred             -------CCC--HHH-HHHHHHHhcccCCHHHHHHHHHHchhhcCCCC-ChhHHHHHHHHHHhcCChHHHHHHHHhC-CC
Q 040394          529 -------QPN--EVI-FTTILSACSHTGMVGEGWKCFYSMCRDFKFVP-SMKHYVCMVDLLARAGRLEEALEFMENM-PI  596 (691)
Q Consensus       529 -------~p~--~~~-~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~  596 (691)
                             .||  -.. +..++..+...|++.+|++.++++..   ..| |......+.+.+...|++.+|++.++.. ..
T Consensus       403 ~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~Ae~~le~l~~---~aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l  479 (822)
T PRK14574        403 VYGLPGKEPNDDWIEGQTLLVQSLVALNDLPTAQKKLEDLSS---TAPANQNLRIALASIYLARDLPRKAEQELKAVESL  479 (822)
T ss_pred             ccCCCCCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhh
Confidence                   122  232 33455678899999999999999854   345 4788889999999999999999999877 45


Q ss_pred             CCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhH
Q 040394          597 EPDV-SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYY  637 (691)
Q Consensus       597 ~p~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~  637 (691)
                      .|+. .+....+..+...|++++|..+.+.+.+..|+++.+-
T Consensus       480 ~P~~~~~~~~~~~~al~l~e~~~A~~~~~~l~~~~Pe~~~~~  521 (822)
T PRK14574        480 APRSLILERAQAETAMALQEWHQMELLTDDVISRSPEDIPSQ  521 (822)
T ss_pred             CCccHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhCCCchhHH
Confidence            6654 5666777788889999999999999999999987544

>KOG2003 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.76  E-value=1.1e-14  Score=136.81  Aligned_cols=203  Identities=12%  Similarity=0.184  Sum_probs=164.5

Q ss_pred             hccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcc---cCCHhHHHHHHHHHhcCCChHHHH
Q 040394          441 ASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMR---EKNTVTWSAMIGGYGMQGDGGGSL  517 (691)
Q Consensus       441 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~A~  517 (691)
                      ...|+++.|...+++....+. ......|| +.-.+.+.|+.++|+..|-++.   ..+......+...|....+...|+
T Consensus       501 f~ngd~dka~~~ykeal~nda-sc~ealfn-iglt~e~~~~ldeald~f~klh~il~nn~evl~qianiye~led~aqai  578 (840)
T KOG2003|consen  501 FANGDLDKAAEFYKEALNNDA-SCTEALFN-IGLTAEALGNLDEALDCFLKLHAILLNNAEVLVQIANIYELLEDPAQAI  578 (840)
T ss_pred             eecCcHHHHHHHHHHHHcCch-HHHHHHHH-hcccHHHhcCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhCHHHHH
Confidence            356788888888888876653 33333333 3445678899999999987765   356777777888888899999999


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcC-CCCChhHHHHHHHHHHhcCChHHHHHHHHhC-C
Q 040394          518 ALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFK-FVPSMKHYVCMVDLLARAGRLEEALEFMENM-P  595 (691)
Q Consensus       518 ~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~-~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~  595 (691)
                      +++.+.... ++.|+.....+...|-+.|+-..|.+.+-.   .+. ++-+..+...|..-|....-+++|+.+|++. -
T Consensus       579 e~~~q~~sl-ip~dp~ilskl~dlydqegdksqafq~~yd---syryfp~nie~iewl~ayyidtqf~ekai~y~ekaal  654 (840)
T KOG2003|consen  579 ELLMQANSL-IPNDPAILSKLADLYDQEGDKSQAFQCHYD---SYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAAL  654 (840)
T ss_pred             HHHHHhccc-CCCCHHHHHHHHHHhhcccchhhhhhhhhh---cccccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHh
Confidence            999877664 455677888888899999999999998763   333 4456888888999999999999999999998 5


Q ss_pred             CCCCHHHHHHHHHHHH-hcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCC
Q 040394          596 IEPDVSLFGAFLHGCG-LYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGR  649 (691)
Q Consensus       596 ~~p~~~~~~~l~~~~~-~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  649 (691)
                      +.|+..-|..++..|. +.|++.+|.+++++..+..|.+......|..++...|.
T Consensus       655 iqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrkfpedldclkflvri~~dlgl  709 (840)
T KOG2003|consen  655 IQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRKFPEDLDCLKFLVRIAGDLGL  709 (840)
T ss_pred             cCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCccchHHHHHHHHHhccccc
Confidence            8899999999998876 68999999999999999999999999999998887774

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

Probab=99.73  E-value=2.8e-11  Score=119.51  Aligned_cols=489  Identities=12%  Similarity=0.079  Sum_probs=386.7

Q ss_pred             HhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHH
Q 040394          122 FLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQ  201 (691)
Q Consensus       122 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  201 (691)
                      ......++|.-++.+..+. ++.+.    -+.-++++..-++.|.++++...+.-+.+..+|.+-...=-..|+.+...+
T Consensus       387 VelE~~~darilL~rAvec-cp~s~----dLwlAlarLetYenAkkvLNkaRe~iptd~~IWitaa~LEE~ngn~~mv~k  461 (913)
T KOG0495|consen  387 VELEEPEDARILLERAVEC-CPQSM----DLWLALARLETYENAKKVLNKAREIIPTDREIWITAAKLEEANGNVDMVEK  461 (913)
T ss_pred             HhccChHHHHHHHHHHHHh-ccchH----HHHHHHHHHHHHHHHHHHHHHHHhhCCCChhHHHHHHHHHHhcCCHHHHHH
Confidence            3456677788888888876 33333    344566777888999999999888766699999888888888899999888


Q ss_pred             HHhccC--------CCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCC--hhhHHHHHHHHHccCChhhHHHHHHH
Q 040394          202 VFDETL--------DKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGN--QITLGSLVTACAKLRALHQGKWLHGY  271 (691)
Q Consensus       202 ~~~~~~--------~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~--~~t~~~li~~~~~~~~~~~a~~~~~~  271 (691)
                      +.++-.        .-|...|-.=...+-..|..--+..+......-|+.-.  ..|+..-...|.+.+.++-|..+|..
T Consensus       462 ii~rgl~~L~~ngv~i~rdqWl~eAe~~e~agsv~TcQAIi~avigigvEeed~~~tw~~da~~~~k~~~~~carAVya~  541 (913)
T KOG0495|consen  462 IIDRGLSELQANGVEINRDQWLKEAEACEDAGSVITCQAIIRAVIGIGVEEEDRKSTWLDDAQSCEKRPAIECARAVYAH  541 (913)
T ss_pred             HHHHHHHHHhhcceeecHHHHHHHHHHHhhcCChhhHHHHHHHHHhhccccchhHhHHhhhHHHHHhcchHHHHHHHHHH
Confidence            887642        12555666666677777888888888888777666532  45788888889999999999999998


Q ss_pred             HHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhc---CCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHH
Q 040394          272 ILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDEL---CSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHV  348 (691)
Q Consensus       272 ~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  348 (691)
                      .++- ++.+..+|...+..--..|..+.-..+|++.   ++.....|-...+.+...|+...|..++....+.... +..
T Consensus       542 alqv-fp~k~slWlra~~~ek~hgt~Esl~Allqkav~~~pkae~lwlM~ake~w~agdv~~ar~il~~af~~~pn-see  619 (913)
T KOG0495|consen  542 ALQV-FPCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQCPKAEILWLMYAKEKWKAGDVPAARVILDQAFEANPN-SEE  619 (913)
T ss_pred             HHhh-ccchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHhCCcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCC-cHH
Confidence            8765 2446678888887777788999999999887   4456667888888888999999999999988876333 567


Q ss_pred             HHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCC
Q 040394          349 TIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSP  428 (691)
Q Consensus       349 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p  428 (691)
                      .+..-+..-.....++.|+.+|......+ ++..+|..-+....-.++.++|.+++++..+.               ++.
T Consensus       620 iwlaavKle~en~e~eraR~llakar~~s-gTeRv~mKs~~~er~ld~~eeA~rllEe~lk~---------------fp~  683 (913)
T KOG0495|consen  620 IWLAAVKLEFENDELERARDLLAKARSIS-GTERVWMKSANLERYLDNVEEALRLLEEALKS---------------FPD  683 (913)
T ss_pred             HHHHHHHHhhccccHHHHHHHHHHHhccC-CcchhhHHHhHHHHHhhhHHHHHHHHHHHHHh---------------CCc
Confidence            78888888889999999999998876632 26677777777888889999999999988764               333


Q ss_pred             CHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-CHhHHHHHHH
Q 040394          429 DAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--K-NTVTWSAMIG  505 (691)
Q Consensus       429 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~li~  505 (691)
                      =...|..+.+.+-+.++++.|...|..-.+.-  |..+..+..|...=.+.|.+-.|..+++...-  | |...|-..|+
T Consensus       684 f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~c--P~~ipLWllLakleEk~~~~~rAR~ildrarlkNPk~~~lwle~Ir  761 (913)
T KOG0495|consen  684 FHKLWLMLGQIEEQMENIEMAREAYLQGTKKC--PNSIPLWLLLAKLEEKDGQLVRARSILDRARLKNPKNALLWLESIR  761 (913)
T ss_pred             hHHHHHHHhHHHHHHHHHHHHHHHHHhccccC--CCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcCCCcchhHHHHHH
Confidence            34567777888889999999999988777665  78888999999999999999999999998763  3 7789999999


Q ss_pred             HHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChH
Q 040394          506 GYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLE  585 (691)
Q Consensus       506 ~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~  585 (691)
                      .-.+.|+.+.|..+..+..+. ++.+...|..-|....+.++-......++      .+.-|.+..-.+...+....+++
T Consensus       762 ~ElR~gn~~~a~~lmakALQe-cp~sg~LWaEaI~le~~~~rkTks~DALk------kce~dphVllaia~lfw~e~k~~  834 (913)
T KOG0495|consen  762 MELRAGNKEQAELLMAKALQE-CPSSGLLWAEAIWLEPRPQRKTKSIDALK------KCEHDPHVLLAIAKLFWSEKKIE  834 (913)
T ss_pred             HHHHcCCHHHHHHHHHHHHHh-CCccchhHHHHHHhccCcccchHHHHHHH------hccCCchhHHHHHHHHHHHHHHH
Confidence            999999999999999888875 55566777777777766666444444444      24667777888888999999999


Q ss_pred             HHHHHHHhC-CCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHH
Q 040394          586 EALEFMENM-PIEPDV-SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSN  642 (691)
Q Consensus       586 ~A~~~~~~~-~~~p~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~  642 (691)
                      +|.+.|.+. ...||. .+|--+..-+.++|.-++-.+++.+....+|.+...|..+..
T Consensus       835 kar~Wf~Ravk~d~d~GD~wa~fykfel~hG~eed~kev~~~c~~~EP~hG~~W~avSK  893 (913)
T KOG0495|consen  835 KAREWFERAVKKDPDNGDAWAWFYKFELRHGTEEDQKEVLKKCETAEPTHGELWQAVSK  893 (913)
T ss_pred             HHHHHHHHHHccCCccchHHHHHHHHHHHhCCHHHHHHHHHHHhccCCCCCcHHHHHhh
Confidence            999999998 666665 578888888899999999999999999999998888876654

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.73  E-value=5.8e-13  Score=124.62  Aligned_cols=421  Identities=12%  Similarity=0.127  Sum_probs=279.1

Q ss_pred             HHHhhc--cCchhHHHHHHHHHHhCCCCch-hhhHHHHH--HhcCCChHHH-HHHhccCCC---CCcchHHHHHHHHHhC
Q 040394           54 NLLGLC--KSTGSLKAFHALLIVDGLTNDK-CNTKLVSM--YGSFGHVKYA-RSVFDSMPN---PDFYSFQVMIRWYFLN  124 (691)
Q Consensus        54 ~ll~~~--~~~~~a~~~~~~~~~~~~~~~~-~~~~l~~~--~~~~g~~~~A-~~~~~~~~~---~~~~~~~~ll~~~~~~  124 (691)
                      +|+.-.  +.+..+--+++.+.+.+.+.++ +-..|.+.  |-...+..-| ++.|-.|..   .+..+|        +.
T Consensus       121 nL~kmIS~~EvKDs~ilY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sW--------K~  192 (625)
T KOG4422|consen  121 NLLKMISSREVKDSCILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSW--------KS  192 (625)
T ss_pred             HHHHHHhhcccchhHHHHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhcccccccccccc--------cc
Confidence            344444  6677788888888888887777 55444432  3333333322 334444542   333344        23


Q ss_pred             CChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCC-ChhHHHHHHHHhHhcCChHHHHHHH
Q 040394          125 DLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGP-DSFVLTGLVDMYAKCRDIGSSRQVF  203 (691)
Q Consensus       125 ~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~  203 (691)
                      |.+.+   +|-+.    .+-+..||.++|.++|+--..+.|.+++++....... +..++|.+|.+-.-..+    .+++
T Consensus       193 G~vAd---L~~E~----~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~Lv  261 (625)
T KOG4422|consen  193 GAVAD---LLFET----LPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKLV  261 (625)
T ss_pred             ccHHH---HHHhh----cCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHHH
Confidence            33332   22222    2446678888888888888888888888887766555 88888888876554433    4455


Q ss_pred             hcc----CCCChhhHHHHHHHHHhCCChhH----HHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhh-HHHHHHHHHH
Q 040394          204 DET----LDKNVVSWTSMIAGYVQNDCAQE----GLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQ-GKWLHGYILK  274 (691)
Q Consensus       204 ~~~----~~~~~~~~~~li~~~~~~g~~~~----A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~-a~~~~~~~~~  274 (691)
                      .+|    ..||..|+|+++.+..+.|+++.    |++++.+|++-|+.|...+|..+|..+++.++..+ +..++.++..
T Consensus       262 ~EMisqkm~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N  341 (625)
T KOG4422|consen  262 AEMISQKMTPNLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQN  341 (625)
T ss_pred             HHHHHhhcCCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHH
Confidence            555    55899999999999999998765    56788999999999999999999999999888755 4444444443


Q ss_pred             ----HCCCC----chHHHHHHHHHHHhcCCHHHHHHHHHhcC--------CCC---hhHHHHHHHHHHhcCCchhHHHHH
Q 040394          275 ----IGIEI----NSHLVTALLDMYVKCGNIRDARSVFDELC--------SID---LVSWTAMIVGYTQSGYPDKALKLF  335 (691)
Q Consensus       275 ----~g~~~----~~~~~~~li~~~~~~g~~~~A~~~~~~~~--------~~~---~~~~~~li~~~~~~g~~~~a~~~~  335 (691)
                          ..++|    |...+..-+..|.+..+.+-|..+-.-+.        .++   ..-|..+....|+....+.-..+|
T Consensus       342 ~ltGK~fkp~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y  421 (625)
T KOG4422|consen  342 SLTGKTFKPITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWY  421 (625)
T ss_pred             hhccCcccCCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                22322    34556777888888888888887765541        122   234666777888888999999999


Q ss_pred             HHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCC-chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchh
Q 040394          336 TDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLE-DYTVINALVDMYAKCHVIADARYIFETTSEKDVIA  414 (691)
Q Consensus       336 ~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~  414 (691)
                      +.|.-.-+-|+..+...++++....|.++-...++..++..|.. ......-++..+++.                    
T Consensus       422 ~~lVP~~y~p~~~~m~~~lrA~~v~~~~e~ipRiw~D~~~~ght~r~~l~eeil~~L~~~--------------------  481 (625)
T KOG4422|consen  422 EDLVPSAYFPHSQTMIHLLRALDVANRLEVIPRIWKDSKEYGHTFRSDLREEILMLLARD--------------------  481 (625)
T ss_pred             HHhccceecCCchhHHHHHHHHhhcCcchhHHHHHHHHHHhhhhhhHHHHHHHHHHHhcC--------------------
Confidence            99999889999999999999999999999999999888877754 333322232222221                    


Q ss_pred             HHHHHHhhhCCCCCCHH---HHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHh
Q 040394          415 WNSIISGLDDNVSPDAV---TLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDA  491 (691)
Q Consensus       415 ~~~li~~~~~~~~p~~~---~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  491 (691)
                                ...|+..   -+.....-|. ..-.+..+..-.++.+.   ...+...+.+.-.+.+.|+.++|.++|..
T Consensus       482 ----------k~hp~tp~r~Ql~~~~ak~a-ad~~e~~e~~~~R~r~~---~~~~t~l~~ia~Ll~R~G~~qkA~e~l~l  547 (625)
T KOG4422|consen  482 ----------KLHPLTPEREQLQVAFAKCA-ADIKEAYESQPIRQRAQ---DWPATSLNCIAILLLRAGRTQKAWEMLGL  547 (625)
T ss_pred             ----------CCCCCChHHHHHHHHHHHHH-HHHHHHHHhhHHHHHhc---cCChhHHHHHHHHHHHcchHHHHHHHHHH
Confidence                      1233322   2222222221 11222223333344444   34566677788889999999999999988


Q ss_pred             ccc-----CCHhHHH---HHHHHHhcCCChHHHHHHHHHHHHCC
Q 040394          492 MRE-----KNTVTWS---AMIGGYGMQGDGGGSLALFSDMLNEE  527 (691)
Q Consensus       492 ~~~-----~~~~~~~---~li~~~~~~~~~~~A~~~~~~m~~~g  527 (691)
                      +.+     |.....|   .++..-.+.+++..|...++-|...+
T Consensus       548 ~~~~~~~ip~~p~lnAm~El~d~a~~~~spsqA~~~lQ~a~~~n  591 (625)
T KOG4422|consen  548 FLRKHNKIPRSPLLNAMAELMDSAKVSNSPSQAIEVLQLASAFN  591 (625)
T ss_pred             HHhcCCcCCCCcchhhHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Confidence            743     2333444   45666677788888888888886654

>KOG4318 consensus Bicoid mRNA stability factor [RNA processing and modification]

Probab=99.70  E-value=2.2e-12  Score=131.42  Aligned_cols=86  Identities=9%  Similarity=0.027  Sum_probs=77.4

Q ss_pred             CChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHH
Q 040394          209 KNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALL  288 (691)
Q Consensus       209 ~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li  288 (691)
                      ++..+|..++.+-.-+|+.+.|..++.+|++.|++.+.+-|-.++-+   .++...+..++.-|.+.|+.|+..|+...+
T Consensus       202 ~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyv  278 (1088)
T KOG4318|consen  202 PTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYV  278 (1088)
T ss_pred             CChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHH
Confidence            78889999999999999999999999999999999998888888776   888899999999999999999999999888


Q ss_pred             HHHHhcCCH
Q 040394          289 DMYVKCGNI  297 (691)
Q Consensus       289 ~~~~~~g~~  297 (691)
                      ..+.++|..
T Consensus       279 ip~l~N~~t  287 (1088)
T KOG4318|consen  279 IPQLSNGQT  287 (1088)
T ss_pred             Hhhhcchhh
Confidence            888776653

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

Probab=99.66  E-value=2e-11  Score=115.93  Aligned_cols=479  Identities=11%  Similarity=0.067  Sum_probs=301.2

Q ss_pred             cCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCC--CCh-hhHHHHHHHHHhCCChhHHHHHHH
Q 040394          159 LRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLD--KNV-VSWTSMIAGYVQNDCAQEGLVLFN  235 (691)
Q Consensus       159 ~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~-~~~~~li~~~~~~g~~~~A~~~~~  235 (691)
                      .+++..|.++|+..+..+..+...|-..+.+=.++..+..|..+|+..+.  |-+ ..|-..+-.--..|++..|.++|+
T Consensus        86 q~e~~RARSv~ERALdvd~r~itLWlkYae~Emknk~vNhARNv~dRAvt~lPRVdqlWyKY~ymEE~LgNi~gaRqife  165 (677)
T KOG1915|consen   86 QKEIQRARSVFERALDVDYRNITLWLKYAEFEMKNKQVNHARNVWDRAVTILPRVDQLWYKYIYMEEMLGNIAGARQIFE  165 (677)
T ss_pred             HHHHHHHHHHHHHHHhcccccchHHHHHHHHHHhhhhHhHHHHHHHHHHHhcchHHHHHHHHHHHHHHhcccHHHHHHHH
Confidence            44455555555555555544555555555555555555555555555322  111 122223333334456666666666


Q ss_pred             HHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCC------
Q 040394          236 RMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCS------  309 (691)
Q Consensus       236 ~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~------  309 (691)
                      +..+  ..|+...+.+.|+.=.+.+.++.|..+++..+-.  .|++..|-.....=.++|....|..+|+...+      
T Consensus       166 rW~~--w~P~eqaW~sfI~fElRykeieraR~IYerfV~~--HP~v~~wikyarFE~k~g~~~~aR~VyerAie~~~~d~  241 (677)
T KOG1915|consen  166 RWME--WEPDEQAWLSFIKFELRYKEIERARSIYERFVLV--HPKVSNWIKYARFEEKHGNVALARSVYERAIEFLGDDE  241 (677)
T ss_pred             HHHc--CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhee--cccHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhhhHH
Confidence            5544  4566666666666666666666666666655432  46666666666666666666666666655422      


Q ss_pred             CChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCc--HHHHHHHHHHHhcCCChhhHH--------HHHHHHHHhCCC
Q 040394          310 IDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPN--HVTIASVLSASAQLGNLNMGR--------MVHSLGIRLGLE  379 (691)
Q Consensus       310 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~t~~~ll~~~~~~~~~~~a~--------~~~~~~~~~~~~  379 (691)
                      -+...+.+...--.+...++.|.-+|+-.++. ++.+  ...|..+...=-+-|+....+        .-++..++.++-
T Consensus       242 ~~e~lfvaFA~fEe~qkE~ERar~iykyAld~-~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk~qYE~~v~~np~  320 (677)
T KOG1915|consen  242 EAEILFVAFAEFEERQKEYERARFIYKYALDH-IPKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRKFQYEKEVSKNPY  320 (677)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhhhHHHHHHHhCCC
Confidence            11123333333334455666666666665554 1111  233444444434445433222        235667777777


Q ss_pred             chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHH-------HHHHHHHHH---hccCcHHHH
Q 040394          380 DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAV-------TLVSVISAC---ASLGAVQVG  449 (691)
Q Consensus       380 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~-------~~~~ll~~~---~~~~~~~~a  449 (691)
                      +..++-..++.-...|+.+...++|++....               ++|-..       .|.-+=-+|   ....+++.+
T Consensus       321 nYDsWfdylrL~e~~g~~~~Ire~yErAIan---------------vpp~~ekr~W~RYIYLWinYalyeEle~ed~ert  385 (677)
T KOG1915|consen  321 NYDSWFDYLRLEESVGDKDRIRETYERAIAN---------------VPPASEKRYWRRYIYLWINYALYEELEAEDVERT  385 (677)
T ss_pred             CchHHHHHHHHHHhcCCHHHHHHHHHHHHcc---------------CCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Confidence            8888888889989999999999999998764               666331       222221222   356799999


Q ss_pred             HHHHHHHHHcCCCCCchhHHHHHHHHH----HhcCCHHHHHHHHHhccc--CCHhHHHHHHHHHhcCCChHHHHHHHHHH
Q 040394          450 SSLHAYSTKQGLLSSNVYVGTALLNFY----AKCGDAQSARMVFDAMRE--KNTVTWSAMIGGYGMQGDGGGSLALFSDM  523 (691)
Q Consensus       450 ~~~~~~~~~~~~~~~~~~~~~~l~~~~----~~~g~~~~A~~~~~~~~~--~~~~~~~~li~~~~~~~~~~~A~~~~~~m  523 (691)
                      .++++...+.  +|....++.-+=-+|    .++.++..|.+++.....  |-..++...|..-.+.++++.+..++++.
T Consensus       386 r~vyq~~l~l--IPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AIG~cPK~KlFk~YIelElqL~efDRcRkLYEkf  463 (677)
T KOG1915|consen  386 RQVYQACLDL--IPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAIGKCPKDKLFKGYIELELQLREFDRCRKLYEKF  463 (677)
T ss_pred             HHHHHHHHhh--cCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHhccCCchhHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            9999999883  377777776654444    477899999999988774  67778888899889999999999999999


Q ss_pred             HHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCHHH
Q 040394          524 LNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PIEPDVSL  602 (691)
Q Consensus       524 ~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~~~  602 (691)
                      ++-+ +-|..+|......-...|+.+.|..+|.-.+....+.-....|...|+.-...|.+++|..+++++ ...+-...
T Consensus       464 le~~-Pe~c~~W~kyaElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYerlL~rt~h~kv  542 (677)
T KOG1915|consen  464 LEFS-PENCYAWSKYAELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARALYERLLDRTQHVKV  542 (677)
T ss_pred             HhcC-hHhhHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHHHHHHhcccchH
Confidence            9853 335577877777777889999999999987655444444567777888888999999999999998 44555557


Q ss_pred             HHHHHHHHH-----hcC-----------CHHHHHHHHHHHHh----cCCCCc--hhHHHHHHHHHhCCCcHHHHHHHHHH
Q 040394          603 FGAFLHGCG-----LYS-----------RFDLGEVMIKKMLE----LHPDKA--CYYVLVSNLYASDGRWIRVNQVRELM  660 (691)
Q Consensus       603 ~~~l~~~~~-----~~g-----------~~~~A~~~~~~~~~----~~p~~~--~~~~~l~~~~~~~g~~~~A~~~~~~~  660 (691)
                      |-++..--.     +.+           ....|..+|+++..    ..|...  .....+-+.-...|...+...+-.+|
T Consensus       543 WisFA~fe~s~~~~~~~~~~~~~e~~~~~~~~AR~iferAn~~~k~~~~KeeR~~LLEaw~~~E~~~G~~~d~~~V~s~m  622 (677)
T KOG1915|consen  543 WISFAKFEASASEGQEDEDLAELEITDENIKRARKIFERANTYLKESTPKEERLMLLEAWKNMEETFGTEGDVERVQSKM  622 (677)
T ss_pred             HHhHHHHhccccccccccchhhhhcchhHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCchhhHHHHHHhc
Confidence            766654332     334           57788999998876    233211  22233334444556655555555554

>KOG4318 consensus Bicoid mRNA stability factor [RNA processing and modification]

Probab=99.66  E-value=8.4e-13  Score=134.47  Aligned_cols=134  Identities=16%  Similarity=0.113  Sum_probs=97.7

Q ss_pred             HHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhCC-----CCCCHHHHHHHHHH
Q 040394          535 FTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMP-----IEPDVSLFGAFLHG  609 (691)
Q Consensus       535 ~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~~-----~~p~~~~~~~l~~~  609 (691)
                      -+.++..|+...+..+++..-+.. +..-+.   ..|..||+.++.....+.|..+.++..     ...|..-+..+.+.
T Consensus       462 ~~ql~l~l~se~n~lK~l~~~eky-e~~lf~---g~ya~Li~l~~~hdkle~Al~~~~e~d~~d~s~~Ld~~~m~~l~dL  537 (1088)
T KOG4318|consen  462 ANQLHLTLNSEYNKLKILCDEEKY-EDLLFA---GLYALLIKLMDLHDKLEYALSFVDEIDTRDESIHLDLPLMTSLQDL  537 (1088)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH-HHHHhh---hHHHHHhhhHHHHHHHHHHHhchhhhcccchhhhcccHhHHHHHHH
Confidence            334555555555555555443333 222222   678899999999999999999999883     34466677888899


Q ss_pred             HHhcCCHHHHHHHHHHHHh---cCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCccCCCeeE
Q 040394          610 CGLYSRFDLGEVMIKKMLE---LHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSL  673 (691)
Q Consensus       610 ~~~~g~~~~A~~~~~~~~~---~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~~~~~~~~  673 (691)
                      +.+.+....+..+++++.+   ..|....+...+.+.....|+.+.-.+..+-+...|+.. +|-.|
T Consensus       538 L~r~~~l~dl~tiL~e~ks~a~n~~~~a~~~f~~lns~a~agqqe~Lkkl~d~lvslgl~e-tgPl~  603 (1088)
T KOG4318|consen  538 LQRLAILYDLSTILYEDKSSAENEPLVAIILFPLLNSGAPAGQQEKLKKLADILVSLGLSE-TGPLW  603 (1088)
T ss_pred             HHHhHHHHHHHHHHhhhhHHhhCCchHHHHHHHHHhhhhhccCHHHHHHHHHHHHHhhhhh-cccce
Confidence            9999999999999999887   344445556666677788899999999999999999877 44433

>KOG2003 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.61  E-value=1.1e-12  Score=123.61  Aligned_cols=458  Identities=12%  Similarity=0.055  Sum_probs=281.8

Q ss_pred             HHHHcccCChhHHHHHHHHHHHhC-CCC-hhHHHHHHHHhHhcCChHHHHHHHhccCC--C--C----hhhHHHHHHHHH
Q 040394          153 LKACCELRDIDEGMKVHCEIVKVG-GPD-SFVLTGLVDMYAKCRDIGSSRQVFDETLD--K--N----VVSWTSMIAGYV  222 (691)
Q Consensus       153 l~~~~~~~~~~~a~~~~~~~~~~~-~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~--~----~~~~~~li~~~~  222 (691)
                      ..-|.......+|...++-+++.. +|+ ...-..+.+.+.+...+.+|++.++...+  |  +    +...+.+.-.+.
T Consensus       208 aqqy~~ndm~~ealntyeiivknkmf~nag~lkmnigni~~kkr~fskaikfyrmaldqvpsink~~rikil~nigvtfi  287 (840)
T KOG2003|consen  208 AQQYEANDMTAEALNTYEIIVKNKMFPNAGILKMNIGNIHFKKREFSKAIKFYRMALDQVPSINKDMRIKILNNIGVTFI  287 (840)
T ss_pred             HHHhhhhHHHHHHhhhhhhhhcccccCCCceeeeeecceeeehhhHHHHHHHHHHHHhhccccchhhHHHHHhhcCeeEE
Confidence            344555556677777777777655 443 23334455667777777777777754422  1  1    224445555667


Q ss_pred             hCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHH
Q 040394          223 QNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARS  302 (691)
Q Consensus       223 ~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~  302 (691)
                      +.|++++|+..|+...+.  .|+-.+-..++-++...|+-++..+.|..|+..-..||..-|-       +..       
T Consensus       288 q~gqy~dainsfdh~m~~--~pn~~a~~nl~i~~f~i~d~ekmkeaf~kli~ip~~~dddkyi-------~~~-------  351 (840)
T KOG2003|consen  288 QAGQYDDAINSFDHCMEE--APNFIAALNLIICAFAIGDAEKMKEAFQKLIDIPGEIDDDKYI-------KEK-------  351 (840)
T ss_pred             ecccchhhHhhHHHHHHh--CccHHhhhhhhhhheecCcHHHHHHHHHHHhcCCCCCCccccc-------CCc-------
Confidence            778888888877776653  3665554455555555677777777777776544334332210       000       


Q ss_pred             HHHhcCCCChhHHHHHH-----HHHHhcC--CchhHHHHHHHhhHCCCCCcHHH-HHHHHHHHhcCCChhhHHHHHHHHH
Q 040394          303 VFDELCSIDLVSWTAMI-----VGYTQSG--YPDKALKLFTDKKWADFFPNHVT-IASVLSASAQLGNLNMGRMVHSLGI  374 (691)
Q Consensus       303 ~~~~~~~~~~~~~~~li-----~~~~~~g--~~~~a~~~~~~m~~~g~~p~~~t-~~~ll~~~~~~~~~~~a~~~~~~~~  374 (691)
                           ..|+....+.-|     +..-+.+  +.++++-.--+++.--+.||-.. +..-+..+-.....+.|..      
T Consensus       352 -----ddp~~~ll~eai~nd~lk~~ek~~ka~aek~i~ta~kiiapvi~~~fa~g~dwcle~lk~s~~~~la~d------  420 (840)
T KOG2003|consen  352 -----DDPDDNLLNEAIKNDHLKNMEKENKADAEKAIITAAKIIAPVIAPDFAAGCDWCLESLKASQHAELAID------  420 (840)
T ss_pred             -----CCcchHHHHHHHhhHHHHHHHHhhhhhHHHHHHHHHHHhccccccchhcccHHHHHHHHHhhhhhhhhh------
Confidence                 112222211111     1111111  11222222222222222333211 1111111111111111111      


Q ss_pred             HhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHH
Q 040394          375 RLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHA  454 (691)
Q Consensus       375 ~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~  454 (691)
                              .--.-...|.+.|+++.|.++++-..++|..+-            .-..+-.+.+.-+....++..|.++-+
T Consensus       421 --------lei~ka~~~lk~~d~~~aieilkv~~~kdnk~~------------saaa~nl~~l~flqggk~~~~aqqyad  480 (840)
T KOG2003|consen  421 --------LEINKAGELLKNGDIEGAIEILKVFEKKDNKTA------------SAAANNLCALRFLQGGKDFADAQQYAD  480 (840)
T ss_pred             --------hhhhHHHHHHhccCHHHHHHHHHHHHhccchhh------------HHHhhhhHHHHHHhcccchhHHHHHHH
Confidence                    111223457789999999999988876642111            111111222333333446777777777


Q ss_pred             HHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHH---HHHHhcCCChHHHHHHHHHHHHCCCCCC
Q 040394          455 YSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAM---IGGYGMQGDGGGSLALFSDMLNEEVQPN  531 (691)
Q Consensus       455 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~l---i~~~~~~~~~~~A~~~~~~m~~~g~~p~  531 (691)
                      .....+  .-++.....-.+.-...|+++.|...+.+....|...-.+|   .-.+-..|+.++|++.|-++..- +..+
T Consensus       481 ~aln~d--ryn~~a~~nkgn~~f~ngd~dka~~~ykeal~ndasc~ealfniglt~e~~~~ldeald~f~klh~i-l~nn  557 (840)
T KOG2003|consen  481 IALNID--RYNAAALTNKGNIAFANGDLDKAAEFYKEALNNDASCTEALFNIGLTAEALGNLDEALDCFLKLHAI-LLNN  557 (840)
T ss_pred             HHhccc--ccCHHHhhcCCceeeecCcHHHHHHHHHHHHcCchHHHHHHHHhcccHHHhcCHHHHHHHHHHHHHH-HHhh
Confidence            666554  34444444444445567999999999999998776544443   33567789999999999888763 3445


Q ss_pred             HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHh-CC-CCCCHHHHHHHHH
Q 040394          532 EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMEN-MP-IEPDVSLFGAFLH  608 (691)
Q Consensus       532 ~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~-~~-~~p~~~~~~~l~~  608 (691)
                      ......+...|....+...|++++-+.   ..+.|+ +.+..-|.+.|-+.|+-..|.+..-. .. ++.+..+...|..
T Consensus       558 ~evl~qianiye~led~aqaie~~~q~---~slip~dp~ilskl~dlydqegdksqafq~~ydsyryfp~nie~iewl~a  634 (840)
T KOG2003|consen  558 AEVLVQIANIYELLEDPAQAIELLMQA---NSLIPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRYFPCNIETIEWLAA  634 (840)
T ss_pred             HHHHHHHHHHHHHhhCHHHHHHHHHHh---cccCCCCHHHHHHHHHHhhcccchhhhhhhhhhcccccCcchHHHHHHHH
Confidence            667777778888889999999998755   245555 88999999999999999999887544 44 5557778888888


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          609 GCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       609 ~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      .|....=+++++.+|+++--+.|+....-..++.++.+.|+|.+|.++++.+.+.
T Consensus       635 yyidtqf~ekai~y~ekaaliqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrk  689 (840)
T KOG2003|consen  635 YYIDTQFSEKAINYFEKAALIQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRK  689 (840)
T ss_pred             HHHhhHHHHHHHHHHHHHHhcCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHh
Confidence            8988888999999999999999997777778888999999999999999988764

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

Probab=99.58  E-value=1.6e-12  Score=117.49  Aligned_cols=303  Identities=12%  Similarity=0.093  Sum_probs=222.2

Q ss_pred             hhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhcc
Q 040394          364 NMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASL  443 (691)
Q Consensus       364 ~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~  443 (691)
                      ++|...|-++.+..+.+..+.-+|.+.|.+.|..|.|+.+-..+.++...++           .--....-.|..-|...
T Consensus        52 dKAvdlF~e~l~~d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~-----------~qr~lAl~qL~~Dym~a  120 (389)
T COG2956          52 DKAVDLFLEMLQEDPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTF-----------EQRLLALQQLGRDYMAA  120 (389)
T ss_pred             chHHHHHHHHHhcCchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCch-----------HHHHHHHHHHHHHHHHh
Confidence            3333333333333333444456677777777777777777776654411000           00112445566778888


Q ss_pred             CcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCH--------hHHHHHHHHHhcCCChHH
Q 040394          444 GAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNT--------VTWSAMIGGYGMQGDGGG  515 (691)
Q Consensus       444 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~--------~~~~~li~~~~~~~~~~~  515 (691)
                      |-+|.|+.+|..+.+.+  .--......|+..|-...+|++|..+-+++.+-+.        ..|..|...+....+.+.
T Consensus       121 Gl~DRAE~~f~~L~de~--efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~  198 (389)
T COG2956         121 GLLDRAEDIFNQLVDEG--EFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDR  198 (389)
T ss_pred             hhhhHHHHHHHHHhcch--hhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHH
Confidence            89999999999888866  45666778889999999999999999887764322        256667777778899999


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHH-HhcccCCHHHHHHHHHHchhhcCCCCC--hhHHHHHHHHHHhcCChHHHHHHHH
Q 040394          516 SLALFSDMLNEEVQPNEVIFTTILS-ACSHTGMVGEGWKCFYSMCRDFKFVPS--MKHYVCMVDLLARAGRLEEALEFME  592 (691)
Q Consensus       516 A~~~~~~m~~~g~~p~~~~~~~ll~-~~~~~g~~~~A~~~~~~m~~~~~~~p~--~~~~~~li~~~~~~g~~~~A~~~~~  592 (691)
                      |..++.+..+.  .|+.+--++++. .....|+++.|.+.++.+.+.   .|+  ..+...|..+|...|+.++...++.
T Consensus       199 A~~~l~kAlqa--~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQ---n~~yl~evl~~L~~~Y~~lg~~~~~~~fL~  273 (389)
T COG2956         199 ARELLKKALQA--DKKCVRASIILGRVELAKGDYQKAVEALERVLEQ---NPEYLSEVLEMLYECYAQLGKPAEGLNFLR  273 (389)
T ss_pred             HHHHHHHHHhh--CccceehhhhhhHHHHhccchHHHHHHHHHHHHh---ChHHHHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence            99999999885  566655555554 778899999999999988543   454  6788889999999999999999998


Q ss_pred             hC-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHH---hCCCcHHHHHHHHHHHhCCCccC
Q 040394          593 NM-PIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYA---SDGRWIRVNQVRELMKQRGLSKS  668 (691)
Q Consensus       593 ~~-~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~---~~g~~~~A~~~~~~~~~~g~~~~  668 (691)
                      ++ ...++...-..+...-....-.+.|...+.+-+...|+ ...+..+.....   +.|.+.+..-.++.|...-++..
T Consensus       274 ~~~~~~~g~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~r~Pt-~~gf~rl~~~~l~daeeg~~k~sL~~lr~mvge~l~~~  352 (389)
T COG2956         274 RAMETNTGADAELMLADLIELQEGIDAAQAYLTRQLRRKPT-MRGFHRLMDYHLADAEEGRAKESLDLLRDMVGEQLRRK  352 (389)
T ss_pred             HHHHccCCccHHHHHHHHHHHhhChHHHHHHHHHHHhhCCc-HHHHHHHHHhhhccccccchhhhHHHHHHHHHHHHhhc
Confidence            87 55566666666666656666678889999998999999 444444444332   44668888999999999999999


Q ss_pred             CCeeEEEeCCeeeEEee
Q 040394          669 PGCSLVDLDIANDFSFS  685 (691)
Q Consensus       669 ~~~~~~~~~~~~~~~~~  685 (691)
                      |.+..-+++..+|+|+-
T Consensus       353 ~~YRC~~CGF~a~~l~W  369 (389)
T COG2956         353 PRYRCQNCGFTAHTLYW  369 (389)
T ss_pred             CCceecccCCcceeeee
Confidence            99999999999999974

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

Probab=99.58  E-value=4e-10  Score=107.36  Aligned_cols=454  Identities=11%  Similarity=0.108  Sum_probs=337.4

Q ss_pred             HHHHHHHHhHhcCChHHHHHHHhccCC---CChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChh-hHHHHHHHHH
Q 040394          182 VLTGLVDMYAKCRDIGSSRQVFDETLD---KNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQI-TLGSLVTACA  257 (691)
Q Consensus       182 ~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~-t~~~li~~~~  257 (691)
                      .|-....-=...+++..|..+|+....   +++..|-.-+..-.++..+..|..++++....  -|-+. .+---+..=-
T Consensus        75 ~WikYaqwEesq~e~~RARSv~ERALdvd~r~itLWlkYae~Emknk~vNhARNv~dRAvt~--lPRVdqlWyKY~ymEE  152 (677)
T KOG1915|consen   75 VWIKYAQWEESQKEIQRARSVFERALDVDYRNITLWLKYAEFEMKNKQVNHARNVWDRAVTI--LPRVDQLWYKYIYMEE  152 (677)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHhhhhHhHHHHHHHHHHHh--cchHHHHHHHHHHHHH
Confidence            333333333456778889999998755   57778888888889999999999999998763  34332 2333333345


Q ss_pred             ccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhc--CCCChhHHHHHHHHHHhcCCchhHHHHH
Q 040394          258 KLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDEL--CSIDLVSWTAMIVGYTQSGYPDKALKLF  335 (691)
Q Consensus       258 ~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~--~~~~~~~~~~li~~~~~~g~~~~a~~~~  335 (691)
                      ..|++..|.++|+...+  ..|+...|++.|+.=.+-+.++.|..+++..  +.|++.+|--...--.++|+...+..+|
T Consensus       153 ~LgNi~gaRqiferW~~--w~P~eqaW~sfI~fElRykeieraR~IYerfV~~HP~v~~wikyarFE~k~g~~~~aR~Vy  230 (677)
T KOG1915|consen  153 MLGNIAGARQIFERWME--WEPDEQAWLSFIKFELRYKEIERARSIYERFVLVHPKVSNWIKYARFEEKHGNVALARSVY  230 (677)
T ss_pred             HhcccHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHheecccHHHHHHHHHHHHhcCcHHHHHHHH
Confidence            67999999999998865  5899999999999999999999999999986  7799999988888888999999999999


Q ss_pred             HHhhHC-CC-CCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCC--chhHHHHHHHHhHhcCChHHHHHHH-------
Q 040394          336 TDKKWA-DF-FPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLE--DYTVINALVDMYAKCHVIADARYIF-------  404 (691)
Q Consensus       336 ~~m~~~-g~-~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~a~~~~-------  404 (691)
                      ....+. |- .-+...|.+....=..+..++.|..++..+++.-+.  ....|..+...--+-|+.....+..       
T Consensus       231 erAie~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk~q  310 (677)
T KOG1915|consen  231 ERAIEFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYALDHIPKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRKFQ  310 (677)
T ss_pred             HHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhhhH
Confidence            887664 11 112334444444455677889999999999998887  5777777777777777765544332       


Q ss_pred             -HhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCch--hHHHHHHHH------
Q 040394          405 -ETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNV--YVGTALLNF------  475 (691)
Q Consensus       405 -~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--~~~~~l~~~------  475 (691)
                       +.+.+.               -+-|-.+|--.+..-...|+.+...++++..+..-  ||-.  ..+.-.|..      
T Consensus       311 YE~~v~~---------------np~nYDsWfdylrL~e~~g~~~~Ire~yErAIanv--pp~~ekr~W~RYIYLWinYal  373 (677)
T KOG1915|consen  311 YEKEVSK---------------NPYNYDSWFDYLRLEESVGDKDRIRETYERAIANV--PPASEKRYWRRYIYLWINYAL  373 (677)
T ss_pred             HHHHHHh---------------CCCCchHHHHHHHHHHhcCCHHHHHHHHHHHHccC--CchhHHHHHHHHHHHHHHHHH
Confidence             222222               34566788888888888899999999999999876  3421  122222211      


Q ss_pred             --HHhcCCHHHHHHHHHhccc--C-CHhH----HHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccC
Q 040394          476 --YAKCGDAQSARMVFDAMRE--K-NTVT----WSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTG  546 (691)
Q Consensus       476 --~~~~g~~~~A~~~~~~~~~--~-~~~~----~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g  546 (691)
                        =....+.+.+.++|+...+  | ...|    |-....-..++.+...|.+++...+  |.-|...+|...|..-.+.+
T Consensus       374 yeEle~ed~ertr~vyq~~l~lIPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AI--G~cPK~KlFk~YIelElqL~  451 (677)
T KOG1915|consen  374 YEELEAEDVERTRQVYQACLDLIPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAI--GKCPKDKLFKGYIELELQLR  451 (677)
T ss_pred             HHHHHhhhHHHHHHHHHHHHhhcCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHh--ccCCchhHHHHHHHHHHHHh
Confidence              1246788889999987764  2 2233    4444555567899999999999876  57899999999999999999


Q ss_pred             CHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHH----HHHHHHHHHHhcCCHHHHHH
Q 040394          547 MVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENMPIEPDVS----LFGAFLHGCGLYSRFDLGEV  621 (691)
Q Consensus       547 ~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~----~~~~l~~~~~~~g~~~~A~~  621 (691)
                      .+|.+..++++.+   ...|. ..+|......-...|+.+.|..+|.-+-..|...    .|.+.|.--...|.++.|..
T Consensus       452 efDRcRkLYEkfl---e~~Pe~c~~W~kyaElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~  528 (677)
T KOG1915|consen  452 EFDRCRKLYEKFL---EFSPENCYAWSKYAELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARA  528 (677)
T ss_pred             hHHHHHHHHHHHH---hcChHhhHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHH
Confidence            9999999999874   45664 6778777777788899999999999985455433    45555555567899999999


Q ss_pred             HHHHHHhcCCCCchhHHHHHHHHH-----hCC-----------CcHHHHHHHHHHHh
Q 040394          622 MIKKMLELHPDKACYYVLVSNLYA-----SDG-----------RWIRVNQVRELMKQ  662 (691)
Q Consensus       622 ~~~~~~~~~p~~~~~~~~l~~~~~-----~~g-----------~~~~A~~~~~~~~~  662 (691)
                      +++++++..+. ..+|...+..-.     ..|           +...|..+|++...
T Consensus       529 LYerlL~rt~h-~kvWisFA~fe~s~~~~~~~~~~~~~e~~~~~~~~AR~iferAn~  584 (677)
T KOG1915|consen  529 LYERLLDRTQH-VKVWISFAKFEASASEGQEDEDLAELEITDENIKRARKIFERANT  584 (677)
T ss_pred             HHHHHHHhccc-chHHHhHHHHhccccccccccchhhhhcchhHHHHHHHHHHHHHH
Confidence            99999998888 447777776555     444           56678888877654

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

Probab=99.58  E-value=9.3e-12  Score=121.18  Aligned_cols=262  Identities=15%  Similarity=0.055  Sum_probs=207.1

Q ss_pred             chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHc
Q 040394          380 DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQ  459 (691)
Q Consensus       380 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  459 (691)
                      +..+.....+-+...+++.+..++++.+.+.|               +++...+..-|.++...|+..+-..+-..+++.
T Consensus       243 ~~dll~~~ad~~y~~c~f~~c~kit~~lle~d---------------pfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~  307 (611)
T KOG1173|consen  243 NLDLLAEKADRLYYGCRFKECLKITEELLEKD---------------PFHLPCLPLHIACLYELGKSNKLFLLSHKLVDL  307 (611)
T ss_pred             cHHHHHHHHHHHHHcChHHHHHHHhHHHHhhC---------------CCCcchHHHHHHHHHHhcccchHHHHHHHHHHh
Confidence            66666777788888899999999999988875               445555555566777888877777777778777


Q ss_pred             CCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC---CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHH-HH
Q 040394          460 GLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK---NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEV-IF  535 (691)
Q Consensus       460 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~-~~  535 (691)
                      -  |..+.+|-++.-.|...|+.++|.+.|.+...-   =...|-.+...|+-.|..++|+..+...-+.  -|... .+
T Consensus       308 y--P~~a~sW~aVg~YYl~i~k~seARry~SKat~lD~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl--~~G~hlP~  383 (611)
T KOG1173|consen  308 Y--PSKALSWFAVGCYYLMIGKYSEARRYFSKATTLDPTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARL--MPGCHLPS  383 (611)
T ss_pred             C--CCCCcchhhHHHHHHHhcCcHHHHHHHHHHhhcCccccHHHHHHhHHhhhcchHHHHHHHHHHHHHh--ccCCcchH
Confidence            6  788888889988888899999999999876643   3468999999999999999999988887763  23221 22


Q ss_pred             HHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhCC-----CCC----CHHHHHH
Q 040394          536 TTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENMP-----IEP----DVSLFGA  605 (691)
Q Consensus       536 ~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~~-----~~p----~~~~~~~  605 (691)
                      -.+---|.+.++.+.|.++|.+.   .++.|+ +...+-+.-+....+.+.+|..+|+..-     ..+    =..+++.
T Consensus       384 LYlgmey~~t~n~kLAe~Ff~~A---~ai~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~N  460 (611)
T KOG1173|consen  384 LYLGMEYMRTNNLKLAEKFFKQA---LAIAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNN  460 (611)
T ss_pred             HHHHHHHHHhccHHHHHHHHHHH---HhcCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHh
Confidence            22333677889999999999844   477776 6677777777778889999999888771     111    2346788


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          606 FLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       606 l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      |..+|.+.+.+++|+..+++++.+.|.++.++..++.+|.-.|+++.|++.|.+.+..
T Consensus       461 LGH~~Rkl~~~~eAI~~~q~aL~l~~k~~~~~asig~iy~llgnld~Aid~fhKaL~l  518 (611)
T KOG1173|consen  461 LGHAYRKLNKYEEAIDYYQKALLLSPKDASTHASIGYIYHLLGNLDKAIDHFHKALAL  518 (611)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcChHHHHHHHHHHHhc
Confidence            8899999999999999999999999999999999999999999999999999887653

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

Probab=99.57  E-value=9.4e-15  Score=141.79  Aligned_cols=257  Identities=15%  Similarity=0.148  Sum_probs=113.4

Q ss_pred             HHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHH-HHHHHHhccCcHHHHHHHHHHHHHcCCCCC
Q 040394          386 ALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLV-SVISACASLGAVQVGSSLHAYSTKQGLLSS  464 (691)
Q Consensus       386 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~-~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~  464 (691)
                      .+...+.+.|++++|.+++++....              ..+|+...|- .+...+...++.+.|...++.+...+  +.
T Consensus        13 ~~A~~~~~~~~~~~Al~~L~~~~~~--------------~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~--~~   76 (280)
T PF13429_consen   13 RLARLLYQRGDYEKALEVLKKAAQK--------------IAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASD--KA   76 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccccccccccccccccccccccc--------------ccccccccccccccccccccccccccccccccccccc--cc
Confidence            4577888899999999999654433              1135554444 44556667899999999999999887  56


Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhccc--CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCC-CCCCHHHHHHHHHH
Q 040394          465 NVYVGTALLNFYAKCGDAQSARMVFDAMRE--KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEE-VQPNEVIFTTILSA  541 (691)
Q Consensus       465 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g-~~p~~~~~~~ll~~  541 (691)
                      ++..+..++.. ...+++++|..++...-+  ++...+..++..+...++++++.++++++.... .+++...|..+...
T Consensus        77 ~~~~~~~l~~l-~~~~~~~~A~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~  155 (280)
T PF13429_consen   77 NPQDYERLIQL-LQDGDPEEALKLAEKAYERDGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEI  155 (280)
T ss_dssp             ------------------------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHH
T ss_pred             ccccccccccc-cccccccccccccccccccccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHH
Confidence            77778888887 789999999999887643  466778888899999999999999999987643 34566677778888


Q ss_pred             hcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC--CCCCCHHHHHHHHHHHHhcCCHHH
Q 040394          542 CSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM--PIEPDVSLFGAFLHGCGLYSRFDL  618 (691)
Q Consensus       542 ~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~--~~~p~~~~~~~l~~~~~~~g~~~~  618 (691)
                      +.+.|+.++|.+.+++.++   ..|+ ......++..+...|+.+++.++++..  ..+.|...|..+..++...|+.++
T Consensus       156 ~~~~G~~~~A~~~~~~al~---~~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~  232 (280)
T PF13429_consen  156 YEQLGDPDKALRDYRKALE---LDPDDPDARNALAWLLIDMGDYDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEE  232 (280)
T ss_dssp             HHHCCHHHHHHHHHHHHHH---H-TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHH
T ss_pred             HHHcCCHHHHHHHHHHHHH---cCCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCcCHHHHHHHHHHHhcccccccc
Confidence            9999999999999997754   4676 778888999999999999988888777  234566678899999999999999


Q ss_pred             HHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          619 GEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       619 A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      |...++++.+.+|+|+.....++.++...|+.++|.+++++..+
T Consensus       233 Al~~~~~~~~~~p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~~~  276 (280)
T PF13429_consen  233 ALEYLEKALKLNPDDPLWLLAYADALEQAGRKDEALRLRRQALR  276 (280)
T ss_dssp             HHHHHHHHHHHSTT-HHHHHHHHHHHT-----------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccc
Confidence            99999999999999999999999999999999999999887754

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

Probab=99.56  E-value=1.4e-11  Score=117.52  Aligned_cols=213  Identities=14%  Similarity=0.135  Sum_probs=151.5

Q ss_pred             ccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHH
Q 040394          442 SLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLA  518 (691)
Q Consensus       442 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~  518 (691)
                      -.|+.-.+..-|+..++..  +.+...|--+..+|....+.++..+.|++..+   .|..+|..-...+.-.+++++|..
T Consensus       338 L~g~~~~a~~d~~~~I~l~--~~~~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~flL~q~e~A~a  415 (606)
T KOG0547|consen  338 LKGDSLGAQEDFDAAIKLD--PAFNSLYIKRAAAYADENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFLLQQYEEAIA  415 (606)
T ss_pred             hcCCchhhhhhHHHHHhcC--cccchHHHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHHHHHHHHHHH
Confidence            3567777777777777776  34444466666777888888888888877664   255667666666666777888888


Q ss_pred             HHHHHHHCCCCCCH-HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CC
Q 040394          519 LFSDMLNEEVQPNE-VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PI  596 (691)
Q Consensus       519 ~~~~m~~~g~~p~~-~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~  596 (691)
                      =|++.++  +.|+. ..|.-+--+..+.+.++++...|++..++  ++.-+..|+.....+...+++++|.+.|+.. ..
T Consensus       416 DF~Kai~--L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk--FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~L  491 (606)
T KOG0547|consen  416 DFQKAIS--LDPENAYAYIQLCCALYRQHKIAESMKTFEEAKKK--FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIEL  491 (606)
T ss_pred             HHHHHhh--cChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhh
Confidence            8888776  34543 34444444555777888888888887554  3334677888888888888888888888876 44


Q ss_pred             CCC---------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHH
Q 040394          597 EPD---------VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMK  661 (691)
Q Consensus       597 ~p~---------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  661 (691)
                      .|+         +.+...++.. .-.+|+..|.++++++.+++|.....+..|+.+..++|+.++|+++|++-.
T Consensus       492 E~~~~~~~v~~~plV~Ka~l~~-qwk~d~~~a~~Ll~KA~e~Dpkce~A~~tlaq~~lQ~~~i~eAielFEksa  564 (606)
T KOG0547|consen  492 EPREHLIIVNAAPLVHKALLVL-QWKEDINQAENLLRKAIELDPKCEQAYETLAQFELQRGKIDEAIELFEKSA  564 (606)
T ss_pred             ccccccccccchhhhhhhHhhh-chhhhHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            443         2222222222 234899999999999999999988899999999999999999999988754

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.55  E-value=9.6e-12  Score=126.34  Aligned_cols=216  Identities=7%  Similarity=-0.008  Sum_probs=127.6

Q ss_pred             HHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC---CH--------hHHHHHHHH
Q 040394          438 SACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK---NT--------VTWSAMIGG  506 (691)
Q Consensus       438 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~--------~~~~~li~~  506 (691)
                      ..+...|+.+.|...++.+.+..  |.++.....+...|.+.|++++|.+++..+.+.   +.        ..|..++..
T Consensus       161 ~l~l~~g~~~~Al~~l~~~~~~~--P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~  238 (398)
T PRK10747        161 RIQLARNENHAARHGVDKLLEVA--PRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQ  238 (398)
T ss_pred             HHHHHCCCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH
Confidence            34445555555555555555555  455555556666666666666666665555532   11        122233333


Q ss_pred             HhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHH
Q 040394          507 YGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEE  586 (691)
Q Consensus       507 ~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~  586 (691)
                      .....+.+...++++.+-+. .+.+......+..++...|+.++|.+.+++..+   ..|+....  ++.+....++.++
T Consensus       239 ~~~~~~~~~l~~~w~~lp~~-~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~---~~~~~~l~--~l~~~l~~~~~~~  312 (398)
T PRK10747        239 AMADQGSEGLKRWWKNQSRK-TRHQVALQVAMAEHLIECDDHDTAQQIILDGLK---RQYDERLV--LLIPRLKTNNPEQ  312 (398)
T ss_pred             HHHhcCHHHHHHHHHhCCHH-HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh---cCCCHHHH--HHHhhccCCChHH
Confidence            33344445555555554332 234555666666677777777777777765532   23443221  2233344577777


Q ss_pred             HHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          587 ALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       587 A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      +++..++. ...| |...+..+...|.+.+++++|...|+++.+..|+ ...+..++.++.+.|+.++|.+.+++-+.
T Consensus       313 al~~~e~~lk~~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~-~~~~~~La~~~~~~g~~~~A~~~~~~~l~  389 (398)
T PRK10747        313 LEKVLRQQIKQHGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQRPD-AYDYAWLADALDRLHKPEEAAAMRRDGLM  389 (398)
T ss_pred             HHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            77777766 3334 3445667777777888888888888888888877 45556777788888888888777776644

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.54  E-value=1.1e-11  Score=125.97  Aligned_cols=284  Identities=12%  Similarity=0.039  Sum_probs=200.5

Q ss_pred             cCCHHHHHHHHHhcCCC--Chh-HHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHH--HHHHHHhcCCChhhHHH
Q 040394          294 CGNIRDARSVFDELCSI--DLV-SWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIA--SVLSASAQLGNLNMGRM  368 (691)
Q Consensus       294 ~g~~~~A~~~~~~~~~~--~~~-~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~--~ll~~~~~~~~~~~a~~  368 (691)
                      .|+++.|.+.+......  +.. .|-....+..+.|+++.|.+.+.++.+.  .|+.....  .....+...|+++.|..
T Consensus        97 eGd~~~A~k~l~~~~~~~~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~~Al~  174 (398)
T PRK10747         97 EGDYQQVEKLMTRNADHAEQPVVNYLLAAEAAQQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENHAARH  174 (398)
T ss_pred             CCCHHHHHHHHHHHHhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHHHHHH
Confidence            58888888888776432  222 3333334457889999999999998764  55654333  33457888899999999


Q ss_pred             HHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHH
Q 040394          369 VHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQV  448 (691)
Q Consensus       369 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~  448 (691)
                      .++...+..|.++.+...+...|.+.|++++|..++..+.+..              .. +......+-           
T Consensus       175 ~l~~~~~~~P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~--------------~~-~~~~~~~l~-----------  228 (398)
T PRK10747        175 GVDKLLEVAPRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAH--------------VG-DEEHRAMLE-----------  228 (398)
T ss_pred             HHHHHHhcCCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcC--------------CC-CHHHHHHHH-----------
Confidence            9999999998899999999999999999999999999988762              11 111111000           


Q ss_pred             HHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHH
Q 040394          449 GSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLN  525 (691)
Q Consensus       449 a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~  525 (691)
                                       ...|..++.......+.+...++++.+.+   .++.....+...+...|+.++|.+++++..+
T Consensus       229 -----------------~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~  291 (398)
T PRK10747        229 -----------------QQAWIGLMDQAMADQGSEGLKRWWKNQSRKTRHQVALQVAMAEHLIECDDHDTAQQIILDGLK  291 (398)
T ss_pred             -----------------HHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence                             01111222222223344555555555543   3666777778888888888888888888877


Q ss_pred             CCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCHHHH
Q 040394          526 EEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEPDVSLF  603 (691)
Q Consensus       526 ~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~~~~  603 (691)
                      .  .|+....  ++.+....++.+++.+..+...+.   .|+ ...+..+...+.+.|++++|.+.|++. ...|+...+
T Consensus       292 ~--~~~~~l~--~l~~~l~~~~~~~al~~~e~~lk~---~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~~~~~  364 (398)
T PRK10747        292 R--QYDERLV--LLIPRLKTNNPEQLEKVLRQQIKQ---HGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQRPDAYDY  364 (398)
T ss_pred             c--CCCHHHH--HHHhhccCCChHHHHHHHHHHHhh---CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCHHHH
Confidence            3  5555322  233444568888888888877543   454 556778888888999999999998888 777888888


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhc
Q 040394          604 GAFLHGCGLYSRFDLGEVMIKKMLEL  629 (691)
Q Consensus       604 ~~l~~~~~~~g~~~~A~~~~~~~~~~  629 (691)
                      ..+...+.+.|+.++|.+++++.+.+
T Consensus       365 ~~La~~~~~~g~~~~A~~~~~~~l~~  390 (398)
T PRK10747        365 AWLADALDRLHKPEEAAAMRRDGLML  390 (398)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            88888899999999999999988774

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

Probab=99.51  E-value=4.5e-11  Score=114.24  Aligned_cols=337  Identities=11%  Similarity=-0.014  Sum_probs=199.2

Q ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHHcCCCCC-cchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHh
Q 040394          114 FQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHD-NFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAK  192 (691)
Q Consensus       114 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~  192 (691)
                      +-...+-|.++|.+++|++.|.+.++.  .|+ +.-|.....+|...|+++++.+--...++..|.-+.++..-..++-.
T Consensus       118 lK~~GN~~f~~kkY~eAIkyY~~AI~l--~p~epiFYsNraAcY~~lgd~~~Vied~TkALEl~P~Y~KAl~RRA~A~E~  195 (606)
T KOG0547|consen  118 LKTKGNKFFRNKKYDEAIKYYTQAIEL--CPDEPIFYSNRAACYESLGDWEKVIEDCTKALELNPDYVKALLRRASAHEQ  195 (606)
T ss_pred             HHhhhhhhhhcccHHHHHHHHHHHHhc--CCCCchhhhhHHHHHHHHhhHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHh
Confidence            344556778899999999999999986  677 67788888899999999999999998888887788888888899999


Q ss_pred             cCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHH---------HHhCC--CCCChhhHHHHHHHHHcc--
Q 040394          193 CRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNR---------MREGF--VEGNQITLGSLVTACAKL--  259 (691)
Q Consensus       193 ~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~---------m~~~~--~~p~~~t~~~li~~~~~~--  259 (691)
                      .|++++|+.=+         |-.++..++..+.-..-+.+++++         |.+++  +-|......+....+...  
T Consensus       196 lg~~~eal~D~---------tv~ci~~~F~n~s~~~~~eR~Lkk~a~~ka~e~~k~nr~p~lPS~~fi~syf~sF~~~~~  266 (606)
T KOG0547|consen  196 LGKFDEALFDV---------TVLCILEGFQNASIEPMAERVLKKQAMKKAKEKLKENRPPVLPSATFIASYFGSFHADPK  266 (606)
T ss_pred             hccHHHHHHhh---------hHHHHhhhcccchhHHHHHHHHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHhhcccccc
Confidence            99999885322         222222222222211222222221         22122  335554444444433211  


Q ss_pred             ----CChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHh-cCCHHHHHHHHHhc--------CCC--Ch------hHHHHH
Q 040394          260 ----RALHQGKWLHGYILKIGIEINSHLVTALLDMYVK-CGNIRDARSVFDEL--------CSI--DL------VSWTAM  318 (691)
Q Consensus       260 ----~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~-~g~~~~A~~~~~~~--------~~~--~~------~~~~~l  318 (691)
                          ...+++-..+....+              ..+.. ...+..|...+.+-        ...  |.      .+...-
T Consensus       267 ~~~~~~~~ksDa~l~~~l~--------------~l~~~~~e~Y~~a~~~~te~~~~~~~~~~~n~~d~~le~~A~al~~~  332 (606)
T KOG0547|consen  267 PLFDNKSDKSDAALAEALE--------------ALEKGLEEGYLKAYDKATEECLGSESSLSVNEIDAELEYMAEALLLR  332 (606)
T ss_pred             ccccCCCccchhhHHHHHH--------------HHHhhCchhHHHHHHHHHHHhhhhhhhccccccchhHHHHHHHHHHh
Confidence                011111111111100              00000 01223333332221        111  11      111111


Q ss_pred             HHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChH
Q 040394          319 IVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIA  398 (691)
Q Consensus       319 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  398 (691)
                      ..-+.-.|+...|..-|+..+.....++.- |..+...|....+.++..+.|..+.+.++.++.+|..-..++.-.++++
T Consensus       333 gtF~fL~g~~~~a~~d~~~~I~l~~~~~~l-yI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~flL~q~e  411 (606)
T KOG0547|consen  333 GTFHFLKGDSLGAQEDFDAAIKLDPAFNSL-YIKRAAAYADENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFLLQQYE  411 (606)
T ss_pred             hhhhhhcCCchhhhhhHHHHHhcCcccchH-HHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHHHHHHH
Confidence            122344678888888888887764333332 6667777888888888888888888888888888877777777778888


Q ss_pred             HHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHh
Q 040394          399 DARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAK  478 (691)
Q Consensus       399 ~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  478 (691)
                      +|..=|++..+-+               +-+...|..+--+.-+.+++++++..|++.++.-  |..+..|+.....+..
T Consensus       412 ~A~aDF~Kai~L~---------------pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkkF--P~~~Evy~~fAeiLtD  474 (606)
T KOG0547|consen  412 EAIADFQKAISLD---------------PENAYAYIQLCCALYRQHKIAESMKTFEEAKKKF--PNCPEVYNLFAEILTD  474 (606)
T ss_pred             HHHHHHHHHhhcC---------------hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC--CCCchHHHHHHHHHhh
Confidence            8888887776432               1223344444444445666666666666666554  5666666666666666


Q ss_pred             cCCHHHHHHHHHhcc
Q 040394          479 CGDAQSARMVFDAMR  493 (691)
Q Consensus       479 ~g~~~~A~~~~~~~~  493 (691)
                      .++++.|.+.|+...
T Consensus       475 qqqFd~A~k~YD~ai  489 (606)
T KOG0547|consen  475 QQQFDKAVKQYDKAI  489 (606)
T ss_pred             HHhHHHHHHHHHHHH
Confidence            666666666665544

>TIGR00540 hemY_coli hemY protein

Probab=99.51  E-value=3.1e-11  Score=123.41  Aligned_cols=283  Identities=14%  Similarity=0.001  Sum_probs=147.1

Q ss_pred             HhcCCchhHHHHHHHhhHCCCCCcHHH-HHHHHHHHhcCCChhhHHHHHHHHHHhCCCc-hhHHHHHHHHhHhcCChHHH
Q 040394          323 TQSGYPDKALKLFTDKKWADFFPNHVT-IASVLSASAQLGNLNMGRMVHSLGIRLGLED-YTVINALVDMYAKCHVIADA  400 (691)
Q Consensus       323 ~~~g~~~~a~~~~~~m~~~g~~p~~~t-~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~a  400 (691)
                      ...|+++.|.+.+.+..+.  .|+... +.....+....|+.+.+...+....+..+.+ ..+.......+...|+++.|
T Consensus        95 ~~~g~~~~A~~~l~~~~~~--~~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~~A  172 (409)
T TIGR00540        95 LAEGDYAKAEKLIAKNADH--AAEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQNELHAA  172 (409)
T ss_pred             HhCCCHHHHHHHHHHHhhc--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHHHH
Confidence            4578888888888776554  454433 3333446667777777777777776655442 33444456666777777777


Q ss_pred             HHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHH-HHHHH---
Q 040394          401 RYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTA-LLNFY---  476 (691)
Q Consensus       401 ~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~-l~~~~---  476 (691)
                      ...++.+.+.               -+-+...+..+...+...|+++.+.+.+..+.+.+.  .+...+.. -...+   
T Consensus       173 l~~l~~l~~~---------------~P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~--~~~~~~~~l~~~a~~~~  235 (409)
T TIGR00540       173 RHGVDKLLEM---------------APRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGL--FDDEEFADLEQKAEIGL  235 (409)
T ss_pred             HHHHHHHHHh---------------CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCC--CCHHHHHHHHHHHHHHH
Confidence            7777776654               122444566666666777777777777777776653  22222211 11111   


Q ss_pred             H----hcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHH
Q 040394          477 A----KCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVG  549 (691)
Q Consensus       477 ~----~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~  549 (691)
                      .    .....+...+.++...+   .+...+..+...+...|+.++|.+.+++..+.  .||.....             
T Consensus       236 l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~--~pd~~~~~-------------  300 (409)
T TIGR00540       236 LDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKK--LGDDRAIS-------------  300 (409)
T ss_pred             HHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhh--CCCcccch-------------
Confidence            1    11122233333333332   24455555555555555555555555555553  23322100             


Q ss_pred             HHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCH---HHHHHHHHHHHhcCCHHHHHHHHH-
Q 040394          550 EGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PIEPDV---SLFGAFLHGCGLYSRFDLGEVMIK-  624 (691)
Q Consensus       550 ~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~---~~~~~l~~~~~~~g~~~~A~~~~~-  624 (691)
                                          ......-.....++.+.+.+.+++. ...|+.   ....++.+.+.+.|++++|.+.|+ 
T Consensus       301 --------------------~~~l~~~~~l~~~~~~~~~~~~e~~lk~~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~  360 (409)
T TIGR00540       301 --------------------LPLCLPIPRLKPEDNEKLEKLIEKQAKNVDDKPKCCINRALGQLLMKHGEFIEAADAFKN  360 (409)
T ss_pred             --------------------hHHHHHhhhcCCCChHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHcccHHHHHHHHHH
Confidence                                0000111112223444444444443 222222   344556666666666666666666 


Q ss_pred             -HHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHH
Q 040394          625 -KMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELM  660 (691)
Q Consensus       625 -~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  660 (691)
                       .+.+..|+ +..+..++.++.+.|+.++|.+++++.
T Consensus       361 a~a~~~~p~-~~~~~~La~ll~~~g~~~~A~~~~~~~  396 (409)
T TIGR00540       361 VAACKEQLD-ANDLAMAADAFDQAGDKAEAAAMRQDS  396 (409)
T ss_pred             hHHhhcCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence             34445565 333446666666666666666666554

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.

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

Probab=99.50  E-value=3.1e-08  Score=98.36  Aligned_cols=544  Identities=11%  Similarity=0.112  Sum_probs=341.1

Q ss_pred             hhhHHHHHHhcCCChHHHHHHhccCCC-----CCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHH
Q 040394           82 CNTKLVSMYGSFGHVKYARSVFDSMPN-----PDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKAC  156 (691)
Q Consensus        82 ~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~  156 (691)
                      .|-...+.+.++|++..-+..|++...     .....|...+.-....+-++-++.+|++.++-    ++..-+.-|..+
T Consensus       104 Iwl~Ylq~l~~Q~~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rvyrRYLk~----~P~~~eeyie~L  179 (835)
T KOG2047|consen  104 IWLDYLQFLIKQGLITRTRRTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRVYRRYLKV----APEAREEYIEYL  179 (835)
T ss_pred             HHHHHHHHHHhcchHHHHHHHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHHHHHHHhc----CHHHHHHHHHHH
Confidence            566667778888998888888886532     45567888888888888888999999988764    333466667788


Q ss_pred             cccCChhHHHHHHHHHHHh-------CCCChhHHHHHHHHhHhcCCh---HHHHHHHhccCCC--C--hhhHHHHHHHHH
Q 040394          157 CELRDIDEGMKVHCEIVKV-------GGPDSFVLTGLVDMYAKCRDI---GSSRQVFDETLDK--N--VVSWTSMIAGYV  222 (691)
Q Consensus       157 ~~~~~~~~a~~~~~~~~~~-------~~~~~~~~~~l~~~~~~~g~~---~~A~~~~~~~~~~--~--~~~~~~li~~~~  222 (691)
                      +..+++++|.+.+...+..       |+.+-..|..+.+...+.-+.   -....+++.+..+  |  ...|++|.+.|.
T Consensus       180 ~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdYYI  259 (835)
T KOG2047|consen  180 AKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADYYI  259 (835)
T ss_pred             HhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHHHH
Confidence            8889999998888877642       333667777777777665432   2334455555442  2  357999999999


Q ss_pred             hCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHH-HHCCCCchHHHHHHHHHHHhcCCHHHHH
Q 040394          223 QNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYIL-KIGIEINSHLVTALLDMYVKCGNIRDAR  301 (691)
Q Consensus       223 ~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~-~~g~~~~~~~~~~li~~~~~~g~~~~A~  301 (691)
                      +.|.+++|.++|++....-  .+..-|..+.++|+......-+... +... +.|-+-+..             +++-..
T Consensus       260 r~g~~ekarDvyeeai~~v--~tvrDFt~ifd~Ya~FEE~~~~~~m-e~a~~~~~n~ed~~-------------dl~~~~  323 (835)
T KOG2047|consen  260 RSGLFEKARDVYEEAIQTV--MTVRDFTQIFDAYAQFEESCVAAKM-ELADEESGNEEDDV-------------DLELHM  323 (835)
T ss_pred             HhhhhHHHHHHHHHHHHhh--eehhhHHHHHHHHHHHHHHHHHHHH-hhhhhcccChhhhh-------------hHHHHH
Confidence            9999999999999876532  2444566666666543222111111 0000 111111111             122222


Q ss_pred             HHHHhc---------------CCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCc------HHHHHHHHHHHhcC
Q 040394          302 SVFDEL---------------CSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPN------HVTIASVLSASAQL  360 (691)
Q Consensus       302 ~~~~~~---------------~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~------~~t~~~ll~~~~~~  360 (691)
                      .-|+.+               ...++..|..-+.  +..|+..+-...+.+.... +.|.      ...|..+...|-..
T Consensus       324 a~~e~lm~rr~~~lNsVlLRQn~~nV~eW~kRV~--l~e~~~~~~i~tyteAv~~-vdP~ka~Gs~~~Lw~~faklYe~~  400 (835)
T KOG2047|consen  324 ARFESLMNRRPLLLNSVLLRQNPHNVEEWHKRVK--LYEGNAAEQINTYTEAVKT-VDPKKAVGSPGTLWVEFAKLYENN  400 (835)
T ss_pred             HHHHHHHhccchHHHHHHHhcCCccHHHHHhhhh--hhcCChHHHHHHHHHHHHc-cCcccCCCChhhHHHHHHHHHHhc
Confidence            223222               1234445544443  3456777777888877665 3332      24577788889999


Q ss_pred             CChhhHHHHHHHHHHhCCCc----hhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHH-----
Q 040394          361 GNLNMGRMVHSLGIRLGLED----YTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAV-----  431 (691)
Q Consensus       361 ~~~~~a~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~-----  431 (691)
                      |+++.|+.+|+...+...+.    ..+|.....+-.+..+++.|+++.++...-.   -+..+..|..+.++...     
T Consensus       401 ~~l~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP---~~~~~~~yd~~~pvQ~rlhrSl  477 (835)
T KOG2047|consen  401 GDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRATHVP---TNPELEYYDNSEPVQARLHRSL  477 (835)
T ss_pred             CcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCC---CchhhhhhcCCCcHHHHHHHhH
Confidence            99999999999998877662    4566666677777888999999888754321   11112333333333333     


Q ss_pred             -HHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc----CCHh-HHHHHHH
Q 040394          432 -TLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE----KNTV-TWSAMIG  505 (691)
Q Consensus       432 -~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----~~~~-~~~~li~  505 (691)
                       .|...+..--..|-++....+++.+.+..+  .++.+.-.....+....-++++.+++++-..    |++. .|+..+.
T Consensus       478 kiWs~y~DleEs~gtfestk~vYdriidLri--aTPqii~NyAmfLEeh~yfeesFk~YErgI~LFk~p~v~diW~tYLt  555 (835)
T KOG2047|consen  478 KIWSMYADLEESLGTFESTKAVYDRIIDLRI--ATPQIIINYAMFLEEHKYFEESFKAYERGISLFKWPNVYDIWNTYLT  555 (835)
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHHhc--CCHHHHHHHHHHHHhhHHHHHHHHHHHcCCccCCCccHHHHHHHHHH
Confidence             344445555567888999999999999886  4455444455556667778999999998664    4443 6777665


Q ss_pred             HHhc---CCChHHHHHHHHHHHHCCCCCCHHHHHHHHH--HhcccCCHHHHHHHHHHchhhcCCCCC--hhHHHHHHHHH
Q 040394          506 GYGM---QGDGGGSLALFSDMLNEEVQPNEVIFTTILS--ACSHTGMVGEGWKCFYSMCRDFKFVPS--MKHYVCMVDLL  578 (691)
Q Consensus       506 ~~~~---~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~--~~~~~g~~~~A~~~~~~m~~~~~~~p~--~~~~~~li~~~  578 (691)
                      -+.+   ....+.|..+|++..+ |.+|...-+-.++-  .-.+.|....|..++++...  ++.+.  ..+|+..|.--
T Consensus       556 kfi~rygg~klEraRdLFEqaL~-~Cpp~~aKtiyLlYA~lEEe~GLar~amsiyerat~--~v~~a~~l~myni~I~ka  632 (835)
T KOG2047|consen  556 KFIKRYGGTKLERARDLFEQALD-GCPPEHAKTIYLLYAKLEEEHGLARHAMSIYERATS--AVKEAQRLDMYNIYIKKA  632 (835)
T ss_pred             HHHHHhcCCCHHHHHHHHHHHHh-cCCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHh--cCCHHHHHHHHHHHHHHH
Confidence            5543   3578999999999999 67776543322222  22346888899999998632  45554  56777777543


Q ss_pred             HhcCChHHHHHHHHhC-CCCCCHHHH---HHHHHHHHhcCCHHHHHHHHHHHHhc-CCC-CchhHHHHHHHHHhCCCcHH
Q 040394          579 ARAGRLEEALEFMENM-PIEPDVSLF---GAFLHGCGLYSRFDLGEVMIKKMLEL-HPD-KACYYVLVSNLYASDGRWIR  652 (691)
Q Consensus       579 ~~~g~~~~A~~~~~~~-~~~p~~~~~---~~l~~~~~~~g~~~~A~~~~~~~~~~-~p~-~~~~~~~l~~~~~~~g~~~~  652 (691)
                      ...=-+....+++++. ..-||...-   ......-.+.|..+.|..++...-++ +|. +..+|...-..-.+-|+-+.
T Consensus       633 ae~yGv~~TR~iYekaIe~Lp~~~~r~mclrFAdlEtklGEidRARaIya~~sq~~dPr~~~~fW~twk~FEvrHGnedT  712 (835)
T KOG2047|consen  633 AEIYGVPRTREIYEKAIESLPDSKAREMCLRFADLETKLGEIDRARAIYAHGSQICDPRVTTEFWDTWKEFEVRHGNEDT  712 (835)
T ss_pred             HHHhCCcccHHHHHHHHHhCChHHHHHHHHHHHHHhhhhhhHHHHHHHHHhhhhcCCCcCChHHHHHHHHHHHhcCCHHH
Confidence            3222222233344443 233444332   22233345678888898888887774 444 24567777677777888444


Q ss_pred             HHHH
Q 040394          653 VNQV  656 (691)
Q Consensus       653 A~~~  656 (691)
                      ..+.
T Consensus       713 ~keM  716 (835)
T KOG2047|consen  713 YKEM  716 (835)
T ss_pred             HHHH
Confidence            4333

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

Probab=99.50  E-value=6.7e-10  Score=105.73  Aligned_cols=285  Identities=11%  Similarity=0.103  Sum_probs=187.8

Q ss_pred             HHhcCCChhhHHHHHHHHHHhCCC-chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHH
Q 040394          356 ASAQLGNLNMGRMVHSLGIRLGLE-DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLV  434 (691)
Q Consensus       356 ~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~  434 (691)
                      ++......+++.+-.......|.+ +...-+....+.-...++++|..+|+++.+.|+-            ---|..+|+
T Consensus       236 a~~el~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPY------------Rl~dmdlyS  303 (559)
T KOG1155|consen  236 AYQELHQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPY------------RLDDMDLYS  303 (559)
T ss_pred             HHHHHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCC------------cchhHHHHh
Confidence            444445566666666666666666 5544555555566667777777777777765531            112445666


Q ss_pred             HHHHHHhccCcHH-HHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC---CHhHHHHHHHHHhcC
Q 040394          435 SVISACASLGAVQ-VGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK---NTVTWSAMIGGYGMQ  510 (691)
Q Consensus       435 ~ll~~~~~~~~~~-~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~li~~~~~~  510 (691)
                      .++-.-....++. .|..++    ..+  .-.+.+...+.+.|.-.++.+.|...|++..+-   ....|+.+.+-|...
T Consensus       304 N~LYv~~~~skLs~LA~~v~----~id--KyR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLNp~~~~aWTLmGHEyvEm  377 (559)
T KOG1155|consen  304 NVLYVKNDKSKLSYLAQNVS----NID--KYRPETCCIIANYYSLRSEHEKAVMYFKRALKLNPKYLSAWTLMGHEYVEM  377 (559)
T ss_pred             HHHHHHhhhHHHHHHHHHHH----Hhc--cCCccceeeehhHHHHHHhHHHHHHHHHHHHhcCcchhHHHHHhhHHHHHh
Confidence            6554432222111 122211    111  344566666777777788888888888877653   345777788888888


Q ss_pred             CChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHH
Q 040394          511 GDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALE  589 (691)
Q Consensus       511 ~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~  589 (691)
                      ++...|++.+++..+-. +-|-..|..+-++|.-.+...=|+-+|++.   ..++|+ ...|.+|...|.+.++.++|++
T Consensus       378 KNt~AAi~sYRrAvdi~-p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA---~~~kPnDsRlw~aLG~CY~kl~~~~eAiK  453 (559)
T KOG1155|consen  378 KNTHAAIESYRRAVDIN-PRDYRAWYGLGQAYEIMKMHFYALYYFQKA---LELKPNDSRLWVALGECYEKLNRLEEAIK  453 (559)
T ss_pred             cccHHHHHHHHHHHhcC-chhHHHHhhhhHHHHHhcchHHHHHHHHHH---HhcCCCchHHHHHHHHHHHHhccHHHHHH
Confidence            88888888888887742 446677777888888888888888888754   356675 7788888888888888888888


Q ss_pred             HHHhC--CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-------cCCCCchhHHHHHHHHHhCCCcHHHHHHHHHH
Q 040394          590 FMENM--PIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLE-------LHPDKACYYVLVSNLYASDGRWIRVNQVRELM  660 (691)
Q Consensus       590 ~~~~~--~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-------~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  660 (691)
                      .|.+.  ....+...+..|...+-+-++.++|...+++-++       ..|+.......|+.-+.+.+++++|..+....
T Consensus       454 Cykrai~~~dte~~~l~~LakLye~l~d~~eAa~~yek~v~~~~~eg~~~~~t~ka~~fLA~~f~k~~~~~~As~Ya~~~  533 (559)
T KOG1155|consen  454 CYKRAILLGDTEGSALVRLAKLYEELKDLNEAAQYYEKYVEVSELEGEIDDETIKARLFLAEYFKKMKDFDEASYYATLV  533 (559)
T ss_pred             HHHHHHhccccchHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHhhcchHHHHHHHHHH
Confidence            88877  2333557778888888888888888888887776       34444445555777777888888877665554


Q ss_pred             Hh
Q 040394          661 KQ  662 (691)
Q Consensus       661 ~~  662 (691)
                      ..
T Consensus       534 ~~  535 (559)
T KOG1155|consen  534 LK  535 (559)
T ss_pred             hc
Confidence            43

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

Probab=99.50  E-value=1.1e-10  Score=113.79  Aligned_cols=494  Identities=11%  Similarity=0.004  Sum_probs=306.7

Q ss_pred             hhHHHHHhhc---cCchhHHHHHHHHHHhCCCCchhhhHHHHHHhcCCChHHHHHHhcc--CCCCCcchHHHHHHHHHhC
Q 040394           50 IPCLNLLGLC---KSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDS--MPNPDFYSFQVMIRWYFLN  124 (691)
Q Consensus        50 ~~~~~ll~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~--~~~~~~~~~~~ll~~~~~~  124 (691)
                      ..+..+.+-+   .+...|..+-+.+...+..|.. .--++++|.-.|+++.|..+...  +.+.|..+.......+.+.
T Consensus        17 ~~~~~~~r~~l~q~~y~~a~f~adkV~~l~~dp~d-~~~~aq~l~~~~~y~ra~~lit~~~le~~d~~cryL~~~~l~~l   95 (611)
T KOG1173|consen   17 EKYRRLVRDALMQHRYKTALFWADKVAGLTNDPAD-IYWLAQVLYLGRQYERAAHLITTYKLEKRDIACRYLAAKCLVKL   95 (611)
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHhccCChHH-HHHHHHHHHhhhHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHH
Confidence            3344444433   3455566666666555533333 33477888888999999888764  4467888888899999999


Q ss_pred             CChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHh
Q 040394          125 DLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFD  204 (691)
Q Consensus       125 ~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  204 (691)
                      .++++|..++..-.   +.-++..|-..=.  ...-..+.+.+....-.     ....+-.-...|......++|..-|.
T Consensus        96 k~~~~al~vl~~~~---~~~~~f~yy~~~~--~~~l~~n~~~~~~~~~~-----essic~lRgk~y~al~n~~~ar~~Y~  165 (611)
T KOG1173|consen   96 KEWDQALLVLGRGH---VETNPFSYYEKDA--ANTLELNSAGEDLMINL-----ESSICYLRGKVYVALDNREEARDKYK  165 (611)
T ss_pred             HHHHHHHHHhcccc---hhhcchhhcchhh--hceeccCcccccccccc-----hhceeeeeeehhhhhccHHHHHHHHH
Confidence            99999998887321   0001111100000  00000011110000000     11111111223333445556655555


Q ss_pred             ccCCCChhhHHHHHHHHHhC-CChhHHHHHHHHHHhC-CCCCChhhHHHHHHHH-HccCChhhHHHHHHHHHHHCCCCch
Q 040394          205 ETLDKNVVSWTSMIAGYVQN-DCAQEGLVLFNRMREG-FVEGNQITLGSLVTAC-AKLRALHQGKWLHGYILKIGIEINS  281 (691)
Q Consensus       205 ~~~~~~~~~~~~li~~~~~~-g~~~~A~~~~~~m~~~-~~~p~~~t~~~li~~~-~~~~~~~~a~~~~~~~~~~g~~~~~  281 (691)
                      +..--|+..+..+...-... -...+-.++++...-. -.+-+......+.... ++..+.+ ....-.+-.-.|..-+.
T Consensus       166 ~Al~~D~~c~Ea~~~lvs~~mlt~~Ee~~ll~~l~~a~~~~ed~e~l~~lyel~~~k~~n~~-~~~r~~~~sl~~l~~~~  244 (611)
T KOG1173|consen  166 EALLADAKCFEAFEKLVSAHMLTAQEEFELLESLDLAMLTKEDVERLEILYELKLCKNRNEE-SLTRNEDESLIGLAENL  244 (611)
T ss_pred             HHHhcchhhHHHHHHHHHHHhcchhHHHHHHhcccHHhhhhhHHHHHHHHHHhhhhhhcccc-ccccCchhhhhhhhhcH
Confidence            54444444443332221110 0011112222211000 0111222222222221 1111100 00000001112345566


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhcCC---CChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHh
Q 040394          282 HLVTALLDMYVKCGNIRDARSVFDELCS---IDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASA  358 (691)
Q Consensus       282 ~~~~~li~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~  358 (691)
                      .+...-.+-+...+++.+..++++.+.+   .+...+..=|..+...|+..+-..+=..|.+. .+-...+|-.+..-|.
T Consensus       245 dll~~~ad~~y~~c~f~~c~kit~~lle~dpfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~-yP~~a~sW~aVg~YYl  323 (611)
T KOG1173|consen  245 DLLAEKADRLYYGCRFKECLKITEELLEKDPFHLPCLPLHIACLYELGKSNKLFLLSHKLVDL-YPSKALSWFAVGCYYL  323 (611)
T ss_pred             HHHHHHHHHHHHcChHHHHHHHhHHHHhhCCCCcchHHHHHHHHHHhcccchHHHHHHHHHHh-CCCCCcchhhHHHHHH
Confidence            7777777888899999999999998844   44556666677888999988888888888776 3445678888888888


Q ss_pred             cCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHH
Q 040394          359 QLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVIS  438 (691)
Q Consensus       359 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~  438 (691)
                      ..|+.++|+.++.+....++.-...|-.+...|+-.|..++|+..+....+-               ++-...-+.-+.-
T Consensus       324 ~i~k~seARry~SKat~lD~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl---------------~~G~hlP~LYlgm  388 (611)
T KOG1173|consen  324 MIGKYSEARRYFSKATTLDPTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARL---------------MPGCHLPSLYLGM  388 (611)
T ss_pred             HhcCcHHHHHHHHHHhhcCccccHHHHHHhHHhhhcchHHHHHHHHHHHHHh---------------ccCCcchHHHHHH
Confidence            8899999999999999988887778889999999999999998877654321               1111112233444


Q ss_pred             HHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC----------CHhHHHHHHHHHh
Q 040394          439 ACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK----------NTVTWSAMIGGYG  508 (691)
Q Consensus       439 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----------~~~~~~~li~~~~  508 (691)
                      -|.+.++...|.++|.......  |.++.+.+-+.-.....+.+.+|..+|+....+          -..+++.|..+|.
T Consensus       389 ey~~t~n~kLAe~Ff~~A~ai~--P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~R  466 (611)
T KOG1173|consen  389 EYMRTNNLKLAEKFFKQALAIA--PSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYR  466 (611)
T ss_pred             HHHHhccHHHHHHHHHHHHhcC--CCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHH
Confidence            5778899999999999998877  889999999988888899999999999876631          3446788889999


Q ss_pred             cCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHH
Q 040394          509 MQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDL  577 (691)
Q Consensus       509 ~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~  577 (691)
                      +.+.+++|+..+++.+.. .+-|..++.++.-.+...|+++.|.+.|.   +...+.|+-.+-..++..
T Consensus       467 kl~~~~eAI~~~q~aL~l-~~k~~~~~asig~iy~llgnld~Aid~fh---KaL~l~p~n~~~~~lL~~  531 (611)
T KOG1173|consen  467 KLNKYEEAIDYYQKALLL-SPKDASTHASIGYIYHLLGNLDKAIDHFH---KALALKPDNIFISELLKL  531 (611)
T ss_pred             HHhhHHHHHHHHHHHHHc-CCCchhHHHHHHHHHHHhcChHHHHHHHH---HHHhcCCccHHHHHHHHH
Confidence            999999999999988875 35567788888888888999999999998   455788887666665553

>TIGR00540 hemY_coli hemY protein

Probab=99.49  E-value=1.1e-10  Score=119.51  Aligned_cols=285  Identities=12%  Similarity=0.031  Sum_probs=184.4

Q ss_pred             HhcCCHHHHHHHHHhcCC--CCh-hHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHH--HHHHHHHHHhcCCChhhH
Q 040394          292 VKCGNIRDARSVFDELCS--IDL-VSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHV--TIASVLSASAQLGNLNMG  366 (691)
Q Consensus       292 ~~~g~~~~A~~~~~~~~~--~~~-~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~--t~~~ll~~~~~~~~~~~a  366 (691)
                      ...|+++.|.+.+.+..+  |+. ..+-....+..+.|+++.|.+.+.+..+.  .|+..  .-......+...|+++.|
T Consensus        95 ~~~g~~~~A~~~l~~~~~~~~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~--~p~~~l~~~~~~a~l~l~~~~~~~A  172 (409)
T TIGR00540        95 LAEGDYAKAEKLIAKNADHAAEPVLNLIKAAEAAQQRGDEARANQHLEEAAEL--AGNDNILVEIARTRILLAQNELHAA  172 (409)
T ss_pred             HhCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCcCchHHHHHHHHHHHHCCCHHHH
Confidence            467999999999988733  333 33444456788899999999999998765  35543  333446788889999999


Q ss_pred             HHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHH-HHHHH---hc
Q 040394          367 RMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVS-VISAC---AS  442 (691)
Q Consensus       367 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~-ll~~~---~~  442 (691)
                      ...++.+.+..|.++.+...+...+...|++++|.+.+....+.              ++ ++...+.. -..+.   ..
T Consensus       173 l~~l~~l~~~~P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~--------------~~-~~~~~~~~l~~~a~~~~l~  237 (409)
T TIGR00540       173 RHGVDKLLEMAPRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKA--------------GL-FDDEEFADLEQKAEIGLLD  237 (409)
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHc--------------CC-CCHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999998876              22 23333321 11111   22


Q ss_pred             cCcHHHHHHHHHHHHHcCC--CCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--CCHhH---HHHHHHHHhcCCChHH
Q 040394          443 LGAVQVGSSLHAYSTKQGL--LSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--KNTVT---WSAMIGGYGMQGDGGG  515 (691)
Q Consensus       443 ~~~~~~a~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~---~~~li~~~~~~~~~~~  515 (691)
                      .+..+.+...+..+.+...  .+.++..+..+...+...|+.++|.+++++..+  ||...   ...........++.+.
T Consensus       238 ~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~pd~~~~~~~~l~~~~~l~~~~~~~  317 (409)
T TIGR00540       238 EAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKLGDDRAISLPLCLPIPRLKPEDNEK  317 (409)
T ss_pred             HHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhCCCcccchhHHHHHhhhcCCCChHH
Confidence            2333333345555554431  024888999999999999999999999999875  33221   0111111122333333


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHh--
Q 040394          516 SLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMEN--  593 (691)
Q Consensus       516 A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~--  593 (691)
                      +.+.+++..+.  .|+.                                 |+.....++...+.+.|++++|.+.|++  
T Consensus       318 ~~~~~e~~lk~--~p~~---------------------------------~~~~ll~sLg~l~~~~~~~~~A~~~le~a~  362 (409)
T TIGR00540       318 LEKLIEKQAKN--VDDK---------------------------------PKCCINRALGQLLMKHGEFIEAADAFKNVA  362 (409)
T ss_pred             HHHHHHHHHHh--CCCC---------------------------------hhHHHHHHHHHHHHHcccHHHHHHHHHHhH
Confidence            43333333331  2222                                 2113444556666666666666666662  


Q ss_pred             C-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040394          594 M-PIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLE  628 (691)
Q Consensus       594 ~-~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  628 (691)
                      . ...|+...+..+...+.+.|+.++|.+++++.+.
T Consensus       363 a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~l~  398 (409)
T TIGR00540       363 ACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDSLG  398 (409)
T ss_pred             HhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            2 4556666666666666666666666666666544

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.

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

Probab=99.48  E-value=1.3e-13  Score=133.76  Aligned_cols=256  Identities=13%  Similarity=0.034  Sum_probs=83.5

Q ss_pred             HHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHH-HHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCC
Q 040394          218 IAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGS-LVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGN  296 (691)
Q Consensus       218 i~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~-li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~  296 (691)
                      ...+.+.|++++|++++++......+|+...|-. +...+...++.+.|...++.+...+.. +...+..++.. ...++
T Consensus        15 A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~~-~~~~~~~l~~l-~~~~~   92 (280)
T PF13429_consen   15 ARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASDKA-NPQDYERLIQL-LQDGD   92 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccc-ccccc
Confidence            4444555666666666544333221233333322 223334455566666666666554422 44445555555 56677


Q ss_pred             HHHHHHHHHhc--CCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCC-CCCcHHHHHHHHHHHhcCCChhhHHHHHHHH
Q 040394          297 IRDARSVFDEL--CSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWAD-FFPNHVTIASVLSASAQLGNLNMGRMVHSLG  373 (691)
Q Consensus       297 ~~~A~~~~~~~--~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~  373 (691)
                      +++|.++++..  ..++...+..++..+.+.++++++.++++...... ..++...|..+...+.+.|+.++|...++.+
T Consensus        93 ~~~A~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~a  172 (280)
T PF13429_consen   93 PEEALKLAEKAYERDGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKA  172 (280)
T ss_dssp             -------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHH
T ss_pred             ccccccccccccccccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            77777776655  22445556666777777777777777777765432 2345556666666677777777777777777


Q ss_pred             HHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHH
Q 040394          374 IRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLH  453 (691)
Q Consensus       374 ~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~  453 (691)
                      .+..|.+..+.+.++..+...|+.+++..+++.....               .+.|...+..+..++...|+.+.|...+
T Consensus       173 l~~~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~---------------~~~~~~~~~~la~~~~~lg~~~~Al~~~  237 (280)
T PF13429_consen  173 LELDPDDPDARNALAWLLIDMGDYDEAREALKRLLKA---------------APDDPDLWDALAAAYLQLGRYEEALEYL  237 (280)
T ss_dssp             HHH-TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH----------------HTSCCHCHHHHHHHHHHT-HHHHHHHH
T ss_pred             HHcCCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHH---------------CcCHHHHHHHHHHHhccccccccccccc
Confidence            7777776666677777777777776666655554332               1233344555555666666666666666


Q ss_pred             HHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhc
Q 040394          454 AYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAM  492 (691)
Q Consensus       454 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  492 (691)
                      +...+..  |.++.....+.+++...|+.++|..+..+.
T Consensus       238 ~~~~~~~--p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~  274 (280)
T PF13429_consen  238 EKALKLN--PDDPLWLLAYADALEQAGRKDEALRLRRQA  274 (280)
T ss_dssp             HHHHHHS--TT-HHHHHHHHHHHT---------------
T ss_pred             ccccccc--cccccccccccccccccccccccccccccc
Confidence            6666555  556666666666666666666666555443

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

Probab=99.47  E-value=1.5e-11  Score=122.31  Aligned_cols=279  Identities=11%  Similarity=-0.010  Sum_probs=205.5

Q ss_pred             hhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhc
Q 040394          363 LNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACAS  442 (691)
Q Consensus       363 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~  442 (691)
                      ..+|...|......-..+..+...+..+|...+++++|..+|+.+...+..            ..-+..+|.+.+.-+-+
T Consensus       335 ~~~A~~~~~klp~h~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~------------rv~~meiyST~LWHLq~  402 (638)
T KOG1126|consen  335 CREALNLFEKLPSHHYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPY------------RVKGMEIYSTTLWHLQD  402 (638)
T ss_pred             HHHHHHHHHhhHHhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc------------cccchhHHHHHHHHHHh
Confidence            345555555544444445566677777777777777777777777654211            11234556665554432


Q ss_pred             cCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC---CHhHHHHHHHHHhcCCChHHHHHH
Q 040394          443 LGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK---NTVTWSAMIGGYGMQGDGGGSLAL  519 (691)
Q Consensus       443 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~li~~~~~~~~~~~A~~~  519 (691)
                      .-   .--.+-+.+.+..  +..+.+|-++.+.|.-+++.+.|++.|++..+-   ...+|+.+..-+.....+|.|...
T Consensus       403 ~v---~Ls~Laq~Li~~~--~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~  477 (638)
T KOG1126|consen  403 EV---ALSYLAQDLIDTD--PNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKS  477 (638)
T ss_pred             hH---HHHHHHHHHHhhC--CCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHH
Confidence            11   1112233444554  788889999999999999999999999988763   456888888888888899999999


Q ss_pred             HHHHHHCCCCCCHHHHHH---HHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-
Q 040394          520 FSDMLNEEVQPNEVIFTT---ILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-  594 (691)
Q Consensus       520 ~~~m~~~g~~p~~~~~~~---ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-  594 (691)
                      |+..+    ..|...|++   +--.|.+.++++.|+-.|++.   ..+.|. ......+...+-+.|+.++|+.+++++ 
T Consensus       478 fr~Al----~~~~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA---~~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~  550 (638)
T KOG1126|consen  478 FRKAL----GVDPRHYNAWYGLGTVYLKQEKLEFAEFHFQKA---VEINPSNSVILCHIGRIQHQLKRKDKALQLYEKAI  550 (638)
T ss_pred             HHhhh----cCCchhhHHHHhhhhheeccchhhHHHHHHHhh---hcCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHH
Confidence            98875    445555554   444788999999999999955   367776 667777888899999999999999998 


Q ss_pred             CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          595 PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       595 ~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      ...| |+..--.-+..+...+++++|...++++.++.|++...+..++.+|.+.|+.+.|...+-.+.+-..
T Consensus       551 ~ld~kn~l~~~~~~~il~~~~~~~eal~~LEeLk~~vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~ldp  622 (638)
T KOG1126|consen  551 HLDPKNPLCKYHRASILFSLGRYVEALQELEELKELVPQESSVFALLGKIYKRLGNTDLALLHFSWALDLDP  622 (638)
T ss_pred             hcCCCCchhHHHHHHHHHhhcchHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHccchHHHHhhHHHhcCCC
Confidence            3333 4444445566777889999999999999999999999999999999999999999999988887543

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

Probab=99.47  E-value=1.6e-09  Score=101.65  Aligned_cols=298  Identities=10%  Similarity=-0.031  Sum_probs=216.7

Q ss_pred             HHhcCCchhHHHHHHHhhHCC-CCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHH
Q 040394          322 YTQSGYPDKALKLFTDKKWAD-FFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADA  400 (691)
Q Consensus       322 ~~~~g~~~~a~~~~~~m~~~g-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a  400 (691)
                      .+-.++...+...+--+.... ++-|......+...+...|+.++++..|+.....++.+..........+.+.|+.+..
T Consensus       206 q~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~dpy~i~~MD~Ya~LL~~eg~~e~~  285 (564)
T KOG1174|consen  206 QMFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCANPDNVEAMDLYAVLLGQEGGCEQD  285 (564)
T ss_pred             HHHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhCChhhhhhHHHHHHHHHhccCHhhH
Confidence            344455555554444333333 3444555666666777778888888888777777766444444455556667777766


Q ss_pred             HHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcC
Q 040394          401 RYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCG  480 (691)
Q Consensus       401 ~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  480 (691)
                      ..+...+...+               .-+..-|..-........+.+.|..+-++.++.+  +.+...+-.-...+...|
T Consensus       286 ~~L~~~Lf~~~---------------~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~--~r~~~alilKG~lL~~~~  348 (564)
T KOG1174|consen  286 SALMDYLFAKV---------------KYTASHWFVHAQLLYDEKKFERALNFVEKCIDSE--PRNHEALILKGRLLIALE  348 (564)
T ss_pred             HHHHHHHHhhh---------------hcchhhhhhhhhhhhhhhhHHHHHHHHHHHhccC--cccchHHHhccHHHHhcc
Confidence            66555554321               1122223333344456778889999999888877  677777766678888999


Q ss_pred             CHHHHHHHHHhccc--C-CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHH-HHhc-ccCCHHHHHHHH
Q 040394          481 DAQSARMVFDAMRE--K-NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTIL-SACS-HTGMVGEGWKCF  555 (691)
Q Consensus       481 ~~~~A~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll-~~~~-~~g~~~~A~~~~  555 (691)
                      +.++|.-.|+....  | +..+|..|+..|...|.+.+|..+-....+. ++-+..+.+.+- ..|. ....-++|.+++
T Consensus       349 R~~~A~IaFR~Aq~Lap~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~  427 (564)
T KOG1174|consen  349 RHTQAVIAFRTAQMLAPYRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRMREKAKKFA  427 (564)
T ss_pred             chHHHHHHHHHHHhcchhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchhHHHHHHHH
Confidence            99999999997664  3 7889999999999999999999887776654 455556665552 3332 334457889998


Q ss_pred             HHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC
Q 040394          556 YSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK  633 (691)
Q Consensus       556 ~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~  633 (691)
                      +   +...+.|+ ....+.+...+...|+.++++.++++. ...||....+.|.+.+...+.+.+|...|..+++++|++
T Consensus       428 e---k~L~~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr~dP~~  504 (564)
T KOG1174|consen  428 E---KSLKINPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLIIFPDVNLHNHLGDIMRAQNEPQKAMEYYYKALRQDPKS  504 (564)
T ss_pred             H---hhhccCCccHHHHHHHHHHHHhhCccchHHHHHHHHHhhccccHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCccc
Confidence            8   44578888 677788889999999999999999998 778999999999999999999999999999999999998


Q ss_pred             chhHHHH
Q 040394          634 ACYYVLV  640 (691)
Q Consensus       634 ~~~~~~l  640 (691)
                      ..+...+
T Consensus       505 ~~sl~Gl  511 (564)
T KOG1174|consen  505 KRTLRGL  511 (564)
T ss_pred             hHHHHHH
Confidence            7666555

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.42  E-value=6.5e-08  Score=100.67  Aligned_cols=602  Identities=14%  Similarity=0.119  Sum_probs=342.6

Q ss_pred             hhhhhhcccCCCccccccccccCCCCCCCCCChHHHHhhhcCCCc--hhHHHHHhhc--cCchh--------------HH
Q 040394            5 SLLQRHVSRTKKPKLQLRFFSYTNQQTPTQHELDQTFASFHSLPS--IPCLNLLGLC--KSTGS--------------LK   66 (691)
Q Consensus         5 ~~~~~~~~~~~~p~~a~~~~~~~~~~~~~~~~~~~a~~~~~~~~~--~~~~~ll~~~--~~~~~--------------a~   66 (691)
                      .+++.+..  .+|+.+..|-.-..+..+...+++.-..+|.+.+.  .....+|.+.  .+++.              |.
T Consensus       515 flLq~l~r--~sPD~~~qFa~~l~Q~~~~~~die~I~DlFme~N~iQq~TSFLLdaLK~~~Pd~g~LQTrLLE~NL~~aP  592 (1666)
T KOG0985|consen  515 FLLQQLKR--SSPDQALQFAMMLVQDEEPLADIEQIVDLFMELNLIQQCTSFLLDALKLNSPDEGHLQTRLLEMNLVHAP  592 (1666)
T ss_pred             HHHHHHHc--cChhHHHHHHHHhhccCCCcccHHHHHHHHHHHHhhhhhHHHHHHHhcCCChhhhhHHHHHHHHHhccch
Confidence            34444443  68888888887777767777778877777776221  1122234444  11221              22


Q ss_pred             HHHHHHHHhCCCCchhhhHHHHHHhcCCChHHHHHHhccCCC--CCcchHHHH-----HHHHHhCCChhHHHHHHHHHHH
Q 040394           67 AFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPN--PDFYSFQVM-----IRWYFLNDLYKDIVEFYKCMRK  139 (691)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~~~~l-----l~~~~~~~~~~~a~~~~~~m~~  139 (691)
                      ++.+.++-+++...--+..+.+.|.++|-...|++.+..+..  +.++ ...+     +-.|...-.++++.+.++.|..
T Consensus       593 qVADAILgN~mFtHyDra~IAqLCEKAGL~qraLehytDl~DIKR~vV-hth~L~pEwLv~yFg~lsve~s~eclkaml~  671 (1666)
T KOG0985|consen  593 QVADAILGNDMFTHYDRAEIAQLCEKAGLLQRALEHYTDLYDIKRVVV-HTHLLNPEWLVNYFGSLSVEDSLECLKAMLS  671 (1666)
T ss_pred             HHHHHHHhccccccccHHHHHHHHHhcchHHHHHHhcccHHHHHHHHH-HhccCCHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            222222333322221356788999999999999999887753  1111 1111     2234455678999999999999


Q ss_pred             cCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHh-----------CCC-ChhHHHHHHHHhHhcCChHHHHHHHhccC
Q 040394          140 RLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKV-----------GGP-DSFVLTGLVDMYAKCRDIGSSRQVFDETL  207 (691)
Q Consensus       140 ~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-----------~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  207 (691)
                      .+++.+..+...+..-|+..=-.+.-.++|+.....           ... |+.+.--.|.+.|+.|++.+.+++.++-.
T Consensus       672 ~NirqNlQi~VQvatky~eqlg~~~li~lFE~fks~eGL~yfLgSivn~seDpevh~KYIqAA~kt~QikEvERicresn  751 (1666)
T KOG0985|consen  672 ANIRQNLQIVVQVATKYHEQLGAQALIELFESFKSYEGLYYFLGSIVNFSEDPEVHFKYIQAACKTGQIKEVERICRESN  751 (1666)
T ss_pred             HHHHhhhHHHHHHHHHHHHHhCHHHHHHHHHhhccchhHHHHHHHHhccccCchHHHHHHHHHHhhccHHHHHHHHhccc
Confidence            999989888888888887776677777888776542           123 88888899999999999999999987541


Q ss_pred             C-------------------C-----C-------hhhH------HHHHHHHHhCCChhHHHHHHHHHHhCCCCCCh----
Q 040394          208 D-------------------K-----N-------VVSW------TSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQ----  246 (691)
Q Consensus       208 ~-------------------~-----~-------~~~~------~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~----  246 (691)
                      -                   |     |       .+.|      ...|..|.+.=++.+.-.+.-.+..-++.-+.    
T Consensus       752 ~YdpErvKNfLkeAkL~DqlPLiiVCDRf~fVhdlvlYLyrnn~~kyIE~yVQkvNps~~p~VvG~LLD~dC~E~~ik~L  831 (1666)
T KOG0985|consen  752 CYDPERVKNFLKEAKLTDQLPLIIVCDRFDFVHDLVLYLYRNNLQKYIEIYVQKVNPSRTPQVVGALLDVDCSEDFIKNL  831 (1666)
T ss_pred             cCCHHHHHHHHHhccccccCceEEEecccccHHHHHHHHHHhhHHHHHHHHHhhcCCcccchhhhhhhcCCCcHHHHHHH
Confidence            0                   1     1       1111      11233333333322222222222211111000    


Q ss_pred             -------hhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhc------------
Q 040394          247 -------ITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDEL------------  307 (691)
Q Consensus       247 -------~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~------------  307 (691)
                             ..-..+..-+-+.+++..-..+++.....|.+ |..++|+|...|...++-.+-  ++++-            
T Consensus       832 i~~v~gq~~~deLv~EvEkRNRLklLlp~LE~~i~eG~~-d~a~hnAlaKIyIDSNNnPE~--fLkeN~yYDs~vVGkYC  908 (1666)
T KOG0985|consen  832 ILSVRGQFPVDELVEEVEKRNRLKLLLPWLESLIQEGSQ-DPATHNALAKIYIDSNNNPER--FLKENPYYDSKVVGKYC  908 (1666)
T ss_pred             HHHHhccCChHHHHHHHHhhhhHHHHHHHHHHHHhccCc-chHHHhhhhheeecCCCChHH--hcccCCcchhhHHhhhh
Confidence                   01122334445566666667777777888865 889999999988876653321  11111            


Q ss_pred             CCCChh----HH------HHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhC
Q 040394          308 CSIDLV----SW------TAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLG  377 (691)
Q Consensus       308 ~~~~~~----~~------~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~  377 (691)
                      .++|+.    +|      .-||..+-.+..+..--+.+   .   -+.|...|..++.     ..-..-+++.+...+.+
T Consensus       909 EKRDP~lA~vaYerGqcD~elI~vcNeNSlfK~~aRYl---v---~R~D~~LW~~VL~-----e~n~~rRqLiDqVv~ta  977 (1666)
T KOG0985|consen  909 EKRDPHLACVAYERGQCDLELINVCNENSLFKSQARYL---V---ERSDPDLWAKVLN-----EENPYRRQLIDQVVQTA  977 (1666)
T ss_pred             cccCCceEEEeecccCCcHHHHHhcCchhHHHHHHHHH---H---hccChHHHHHHHh-----ccChHHHHHHHHHHHhc
Confidence            111111    01      11222221111111100000   0   0223334443332     11111233444444444


Q ss_pred             CC---chhHHHHHHHHhHhcCChHHHHHHHHhCCCCC-chh-----HHHHHHhhhCCCCCCHHH---H---------HHH
Q 040394          378 LE---DYTVINALVDMYAKCHVIADARYIFETTSEKD-VIA-----WNSIISGLDDNVSPDAVT---L---------VSV  436 (691)
Q Consensus       378 ~~---~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~-~~~-----~~~li~~~~~~~~p~~~~---~---------~~l  436 (691)
                      .+   ++...+..+.++...+-..+-.++++++.-.+ +.+     -|.+|-.   .++.|..-   |         -.+
T Consensus       978 l~E~~dPe~vS~tVkAfMtadLp~eLIELLEKIvL~~S~Fse~~nLQnLLiLt---Aikad~trVm~YI~rLdnyDa~~i 1054 (1666)
T KOG0985|consen  978 LPETQDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSENRNLQNLLILT---AIKADRTRVMEYINRLDNYDAPDI 1054 (1666)
T ss_pred             CCccCChHHHHHHHHHHHhcCCcHHHHHHHHHHhcCCcccccchhhhhhHHHH---HhhcChHHHHHHHHHhccCCchhH
Confidence            33   45555555555555555555555555543211 100     0000000   00001000   0         011


Q ss_pred             HHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHH
Q 040394          437 ISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGS  516 (691)
Q Consensus       437 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A  516 (691)
                      ...+...+-+++|..+|++.      ..+....+.|+.   ..+..+.|.+.-++..+  ...|+.+..+-.+.|...+|
T Consensus      1055 a~iai~~~LyEEAF~ifkkf------~~n~~A~~VLie---~i~~ldRA~efAe~~n~--p~vWsqlakAQL~~~~v~dA 1123 (1666)
T KOG0985|consen 1055 AEIAIENQLYEEAFAIFKKF------DMNVSAIQVLIE---NIGSLDRAYEFAERCNE--PAVWSQLAKAQLQGGLVKDA 1123 (1666)
T ss_pred             HHHHhhhhHHHHHHHHHHHh------cccHHHHHHHHH---HhhhHHHHHHHHHhhCC--hHHHHHHHHHHHhcCchHHH
Confidence            22334445566666666554      233444444443   34566777776666655  45788999999999999999


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhCCC
Q 040394          517 LALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPI  596 (691)
Q Consensus       517 ~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~~~  596 (691)
                      ++-|-+      .-|+..|..+++.+.+.|.+++-.+++... ++..-.|.+.+  .||-+|++.++..+-.+++.    
T Consensus      1124 ieSyik------adDps~y~eVi~~a~~~~~~edLv~yL~Ma-Rkk~~E~~id~--eLi~AyAkt~rl~elE~fi~---- 1190 (1666)
T KOG0985|consen 1124 IESYIK------ADDPSNYLEVIDVASRTGKYEDLVKYLLMA-RKKVREPYIDS--ELIFAYAKTNRLTELEEFIA---- 1190 (1666)
T ss_pred             HHHHHh------cCCcHHHHHHHHHHHhcCcHHHHHHHHHHH-HHhhcCccchH--HHHHHHHHhchHHHHHHHhc----
Confidence            887753      346678899999999999999999988865 55455666544  78889999999988877764    


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHH
Q 040394          597 EPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRE  658 (691)
Q Consensus       597 ~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~  658 (691)
                      -||......+..-|...|.++.|.-++..        ..-|..|+..+...|.+..|...-+
T Consensus      1191 gpN~A~i~~vGdrcf~~~~y~aAkl~y~~--------vSN~a~La~TLV~LgeyQ~AVD~aR 1244 (1666)
T KOG0985|consen 1191 GPNVANIQQVGDRCFEEKMYEAAKLLYSN--------VSNFAKLASTLVYLGEYQGAVDAAR 1244 (1666)
T ss_pred             CCCchhHHHHhHHHhhhhhhHHHHHHHHH--------hhhHHHHHHHHHHHHHHHHHHHHhh
Confidence            46777777788888888888888777764        4455666666666666666654443

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.42  E-value=2.7e-08  Score=91.61  Aligned_cols=414  Identities=8%  Similarity=0.002  Sum_probs=186.2

Q ss_pred             HcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHH
Q 040394          156 CCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFN  235 (691)
Q Consensus       156 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~  235 (691)
                      +-+.|++++|..++..+.+..-++...+..|.-++.-.|.+.+|..+-.+.++ ++..-..|...-.+-|+-++-..+-+
T Consensus        67 ~fhLgdY~~Al~~Y~~~~~~~~~~~el~vnLAcc~FyLg~Y~eA~~~~~ka~k-~pL~~RLlfhlahklndEk~~~~fh~  145 (557)
T KOG3785|consen   67 YFHLGDYEEALNVYTFLMNKDDAPAELGVNLACCKFYLGQYIEAKSIAEKAPK-TPLCIRLLFHLAHKLNDEKRILTFHS  145 (557)
T ss_pred             HHhhccHHHHHHHHHHHhccCCCCcccchhHHHHHHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHHHhCcHHHHHHHHH
Confidence            34556666666666555554444445555555555555555665555544322 12222223333334444444333333


Q ss_pred             HHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHH-HHHHHhcCCHHHHHHHHHhc---CCCC
Q 040394          236 RMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTAL-LDMYVKCGNIRDARSVFDEL---CSID  311 (691)
Q Consensus       236 ~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l-i~~~~~~g~~~~A~~~~~~~---~~~~  311 (691)
                      .+...     ...-.++.+..-..-..++|.+++...+..+  |+-...|.- .-+|.+..-++-+.++++-.   ...+
T Consensus       146 ~LqD~-----~EdqLSLAsvhYmR~HYQeAIdvYkrvL~dn--~ey~alNVy~ALCyyKlDYydvsqevl~vYL~q~pdS  218 (557)
T KOG3785|consen  146 SLQDT-----LEDQLSLASVHYMRMHYQEAIDVYKRVLQDN--PEYIALNVYMALCYYKLDYYDVSQEVLKVYLRQFPDS  218 (557)
T ss_pred             HHhhh-----HHHHHhHHHHHHHHHHHHHHHHHHHHHHhcC--hhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHhCCCc
Confidence            33221     0111111121112223445555555544321  222222222 22344444455555554433   2223


Q ss_pred             hhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHH-HHH-HHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHH
Q 040394          312 LVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIAS-VLS-ASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVD  389 (691)
Q Consensus       312 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~-ll~-~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  389 (691)
                      +.+.|.......+.-....|.+-.+++.+.+-..  ..+.. +++ -+..-.+-+.|.+++--+.+.-|   .+.-.++-
T Consensus       219 tiA~NLkacn~fRl~ngr~ae~E~k~ladN~~~~--~~f~~~l~rHNLVvFrngEgALqVLP~L~~~IP---EARlNL~i  293 (557)
T KOG3785|consen  219 TIAKNLKACNLFRLINGRTAEDEKKELADNIDQE--YPFIEYLCRHNLVVFRNGEGALQVLPSLMKHIP---EARLNLII  293 (557)
T ss_pred             HHHHHHHHHHHhhhhccchhHHHHHHHHhccccc--chhHHHHHHcCeEEEeCCccHHHhchHHHhhCh---Hhhhhhee
Confidence            3344444444444333333333333433332111  11111 111 11122333445554443333322   22334556


Q ss_pred             HhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHH-----HHhccCcHHHHHHHHHHHHHcCCCCC
Q 040394          390 MYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVIS-----ACASLGAVQVGSSLHAYSTKQGLLSS  464 (691)
Q Consensus       390 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~-----~~~~~~~~~~a~~~~~~~~~~~~~~~  464 (691)
                      -|.+.|++++|..+.++...                ..|-......+..     -......+.-|.+.|+..-..+....
T Consensus       294 YyL~q~dVqeA~~L~Kdl~P----------------ttP~EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecD  357 (557)
T KOG3785|consen  294 YYLNQNDVQEAISLCKDLDP----------------TTPYEYILKGVVFAALGQETGSREHLKIAQQFFQLVGESALECD  357 (557)
T ss_pred             eecccccHHHHHHHHhhcCC----------------CChHHHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccc
Confidence            67788888888888887752                3454444333333     23334456677777777766654233


Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHH-H
Q 040394          465 NVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTIL-S  540 (691)
Q Consensus       465 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll-~  540 (691)
                      +..--.++...+.-..++++.+..++.+..   .|-..--.+..+++..|++.+|.++|-+.....+ -|..+|.+++ +
T Consensus       358 TIpGRQsmAs~fFL~~qFddVl~YlnSi~sYF~NdD~Fn~N~AQAk~atgny~eaEelf~~is~~~i-kn~~~Y~s~LAr  436 (557)
T KOG3785|consen  358 TIPGRQSMASYFFLSFQFDDVLTYLNSIESYFTNDDDFNLNLAQAKLATGNYVEAEELFIRISGPEI-KNKILYKSMLAR  436 (557)
T ss_pred             cccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhHHHHHHHHhcChHHHHHHHhhhcChhh-hhhHHHHHHHHH
Confidence            333334455555555566666666665553   2222222355666666666666666655543322 2334444433 3


Q ss_pred             HhcccCCHHHHHHHHHHchhhcCCCCChh-HHHHHHHHHHhcCChHHHHHHHHhC-CCCCCHHHH
Q 040394          541 ACSHTGMVGEGWKCFYSMCRDFKFVPSMK-HYVCMVDLLARAGRLEEALEFMENM-PIEPDVSLF  603 (691)
Q Consensus       541 ~~~~~g~~~~A~~~~~~m~~~~~~~p~~~-~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~~~~  603 (691)
                      +|.+.+.++.|+.++-++    +-..+.. ....+...|.+++.+--|-+.|+.+ ...|++..|
T Consensus       437 Cyi~nkkP~lAW~~~lk~----~t~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~lDP~pEnW  497 (557)
T KOG3785|consen  437 CYIRNKKPQLAWDMMLKT----NTPSERFSLLQLIANDCYKANEFYYAAKAFDELEILDPTPENW  497 (557)
T ss_pred             HHHhcCCchHHHHHHHhc----CCchhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHccCCCcccc
Confidence            556666666666655443    1111111 2222334455555555555555544 345555555

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

Probab=99.41  E-value=1.7e-07  Score=93.31  Aligned_cols=503  Identities=11%  Similarity=0.086  Sum_probs=321.4

Q ss_pred             cCchhHHHHHHHHHHhCC-CCch-hhhHHHHHHhcCCChHHHHHHhccCCCCCcchHHHHHHHHHhCCChhHHHHHHHHH
Q 040394           60 KSTGSLKAFHALLIVDGL-TNDK-CNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCM  137 (691)
Q Consensus        60 ~~~~~a~~~~~~~~~~~~-~~~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m  137 (691)
                      +.+..-+..++..+..-+ .... +|...+......|-.+.+.+++++...-++..-+--+.-++..+++++|-+.|...
T Consensus       116 ~~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rvyrRYLk~~P~~~eeyie~L~~~d~~~eaa~~la~v  195 (835)
T KOG2047|consen  116 GLITRTRRTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRVYRRYLKVAPEAREEYIEYLAKSDRLDEAAQRLATV  195 (835)
T ss_pred             chHHHHHHHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhccchHHHHHHHHHh
Confidence            666677777777665432 2233 89999999999999999999999877666666788888899999999999999887


Q ss_pred             HHc------CCCCCcchHHHHHHHHcccCChh---HHHHHHHHHHHhCCC-ChhHHHHHHHHhHhcCChHHHHHHHhccC
Q 040394          138 RKR------LKEHDNFVFSKVLKACCELRDID---EGMKVHCEIVKVGGP-DSFVLTGLVDMYAKCRDIGSSRQVFDETL  207 (691)
Q Consensus       138 ~~~------~~~~~~~~~~~ll~~~~~~~~~~---~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  207 (691)
                      +..      ..+.+...|..+-...++..+.-   ....+++.+...-.+ -...|++|.+.|.+.|.++.|..++++..
T Consensus       196 ln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdYYIr~g~~ekarDvyeeai  275 (835)
T KOG2047|consen  196 LNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADYYIRSGLFEKARDVYEEAI  275 (835)
T ss_pred             cCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence            543      22445556666666655544332   244555555544444 56789999999999999999999999865


Q ss_pred             CC--ChhhHHHHHHHHHh----------------CCC------hhHHHHHHHHHHhCCC-----------CCChhhHHHH
Q 040394          208 DK--NVVSWTSMIAGYVQ----------------NDC------AQEGLVLFNRMREGFV-----------EGNQITLGSL  252 (691)
Q Consensus       208 ~~--~~~~~~~li~~~~~----------------~g~------~~~A~~~~~~m~~~~~-----------~p~~~t~~~l  252 (691)
                      ..  .+.-++.+-+.|++                .|+      ++-.+.-|+.+...+.           +-++.+|..-
T Consensus       276 ~~v~tvrDFt~ifd~Ya~FEE~~~~~~me~a~~~~~n~ed~~dl~~~~a~~e~lm~rr~~~lNsVlLRQn~~nV~eW~kR  355 (835)
T KOG2047|consen  276 QTVMTVRDFTQIFDAYAQFEESCVAAKMELADEESGNEEDDVDLELHMARFESLMNRRPLLLNSVLLRQNPHNVEEWHKR  355 (835)
T ss_pred             HhheehhhHHHHHHHHHHHHHHHHHHHHhhhhhcccChhhhhhHHHHHHHHHHHHhccchHHHHHHHhcCCccHHHHHhh
Confidence            42  22223333333321                111      2222333444333211           0011122111


Q ss_pred             HHHHHccCChhhHHHHHHHHHHHCCCC------chHHHHHHHHHHHhcCCHHHHHHHHHhcCCCCh-------hHHHHHH
Q 040394          253 VTACAKLRALHQGKWLHGYILKIGIEI------NSHLVTALLDMYVKCGNIRDARSVFDELCSIDL-------VSWTAMI  319 (691)
Q Consensus       253 i~~~~~~~~~~~a~~~~~~~~~~g~~~------~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~-------~~~~~li  319 (691)
                      +  -+..|+..+....+.+..+. +.|      -...|..+.+.|-..|+++.|..+|++..+-+-       .+|....
T Consensus       356 V--~l~e~~~~~~i~tyteAv~~-vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~wa  432 (835)
T KOG2047|consen  356 V--KLYEGNAAEQINTYTEAVKT-VDPKKAVGSPGTLWVEFAKLYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWA  432 (835)
T ss_pred             h--hhhcCChHHHHHHHHHHHHc-cCcccCCCChhhHHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHH
Confidence            1  12345555666666666553 222      235688889999999999999999999844322       3566666


Q ss_pred             HHHHhcCCchhHHHHHHHhhHCCCC----------C-------cHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchh
Q 040394          320 VGYTQSGYPDKALKLFTDKKWADFF----------P-------NHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYT  382 (691)
Q Consensus       320 ~~~~~~g~~~~a~~~~~~m~~~g~~----------p-------~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~  382 (691)
                      ..-.+..+++.|+++++......-.          |       +...|+..+..--..|-++..+.+++.+.+..+.++.
T Consensus       433 emElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~~pvQ~rlhrSlkiWs~y~DleEs~gtfestk~vYdriidLriaTPq  512 (835)
T KOG2047|consen  433 EMELRHENFEAALKLMRRATHVPTNPELEYYDNSEPVQARLHRSLKIWSMYADLEESLGTFESTKAVYDRIIDLRIATPQ  512 (835)
T ss_pred             HHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcCCCcHHHHHHHhHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhcCCHH
Confidence            6667788899999988776432111          1       2234555555555667888889999999998888777


Q ss_pred             HHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCH-HHHHHHHHHHh---ccCcHHHHHHHHHHHHH
Q 040394          383 VINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDA-VTLVSVISACA---SLGAVQVGSSLHAYSTK  458 (691)
Q Consensus       383 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~-~~~~~ll~~~~---~~~~~~~a~~~~~~~~~  458 (691)
                      +.......+-...-++++.++|++-..--              -.|+. ..|+.-+.-+.   ....++.|..+|++..+
T Consensus       513 ii~NyAmfLEeh~yfeesFk~YErgI~LF--------------k~p~v~diW~tYLtkfi~rygg~klEraRdLFEqaL~  578 (835)
T KOG2047|consen  513 IIINYAMFLEEHKYFEESFKAYERGISLF--------------KWPNVYDIWNTYLTKFIKRYGGTKLERARDLFEQALD  578 (835)
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHcCCccC--------------CCccHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh
Confidence            76666777777788899999998866531              12333 24444444333   23478999999999998


Q ss_pred             cCCCCCchhHHHHHHHHHH----hcCCHHHHHHHHHhcccC-----CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCC
Q 040394          459 QGLLSSNVYVGTALLNFYA----KCGDAQSARMVFDAMREK-----NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQ  529 (691)
Q Consensus       459 ~~~~~~~~~~~~~l~~~~~----~~g~~~~A~~~~~~~~~~-----~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~  529 (691)
                       +. ||..  ...+--.|+    +-|-...|..++++....     -...||+.|.-....=-+.....+|++.++.  -
T Consensus       579 -~C-pp~~--aKtiyLlYA~lEEe~GLar~amsiyerat~~v~~a~~l~myni~I~kaae~yGv~~TR~iYekaIe~--L  652 (835)
T KOG2047|consen  579 -GC-PPEH--AKTIYLLYAKLEEEHGLARHAMSIYERATSAVKEAQRLDMYNIYIKKAAEIYGVPRTREIYEKAIES--L  652 (835)
T ss_pred             -cC-CHHH--HHHHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHhCCcccHHHHHHHHHh--C
Confidence             54 4332  222222333    457778888888886642     2346788776555544556667788888774  6


Q ss_pred             CCHHHHHHHHH---HhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChH
Q 040394          530 PNEVIFTTILS---ACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLE  585 (691)
Q Consensus       530 p~~~~~~~ll~---~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~  585 (691)
                      |+...-...+.   .-++.|..+.|..++....+-..-..+...|.+.=..=.+.|+-+
T Consensus       653 p~~~~r~mclrFAdlEtklGEidRARaIya~~sq~~dPr~~~~fW~twk~FEvrHGned  711 (835)
T KOG2047|consen  653 PDSKAREMCLRFADLETKLGEIDRARAIYAHGSQICDPRVTTEFWDTWKEFEVRHGNED  711 (835)
T ss_pred             ChHHHHHHHHHHHHHhhhhhhHHHHHHHHHhhhhcCCCcCChHHHHHHHHHHHhcCCHH
Confidence            76655443333   446778888888888766333222223566777767777778733

>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]

Probab=99.41  E-value=7.1e-10  Score=104.03  Aligned_cols=216  Identities=12%  Similarity=0.099  Sum_probs=102.7

Q ss_pred             HHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCC-----------HhHHHHHHH
Q 040394          437 ISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKN-----------TVTWSAMIG  505 (691)
Q Consensus       437 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-----------~~~~~~li~  505 (691)
                      .......|+.+.|..-...+.+.+  |.++.......++|.+.|++.+...++..+.+..           ..+|+.+++
T Consensus       160 arlll~~~d~~aA~~~v~~ll~~~--pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~  237 (400)
T COG3071         160 ARLLLNRRDYPAARENVDQLLEMT--PRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQ  237 (400)
T ss_pred             HHHHHhCCCchhHHHHHHHHHHhC--cCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHH
Confidence            333444444444444444444444  4444455555555555555555555555544321           124444555


Q ss_pred             HHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChH
Q 040394          506 GYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLE  585 (691)
Q Consensus       506 ~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~  585 (691)
                      -....+..+.-...|++.-.. .+-++..-..++.-+...|+.++|.++..+..++ +..|+   ...++ ...+-++.+
T Consensus       238 q~~~~~~~~gL~~~W~~~pr~-lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~-~~D~~---L~~~~-~~l~~~d~~  311 (400)
T COG3071         238 QARDDNGSEGLKTWWKNQPRK-LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKR-QWDPR---LCRLI-PRLRPGDPE  311 (400)
T ss_pred             HHhccccchHHHHHHHhccHH-hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHh-ccChh---HHHHH-hhcCCCCch
Confidence            444444444444444444332 2333334444445555555555555555544322 33333   11111 122333333


Q ss_pred             HHHHHHHhC--CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHH
Q 040394          586 EALEFMENM--PIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMK  661 (691)
Q Consensus       586 ~A~~~~~~~--~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  661 (691)
                      .-++..++.  ..+.++-.+.+|...|.+++.+.+|...|+.+++..|+ ...+..++.++.+.|+..+|....++.+
T Consensus       312 ~l~k~~e~~l~~h~~~p~L~~tLG~L~~k~~~w~kA~~~leaAl~~~~s-~~~~~~la~~~~~~g~~~~A~~~r~e~L  388 (400)
T COG3071         312 PLIKAAEKWLKQHPEDPLLLSTLGRLALKNKLWGKASEALEAALKLRPS-ASDYAELADALDQLGEPEEAEQVRREAL  388 (400)
T ss_pred             HHHHHHHHHHHhCCCChhHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCC-hhhHHHHHHHHHHcCChHHHHHHHHHHH
Confidence            333332222  11122245555666666666666666666666666665 5556666666666666666666655544

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

Probab=99.41  E-value=7.2e-09  Score=98.90  Aligned_cols=352  Identities=9%  Similarity=0.028  Sum_probs=193.2

Q ss_pred             ChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhH--HHHHHHH
Q 040394          179 DSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITL--GSLVTAC  256 (691)
Q Consensus       179 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~--~~li~~~  256 (691)
                      |...+-.....+.+.|....|+..|.+....-+..|.+-+....--.+.+.+.    .... |...|..-+  -.+..++
T Consensus       163 D~fllYL~Gvv~k~~~~~s~A~~sfv~~v~~~P~~W~AWleL~~lit~~e~~~----~l~~-~l~~~~h~M~~~F~~~a~  237 (559)
T KOG1155|consen  163 DEFLLYLYGVVLKELGLLSLAIDSFVEVVNRYPWFWSAWLELSELITDIEILS----ILVV-GLPSDMHWMKKFFLKKAY  237 (559)
T ss_pred             hhHHHHHHHHHHHhhchHHHHHHHHHHHHhcCCcchHHHHHHHHhhchHHHHH----HHHh-cCcccchHHHHHHHHHHH
Confidence            66666666666777888899998888776544444444433322222222222    2211 121121111  1233344


Q ss_pred             HccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCC------ChhHHHHHHHHHHhcCCchh
Q 040394          257 AKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSI------DLVSWTAMIVGYTQSGYPDK  330 (691)
Q Consensus       257 ~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~------~~~~~~~li~~~~~~g~~~~  330 (691)
                      -.....+++.+-.......|+..+...-+....+.-...++|+|+.+|+++.+.      |..+|+.++-  .++.+.. 
T Consensus       238 ~el~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LY--v~~~~sk-  314 (559)
T KOG1155|consen  238 QELHQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLY--VKNDKSK-  314 (559)
T ss_pred             HHHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHH--HHhhhHH-
Confidence            555577777777777888887767666666666667778888888888888443      4456655543  3322211 


Q ss_pred             HHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCC
Q 040394          331 ALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEK  410 (691)
Q Consensus       331 a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  410 (691)
                       +..+.+-...--+--+.|...+.+-|+-.++-++|..+|+.+.+.++....+++.+..-                    
T Consensus       315 -Ls~LA~~v~~idKyR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLNp~~~~aWTLmGHE--------------------  373 (559)
T KOG1155|consen  315 -LSYLAQNVSNIDKYRPETCCIIANYYSLRSEHEKAVMYFKRALKLNPKYLSAWTLMGHE--------------------  373 (559)
T ss_pred             -HHHHHHHHHHhccCCccceeeehhHHHHHHhHHHHHHHHHHHHhcCcchhHHHHHhhHH--------------------
Confidence             11111111110122233444444445555555555555555555555544444444444                    


Q ss_pred             CchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHH
Q 040394          411 DVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFD  490 (691)
Q Consensus       411 ~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  490 (691)
                                                   |....+...|.+-++..++..  |.|-..|-.|.++|.-.+...-|+-.|+
T Consensus       374 -----------------------------yvEmKNt~AAi~sYRrAvdi~--p~DyRAWYGLGQaYeim~Mh~YaLyYfq  422 (559)
T KOG1155|consen  374 -----------------------------YVEMKNTHAAIESYRRAVDIN--PRDYRAWYGLGQAYEIMKMHFYALYYFQ  422 (559)
T ss_pred             -----------------------------HHHhcccHHHHHHHHHHHhcC--chhHHHHhhhhHHHHHhcchHHHHHHHH
Confidence                                         444445555555555555544  5566666666666666666666666666


Q ss_pred             hccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhc---C-
Q 040394          491 AMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDF---K-  563 (691)
Q Consensus       491 ~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~---~-  563 (691)
                      +..+   .|...|.+|..+|.+.++.++|++.|.+....| ..+...+..+...+.+.++..+|.+.|++.++..   | 
T Consensus       423 kA~~~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~-dte~~~l~~LakLye~l~d~~eAa~~yek~v~~~~~eg~  501 (559)
T KOG1155|consen  423 KALELKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLG-DTEGSALVRLAKLYEELKDLNEAAQYYEKYVEVSELEGE  501 (559)
T ss_pred             HHHhcCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcc-ccchHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcc
Confidence            5543   266667777777777777777777777766654 3355666667777777777777766666554422   1 


Q ss_pred             CCCC-hhHHHHHHHHHHhcCChHHHHHHH
Q 040394          564 FVPS-MKHYVCMVDLLARAGRLEEALEFM  591 (691)
Q Consensus       564 ~~p~-~~~~~~li~~~~~~g~~~~A~~~~  591 (691)
                      +.|. ......|..-+.+.+++++|....
T Consensus       502 ~~~~t~ka~~fLA~~f~k~~~~~~As~Ya  530 (559)
T KOG1155|consen  502 IDDETIKARLFLAEYFKKMKDFDEASYYA  530 (559)
T ss_pred             cchHHHHHHHHHHHHHHhhcchHHHHHHH
Confidence            1221 222223444455666666665443

>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]

Probab=99.40  E-value=1.5e-09  Score=101.90  Aligned_cols=281  Identities=12%  Similarity=0.036  Sum_probs=187.1

Q ss_pred             cCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCC----CChhhHHHHHHHHHhCCChhHHHHHH
Q 040394          159 LRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLD----KNVVSWTSMIAGYVQNDCAQEGLVLF  234 (691)
Q Consensus       159 ~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----~~~~~~~~li~~~~~~g~~~~A~~~~  234 (691)
                      .|++..|+++..+-.+.+......|..-..+--+.|+.+.+-..+.+..+    ++...+-+........|+++.|..-+
T Consensus        97 eG~~~qAEkl~~rnae~~e~p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~~v  176 (400)
T COG3071          97 EGDFQQAEKLLRRNAEHGEQPVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAARENV  176 (400)
T ss_pred             cCcHHHHHHHHHHhhhcCcchHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHHH
Confidence            35555555555554444433444444444444455555555555554422    22333444445555555555555555


Q ss_pred             HHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCch-------HHHHHHHHHHHhcCCHHHHHHHHHhc
Q 040394          235 NRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINS-------HLVTALLDMYVKCGNIRDARSVFDEL  307 (691)
Q Consensus       235 ~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~-------~~~~~li~~~~~~g~~~~A~~~~~~~  307 (691)
                      .++.+.+.. +.........+|.+.|++.....++..+.+.|.-.|.       .+|..+++-....+..+.-...++..
T Consensus       177 ~~ll~~~pr-~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~  255 (400)
T COG3071         177 DQLLEMTPR-HPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQ  255 (400)
T ss_pred             HHHHHhCcC-ChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhc
Confidence            555544322 3344555555555666666666666666555543332       45666777666666666666777777


Q ss_pred             CC---CChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHH
Q 040394          308 CS---IDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVI  384 (691)
Q Consensus       308 ~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  384 (691)
                      +.   .++..-.+++.-+.+.|+.++|.++..+-.+.+..|+.    ..+-.+.+.++...-.+..+...+..+.++..+
T Consensus       256 pr~lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L----~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p~L~  331 (400)
T COG3071         256 PRKLRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRL----CRLIPRLRPGDPEPLIKAAEKWLKQHPEDPLLL  331 (400)
T ss_pred             cHHhhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhH----HHHHhhcCCCCchHHHHHHHHHHHhCCCChhHH
Confidence            33   45667777888899999999999999999988877772    233466777888888888888888888888999


Q ss_pred             HHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcC
Q 040394          385 NALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQG  460 (691)
Q Consensus       385 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  460 (691)
                      .+|...|.+.+.+.+|...|+...+                ..|+..+|+.+.+++.+.|+.+.|.+..++....-
T Consensus       332 ~tLG~L~~k~~~w~kA~~~leaAl~----------------~~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~~~  391 (400)
T COG3071         332 STLGRLALKNKLWGKASEALEAALK----------------LRPSASDYAELADALDQLGEPEEAEQVRREALLLT  391 (400)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHh----------------cCCChhhHHHHHHHHHHcCChHHHHHHHHHHHHHh
Confidence            9999999999999999999997664                57888889989899999999888888888766433

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.36  E-value=1.4e-08  Score=100.06  Aligned_cols=191  Identities=10%  Similarity=0.103  Sum_probs=115.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHhcccCC-HhHHHHHHHHHh--cCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCC
Q 040394          471 ALLNFYAKCGDAQSARMVFDAMREKN-TVTWSAMIGGYG--MQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGM  547 (691)
Q Consensus       471 ~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~li~~~~--~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~  547 (691)
                      .++.+|.  +..+.+.++........ ...+.+++....  +......+.+++...-+....-.....-..++.....|+
T Consensus       314 ~lL~l~t--nk~~q~r~~~a~lp~~~p~~~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is~gn  391 (652)
T KOG2376|consen  314 ALLALFT--NKMDQVRELSASLPGMSPESLFPILLQEATKVREKKHKKAIELLLQFADGHPEKSKVVLLLRAQLKISQGN  391 (652)
T ss_pred             HHHHHHh--hhHHHHHHHHHhCCccCchHHHHHHHHHHHHHHHHHHhhhHHHHHHHhccCCchhHHHHHHHHHHHHhcCC
Confidence            3444443  45566666666665432 344445444332  223466777777777664222223455556667788899


Q ss_pred             HHHHHHHHH--------HchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-----CCCCCHH----HHHHHHHHH
Q 040394          548 VGEGWKCFY--------SMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-----PIEPDVS----LFGAFLHGC  610 (691)
Q Consensus       548 ~~~A~~~~~--------~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-----~~~p~~~----~~~~l~~~~  610 (691)
                      ++.|.+++.        .+ .+.+..  +.+...++..+.+.++.+.|..++.+.     ...+...    ++..+..--
T Consensus       392 ~~~A~~il~~~~~~~~ss~-~~~~~~--P~~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~  468 (652)
T KOG2376|consen  392 PEVALEILSLFLESWKSSI-LEAKHL--PGTVGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSLMREAAEFK  468 (652)
T ss_pred             HHHHHHHHHHHhhhhhhhh-hhhccC--hhHHHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhHHHHHhHHH
Confidence            999999888        44 232333  445556777788877766666666555     1112222    333333334


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCccCCCee
Q 040394          611 GLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCS  672 (691)
Q Consensus       611 ~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~~~~~~~  672 (691)
                      .+.|+.++|..+++++.+.+|++......++.+|++. +.+.|..+-     +.+.|.++..
T Consensus       469 lr~G~~~ea~s~leel~k~n~~d~~~l~~lV~a~~~~-d~eka~~l~-----k~L~p~~~l~  524 (652)
T KOG2376|consen  469 LRHGNEEEASSLLEELVKFNPNDTDLLVQLVTAYARL-DPEKAESLS-----KKLPPLKGLK  524 (652)
T ss_pred             HhcCchHHHHHHHHHHHHhCCchHHHHHHHHHHHHhc-CHHHHHHHh-----hcCCCcccch
Confidence            5779999999999999999999999988888887654 455555443     3444555443

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

Probab=99.36  E-value=2.4e-10  Score=114.00  Aligned_cols=280  Identities=9%  Similarity=-0.027  Sum_probs=189.0

Q ss_pred             ChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCC------CChhHHHHHHHHHHhcCCchhHHHH
Q 040394          261 ALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCS------IDLVSWTAMIVGYTQSGYPDKALKL  334 (691)
Q Consensus       261 ~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~------~~~~~~~~li~~~~~~g~~~~a~~~  334 (691)
                      +..+|...|..+.+. +.-+..+...+..+|...+++++|.++|+.+..      .+...|++.+-.+-+.=.   ---+
T Consensus       334 ~~~~A~~~~~klp~h-~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~---Ls~L  409 (638)
T KOG1126|consen  334 NCREALNLFEKLPSH-HYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVA---LSYL  409 (638)
T ss_pred             HHHHHHHHHHhhHHh-cCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHH---HHHH
Confidence            345666666663333 222335556667777777777777777777622      355566666543322111   1111


Q ss_pred             HHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchh
Q 040394          335 FTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIA  414 (691)
Q Consensus       335 ~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~  414 (691)
                      -+++.+. -+-.+.||..+.++|.-+++.+.|.+.|+.+++.++....+|+.+..-+.....+|.|...|+.....|+- 
T Consensus       410 aq~Li~~-~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~~r-  487 (638)
T KOG1126|consen  410 AQDLIDT-DPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKSFRKALGVDPR-  487 (638)
T ss_pred             HHHHHhh-CCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHHHHhhhcCCch-
Confidence            1222221 23356778888888888888888888888888887777777888888888888888888888876543211 


Q ss_pred             HHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc
Q 040394          415 WNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE  494 (691)
Q Consensus       415 ~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  494 (691)
                                    +-..|-.+...|.+.++.+.|+-.|++..+.+  |.+......+...+.+.|+.++|+.++++...
T Consensus       488 --------------hYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~IN--P~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~  551 (638)
T KOG1126|consen  488 --------------HYNAWYGLGTVYLKQEKLEFAEFHFQKAVEIN--PSNSVILCHIGRIQHQLKRKDKALQLYEKAIH  551 (638)
T ss_pred             --------------hhHHHHhhhhheeccchhhHHHHHHHhhhcCC--ccchhHHhhhhHHHHHhhhhhHHHHHHHHHHh
Confidence                          11245556667888888888888888888877  67777777888888888888888888887653


Q ss_pred             ---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHH-HHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC
Q 040394          495 ---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEV-IFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS  567 (691)
Q Consensus       495 ---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~-~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~  567 (691)
                         .|+..--..+..+...+++++|+..++++.+  +.|+.. .|..+...|.+.|+.+.|+.-|..+.   .+.|.
T Consensus       552 ld~kn~l~~~~~~~il~~~~~~~eal~~LEeLk~--~vP~es~v~~llgki~k~~~~~~~Al~~f~~A~---~ldpk  623 (638)
T KOG1126|consen  552 LDPKNPLCKYHRASILFSLGRYVEALQELEELKE--LVPQESSVFALLGKIYKRLGNTDLALLHFSWAL---DLDPK  623 (638)
T ss_pred             cCCCCchhHHHHHHHHHhhcchHHHHHHHHHHHH--hCcchHHHHHHHHHHHHHHccchHHHHhhHHHh---cCCCc
Confidence               3555555566677778888888888888888  566664 45555568888888888888887663   34554

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.36  E-value=8.3e-10  Score=111.43  Aligned_cols=201  Identities=14%  Similarity=0.182  Sum_probs=128.3

Q ss_pred             HHHHHhccCcHHHHHHHHHHHHHc-----CC-CCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhc
Q 040394          436 VISACASLGAVQVGSSLHAYSTKQ-----GL-LSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGM  509 (691)
Q Consensus       436 ll~~~~~~~~~~~a~~~~~~~~~~-----~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~  509 (691)
                      +...|...+++++|..+|+++...     |. -+....+++.|..+|.+.|++++|...+++.                 
T Consensus       247 ~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~A-----------------  309 (508)
T KOG1840|consen  247 LALVYRSLGKYDEAVNLYEEALTIREEVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERA-----------------  309 (508)
T ss_pred             HHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHH-----------------
Confidence            444555566666666666555421     20 0223445556666777777777777665543                 


Q ss_pred             CCChHHHHHHHHHHHHCC-CCCCHH-HHHHHHHHhcccCCHHHHHHHHHHchhhcC--CCCC----hhHHHHHHHHHHhc
Q 040394          510 QGDGGGSLALFSDMLNEE-VQPNEV-IFTTILSACSHTGMVGEGWKCFYSMCRDFK--FVPS----MKHYVCMVDLLARA  581 (691)
Q Consensus       510 ~~~~~~A~~~~~~m~~~g-~~p~~~-~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~--~~p~----~~~~~~li~~~~~~  581 (691)
                             ++++++  ..| ..|... .++.+...|...+.+++|..+++...+.+.  +.++    ..+++.|...|...
T Consensus       310 -------l~I~~~--~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~~~~~~a~~~~nl~~l~~~~  380 (508)
T KOG1840|consen  310 -------LEIYEK--LLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAPGEDNVNLAKIYANLAELYLKM  380 (508)
T ss_pred             -------HHHHHH--hhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHh
Confidence                   233333  111 112222 234444456666666666666665443332  2222    45788888999999


Q ss_pred             CChHHHHHHHHhC---------CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHh----cCCC---CchhHHHHHHHH
Q 040394          582 GRLEEALEFMENM---------PIEPD-VSLFGAFLHGCGLYSRFDLGEVMIKKMLE----LHPD---KACYYVLVSNLY  644 (691)
Q Consensus       582 g~~~~A~~~~~~~---------~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----~~p~---~~~~~~~l~~~~  644 (691)
                      |++++|.++++++         +..+. ...++.|...|.+.+++.+|.++|.+...    ..|+   ...+|..|+.+|
T Consensus       381 gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~~~nL~~~Y  460 (508)
T KOG1840|consen  381 GKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYTYLNLAALY  460 (508)
T ss_pred             cchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHH
Confidence            9999998888887         12222 34678888889999999999999998776    3444   456788999999


Q ss_pred             HhCCCcHHHHHHHHHHHh
Q 040394          645 ASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       645 ~~~g~~~~A~~~~~~~~~  662 (691)
                      .+.|++++|.++.+.+..
T Consensus       461 ~~~g~~e~a~~~~~~~~~  478 (508)
T KOG1840|consen  461 RAQGNYEAAEELEEKVLN  478 (508)
T ss_pred             HHcccHHHHHHHHHHHHH
Confidence            999999999999888763

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.34  E-value=3.8e-10  Score=106.92  Aligned_cols=198  Identities=13%  Similarity=0.095  Sum_probs=147.7

Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 040394          465 NVYVGTALLNFYAKCGDAQSARMVFDAMRE--K-NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSA  541 (691)
Q Consensus       465 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~  541 (691)
                      ....+..+...+...|++++|...+++..+  | +...+..+...+...|++++|.+.+++..+.. +.+...+..+...
T Consensus        30 ~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~  108 (234)
T TIGR02521        30 AAKIRVQLALGYLEQGDLEVAKENLDKALEHDPDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGTF  108 (234)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHH
Confidence            345555666667777777777777776553  2 45566667777777788888888887777653 3344566666677


Q ss_pred             hcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHH
Q 040394          542 CSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLG  619 (691)
Q Consensus       542 ~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A  619 (691)
                      +...|++++|.+.+++.............+..+...+...|++++|.+.+++. ...| +...+..+...+...|++++|
T Consensus       109 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A  188 (234)
T TIGR02521       109 LCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKDA  188 (234)
T ss_pred             HHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHcCCHHHH
Confidence            77888888888888877543222223456667788888999999999998887 3334 456788888889999999999


Q ss_pred             HHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          620 EVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       620 ~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      ...++++.+..|+++..+..++.++...|+.++|.++.+.+.+.
T Consensus       189 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  232 (234)
T TIGR02521       189 RAYLERYQQTYNQTAESLWLGIRIARALGDVAAAQRYGAQLQKL  232 (234)
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhh
Confidence            99999999988888888888999999999999999998877653

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.

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

Probab=99.33  E-value=3.2e-09  Score=96.61  Aligned_cols=284  Identities=12%  Similarity=0.045  Sum_probs=179.9

Q ss_pred             CCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCc---hHHHHHHHHHHHhcCCHHHH
Q 040394          224 NDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEIN---SHLVTALLDMYVKCGNIRDA  300 (691)
Q Consensus       224 ~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~---~~~~~~li~~~~~~g~~~~A  300 (691)
                      +++.++|.++|-+|.+... .+..+--++-+.+-+.|..+.|..+++.+.++---+.   ....-.|..-|...|-+|.|
T Consensus        48 s~Q~dKAvdlF~e~l~~d~-~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRA  126 (389)
T COG2956          48 SNQPDKAVDLFLEMLQEDP-ETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRA  126 (389)
T ss_pred             hcCcchHHHHHHHHHhcCc-hhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHH
Confidence            3556666666666655211 1222333444555566666666666666554321111   12334566778888999999


Q ss_pred             HHHHHhcCCCC---hhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcH----HHHHHHHHHHhcCCChhhHHHHHHHH
Q 040394          301 RSVFDELCSID---LVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNH----VTIASVLSASAQLGNLNMGRMVHSLG  373 (691)
Q Consensus       301 ~~~~~~~~~~~---~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~~  373 (691)
                      +.+|..+.+.+   ..+...|+..|-...+|++|++.-+++...+-.+..    ..|..+...+....+++.|...+..+
T Consensus       127 E~~f~~L~de~efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kA  206 (389)
T COG2956         127 EDIFNQLVDEGEFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKA  206 (389)
T ss_pred             HHHHHHHhcchhhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHH
Confidence            99999886532   346777888999999999999999888877655543    34556666667778888888888888


Q ss_pred             HHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHH
Q 040394          374 IRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLH  453 (691)
Q Consensus       374 ~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~  453 (691)
                      .+.++..+.+--.+.+.+...|+++.|.+.++.+.+.|              ..--..+...|..+|...|+.++....+
T Consensus       207 lqa~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn--------------~~yl~evl~~L~~~Y~~lg~~~~~~~fL  272 (389)
T COG2956         207 LQADKKCVRASIILGRVELAKGDYQKAVEALERVLEQN--------------PEYLSEVLEMLYECYAQLGKPAEGLNFL  272 (389)
T ss_pred             HhhCccceehhhhhhHHHHhccchHHHHHHHHHHHHhC--------------hHHHHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            88888877777778888888888888888888887663              1122345566777777778887777777


Q ss_pred             HHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhc-c-cCCHhHHHHHHHHHhc---CCChHHHHHHHHHHHH
Q 040394          454 AYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAM-R-EKNTVTWSAMIGGYGM---QGDGGGSLALFSDMLN  525 (691)
Q Consensus       454 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~-~-~~~~~~~~~li~~~~~---~~~~~~A~~~~~~m~~  525 (691)
                      ..+.+..   +....-..+.+.-......+.|...+.+- . +|+...+..+|.....   .|...+-+..++.|..
T Consensus       273 ~~~~~~~---~g~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~r~Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~mvg  346 (389)
T COG2956         273 RRAMETN---TGADAELMLADLIELQEGIDAAQAYLTRQLRRKPTMRGFHRLMDYHLADAEEGRAKESLDLLRDMVG  346 (389)
T ss_pred             HHHHHcc---CCccHHHHHHHHHHHhhChHHHHHHHHHHHhhCCcHHHHHHHHHhhhccccccchhhhHHHHHHHHH
Confidence            7776654   23333334444444444444554444332 2 3566666666655443   2334444555555554

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=99.32  E-value=6.4e-08  Score=98.52  Aligned_cols=485  Identities=13%  Similarity=0.080  Sum_probs=252.5

Q ss_pred             hCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHH---cccCChhHH-------------------HHH----HHHHHHhC
Q 040394          123 LNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKAC---CELRDIDEG-------------------MKV----HCEIVKVG  176 (691)
Q Consensus       123 ~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~---~~~~~~~~a-------------------~~~----~~~~~~~~  176 (691)
                      ..++.+.++.-+......+...++.++..+...+   ...++.+++                   ...    +.++....
T Consensus       239 ~~~~~~~~i~s~~~~l~~~w~~~~l~ka~l~~~~~~f~~~~~~Ee~~Lllli~es~i~Re~~~d~ilslm~~~~k~r~~~  318 (799)
T KOG4162|consen  239 KLSGPKEAIKSYRRALLRSWSLDPLTKARLYKGFALFLPKSGQEEVILLLLIEESLIPRENIEDAILSLMLLLRKLRLKK  318 (799)
T ss_pred             CCCCchHHHHhhhHHhhcccccchhHHHHHhhcccccCCCCcHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHHHHhh
Confidence            3455566666666655555555555555444332   233444444                   211    11111222


Q ss_pred             CC-ChhHHHHHHHHhHhcCChHHHHHHHhccCC---CChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHH
Q 040394          177 GP-DSFVLTGLVDMYAKCRDIGSSRQVFDETLD---KNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSL  252 (691)
Q Consensus       177 ~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~l  252 (691)
                      +. |+.+|..|.-++.++|++..+.+.|++...   .....|+.+-..+...|.-..|..+++.-......|+..+--.+
T Consensus       319 ~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~~Lm  398 (799)
T KOG4162|consen  319 FQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFSFGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISVLLM  398 (799)
T ss_pred             hcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchHHHH
Confidence            33 667777777777777777777777776533   24456777777777777777777777765543333433333333


Q ss_pred             HH-HHH-ccCChhhHHHHHHHHHHHC--C--CCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcC
Q 040394          253 VT-ACA-KLRALHQGKWLHGYILKIG--I--EINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSG  326 (691)
Q Consensus       253 i~-~~~-~~~~~~~a~~~~~~~~~~g--~--~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g  326 (691)
                      +. .|. +.+..+++..+-.......  .  ......|..+.-+|...-.            ..+..+        -+..
T Consensus       399 asklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~------------~a~~~s--------eR~~  458 (799)
T KOG4162|consen  399 ASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQAR------------QANLKS--------ERDA  458 (799)
T ss_pred             HHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhh------------cCCChH--------HHHH
Confidence            33 232 4455555555555554411  0  1112222222222221100            000000        0111


Q ss_pred             CchhHHHHHHHhhHCC-CCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCC-chhHHHHHHHHhHhcCChHHHHHHH
Q 040394          327 YPDKALKLFTDKKWAD-FFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLE-DYTVINALVDMYAKCHVIADARYIF  404 (691)
Q Consensus       327 ~~~~a~~~~~~m~~~g-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~  404 (691)
                      ...++++.+++..+.+ -.|+..-|..+  -++..++++.|....++..+.+.. +...+..+.-.+...+++.+|..+.
T Consensus       459 ~h~kslqale~av~~d~~dp~~if~lal--q~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vv  536 (799)
T KOG4162|consen  459 LHKKSLQALEEAVQFDPTDPLVIFYLAL--QYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVV  536 (799)
T ss_pred             HHHHHHHHHHHHHhcCCCCchHHHHHHH--HHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHH
Confidence            2234555555554432 23333333332  234455666666666666666444 6666666666677777777776666


Q ss_pred             HhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHH
Q 040394          405 ETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQS  484 (691)
Q Consensus       405 ~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  484 (691)
                      +.....-               .-|......-++.-..-++.+++......+...---.+.          ....++-..
T Consensus       537 d~al~E~---------------~~N~~l~~~~~~i~~~~~~~e~~l~t~~~~L~~we~~~~----------~q~~~~~g~  591 (799)
T KOG4162|consen  537 DAALEEF---------------GDNHVLMDGKIHIELTFNDREEALDTCIHKLALWEAEYG----------VQQTLDEGK  591 (799)
T ss_pred             HHHHHHh---------------hhhhhhchhhhhhhhhcccHHHHHHHHHHHHHHHHhhhh----------Hhhhhhhhh
Confidence            6543320               000000011111111234455554444433321100000          000111112


Q ss_pred             HHHHHHhcc----cC--CHhHHHHHHHHHh---cCCChHHHHHHHHHHHHCCCC--CCH------HHHHHHHHHhcccCC
Q 040394          485 ARMVFDAMR----EK--NTVTWSAMIGGYG---MQGDGGGSLALFSDMLNEEVQ--PNE------VIFTTILSACSHTGM  547 (691)
Q Consensus       485 A~~~~~~~~----~~--~~~~~~~li~~~~---~~~~~~~A~~~~~~m~~~g~~--p~~------~~~~~ll~~~~~~g~  547 (691)
                      ..+....+.    ++  ...++.-+..-..   +.-..+..      |...-+.  |+.      ..|......+.+.+.
T Consensus       592 ~~~lk~~l~la~~q~~~a~s~sr~ls~l~a~~~~~~~se~~------Lp~s~~~~~~~~~~~~~~~lwllaa~~~~~~~~  665 (799)
T KOG4162|consen  592 LLRLKAGLHLALSQPTDAISTSRYLSSLVASQLKSAGSELK------LPSSTVLPGPDSLWYLLQKLWLLAADLFLLSGN  665 (799)
T ss_pred             hhhhhcccccCcccccccchhhHHHHHHHHhhhhhcccccc------cCcccccCCCCchHHHHHHHHHHHHHHHHhcCC
Confidence            222222221    00  1112222111111   11111111      1111112  221      223344456677788


Q ss_pred             HHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCH-HHHHHHHHHHHhcCCHHHHHH--H
Q 040394          548 VGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEPDV-SLFGAFLHGCGLYSRFDLGEV--M  622 (691)
Q Consensus       548 ~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~-~~~~~l~~~~~~~g~~~~A~~--~  622 (691)
                      .++|...+.+..   ++.|- ...|......+...|.+++|.+.|... ...|+. .+..++...+.+.|+...|..  +
T Consensus       666 ~~~a~~CL~Ea~---~~~~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~ldP~hv~s~~Ala~~lle~G~~~la~~~~~  742 (799)
T KOG4162|consen  666 DDEARSCLLEAS---KIDPLSASVYYLRGLLLEVKGQLEEAKEAFLVALALDPDHVPSMTALAELLLELGSPRLAEKRSL  742 (799)
T ss_pred             chHHHHHHHHHH---hcchhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCcchHHHHHH
Confidence            888887777552   34454 556777777888899999999888777 666754 588888889999999888888  9


Q ss_pred             HHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          623 IKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       623 ~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      +..+++.+|.++..|+.++.++.+.|+.++|.+-|....+-
T Consensus       743 L~dalr~dp~n~eaW~~LG~v~k~~Gd~~~Aaecf~aa~qL  783 (799)
T KOG4162|consen  743 LSDALRLDPLNHEAWYYLGEVFKKLGDSKQAAECFQAALQL  783 (799)
T ss_pred             HHHHHhhCCCCHHHHHHHHHHHHHccchHHHHHHHHHHHhh
Confidence            99999999999999999999999999999999999888763

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

Probab=99.31  E-value=1.1e-07  Score=94.80  Aligned_cols=430  Identities=12%  Similarity=0.069  Sum_probs=250.8

Q ss_pred             HHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCC---ChhhHHHHHHHHHhCC
Q 040394          149 FSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDK---NVVSWTSMIAGYVQND  225 (691)
Q Consensus       149 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~li~~~~~~g  225 (691)
                      |..+++.| ..+++....+..+.+++..++...+.....-.+...|+-++|......-.+.   +.+.|..+.-.+....
T Consensus        11 F~~~lk~y-E~kQYkkgLK~~~~iL~k~~eHgeslAmkGL~L~~lg~~~ea~~~vr~glr~d~~S~vCwHv~gl~~R~dK   89 (700)
T KOG1156|consen   11 FRRALKCY-ETKQYKKGLKLIKQILKKFPEHGESLAMKGLTLNCLGKKEEAYELVRLGLRNDLKSHVCWHVLGLLQRSDK   89 (700)
T ss_pred             HHHHHHHH-HHHHHHhHHHHHHHHHHhCCccchhHHhccchhhcccchHHHHHHHHHHhccCcccchhHHHHHHHHhhhh
Confidence            44444544 3456666777777777754556666666666667777777877777665543   5567888888888888


Q ss_pred             ChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHH
Q 040394          226 CAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFD  305 (691)
Q Consensus       226 ~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~  305 (691)
                      ++++|++.|......  .||.                                  ..++.-+.-.-...|+++.....-.
T Consensus        90 ~Y~eaiKcy~nAl~~--~~dN----------------------------------~qilrDlslLQ~QmRd~~~~~~tr~  133 (700)
T KOG1156|consen   90 KYDEAIKCYRNALKI--EKDN----------------------------------LQILRDLSLLQIQMRDYEGYLETRN  133 (700)
T ss_pred             hHHHHHHHHHHHHhc--CCCc----------------------------------HHHHHHHHHHHHHHHhhhhHHHHHH
Confidence            888898888888763  2332                                  1122211111122233333222222


Q ss_pred             hc---CCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCC-CCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCch
Q 040394          306 EL---CSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWAD-FFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDY  381 (691)
Q Consensus       306 ~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~  381 (691)
                      ..   .......|..+..++.-.|++..|..++++..+.. -.|+...|......+                        
T Consensus       134 ~LLql~~~~ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~L------------------------  189 (700)
T KOG1156|consen  134 QLLQLRPSQRASWIGFAVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLL------------------------  189 (700)
T ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHH------------------------
Confidence            22   23355678888888888899999999999887764 245655553332211                        


Q ss_pred             hHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHH-HHHHHHHhccCcHHHHHHHHHHHHHcC
Q 040394          382 TVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTL-VSVISACASLGAVQVGSSLHAYSTKQG  460 (691)
Q Consensus       382 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~-~~ll~~~~~~~~~~~a~~~~~~~~~~~  460 (691)
                          .-.....+.|.+++|.+.+......                ..|...+ ..-...+.+.+++++|..++..+....
T Consensus       190 ----y~n~i~~E~g~~q~ale~L~~~e~~----------------i~Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~rn  249 (700)
T KOG1156|consen  190 ----YQNQILIEAGSLQKALEHLLDNEKQ----------------IVDKLAFEETKADLLMKLGQLEEAVKVYRRLLERN  249 (700)
T ss_pred             ----HHHHHHHHcccHHHHHHHHHhhhhH----------------HHHHHHHhhhHHHHHHHHhhHHhHHHHHHHHHhhC
Confidence                1122344555566666655554322                1122222 122334556677777777777777766


Q ss_pred             CCCCchhHHHHHHHHHHhcCCHHHHH-HHHHhcccC---CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHH
Q 040394          461 LLSSNVYVGTALLNFYAKCGDAQSAR-MVFDAMREK---NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFT  536 (691)
Q Consensus       461 ~~~~~~~~~~~l~~~~~~~g~~~~A~-~~~~~~~~~---~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~  536 (691)
                        |.+...|-.+..++.+-.+.-++. .+|....+.   ....-..=+.......-.+..-.++..+.+.|+++-...+.
T Consensus       250 --Pdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~y~r~e~p~Rlplsvl~~eel~~~vdkyL~~~l~Kg~p~vf~dl~  327 (700)
T KOG1156|consen  250 --PDNLDYYEGLEKALGKIKDMLEALKALYAILSEKYPRHECPRRLPLSVLNGEELKEIVDKYLRPLLSKGVPSVFKDLR  327 (700)
T ss_pred             --chhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhcCcccccchhccHHHhCcchhHHHHHHHHHHHhhcCCCchhhhhH
Confidence              566666666666665333333333 555544321   00000000111111222334456667777777665433333


Q ss_pred             HHHHHhcccCCHH----HHHHHHHHchhhcC---------C-CCChh--HHHHHHHHHHhcCChHHHHHHHHhC-CCCCC
Q 040394          537 TILSACSHTGMVG----EGWKCFYSMCRDFK---------F-VPSMK--HYVCMVDLLARAGRLEEALEFMENM-PIEPD  599 (691)
Q Consensus       537 ~ll~~~~~~g~~~----~A~~~~~~m~~~~~---------~-~p~~~--~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~  599 (691)
                      ++-   -.....+    -+..+...+ ...|         . +|...  ++-.++..+-+.|+++.|..+++.. +-.|+
T Consensus       328 SLy---k~p~k~~~le~Lvt~y~~~L-~~~~~f~~~D~~~~E~PttllWt~y~laqh~D~~g~~~~A~~yId~AIdHTPT  403 (700)
T KOG1156|consen  328 SLY---KDPEKVAFLEKLVTSYQHSL-SGTGMFNFLDDGKQEPPTTLLWTLYFLAQHYDKLGDYEVALEYIDLAIDHTPT  403 (700)
T ss_pred             HHH---hchhHhHHHHHHHHHHHhhc-ccccCCCcccccccCCchHHHHHHHHHHHHHHHcccHHHHHHHHHHHhccCch
Confidence            322   1111111    111122211 1111         1 33433  3345677788999999999999988 76777


Q ss_pred             HH-HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          600 VS-LFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       600 ~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      .. .|..=.+.+.+.|+++.|..+++++.+++-.|..+...-+.-..+..+.++|.++....-+.|.
T Consensus       404 liEly~~KaRI~kH~G~l~eAa~~l~ea~elD~aDR~INsKcAKYmLrAn~i~eA~~~~skFTr~~~  470 (700)
T KOG1156|consen  404 LIELYLVKARIFKHAGLLDEAAAWLDEAQELDTADRAINSKCAKYMLRANEIEEAEEVLSKFTREGF  470 (700)
T ss_pred             HHHHHHHHHHHHHhcCChHHHHHHHHHHHhccchhHHHHHHHHHHHHHccccHHHHHHHHHhhhccc
Confidence            64 5555567788999999999999999998877677776777888899999999999988887774

>PF13041 PPR_2: PPR repeat family

Probab=99.29  E-value=8.2e-12  Score=84.22  Aligned_cols=50  Identities=26%  Similarity=0.485  Sum_probs=39.9

Q ss_pred             CChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHc
Q 040394          209 KNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAK  258 (691)
Q Consensus       209 ~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~  258 (691)
                      ||+.+||++|.+|++.|++++|.++|++|.+.|++||..||+++|++|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            67778888888888888888888888888888888888888888877764

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

Probab=99.29  E-value=2e-07  Score=93.14  Aligned_cols=228  Identities=10%  Similarity=-0.026  Sum_probs=110.3

Q ss_pred             CCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHH
Q 040394          124 NDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVF  203 (691)
Q Consensus       124 ~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  203 (691)
                      .+++.+.+++.+.+.+. .+--..|....--.+...|+.++|....+.-.+.++.+...|..+.-.+....++++|++-|
T Consensus        20 ~kQYkkgLK~~~~iL~k-~~eHgeslAmkGL~L~~lg~~~ea~~~vr~glr~d~~S~vCwHv~gl~~R~dK~Y~eaiKcy   98 (700)
T KOG1156|consen   20 TKQYKKGLKLIKQILKK-FPEHGESLAMKGLTLNCLGKKEEAYELVRLGLRNDLKSHVCWHVLGLLQRSDKKYDEAIKCY   98 (700)
T ss_pred             HHHHHhHHHHHHHHHHh-CCccchhHHhccchhhcccchHHHHHHHHHHhccCcccchhHHHHHHHHhhhhhHHHHHHHH
Confidence            34555555555555542 22222333333333444556666666555555555555556666655555556666666666


Q ss_pred             hccCC---CChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCC-CC
Q 040394          204 DETLD---KNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGI-EI  279 (691)
Q Consensus       204 ~~~~~---~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~-~~  279 (691)
                      .....   .|...|.-+.-.-.+.|+++...+...+..+... .....|..+..+..-.|+...|..++++..+... .|
T Consensus        99 ~nAl~~~~dN~qilrDlslLQ~QmRd~~~~~~tr~~LLql~~-~~ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~~  177 (700)
T KOG1156|consen   99 RNALKIEKDNLQILRDLSLLQIQMRDYEGYLETRNQLLQLRP-SQRASWIGFAVAQHLLGEYKMALEILEEFEKTQNTSP  177 (700)
T ss_pred             HHHHhcCCCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhh-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCC
Confidence            54321   2444444444444455555555555554444211 1233444455555555566666666655554432 33


Q ss_pred             chHHHHHHH------HHHHhcCCHHHHHHHHHhcCCC--Chh-HHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHH
Q 040394          280 NSHLVTALL------DMYVKCGNIRDARSVFDELCSI--DLV-SWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTI  350 (691)
Q Consensus       280 ~~~~~~~li------~~~~~~g~~~~A~~~~~~~~~~--~~~-~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~  350 (691)
                      +...+....      ....+.|..++|.+.+......  |-. .-..-...+.+.+++++|..++..++..  .||..-|
T Consensus       178 s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~i~Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~r--nPdn~~Y  255 (700)
T KOG1156|consen  178 SKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQIVDKLAFEETKADLLMKLGQLEEAVKVYRRLLER--NPDNLDY  255 (700)
T ss_pred             CHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhHHHHHHHHhhhHHHHHHHHhhHHhHHHHHHHHHhh--CchhHHH
Confidence            433333222      2234455555555555443211  111 1122233455666666666666666654  4555555


Q ss_pred             HHHHH
Q 040394          351 ASVLS  355 (691)
Q Consensus       351 ~~ll~  355 (691)
                      ...+.
T Consensus       256 y~~l~  260 (700)
T KOG1156|consen  256 YEGLE  260 (700)
T ss_pred             HHHHH
Confidence            54444

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=99.27  E-value=2.3e-07  Score=93.52  Aligned_cols=512  Identities=11%  Similarity=0.057  Sum_probs=248.7

Q ss_pred             cCchhHHHHHHHHH-------HhCCCCchhhhHHHHHHhcCCChHHHHHHhccCCCCCcchHHHHHHHHHhCCChhHHHH
Q 040394           60 KSTGSLKAFHALLI-------VDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVE  132 (691)
Q Consensus        60 ~~~~~a~~~~~~~~-------~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~  132 (691)
                      ++...++.+|+...       +.|...+.+|.--...-.-..++.+|+.+|-+-.     .-..-+..|-...+|++|+.
T Consensus       504 ~dvak~r~lhd~~eiadeas~~~ggdgt~fykvra~lail~kkfk~ae~ifleqn-----~te~aigmy~~lhkwde~i~  578 (1636)
T KOG3616|consen  504 GDVAKARFLHDILEIADEASIEIGGDGTDFYKVRAMLAILEKKFKEAEMIFLEQN-----ATEEAIGMYQELHKWDEAIA  578 (1636)
T ss_pred             HHHHHHHHHHHHHHHHHHHhHhhCCCCchHHHHHHHHHHHHhhhhHHHHHHHhcc-----cHHHHHHHHHHHHhHHHHHH
Confidence            55666666665432       2222333333322222222345666666653211     11223334444445555554


Q ss_pred             HHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhc--cCCCC
Q 040394          133 FYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDE--TLDKN  210 (691)
Q Consensus       133 ~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~--~~~~~  210 (691)
                      +-+.   .|.+.-...-.+.++++...|+-+.|-++-.        +..--.+-|+.|.+.|.+..|.+....  ....|
T Consensus       579 lae~---~~~p~~eklk~sy~q~l~dt~qd~ka~elk~--------sdgd~laaiqlyika~~p~~a~~~a~n~~~l~~d  647 (1636)
T KOG3616|consen  579 LAEA---KGHPALEKLKRSYLQALMDTGQDEKAAELKE--------SDGDGLAAIQLYIKAGKPAKAARAALNDEELLAD  647 (1636)
T ss_pred             HHHh---cCChHHHHHHHHHHHHHHhcCchhhhhhhcc--------ccCccHHHHHHHHHcCCchHHHHhhcCHHHhhcc
Confidence            4321   2322222233344555555565555544311        111123456778888887777665432  22345


Q ss_pred             hhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHH-HHHHHH
Q 040394          211 VVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHL-VTALLD  289 (691)
Q Consensus       211 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~-~~~li~  289 (691)
                      ......+..++.+..-+++|-++|+++..    |     .-.+.++.+..-+.+|.++-+..    ++..+++ -.....
T Consensus       648 e~il~~ia~alik~elydkagdlfeki~d----~-----dkale~fkkgdaf~kaielarfa----fp~evv~lee~wg~  714 (1636)
T KOG3616|consen  648 EEILEHIAAALIKGELYDKAGDLFEKIHD----F-----DKALECFKKGDAFGKAIELARFA----FPEEVVKLEEAWGD  714 (1636)
T ss_pred             HHHHHHHHHHHHhhHHHHhhhhHHHHhhC----H-----HHHHHHHHcccHHHHHHHHHHhh----CcHHHhhHHHHHhH
Confidence            55555556666666666777777766642    1     11222232322333444332221    1111111 112223


Q ss_pred             HHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHH
Q 040394          290 MYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMV  369 (691)
Q Consensus       290 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~  369 (691)
                      .+...|+++.|..-|-+..     ..-.-+.+-....++.+|+.+++.+....  .-+.-|..+...|...|+++.|+.+
T Consensus       715 hl~~~~q~daainhfiea~-----~~~kaieaai~akew~kai~ildniqdqk--~~s~yy~~iadhyan~~dfe~ae~l  787 (1636)
T KOG3616|consen  715 HLEQIGQLDAAINHFIEAN-----CLIKAIEAAIGAKEWKKAISILDNIQDQK--TASGYYGEIADHYANKGDFEIAEEL  787 (1636)
T ss_pred             HHHHHHhHHHHHHHHHHhh-----hHHHHHHHHhhhhhhhhhHhHHHHhhhhc--cccccchHHHHHhccchhHHHHHHH
Confidence            3444556666655553321     11122445566777888888887776652  2233455566677777888877777


Q ss_pred             HHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHH
Q 040394          370 HSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVG  449 (691)
Q Consensus       370 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a  449 (691)
                      |.+.        ..++..|++|.+.|++..|.++-++..                |.......|..-..-+-..|++.+|
T Consensus       788 f~e~--------~~~~dai~my~k~~kw~da~kla~e~~----------------~~e~t~~~yiakaedldehgkf~ea  843 (1636)
T KOG3616|consen  788 FTEA--------DLFKDAIDMYGKAGKWEDAFKLAEECH----------------GPEATISLYIAKAEDLDEHGKFAEA  843 (1636)
T ss_pred             HHhc--------chhHHHHHHHhccccHHHHHHHHHHhc----------------CchhHHHHHHHhHHhHHhhcchhhh
Confidence            6543        234667788888888888888777664                2233444555555556666777776


Q ss_pred             HHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC-CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCC
Q 040394          450 SSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK-NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEV  528 (691)
Q Consensus       450 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~  528 (691)
                      ++++-.+.     .|+     .-|.+|-+.|..+..+++.++-... =..|...+..-|-..|+...|.+.|-+..+   
T Consensus       844 eqlyiti~-----~p~-----~aiqmydk~~~~ddmirlv~k~h~d~l~dt~~~f~~e~e~~g~lkaae~~flea~d---  910 (1636)
T KOG3616|consen  844 EQLYITIG-----EPD-----KAIQMYDKHGLDDDMIRLVEKHHGDHLHDTHKHFAKELEAEGDLKAAEEHFLEAGD---  910 (1636)
T ss_pred             hheeEEcc-----Cch-----HHHHHHHhhCcchHHHHHHHHhChhhhhHHHHHHHHHHHhccChhHHHHHHHhhhh---
Confidence            66653321     122     2355667777777766666654421 122444555666666777766666544332   


Q ss_pred             CCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHHHHH
Q 040394          529 QPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLH  608 (691)
Q Consensus       529 ~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~  608 (691)
                            |...+..|...+.+++|.++-+   ..-|-....    .+.-...+.=--+.|.+++.+.+.      ...-+.
T Consensus       911 ------~kaavnmyk~s~lw~dayriak---tegg~n~~k----~v~flwaksiggdaavkllnk~gl------l~~~id  971 (1636)
T KOG3616|consen  911 ------FKAAVNMYKASELWEDAYRIAK---TEGGANAEK----HVAFLWAKSIGGDAAVKLLNKHGL------LEAAID  971 (1636)
T ss_pred             ------HHHHHHHhhhhhhHHHHHHHHh---ccccccHHH----HHHHHHHHhhCcHHHHHHHHhhhh------HHHHhh
Confidence                  3334444555556666655543   111111111    111111222222334444444321      111112


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          609 GCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       609 ~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      -.+..+-++-|.++-+-..+  ...+.....++..+...|++++|.+.+-+.++.+-
T Consensus       972 ~a~d~~afd~afdlari~~k--~k~~~vhlk~a~~ledegk~edaskhyveaiklnt 1026 (1636)
T KOG3616|consen  972 FAADNCAFDFAFDLARIAAK--DKMGEVHLKLAMFLEDEGKFEDASKHYVEAIKLNT 1026 (1636)
T ss_pred             hhhcccchhhHHHHHHHhhh--ccCccchhHHhhhhhhccchhhhhHhhHHHhhccc
Confidence            22233444444444332222  12234555666666777777777666666555443

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=99.26  E-value=9.7e-08  Score=96.13  Aligned_cols=422  Identities=13%  Similarity=0.102  Sum_probs=213.5

Q ss_pred             HcccCChhHHHHHHHHHH-------HhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChh
Q 040394          156 CCELRDIDEGMKVHCEIV-------KVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQ  228 (691)
Q Consensus       156 ~~~~~~~~~a~~~~~~~~-------~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~  228 (691)
                      |+..|++.+|..+++-..       +.|.+....|..-.....-..++.+|..+|-+-.     .-...|..|....+|+
T Consensus       500 faai~dvak~r~lhd~~eiadeas~~~ggdgt~fykvra~lail~kkfk~ae~ifleqn-----~te~aigmy~~lhkwd  574 (1636)
T KOG3616|consen  500 FAAIGDVAKARFLHDILEIADEASIEIGGDGTDFYKVRAMLAILEKKFKEAEMIFLEQN-----ATEEAIGMYQELHKWD  574 (1636)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHhhCCCCchHHHHHHHHHHHHhhhhHHHHHHHhcc-----cHHHHHHHHHHHHhHH
Confidence            334455555554444332       2233333444444444444556777777764421     1123345555556677


Q ss_pred             HHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHh--
Q 040394          229 EGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDE--  306 (691)
Q Consensus       229 ~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~--  306 (691)
                      +|+.+-+-.   |.+.-...-.+-+.++...|+-+.|-++-    .    .+-. --+-|..|.+.|..-+|.+....  
T Consensus       575 e~i~lae~~---~~p~~eklk~sy~q~l~dt~qd~ka~elk----~----sdgd-~laaiqlyika~~p~~a~~~a~n~~  642 (1636)
T KOG3616|consen  575 EAIALAEAK---GHPALEKLKRSYLQALMDTGQDEKAAELK----E----SDGD-GLAAIQLYIKAGKPAKAARAALNDE  642 (1636)
T ss_pred             HHHHHHHhc---CChHHHHHHHHHHHHHHhcCchhhhhhhc----c----ccCc-cHHHHHHHHHcCCchHHHHhhcCHH
Confidence            766654332   22111222234455555555555544331    1    0111 12345667777776666554321  


Q ss_pred             cCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCC--chhHH
Q 040394          307 LCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLE--DYTVI  384 (691)
Q Consensus       307 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~  384 (691)
                      ....|......+..++.+..-+++|-++|+++..    |     ...+.++.+..-+-+|.++-+..    .+  -...-
T Consensus       643 ~l~~de~il~~ia~alik~elydkagdlfeki~d----~-----dkale~fkkgdaf~kaielarfa----fp~evv~le  709 (1636)
T KOG3616|consen  643 ELLADEEILEHIAAALIKGELYDKAGDLFEKIHD----F-----DKALECFKKGDAFGKAIELARFA----FPEEVVKLE  709 (1636)
T ss_pred             HhhccHHHHHHHHHHHHhhHHHHhhhhHHHHhhC----H-----HHHHHHHHcccHHHHHHHHHHhh----CcHHHhhHH
Confidence            1223444444445555555555555555555432    1     11222222222233333221111    11  11112


Q ss_pred             HHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC
Q 040394          385 NALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSS  464 (691)
Q Consensus       385 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~  464 (691)
                      ......+...|+++.|...|-+...                       ....+.+......+..|..+++.+.++.   .
T Consensus       710 e~wg~hl~~~~q~daainhfiea~~-----------------------~~kaieaai~akew~kai~ildniqdqk---~  763 (1636)
T KOG3616|consen  710 EAWGDHLEQIGQLDAAINHFIEANC-----------------------LIKAIEAAIGAKEWKKAISILDNIQDQK---T  763 (1636)
T ss_pred             HHHhHHHHHHHhHHHHHHHHHHhhh-----------------------HHHHHHHHhhhhhhhhhHhHHHHhhhhc---c
Confidence            3334445555666666655544321                       1223344455666777777777666553   3


Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcc
Q 040394          465 NVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSH  544 (691)
Q Consensus       465 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~  544 (691)
                      ....|..+.+-|...|+++.|.++|-+.-     .++-.|..|.+.|+++.|.++-.+..  |.......|..-..-+-+
T Consensus       764 ~s~yy~~iadhyan~~dfe~ae~lf~e~~-----~~~dai~my~k~~kw~da~kla~e~~--~~e~t~~~yiakaedlde  836 (1636)
T KOG3616|consen  764 ASGYYGEIADHYANKGDFEIAEELFTEAD-----LFKDAIDMYGKAGKWEDAFKLAEECH--GPEATISLYIAKAEDLDE  836 (1636)
T ss_pred             ccccchHHHHHhccchhHHHHHHHHHhcc-----hhHHHHHHHhccccHHHHHHHHHHhc--CchhHHHHHHHhHHhHHh
Confidence            44556667777777777777777776543     34555677777777777777665543  223333445444455566


Q ss_pred             cCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 040394          545 TGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIK  624 (691)
Q Consensus       545 ~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~  624 (691)
                      .|++.+|.++|-.+     -.|+.     -|.+|-+.|..++.+++.++.....-..|...+..-+-..|+...|+..|-
T Consensus       837 hgkf~eaeqlyiti-----~~p~~-----aiqmydk~~~~ddmirlv~k~h~d~l~dt~~~f~~e~e~~g~lkaae~~fl  906 (1636)
T KOG3616|consen  837 HGKFAEAEQLYITI-----GEPDK-----AIQMYDKHGLDDDMIRLVEKHHGDHLHDTHKHFAKELEAEGDLKAAEEHFL  906 (1636)
T ss_pred             hcchhhhhheeEEc-----cCchH-----HHHHHHhhCcchHHHHHHHHhChhhhhHHHHHHHHHHHhccChhHHHHHHH
Confidence            77777777666543     13442     345667777777777777766322223455556666666777777766665


Q ss_pred             HHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHH
Q 040394          625 KMLELHPDKACYYVLVSNLYASDGRWIRVNQVRE  658 (691)
Q Consensus       625 ~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~  658 (691)
                      ++-+        +..-.++|..++.|++|.++-+
T Consensus       907 ea~d--------~kaavnmyk~s~lw~dayriak  932 (1636)
T KOG3616|consen  907 EAGD--------FKAAVNMYKASELWEDAYRIAK  932 (1636)
T ss_pred             hhhh--------HHHHHHHhhhhhhHHHHHHHHh
Confidence            5332        2233455566666666655443

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.25  E-value=6.3e-06  Score=86.48  Aligned_cols=272  Identities=10%  Similarity=0.063  Sum_probs=133.8

Q ss_pred             CChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHH----HH------HhCCCCCch----hH------HHHHH
Q 040394          361 GNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARY----IF------ETTSEKDVI----AW------NSIIS  420 (691)
Q Consensus       361 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~----~~------~~~~~~~~~----~~------~~li~  420 (691)
                      +++..-..+++.....|..++.++|++...|...++-.+-.-    .|      +-..++|+.    +|      .-+| 
T Consensus       852 NRLklLlp~LE~~i~eG~~d~a~hnAlaKIyIDSNNnPE~fLkeN~yYDs~vVGkYCEKRDP~lA~vaYerGqcD~elI-  930 (1666)
T KOG0985|consen  852 NRLKLLLPWLESLIQEGSQDPATHNALAKIYIDSNNNPERFLKENPYYDSKVVGKYCEKRDPHLACVAYERGQCDLELI-  930 (1666)
T ss_pred             hhHHHHHHHHHHHHhccCcchHHHhhhhheeecCCCChHHhcccCCcchhhHHhhhhcccCCceEEEeecccCCcHHHH-
Confidence            333344456677788888899999999999988776443210    00      011111110    00      0011 


Q ss_pred             hhhCCCCCCHHHHHHHHHHHhccCcHHHHHHH-----------HHHHHHcCC-CCCchhHHHHHHHHHHhcCCHHHHHHH
Q 040394          421 GLDDNVSPDAVTLVSVISACASLGAVQVGSSL-----------HAYSTKQGL-LSSNVYVGTALLNFYAKCGDAQSARMV  488 (691)
Q Consensus       421 ~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~-----------~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~  488 (691)
                          ++-.....|....+-+.++.+.+.-.++           .+.....++ ...++.-...-+.++...+-..+-.++
T Consensus       931 ----~vcNeNSlfK~~aRYlv~R~D~~LW~~VL~e~n~~rRqLiDqVv~tal~E~~dPe~vS~tVkAfMtadLp~eLIEL 1006 (1666)
T KOG0985|consen  931 ----NVCNENSLFKSQARYLVERSDPDLWAKVLNEENPYRRQLIDQVVQTALPETQDPEEVSVTVKAFMTADLPNELIEL 1006 (1666)
T ss_pred             ----HhcCchhHHHHHHHHHHhccChHHHHHHHhccChHHHHHHHHHHHhcCCccCChHHHHHHHHHHHhcCCcHHHHHH
Confidence                1112223344444444445554443333           333343333 124566667778888888888888888


Q ss_pred             HHhcc-cCC-----HhHHHHHHHHH---------------------------hcCCChHHHHHHHHHHHHCCCCCCHHHH
Q 040394          489 FDAMR-EKN-----TVTWSAMIGGY---------------------------GMQGDGGGSLALFSDMLNEEVQPNEVIF  535 (691)
Q Consensus       489 ~~~~~-~~~-----~~~~~~li~~~---------------------------~~~~~~~~A~~~~~~m~~~g~~p~~~~~  535 (691)
                      ++++. +++     ...-|.|+-..                           ..++-+++|+.+|++.     ..+....
T Consensus      1007 LEKIvL~~S~Fse~~nLQnLLiLtAikad~trVm~YI~rLdnyDa~~ia~iai~~~LyEEAF~ifkkf-----~~n~~A~ 1081 (1666)
T KOG0985|consen 1007 LEKIVLDNSVFSENRNLQNLLILTAIKADRTRVMEYINRLDNYDAPDIAEIAIENQLYEEAFAIFKKF-----DMNVSAI 1081 (1666)
T ss_pred             HHHHhcCCcccccchhhhhhHHHHHhhcChHHHHHHHHHhccCCchhHHHHHhhhhHHHHHHHHHHHh-----cccHHHH
Confidence            88876 221     11222222222                           2233344444444432     2222222


Q ss_pred             HHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC
Q 040394          536 TTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSR  615 (691)
Q Consensus       536 ~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~g~  615 (691)
                      +.++.   ..+.+++|.++-++.       -.+..|+.+..+-.+.|...+|++-|-+..   |+..|...+..+.+.|.
T Consensus      1082 ~VLie---~i~~ldRA~efAe~~-------n~p~vWsqlakAQL~~~~v~dAieSyikad---Dps~y~eVi~~a~~~~~ 1148 (1666)
T KOG0985|consen 1082 QVLIE---NIGSLDRAYEFAERC-------NEPAVWSQLAKAQLQGGLVKDAIESYIKAD---DPSNYLEVIDVASRTGK 1148 (1666)
T ss_pred             HHHHH---HhhhHHHHHHHHHhh-------CChHHHHHHHHHHHhcCchHHHHHHHHhcC---CcHHHHHHHHHHHhcCc
Confidence            22222   233444444444332       123456666666666666666666555543   44556666666666666


Q ss_pred             HHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHH
Q 040394          616 FDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQV  656 (691)
Q Consensus       616 ~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~  656 (691)
                      +++-..++.-+.+.... +.+-..|+.+|++.++..+-.++
T Consensus      1149 ~edLv~yL~MaRkk~~E-~~id~eLi~AyAkt~rl~elE~f 1188 (1666)
T KOG0985|consen 1149 YEDLVKYLLMARKKVRE-PYIDSELIFAYAKTNRLTELEEF 1188 (1666)
T ss_pred             HHHHHHHHHHHHHhhcC-ccchHHHHHHHHHhchHHHHHHH
Confidence            66666665555443222 22333344444555554444333

>PF13041 PPR_2: PPR repeat family

Probab=99.24  E-value=2.3e-11  Score=82.02  Aligned_cols=50  Identities=28%  Similarity=0.494  Sum_probs=48.1

Q ss_pred             CChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhc
Q 040394          310 IDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQ  359 (691)
Q Consensus       310 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~  359 (691)
                      ||+++||++|.+|++.|++++|.++|++|.+.|+.||..||+.+|++|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            78999999999999999999999999999999999999999999999874

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.22  E-value=1e-07  Score=87.90  Aligned_cols=470  Identities=11%  Similarity=0.050  Sum_probs=285.9

Q ss_pred             HHHHcccCChhHHHHHHHHHHHhCCC-ChhHHHHHHHHhHhcCChHHHHHHHhccCC---CChhhHHHHHHHHHhCCChh
Q 040394          153 LKACCELRDIDEGMKVHCEIVKVGGP-DSFVLTGLVDMYAKCRDIGSSRQVFDETLD---KNVVSWTSMIAGYVQNDCAQ  228 (691)
Q Consensus       153 l~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~g~~~  228 (691)
                      +.-+....|+..|..+++.-...+-+ ...+-.-+..++.+.|++++|...+..+.+   ++...+-.|..++.-.|.+.
T Consensus        29 Ledfls~rDytGAislLefk~~~~~EEE~~~~lWia~C~fhLgdY~~Al~~Y~~~~~~~~~~~el~vnLAcc~FyLg~Y~  108 (557)
T KOG3785|consen   29 LEDFLSNRDYTGAISLLEFKLNLDREEEDSLQLWIAHCYFHLGDYEEALNVYTFLMNKDDAPAELGVNLACCKFYLGQYI  108 (557)
T ss_pred             HHHHHhcccchhHHHHHHHhhccchhhhHHHHHHHHHHHHhhccHHHHHHHHHHHhccCCCCcccchhHHHHHHHHHHHH
Confidence            44455677888888888877765544 334445567788899999999999987643   56677777877777888899


Q ss_pred             HHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcC
Q 040394          229 EGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELC  308 (691)
Q Consensus       229 ~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~  308 (691)
                      +|..+-....+     +.---..++...-+.|+-++-..+.+.+.+.     ..---+|.......-.+.+|++++.++.
T Consensus       109 eA~~~~~ka~k-----~pL~~RLlfhlahklndEk~~~~fh~~LqD~-----~EdqLSLAsvhYmR~HYQeAIdvYkrvL  178 (557)
T KOG3785|consen  109 EAKSIAEKAPK-----TPLCIRLLFHLAHKLNDEKRILTFHSSLQDT-----LEDQLSLASVHYMRMHYQEAIDVYKRVL  178 (557)
T ss_pred             HHHHHHhhCCC-----ChHHHHHHHHHHHHhCcHHHHHHHHHHHhhh-----HHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            98887666522     2333344555556777777766666665432     1233445555555567899999999884


Q ss_pred             C--CChhHHHHHH-HHHHhcCCchhHHHHHHHhhHCCCCCcHH-HHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHH
Q 040394          309 S--IDLVSWTAMI-VGYTQSGYPDKALKLFTDKKWADFFPNHV-TIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVI  384 (691)
Q Consensus       309 ~--~~~~~~~~li-~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  384 (691)
                      .  |+-...|.-+ -.|.+..-++-+.++++-....  .||+. ..+.......+.=+-..|++-.+.+.+.+.......
T Consensus       179 ~dn~ey~alNVy~ALCyyKlDYydvsqevl~vYL~q--~pdStiA~NLkacn~fRl~ngr~ae~E~k~ladN~~~~~~f~  256 (557)
T KOG3785|consen  179 QDNPEYIALNVYMALCYYKLDYYDVSQEVLKVYLRQ--FPDSTIAKNLKACNLFRLINGRTAEDEKKELADNIDQEYPFI  256 (557)
T ss_pred             hcChhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHh--CCCcHHHHHHHHHHHhhhhccchhHHHHHHHHhcccccchhH
Confidence            3  4444555444 3566777777777777776654  44443 233222222222222223333333333322211111


Q ss_pred             HHHHHH-hHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCC
Q 040394          385 NALVDM-YAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLS  463 (691)
Q Consensus       385 ~~l~~~-~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  463 (691)
                      ..+++. +.--..-+.|++++-.+.+                +-|  ..-..|+--|.+.+++.+|..+.+++.     |
T Consensus       257 ~~l~rHNLVvFrngEgALqVLP~L~~----------------~IP--EARlNL~iYyL~q~dVqeA~~L~Kdl~-----P  313 (557)
T KOG3785|consen  257 EYLCRHNLVVFRNGEGALQVLPSLMK----------------HIP--EARLNLIIYYLNQNDVQEAISLCKDLD-----P  313 (557)
T ss_pred             HHHHHcCeEEEeCCccHHHhchHHHh----------------hCh--HhhhhheeeecccccHHHHHHHHhhcC-----C
Confidence            111110 0011122334444333221                222  233455556788999999988776542     4


Q ss_pred             CchhHHHHHHHHHHhcC-------CHHHHHHHHHhcccC-----CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCC
Q 040394          464 SNVYVGTALLNFYAKCG-------DAQSARMVFDAMREK-----NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPN  531 (691)
Q Consensus       464 ~~~~~~~~l~~~~~~~g-------~~~~A~~~~~~~~~~-----~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~  531 (691)
                      .++.-|-.-.-.++..|       ...-|...|+..-+.     .+..-.++...+.-..++++++-.+...... +..|
T Consensus       314 ttP~EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQsmAs~fFL~~qFddVl~YlnSi~sY-F~Nd  392 (557)
T KOG3785|consen  314 TTPYEYILKGVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQSMASYFFLSFQFDDVLTYLNSIESY-FTND  392 (557)
T ss_pred             CChHHHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHH-hcCc
Confidence            45544433333333333       344566666655432     3445666777777778889999888888775 3344


Q ss_pred             HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHH-HHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHHH-HHH
Q 040394          532 EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHY-VCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAF-LHG  609 (691)
Q Consensus       532 ~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~-~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l-~~~  609 (691)
                      ...-..+.++.+..|++.+|+++|-.+ ....++ |..+| ..|.+.|.+++.++-|++++-++..+.+..+...+ ..-
T Consensus       393 D~Fn~N~AQAk~atgny~eaEelf~~i-s~~~ik-n~~~Y~s~LArCyi~nkkP~lAW~~~lk~~t~~e~fsLLqlIAn~  470 (557)
T KOG3785|consen  393 DDFNLNLAQAKLATGNYVEAEELFIRI-SGPEIK-NKILYKSMLARCYIRNKKPQLAWDMMLKTNTPSERFSLLQLIAND  470 (557)
T ss_pred             chhhhHHHHHHHHhcChHHHHHHHhhh-cChhhh-hhHHHHHHHHHHHHhcCCchHHHHHHHhcCCchhHHHHHHHHHHH
Confidence            443345678999999999999999876 332333 34444 45678889999999999999999755555555444 456


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCccCCC
Q 040394          610 CGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPG  670 (691)
Q Consensus       610 ~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~~~~~  670 (691)
                      |.+.+.+=-|-+.|..+..++|+ +..|.         |+...-..++..+....-.|.|+
T Consensus       471 CYk~~eFyyaaKAFd~lE~lDP~-pEnWe---------GKRGACaG~f~~l~~~~~~~~p~  521 (557)
T KOG3785|consen  471 CYKANEFYYAAKAFDELEILDPT-PENWE---------GKRGACAGLFRQLANHKTDPIPI  521 (557)
T ss_pred             HHHHHHHHHHHHhhhHHHccCCC-ccccC---------CccchHHHHHHHHHcCCCCCCch
Confidence            88899988888899888888888 66664         34444455666665544444443

>PRK12370 invasion protein regulator; Provisional

Probab=99.19  E-value=6.5e-09  Score=110.65  Aligned_cols=246  Identities=11%  Similarity=0.003  Sum_probs=181.1

Q ss_pred             CChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCC-HHHHHHHHHHHh---------ccCcHHHHHHHHHHHHHcCCCCC
Q 040394          395 HVIADARYIFETTSEKDVIAWNSIISGLDDNVSPD-AVTLVSVISACA---------SLGAVQVGSSLHAYSTKQGLLSS  464 (691)
Q Consensus       395 g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~-~~~~~~ll~~~~---------~~~~~~~a~~~~~~~~~~~~~~~  464 (691)
                      +.+++|...|++..+.|                |+ ...+..+..++.         ..++.++|...+++..+.+  |.
T Consensus       275 ~~~~~A~~~~~~Al~ld----------------P~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~ld--P~  336 (553)
T PRK12370        275 YSLQQALKLLTQCVNMS----------------PNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATELD--HN  336 (553)
T ss_pred             HHHHHHHHHHHHHHhcC----------------CccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhcC--CC
Confidence            34678888888887653                44 334444444332         2345899999999999988  78


Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHH-HHHHHHH
Q 040394          465 NVYVGTALLNFYAKCGDAQSARMVFDAMRE--K-NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEV-IFTTILS  540 (691)
Q Consensus       465 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~-~~~~ll~  540 (691)
                      +...+..+...+...|++++|...|++..+  | +...|..+...+...|++++|+..+++..+.  .|+.. .+..++.
T Consensus       337 ~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l--~P~~~~~~~~~~~  414 (553)
T PRK12370        337 NPQALGLLGLINTIHSEYIVGSLLFKQANLLSPISADIKYYYGWNLFMAGQLEEALQTINECLKL--DPTRAAAGITKLW  414 (553)
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCChhhHHHHHH
Confidence            899999999999999999999999999775  4 4668888999999999999999999999985  55532 3333444


Q ss_pred             HhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCHH-HHHHHHHHHHhcCCHH
Q 040394          541 ACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEPDVS-LFGAFLHGCGLYSRFD  617 (691)
Q Consensus       541 ~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~~-~~~~l~~~~~~~g~~~  617 (691)
                      .+...|++++|...+++....  ..|+ ...+..+..+|...|+.++|.+.++++ ...|+.. ..+.+...+...|  +
T Consensus       415 ~~~~~g~~eeA~~~~~~~l~~--~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~~~~~~~~~~l~~~~~~~g--~  490 (553)
T PRK12370        415 ITYYHTGIDDAIRLGDELRSQ--HLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQEITGLIAVNLLYAEYCQNS--E  490 (553)
T ss_pred             HHHhccCHHHHHHHHHHHHHh--ccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhccchhHHHHHHHHHHHhccH--H
Confidence            566689999999999987433  2354 555777888899999999999999998 4455543 4555556667777  4


Q ss_pred             HHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          618 LGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       618 ~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      .|...++++++..-..+.....+..+|.-.|+-+.+..+ +++.+.|.
T Consensus       491 ~a~~~l~~ll~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~  537 (553)
T PRK12370        491 RALPTIREFLESEQRIDNNPGLLPLVLVAHGEAIAEKMW-NKFKNEDN  537 (553)
T ss_pred             HHHHHHHHHHHHhhHhhcCchHHHHHHHHHhhhHHHHHH-HHhhccch
Confidence            888888887763222222222366778888888888777 88877654

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=99.18  E-value=4.2e-07  Score=95.05  Aligned_cols=565  Identities=11%  Similarity=-0.007  Sum_probs=273.9

Q ss_pred             hHHHHHHHHHHhCCCCch--hhhHHHHHHhcCCChHHHHHHhccCCC---CCcchHHHHHHHHHhCCChhHHHHHHHHHH
Q 040394           64 SLKAFHALLIVDGLTNDK--CNTKLVSMYGSFGHVKYARSVFDSMPN---PDFYSFQVMIRWYFLNDLYKDIVEFYKCMR  138 (691)
Q Consensus        64 ~a~~~~~~~~~~~~~~~~--~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  138 (691)
                      .+..++..+......++-  .|..|...|....+...|.+.|++.-+   .+..++......|++..+++.|..+.-..-
T Consensus       474 ~~~al~ali~alrld~~~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLDatdaeaaaa~adtyae~~~we~a~~I~l~~~  553 (1238)
T KOG1127|consen  474 SALALHALIRALRLDVSLAPAFAFLGQIYRDSDDMKRAKKCFDKAFELDATDAEAAAASADTYAEESTWEEAFEICLRAA  553 (1238)
T ss_pred             HHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhhHHHHHHHhhccccHHHHHHHHHHHh
Confidence            445555555544444444  788899999988888899999987755   456678888899999999999988743332


Q ss_pred             HcCC-CCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCCChh-hHHH
Q 040394          139 KRLK-EHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVV-SWTS  216 (691)
Q Consensus       139 ~~~~-~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~  216 (691)
                      +... ..-...|...--.+...++...|..-|+...+..|.|...|..|+.+|.++|++..|.++|++...-++. .|..
T Consensus       554 qka~a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR~dPkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~LrP~s~y~~  633 (1238)
T KOG1127|consen  554 QKAPAFACKENWVQRGPYYLEAHNLHGAVCEFQSALRTDPKDYNLWLGLGEAYPESGRYSHALKVFTKASLLRPLSKYGR  633 (1238)
T ss_pred             hhchHHHHHhhhhhccccccCccchhhHHHHHHHHhcCCchhHHHHHHHHHHHHhcCceehHHHhhhhhHhcCcHhHHHH
Confidence            2210 0011223333334567788889999999988888889999999999999999999999999776442222 2222


Q ss_pred             H--HHHHHhCCChhHHHHHHHHHHhCC------CCCChhhHHHHHHHHHccCChhhHHHHHHHHHH-------HCCCCch
Q 040394          217 M--IAGYVQNDCAQEGLVLFNRMREGF------VEGNQITLGSLVTACAKLRALHQGKWLHGYILK-------IGIEINS  281 (691)
Q Consensus       217 l--i~~~~~~g~~~~A~~~~~~m~~~~------~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~-------~g~~~~~  281 (691)
                      .  ....+..|.+.+|+..+.......      ..--..++..+...+...|-...+..+++.-++       .....+.
T Consensus       634 fk~A~~ecd~GkYkeald~l~~ii~~~s~e~~~q~gLaE~~ir~akd~~~~gf~~kavd~~eksie~f~~~l~h~~~~~~  713 (1238)
T KOG1127|consen  634 FKEAVMECDNGKYKEALDALGLIIYAFSLERTGQNGLAESVIRDAKDSAITGFQKKAVDFFEKSIESFIVSLIHSLQSDR  713 (1238)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHhhhhhH
Confidence            2  223466788888888887764311      111122222222223333333333333332221       1111111


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhcCCCChh--HHHHHHHH-HHhcCCc---h---hHHHHHHHhhHCCCCCcHHHHHH
Q 040394          282 HLVTALLDMYVKCGNIRDARSVFDELCSIDLV--SWTAMIVG-YTQSGYP---D---KALKLFTDKKWADFFPNHVTIAS  352 (691)
Q Consensus       282 ~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~--~~~~li~~-~~~~g~~---~---~a~~~~~~m~~~g~~p~~~t~~~  352 (691)
                      ..|-.+          ..|..+|-... |+.+  .+..++.. +-..+..   |   -+.+.+-.-..  ...+..+|..
T Consensus       714 ~~Wi~a----------sdac~~f~q~e-~~~vn~h~l~il~~q~e~~~~l~~~d~l~Lg~~c~~~hls--l~~~~~~WyN  780 (1238)
T KOG1127|consen  714 LQWIVA----------SDACYIFSQEE-PSIVNMHYLIILSKQLEKTGALKKNDLLFLGYECGIAHLS--LAIHMYPWYN  780 (1238)
T ss_pred             HHHHHH----------hHHHHHHHHhc-ccchHHHHHHHHHHHHHhcccCcchhHHHHHHHHhhHHHH--HhhccchHHH
Confidence            111111          12223333322 2211  11111111 1111111   0   00000000000  0111222222


Q ss_pred             HHHHHhc-------CCC-hhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhC
Q 040394          353 VLSASAQ-------LGN-LNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDD  424 (691)
Q Consensus       353 ll~~~~~-------~~~-~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~  424 (691)
                      +...+.+       .+. ...|...+...++....+...++.|.-. ...|++.-+.--|-+-...              
T Consensus       781 LGinylr~f~~l~et~~~~~~Ai~c~KkaV~L~ann~~~WnaLGVl-sg~gnva~aQHCfIks~~s--------------  845 (1238)
T KOG1127|consen  781 LGINYLRYFLLLGETMKDACTAIRCCKKAVSLCANNEGLWNALGVL-SGIGNVACAQHCFIKSRFS--------------  845 (1238)
T ss_pred             HhHHHHHHHHHcCCcchhHHHHHHHHHHHHHHhhccHHHHHHHHHh-hccchhhhhhhhhhhhhhc--------------
Confidence            2221111       111 1233444444444444444444444333 3334444443333322211              


Q ss_pred             CCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcc-----c---CC
Q 040394          425 NVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMR-----E---KN  496 (691)
Q Consensus       425 ~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-----~---~~  496 (691)
                       .+....+|..+.-.+....+++-|...|.......  |.+...+..........|+.-++..+|..--     +   ++
T Consensus       846 -ep~~~~~W~NlgvL~l~n~d~E~A~~af~~~qSLd--P~nl~~WlG~Ali~eavG~ii~~~~lfaHs~el~~~~gka~~  922 (1238)
T KOG1127|consen  846 -EPTCHCQWLNLGVLVLENQDFEHAEPAFSSVQSLD--PLNLVQWLGEALIPEAVGRIIERLILFAHSDELCSKEGKAKK  922 (1238)
T ss_pred             -cccchhheeccceeEEecccHHHhhHHHHhhhhcC--chhhHHHHHHHHhHHHHHHHHHHHHHHHhhHHhhccccccch
Confidence             23344556666666666667777777777666655  4555555444444455566666666655411     1   12


Q ss_pred             HhHHHHHHHHHhcCCChHHHHHHHHHHHH---------CCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC
Q 040394          497 TVTWSAMIGGYGMQGDGGGSLALFSDMLN---------EEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS  567 (691)
Q Consensus       497 ~~~~~~li~~~~~~~~~~~A~~~~~~m~~---------~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~  567 (691)
                      ..-|-....-...+|+.++-+...+.+-.         .|.+-+...|.+......+.+.+..|.+...+...-...+.+
T Consensus       923 f~Yw~c~te~h~~Ng~~e~~I~t~~ki~sAs~al~~yf~~~p~~~fAy~~~gstlEhL~ey~~a~ela~RliglLe~k~d 1002 (1238)
T KOG1127|consen  923 FQYWLCATEIHLQNGNIEESINTARKISSASLALSYYFLGHPQLCFAYAANGSTLEHLEEYRAALELATRLIGLLELKLD 1002 (1238)
T ss_pred             hhHHHHHHHHHHhccchHHHHHHhhhhhhhHHHHHHHHhcCcchhHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            22233333333444444433322222211         122333345555555555555555555554443322223333


Q ss_pred             hhHHH----HHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCch---hHHHH
Q 040394          568 MKHYV----CMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKAC---YYVLV  640 (691)
Q Consensus       568 ~~~~~----~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~---~~~~l  640 (691)
                      ...|+    ...+.++..|.++.|..-+......-+..+-..-+.. .-.|+++++.+.|++++.+..++..   ....+
T Consensus      1003 ~sqynvak~~~gRL~lslgefe~A~~a~~~~~~evdEdi~gt~l~l-Ffkndf~~sl~~fe~aLsis~se~d~vvLl~kv 1081 (1238)
T KOG1127|consen 1003 ESQYNVAKPDAGRLELSLGEFESAKKASWKEWMEVDEDIRGTDLTL-FFKNDFFSSLEFFEQALSISNSESDKVVLLCKV 1081 (1238)
T ss_pred             hhhhhhhhhhhhhhhhhhcchhhHhhhhcccchhHHHHHhhhhHHH-HHHhHHHHHHHHHHHHhhhcccccchhhhhHHH
Confidence            33444    2334455666666665555544323333322222222 3456777777777777775444333   23334


Q ss_pred             HHHHHhCCCcHHHHHHHHHH
Q 040394          641 SNLYASDGRWIRVNQVRELM  660 (691)
Q Consensus       641 ~~~~~~~g~~~~A~~~~~~~  660 (691)
                      +.+...++.-+.|...+=+.
T Consensus      1082 a~~~g~~~~k~~A~~lLfe~ 1101 (1238)
T KOG1127|consen 1082 AVCMGLARQKNDAQFLLFEV 1101 (1238)
T ss_pred             HHHHhhcccchHHHHHHHHH
Confidence            44445555666665554333

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

Probab=99.18  E-value=7.2e-10  Score=100.62  Aligned_cols=229  Identities=10%  Similarity=0.073  Sum_probs=155.4

Q ss_pred             HHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC
Q 040394          385 NALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSS  464 (691)
Q Consensus       385 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~  464 (691)
                      +.+..+|.+.|.+.+|.+.++.-.+.                .|.+.||..|-++|.+..+++.|..++.+..+.-  |.
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q----------------~~~~dTfllLskvY~ridQP~~AL~~~~~gld~f--P~  288 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQ----------------FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDSF--PF  288 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhc----------------CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhcC--Cc
Confidence            67788888889999998888876643                5777788888888888888888888888877765  66


Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhcccC---CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 040394          465 NVYVGTALLNFYAKCGDAQSARMVFDAMREK---NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSA  541 (691)
Q Consensus       465 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~  541 (691)
                      +..........+...++.++|.++++...+.   ++.....+..+|.-.++++.|+..++++.+.|+ -+...|+.+--+
T Consensus       289 ~VT~l~g~ARi~eam~~~~~a~~lYk~vlk~~~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~-~speLf~NigLC  367 (478)
T KOG1129|consen  289 DVTYLLGQARIHEAMEQQEDALQLYKLVLKLHPINVEAIACIAVGYFYDNNPEMALRYYRRILQMGA-QSPELFCNIGLC  367 (478)
T ss_pred             hhhhhhhhHHHHHHHHhHHHHHHHHHHHHhcCCccceeeeeeeeccccCCChHHHHHHHHHHHHhcC-CChHHHhhHHHH
Confidence            6666667777788888888888888877652   555555666677777888888888888888774 355566666666


Q ss_pred             hcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 040394          542 CSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEV  621 (691)
Q Consensus       542 ~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~  621 (691)
                      |...+++|-++.-|++.... .-.|+                  +|-            ..|..+.......||+..|.+
T Consensus       368 C~yaqQ~D~~L~sf~RAlst-at~~~------------------~aa------------DvWYNlg~vaV~iGD~nlA~r  416 (478)
T KOG1129|consen  368 CLYAQQIDLVLPSFQRALST-ATQPG------------------QAA------------DVWYNLGFVAVTIGDFNLAKR  416 (478)
T ss_pred             HHhhcchhhhHHHHHHHHhh-ccCcc------------------hhh------------hhhhccceeEEeccchHHHHH
Confidence            66677777766666654211 11222                  111            233334444445566666666


Q ss_pred             HHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          622 MIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       622 ~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      .|+-++.-+|++...+..|+.+-.+.|+.++|..+++.....
T Consensus       417 cfrlaL~~d~~h~ealnNLavL~~r~G~i~~Arsll~~A~s~  458 (478)
T KOG1129|consen  417 CFRLALTSDAQHGEALNNLAVLAARSGDILGARSLLNAAKSV  458 (478)
T ss_pred             HHHHHhccCcchHHHHHhHHHHHhhcCchHHHHHHHHHhhhh
Confidence            666666666666666666666666666666666666655543

>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=99.18  E-value=2.3e-07  Score=95.26  Aligned_cols=302  Identities=13%  Similarity=0.075  Sum_probs=147.2

Q ss_pred             HHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCCCh--h-hHHHHHHHHHhC-----C
Q 040394          154 KACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNV--V-SWTSMIAGYVQN-----D  225 (691)
Q Consensus       154 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~--~-~~~~li~~~~~~-----g  225 (691)
                      ..+...|+.++|.+.++.-...-++...........+.+.|+.++|..++..+.+.|+  . -|..+..+..-.     .
T Consensus        12 ~il~e~g~~~~AL~~L~~~~~~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNPdn~~Yy~~L~~~~g~~~~~~~~   91 (517)
T PF12569_consen   12 SILEEAGDYEEALEHLEKNEKQILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRNPDNYDYYRGLEEALGLQLQLSDE   91 (517)
T ss_pred             HHHHHCCCHHHHHHHHHhhhhhCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHhhhcccccc
Confidence            3445566777777666654444444555666666666666666666666666654322  2 233333333211     2


Q ss_pred             ChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCCh-hhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHH
Q 040394          226 CAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRAL-HQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVF  304 (691)
Q Consensus       226 ~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~-~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~  304 (691)
                      +.+...++|+++...-  |.......+.-.+.....+ ..+..++..+...|+++   +++.|-..|....+.+-..+++
T Consensus        92 ~~~~~~~~y~~l~~~y--p~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPs---lF~~lk~Ly~d~~K~~~i~~l~  166 (517)
T PF12569_consen   92 DVEKLLELYDELAEKY--PRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPS---LFSNLKPLYKDPEKAAIIESLV  166 (517)
T ss_pred             cHHHHHHHHHHHHHhC--ccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCch---HHHHHHHHHcChhHHHHHHHHH
Confidence            3455555666654432  3332222222222221122 23334444445555432   2333333333222222222222


Q ss_pred             HhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcH--HHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchh
Q 040394          305 DELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNH--VTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYT  382 (691)
Q Consensus       305 ~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~--~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~  382 (691)
                      ....           ..+...+.+...-      ....-.|+.  .++..+...+...|++++|..+.+.++.+.|..+.
T Consensus       167 ~~~~-----------~~l~~~~~~~~~~------~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~~e  229 (517)
T PF12569_consen  167 EEYV-----------NSLESNGSFSNGD------DEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPTLVE  229 (517)
T ss_pred             HHHH-----------HhhcccCCCCCcc------ccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCcHH
Confidence            2210           0000000000000      000012222  23334444566666666666666666666666666


Q ss_pred             HHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCC
Q 040394          383 VINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLL  462 (691)
Q Consensus       383 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  462 (691)
                      .|..-.+.|-+.|++.+|.+.++....-|               .-|...-+.....+.+.|++++|..++....+.+. 
T Consensus       230 ly~~KarilKh~G~~~~Aa~~~~~Ar~LD---------------~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~-  293 (517)
T PF12569_consen  230 LYMTKARILKHAGDLKEAAEAMDEARELD---------------LADRYINSKCAKYLLRAGRIEEAEKTASLFTREDV-  293 (517)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhCC---------------hhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCC-
Confidence            66677777777777777777666665543               23444445555566666777777777666665553 


Q ss_pred             CCc--------hhHHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040394          463 SSN--------VYVGTALLNFYAKCGDAQSARMVFDAMR  493 (691)
Q Consensus       463 ~~~--------~~~~~~l~~~~~~~g~~~~A~~~~~~~~  493 (691)
                      .+.        .........+|.+.|++..|++.|..+.
T Consensus       294 ~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk~~~~v~  332 (517)
T PF12569_consen  294 DPLSNLNDMQCMWFETECAEAYLRQGDYGLALKRFHAVL  332 (517)
T ss_pred             CcccCHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            221        1222445667777787777777776655

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 [], [].

>PRK12370 invasion protein regulator; Provisional

Probab=99.16  E-value=6e-09  Score=110.88  Aligned_cols=211  Identities=12%  Similarity=0.001  Sum_probs=168.0

Q ss_pred             CcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHh---------cCCHHHHHHHHHhccc--C-CHhHHHHHHHHHhcCC
Q 040394          444 GAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAK---------CGDAQSARMVFDAMRE--K-NTVTWSAMIGGYGMQG  511 (691)
Q Consensus       444 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~---------~g~~~~A~~~~~~~~~--~-~~~~~~~li~~~~~~~  511 (691)
                      ++.+.|...+++..+..  |.+...+..+..+|..         .+++++|...+++..+  | +...|..+...+...|
T Consensus       275 ~~~~~A~~~~~~Al~ld--P~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~ldP~~~~a~~~lg~~~~~~g  352 (553)
T PRK12370        275 YSLQQALKLLTQCVNMS--PNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATELDHNNPQALGLLGLINTIHS  352 (553)
T ss_pred             HHHHHHHHHHHHHHhcC--CccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcc
Confidence            45689999999999887  6777777777665542         3458899999998875  3 6778888888999999


Q ss_pred             ChHHHHHHHHHHHHCCCCCC-HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCCh-hHHHHHHHHHHhcCChHHHHH
Q 040394          512 DGGGSLALFSDMLNEEVQPN-EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSM-KHYVCMVDLLARAGRLEEALE  589 (691)
Q Consensus       512 ~~~~A~~~~~~m~~~g~~p~-~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~-~~~~~li~~~~~~g~~~~A~~  589 (691)
                      ++++|...+++..+.  .|+ ...+..+..++...|++++|...+++..   .+.|+. ..+..++..+...|++++|++
T Consensus       353 ~~~~A~~~~~~Al~l--~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al---~l~P~~~~~~~~~~~~~~~~g~~eeA~~  427 (553)
T PRK12370        353 EYIVGSLLFKQANLL--SPISADIKYYYGWNLFMAGQLEEALQTINECL---KLDPTRAAAGITKLWITYYHTGIDDAIR  427 (553)
T ss_pred             CHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH---hcCCCChhhHHHHHHHHHhccCHHHHHH
Confidence            999999999999985  455 4567777788999999999999999774   456663 233344556777899999999


Q ss_pred             HHHhC--CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          590 FMENM--PIEPD-VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       590 ~~~~~--~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      .+++.  ...|+ ...+..+..++...|+.++|...++++....|++......++..|...|  ++|...++++.+.
T Consensus       428 ~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~~~~~~~~~~l~~~~~~~g--~~a~~~l~~ll~~  502 (553)
T PRK12370        428 LGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQEITGLIAVNLLYAEYCQNS--ERALPTIREFLES  502 (553)
T ss_pred             HHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhccchhHHHHHHHHHHHhccH--HHHHHHHHHHHHH
Confidence            99887  23454 4456777788889999999999999998889988888888888888888  4888888887663

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.16  E-value=1.6e-08  Score=95.71  Aligned_cols=199  Identities=12%  Similarity=0.110  Sum_probs=164.2

Q ss_pred             CCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHH
Q 040394          428 PDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMI  504 (691)
Q Consensus       428 p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li  504 (691)
                      .....+..+...+...|+++.|...+++..+..  |.+...+..+...+...|++++|.+.+++..+   .+...+..+.
T Consensus        29 ~~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~  106 (234)
T TIGR02521        29 KAAKIRVQLALGYLEQGDLEVAKENLDKALEHD--PDDYLAYLALALYYQQLGELEKAEDSFRRALTLNPNNGDVLNNYG  106 (234)
T ss_pred             cHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHH
Confidence            345677888889999999999999999998876  67788888999999999999999999998764   3566788889


Q ss_pred             HHHhcCCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcC
Q 040394          505 GGYGMQGDGGGSLALFSDMLNEEVQP-NEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAG  582 (691)
Q Consensus       505 ~~~~~~~~~~~A~~~~~~m~~~g~~p-~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g  582 (691)
                      ..+...|++++|.+.+++..+....| ....+..+..++...|++++|.+.+++...   ..|+ ...+..+...+...|
T Consensus       107 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~~~~la~~~~~~~  183 (234)
T TIGR02521       107 TFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQ---IDPQRPESLLELAELYYLRG  183 (234)
T ss_pred             HHHHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCcCChHHHHHHHHHHHHcC
Confidence            99999999999999999998753223 334566677788999999999999998753   3444 667888999999999


Q ss_pred             ChHHHHHHHHhC-CC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC
Q 040394          583 RLEEALEFMENM-PI-EPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHP  631 (691)
Q Consensus       583 ~~~~A~~~~~~~-~~-~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p  631 (691)
                      ++++|.+.+++. .. +.+...+..+...+...|+.++|..+.+.+.+..|
T Consensus       184 ~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~  234 (234)
T TIGR02521       184 QYKDARAYLERYQQTYNQTAESLWLGIRIARALGDVAAAQRYGAQLQKLFP  234 (234)
T ss_pred             CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhhCc
Confidence            999999999987 32 34556677777888899999999999988776654

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.

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.16  E-value=5.7e-06  Score=82.11  Aligned_cols=438  Identities=11%  Similarity=0.060  Sum_probs=202.4

Q ss_pred             HHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCC-CChhHHHHHHHHhH--hcCC
Q 040394          119 RWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGG-PDSFVLTGLVDMYA--KCRD  195 (691)
Q Consensus       119 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~l~~~~~--~~g~  195 (691)
                      +.+...+++++|.....++...+ +-+...+..-+-++.+.+++++|..+.+.   .+. .....+ .+=.+||  +.+.
T Consensus        20 n~~~~~~e~e~a~k~~~Kil~~~-pdd~~a~~cKvValIq~~ky~~ALk~ikk---~~~~~~~~~~-~fEKAYc~Yrlnk   94 (652)
T KOG2376|consen   20 NRHGKNGEYEEAVKTANKILSIV-PDDEDAIRCKVVALIQLDKYEDALKLIKK---NGALLVINSF-FFEKAYCEYRLNK   94 (652)
T ss_pred             HHhccchHHHHHHHHHHHHHhcC-CCcHhhHhhhHhhhhhhhHHHHHHHHHHh---cchhhhcchh-hHHHHHHHHHccc
Confidence            33445556666666666665543 33444555555555666666666543332   111 100011 0222333  4566


Q ss_pred             hHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCC-ChhhHHHHHHHHHccCChhhHHHHHHHHHH
Q 040394          196 IGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEG-NQITLGSLVTACAKLRALHQGKWLHGYILK  274 (691)
Q Consensus       196 ~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~~~~  274 (691)
                      .++|+..++-..+-+..+...-...+-+.|++++|+++|+.+.+++..- +...-..++.+-..    ..+    +.+..
T Consensus        95 ~Dealk~~~~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~----l~~----~~~q~  166 (652)
T KOG2376|consen   95 LDEALKTLKGLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAA----LQV----QLLQS  166 (652)
T ss_pred             HHHHHHHHhcccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHh----hhH----HHHHh
Confidence            6666666664333333344444555666666777777776665543321 11111111111000    000    01222


Q ss_pred             HCCCCchHHHHH---HHHHHHhcCCHHHHHHHHHhc--------CCCCh-----h-----HHHHHHHHHHhcCCchhHHH
Q 040394          275 IGIEINSHLVTA---LLDMYVKCGNIRDARSVFDEL--------CSIDL-----V-----SWTAMIVGYTQSGYPDKALK  333 (691)
Q Consensus       275 ~g~~~~~~~~~~---li~~~~~~g~~~~A~~~~~~~--------~~~~~-----~-----~~~~li~~~~~~g~~~~a~~  333 (691)
                      ....| ..+|..   ....+...|++.+|+++++..        ...|.     .     .--.|...+...|+.++|..
T Consensus       167 v~~v~-e~syel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~ea~~  245 (652)
T KOG2376|consen  167 VPEVP-EDSYELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTAEASS  245 (652)
T ss_pred             ccCCC-cchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchHHHHH
Confidence            22222 122222   233455667777777776654        11111     0     12223445667888888888


Q ss_pred             HHHHhhHCCCCCcHHHHHHH---HHHHhcCCChhhH--HHHHHHH-----------HHhCCC-chhHHHHHHHHhHhcCC
Q 040394          334 LFTDKKWADFFPNHVTIASV---LSASAQLGNLNMG--RMVHSLG-----------IRLGLE-DYTVINALVDMYAKCHV  396 (691)
Q Consensus       334 ~~~~m~~~g~~p~~~t~~~l---l~~~~~~~~~~~a--~~~~~~~-----------~~~~~~-~~~~~~~l~~~~~~~g~  396 (691)
                      ++...+... .+|.......   |.+.....++...  ...++..           ....-. ....-+.++.+|  .+.
T Consensus       246 iy~~~i~~~-~~D~~~~Av~~NNLva~~~d~~~~d~~~l~~k~~~~~~l~~~~l~~Ls~~qk~~i~~N~~lL~l~--tnk  322 (652)
T KOG2376|consen  246 IYVDIIKRN-PADEPSLAVAVNNLVALSKDQNYFDGDLLKSKKSQVFKLAEFLLSKLSKKQKQAIYRNNALLALF--TNK  322 (652)
T ss_pred             HHHHHHHhc-CCCchHHHHHhcchhhhccccccCchHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH--hhh
Confidence            888877763 2333222222   2222222222221  1111110           000000 111123333333  334


Q ss_pred             hHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHh--ccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHH
Q 040394          397 IADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACA--SLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLN  474 (691)
Q Consensus       397 ~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~--~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~  474 (691)
                      -+.+.++....+.                ..|.. .+..++..+.  +......+..++....+... .....+....+.
T Consensus       323 ~~q~r~~~a~lp~----------------~~p~~-~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~~p-~~s~~v~L~~aQ  384 (652)
T KOG2376|consen  323 MDQVRELSASLPG----------------MSPES-LFPILLQEATKVREKKHKKAIELLLQFADGHP-EKSKVVLLLRAQ  384 (652)
T ss_pred             HHHHHHHHHhCCc----------------cCchH-HHHHHHHHHHHHHHHHHhhhHHHHHHHhccCC-chhHHHHHHHHH
Confidence            4555555555542                23333 3334444332  22246667777776666552 233455566677


Q ss_pred             HHHhcCCHHHHHHHHHhcc--------c--CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHC--CCCCCHHHHHHHH---
Q 040394          475 FYAKCGDAQSARMVFDAMR--------E--KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNE--EVQPNEVIFTTIL---  539 (691)
Q Consensus       475 ~~~~~g~~~~A~~~~~~~~--------~--~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~--g~~p~~~~~~~ll---  539 (691)
                      .....|+++.|.+++....        +  ..+.+-..++..+.+.++.+.|..++.+...-  .-.+......+++   
T Consensus       385 l~is~gn~~~A~~il~~~~~~~~ss~~~~~~~P~~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~a  464 (652)
T KOG2376|consen  385 LKISQGNPEVALEILSLFLESWKSSILEAKHLPGTVGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSLMREA  464 (652)
T ss_pred             HHHhcCCHHHHHHHHHHHhhhhhhhhhhhccChhHHHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhHHHHH
Confidence            7788888888888887322        1  12233344555555666655566555554431  0112222222222   


Q ss_pred             -HHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC
Q 040394          540 -SACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM  594 (691)
Q Consensus       540 -~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~  594 (691)
                       ..-.+.|+.++|..+++++.+.  ..+|..+...++.+|++. +++.|..+-+.+
T Consensus       465 a~f~lr~G~~~ea~s~leel~k~--n~~d~~~l~~lV~a~~~~-d~eka~~l~k~L  517 (652)
T KOG2376|consen  465 AEFKLRHGNEEEASSLLEELVKF--NPNDTDLLVQLVTAYARL-DPEKAESLSKKL  517 (652)
T ss_pred             hHHHHhcCchHHHHHHHHHHHHh--CCchHHHHHHHHHHHHhc-CHHHHHHHhhcC
Confidence             2223456666666666666432  234456666666666554 556666655555

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

Probab=99.15  E-value=5.2e-07  Score=85.17  Aligned_cols=301  Identities=12%  Similarity=-0.019  Sum_probs=212.9

Q ss_pred             CCCcHHHHHHHHHHHh--cCCChhhHHHHHHHHHH-hCCC-chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHH
Q 040394          343 FFPNHVTIASVLSASA--QLGNLNMGRMVHSLGIR-LGLE-DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSI  418 (691)
Q Consensus       343 ~~p~~~t~~~ll~~~~--~~~~~~~a~~~~~~~~~-~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~l  418 (691)
                      +.|...+....+.+++  -.++-..+...+-.+.. .-.+ +......+.+++...|+.++|...|++....|       
T Consensus       190 ~~~~~dwls~wika~Aq~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~d-------  262 (564)
T KOG1174|consen  190 VPDHFDWLSKWIKALAQMFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCAN-------  262 (564)
T ss_pred             cCCCccHHHHHHHHHHHHHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhCC-------
Confidence            4444444444444333  33444444444333332 3333 89999999999999999999999999987653       


Q ss_pred             HHhhhCCCCCCHHH-HHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCC-
Q 040394          419 ISGLDDNVSPDAVT-LVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKN-  496 (691)
Q Consensus       419 i~~~~~~~~p~~~~-~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-  496 (691)
                               |+..+ ...-.-.+...|+.+....+...+....  ..+...+-.-.......++++.|+.+-++..+.+ 
T Consensus       263 ---------py~i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~--~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~~  331 (564)
T KOG1174|consen  263 ---------PDNVEAMDLYAVLLGQEGGCEQDSALMDYLFAKV--KYTASHWFVHAQLLYDEKKFERALNFVEKCIDSEP  331 (564)
T ss_pred             ---------hhhhhhHHHHHHHHHhccCHhhHHHHHHHHHhhh--hcchhhhhhhhhhhhhhhhHHHHHHHHHHHhccCc
Confidence                     33221 1111122356677777777777666544  2344444444555666788999999998877643 


Q ss_pred             --HhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHH
Q 040394          497 --TVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQP-NEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVC  573 (691)
Q Consensus       497 --~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p-~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~  573 (691)
                        +..|-.-...+...|++++|.-.|+..+..  .| +...|.-++.+|...|.+.+|...-+...+.  +.-+..+...
T Consensus       332 r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~L--ap~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~--~~~sA~~LtL  407 (564)
T KOG1174|consen  332 RNHEALILKGRLLIALERHTQAVIAFRTAQML--APYRLEIYRGLFHSYLAQKRFKEANALANWTIRL--FQNSARSLTL  407 (564)
T ss_pred             ccchHHHhccHHHHhccchHHHHHHHHHHHhc--chhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH--hhcchhhhhh
Confidence              444444456788899999999999998874  54 6689999999999999999998877765443  2233444444


Q ss_pred             HH-HHHH-hcCChHHHHHHHHhC-CCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCC
Q 040394          574 MV-DLLA-RAGRLEEALEFMENM-PIEPDV-SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGR  649 (691)
Q Consensus       574 li-~~~~-~~g~~~~A~~~~~~~-~~~p~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  649 (691)
                      +. .++. ...--++|.+++++. ...|+- ...+.+...|...|..+.++.++++.+...|+ ...+..|+.++...+.
T Consensus       408 ~g~~V~~~dp~~rEKAKkf~ek~L~~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~~~D-~~LH~~Lgd~~~A~Ne  486 (564)
T KOG1174|consen  408 FGTLVLFPDPRMREKAKKFAEKSLKINPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLIIFPD-VNLHNHLGDIMRAQNE  486 (564)
T ss_pred             hcceeeccCchhHHHHHHHHHhhhccCCccHHHHHHHHHHHHhhCccchHHHHHHHHHhhccc-cHHHHHHHHHHHHhhh
Confidence            42 2333 223458899999987 788876 46777888889999999999999999999999 8899999999999999


Q ss_pred             cHHHHHHHHHHHhCCCc
Q 040394          650 WIRVNQVRELMKQRGLS  666 (691)
Q Consensus       650 ~~~A~~~~~~~~~~g~~  666 (691)
                      +.+|.+.|...+..+.+
T Consensus       487 ~Q~am~~y~~ALr~dP~  503 (564)
T KOG1174|consen  487 PQKAMEYYYKALRQDPK  503 (564)
T ss_pred             HHHHHHHHHHHHhcCcc
Confidence            99999999888776553

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=99.13  E-value=4.1e-07  Score=92.83  Aligned_cols=272  Identities=13%  Similarity=0.067  Sum_probs=167.6

Q ss_pred             hhhhhhhhhcccCCCccccccccccCCCCCCCCCChHHHHhhhcC-----CCc-hhHHHHHhhc-------cCchhHH--
Q 040394            2 KLISLLQRHVSRTKKPKLQLRFFSYTNQQTPTQHELDQTFASFHS-----LPS-IPCLNLLGLC-------KSTGSLK--   66 (691)
Q Consensus         2 ~~~~~~~~~~~~~~~p~~a~~~~~~~~~~~~~~~~~~~a~~~~~~-----~~~-~~~~~ll~~~-------~~~~~a~--   66 (691)
                      |.++++..+-+..++|+.+++.|....-.+-.....+.+. +++.     |.+ ..-..++...       ...+.+.  
T Consensus       228 ~~~~~~~~Lw~~~~~~~~~i~s~~~~l~~~w~~~~l~ka~-l~~~~~~f~~~~~~Ee~~Lllli~es~i~Re~~~d~ils  306 (799)
T KOG4162|consen  228 RAVELLPILWKKLSGPKEAIKSYRRALLRSWSLDPLTKAR-LYKGFALFLPKSGQEEVILLLLIEESLIPRENIEDAILS  306 (799)
T ss_pred             HHHHHhHHHhcCCCCchHHHHhhhHHhhcccccchhHHHH-HhhcccccCCCCcHHHHHHHHHHHhhccccccHHHHHHH
Confidence            4456667777788888887777765544333222222221 2222     111 0011111111       2222222  


Q ss_pred             --HHHHHHHHhCCCCch-hhhHHHHHHhcCCChHHHHHHhccCCC---CCcchHHHHHHHHHhCCChhHHHHHHHHHHHc
Q 040394           67 --AFHALLIVDGLTNDK-CNTKLVSMYGSFGHVKYARSVFDSMPN---PDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKR  140 (691)
Q Consensus        67 --~~~~~~~~~~~~~~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~  140 (691)
                        .....+....+.+++ +|..+.-++.+.|+++.+-+.|++...   .....|+.+...|...|....|+.+++.-...
T Consensus       307 lm~~~~k~r~~~~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~~~~~e~w~~~als~saag~~s~Av~ll~~~~~~  386 (799)
T KOG4162|consen  307 LMLLLRKLRLKKFQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFSFGEHERWYQLALSYSAAGSDSKAVNLLRESLKK  386 (799)
T ss_pred             HHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhHHHHHHHHHHHHHhccchHHHHHHHhhccc
Confidence              223334445577788 999999999999999999999998654   44567999999999999999999999887665


Q ss_pred             CCCC-CcchHHHHHHHHc-ccCChhHHHHHHHHHHHh--CC--C-ChhHHHHHHHHhHhc-----------CChHHHHHH
Q 040394          141 LKEH-DNFVFSKVLKACC-ELRDIDEGMKVHCEIVKV--GG--P-DSFVLTGLVDMYAKC-----------RDIGSSRQV  202 (691)
Q Consensus       141 ~~~~-~~~~~~~ll~~~~-~~~~~~~a~~~~~~~~~~--~~--~-~~~~~~~l~~~~~~~-----------g~~~~A~~~  202 (691)
                      ...| +...+...-+.|. +.+..+++...-...+..  +.  . .+..|..+.-+|...           ....++.+.
T Consensus       387 ~~~ps~~s~~Lmasklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqa  466 (799)
T KOG4162|consen  387 SEQPSDISVLLMASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQA  466 (799)
T ss_pred             ccCCCcchHHHHHHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHH
Confidence            3334 3444444445454 456777777766666662  21  1 555666666665532           223445555


Q ss_pred             HhccCCC---ChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHH
Q 040394          203 FDETLDK---NVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILK  274 (691)
Q Consensus       203 ~~~~~~~---~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~  274 (691)
                      +++..+.   |..+---+.--|+..++.+.|.+..++..+-+-.-+...+..+...+...+++.+|..+.+...+
T Consensus       467 le~av~~d~~dp~~if~lalq~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~  541 (799)
T KOG4162|consen  467 LEEAVQFDPTDPLVIFYLALQYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALE  541 (799)
T ss_pred             HHHHHhcCCCCchHHHHHHHHHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHH
Confidence            6655332   22222223334566778888888888888776666777888888888888888888888776654

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

Probab=99.13  E-value=5.8e-09  Score=90.62  Aligned_cols=161  Identities=19%  Similarity=0.176  Sum_probs=117.4

Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCH-HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHH
Q 040394          500 WSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNE-VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDL  577 (691)
Q Consensus       500 ~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~-~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~  577 (691)
                      ...|..+|.+.|+...|..-+++.++.  .|+. .++..+...|.+.|..+.|.+.|+...   .+.|+ ..+.|.....
T Consensus        38 rlqLal~YL~~gd~~~A~~nlekAL~~--DPs~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAl---sl~p~~GdVLNNYG~F  112 (250)
T COG3063          38 RLQLALGYLQQGDYAQAKKNLEKALEH--DPSYYLAHLVRAHYYQKLGENDLADESYRKAL---SLAPNNGDVLNNYGAF  112 (250)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcCChhhHHHHHHHHH---hcCCCccchhhhhhHH
Confidence            344566777777777777777777774  4443 566667777777788888887777543   45666 6677777778


Q ss_pred             HHhcCChHHHHHHHHhCCCCC----CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHH
Q 040394          578 LARAGRLEEALEFMENMPIEP----DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRV  653 (691)
Q Consensus       578 ~~~~g~~~~A~~~~~~~~~~p----~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A  653 (691)
                      +|..|++++|...|++.-..|    -..+|..++.+..+.|+.+.|+..+++.++.+|+++.....++....+.|++-.|
T Consensus       113 LC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~~~~~l~~a~~~~~~~~y~~A  192 (250)
T COG3063         113 LCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQFPPALLELARLHYKAGDYAPA  192 (250)
T ss_pred             HHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCCChHHHHHHHHHHhcccchHH
Confidence            888888888888887772222    2346777777777888888888888888888888888888888888888888888


Q ss_pred             HHHHHHHHhCCC
Q 040394          654 NQVRELMKQRGL  665 (691)
Q Consensus       654 ~~~~~~~~~~g~  665 (691)
                      .-+++.....+.
T Consensus       193 r~~~~~~~~~~~  204 (250)
T COG3063         193 RLYLERYQQRGG  204 (250)
T ss_pred             HHHHHHHHhccc
Confidence            888877776655

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=99.11  E-value=4.8e-06  Score=85.44  Aligned_cols=337  Identities=12%  Similarity=0.058  Sum_probs=191.8

Q ss_pred             hhhHHH--HHHhcCCChHHHHHHhccCCCCCcchHHHHHHHHHhCCChhHHHHHHHHHHHc-C--------CCCCcchHH
Q 040394           82 CNTKLV--SMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKR-L--------KEHDNFVFS  150 (691)
Q Consensus        82 ~~~~l~--~~~~~~g~~~~A~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~-~--------~~~~~~~~~  150 (691)
                      +...++  +.|.--|+.+.|.+..+-++  +...|..|.+.+.+.++.+-|.-.+..|... |        -.|+ .+=.
T Consensus       728 TRkaml~FSfyvtiG~MD~AfksI~~Ik--S~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~-e~ea  804 (1416)
T KOG3617|consen  728 TRKAMLDFSFYVTIGSMDAAFKSIQFIK--SDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE-EDEA  804 (1416)
T ss_pred             HHHhhhceeEEEEeccHHHHHHHHHHHh--hhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc-chhh
Confidence            344444  45667788898887766554  4467899999998888888777666655321 1        1122 2222


Q ss_pred             HHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCC-ChhhHHHHHHHHHhCCChhH
Q 040394          151 KVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDK-NVVSWTSMIAGYVQNDCAQE  229 (691)
Q Consensus       151 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~~~~~~~li~~~~~~g~~~~  229 (691)
                      .+.-.....|.+++|+.+|++-++.        ..|=..|-..|.+++|.++-+.-.+- =..||..-...+-..++.+.
T Consensus       805 kvAvLAieLgMlEeA~~lYr~ckR~--------DLlNKlyQs~g~w~eA~eiAE~~DRiHLr~Tyy~yA~~Lear~Di~~  876 (1416)
T KOG3617|consen  805 KVAVLAIELGMLEEALILYRQCKRY--------DLLNKLYQSQGMWSEAFEIAETKDRIHLRNTYYNYAKYLEARRDIEA  876 (1416)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHH--------HHHHHHHHhcccHHHHHHHHhhccceehhhhHHHHHHHHHhhccHHH
Confidence            2223334678999999999988874        45556777889999999988764332 23466666777777888899


Q ss_pred             HHHHHHHHH----------hCCC---------CCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHH
Q 040394          230 GLVLFNRMR----------EGFV---------EGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDM  290 (691)
Q Consensus       230 A~~~~~~m~----------~~~~---------~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~  290 (691)
                      |++.|++..          ...+         +.|...|..--.-+-..|+.+.|..+|....         -|-+++..
T Consensus       877 AleyyEK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~---------D~fs~VrI  947 (1416)
T KOG3617|consen  877 ALEYYEKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAK---------DYFSMVRI  947 (1416)
T ss_pred             HHHHHHhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhh---------hhhhheee
Confidence            988887632          1110         1122222222233334455555555554433         23456666


Q ss_pred             HHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHH
Q 040394          291 YVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVH  370 (691)
Q Consensus       291 ~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~  370 (691)
                      .|-.|+.++|-++-++  ..|..+...|.+.|-..|++.+|..+|.+..         +|...|+.|-..+--++-.   
T Consensus       948 ~C~qGk~~kAa~iA~e--sgd~AAcYhlaR~YEn~g~v~~Av~FfTrAq---------afsnAIRlcKEnd~~d~L~--- 1013 (1416)
T KOG3617|consen  948 KCIQGKTDKAARIAEE--SGDKAACYHLARMYENDGDVVKAVKFFTRAQ---------AFSNAIRLCKENDMKDRLA--- 1013 (1416)
T ss_pred             EeeccCchHHHHHHHh--cccHHHHHHHHHHhhhhHHHHHHHHHHHHHH---------HHHHHHHHHHhcCHHHHHH---
Confidence            6777788887777665  3566677778888888999999998887643         4455555444333222211   


Q ss_pred             HHHHHhCCCc-----------hhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHH
Q 040394          371 SLGIRLGLED-----------YTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISA  439 (691)
Q Consensus       371 ~~~~~~~~~~-----------~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~  439 (691)
                      ....-.+..+           ..-....+..|-++|.+.+|+++-=+-.+.  .+...+-..+  .-..|+...+....-
T Consensus      1014 nlal~s~~~d~v~aArYyEe~g~~~~~AVmLYHkAGm~~kALelAF~tqQf--~aL~lIa~DL--d~~sDp~ll~RcadF 1089 (1416)
T KOG3617|consen 1014 NLALMSGGSDLVSAARYYEELGGYAHKAVMLYHKAGMIGKALELAFRTQQF--SALDLIAKDL--DAGSDPKLLRRCADF 1089 (1416)
T ss_pred             HHHhhcCchhHHHHHHHHHHcchhhhHHHHHHHhhcchHHHHHHHHhhccc--HHHHHHHHhc--CCCCCHHHHHHHHHH
Confidence            1111111110           001133456677788887777654332221  0111111111  122344445555555


Q ss_pred             HhccCcHHHHHHHHHHH
Q 040394          440 CASLGAVQVGSSLHAYS  456 (691)
Q Consensus       440 ~~~~~~~~~a~~~~~~~  456 (691)
                      ++...+++.|..++-..
T Consensus      1090 F~~~~qyekAV~lL~~a 1106 (1416)
T KOG3617|consen 1090 FENNQQYEKAVNLLCLA 1106 (1416)
T ss_pred             HHhHHHHHHHHHHHHHH
Confidence            55555666655555433

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

Probab=99.09  E-value=6.3e-09  Score=94.66  Aligned_cols=194  Identities=12%  Similarity=0.117  Sum_probs=156.6

Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhccc--CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHH-HHHHh
Q 040394          466 VYVGTALLNFYAKCGDAQSARMVFDAMRE--KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTT-ILSAC  542 (691)
Q Consensus       466 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~-ll~~~  542 (691)
                      -.--+.+..+|.+.|.+.+|.+.|+.-.+  |-+.||-.|-.+|.+..++..|+.++.+-.+.  .|-.+||.. +.+.+
T Consensus       223 wwWk~Q~gkCylrLgm~r~AekqlqssL~q~~~~dTfllLskvY~ridQP~~AL~~~~~gld~--fP~~VT~l~g~ARi~  300 (478)
T KOG1129|consen  223 WWWKQQMGKCYLRLGMPRRAEKQLQSSLTQFPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS--FPFDVTYLLGQARIH  300 (478)
T ss_pred             HHHHHHHHHHHHHhcChhhhHHHHHHHhhcCCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc--CCchhhhhhhhHHHH
Confidence            33345678888899999999998887653  67778888999999999999999999988874  666666544 45577


Q ss_pred             cccCCHHHHHHHHHHchhhcCCCC-ChhHHHHHHHHHHhcCChHHHHHHHHhC---CCCCCHHHHHHHHHHHHhcCCHHH
Q 040394          543 SHTGMVGEGWKCFYSMCRDFKFVP-SMKHYVCMVDLLARAGRLEEALEFMENM---PIEPDVSLFGAFLHGCGLYSRFDL  618 (691)
Q Consensus       543 ~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~~---~~~p~~~~~~~l~~~~~~~g~~~~  618 (691)
                      ...++.++|.++++...+.   .| +++...++...|.-.++++-|+.+++++   | .-++..|..+.-+|.-.++++-
T Consensus       301 eam~~~~~a~~lYk~vlk~---~~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG-~~speLf~NigLCC~yaqQ~D~  376 (478)
T KOG1129|consen  301 EAMEQQEDALQLYKLVLKL---HPINVEAIACIAVGYFYDNNPEMALRYYRRILQMG-AQSPELFCNIGLCCLYAQQIDL  376 (478)
T ss_pred             HHHHhHHHHHHHHHHHHhc---CCccceeeeeeeeccccCCChHHHHHHHHHHHHhc-CCChHHHhhHHHHHHhhcchhh
Confidence            8889999999999977543   44 4677777888888999999999999987   4 3467788888889999999999


Q ss_pred             HHHHHHHHHhcC--CCC-chhHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          619 GEVMIKKMLELH--PDK-ACYYVLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       619 A~~~~~~~~~~~--p~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      +...|++++...  |+. ..+|+.++.+....|++..|.+-|+..+..+-
T Consensus       377 ~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~  426 (478)
T KOG1129|consen  377 VLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDA  426 (478)
T ss_pred             hHHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCc
Confidence            999999999843  432 47899999999999999999999987776543

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.06  E-value=1.7e-07  Score=94.95  Aligned_cols=125  Identities=12%  Similarity=0.086  Sum_probs=66.6

Q ss_pred             HHHHHHHHhccCcHHHHHHHHHHHHHc-----CCC-CCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC-----------
Q 040394          433 LVSVISACASLGAVQVGSSLHAYSTKQ-----GLL-SSNVYVGTALLNFYAKCGDAQSARMVFDAMREK-----------  495 (691)
Q Consensus       433 ~~~ll~~~~~~~~~~~a~~~~~~~~~~-----~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----------  495 (691)
                      ++.+...|+..++++.|..+++...+.     |.. +....+++.|...|.+.|++++|.++++++.+.           
T Consensus       328 l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~  407 (508)
T KOG1840|consen  328 LSELAAILQSMNEYEEAKKLLQKALKIYLDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYG  407 (508)
T ss_pred             HHHHHHHHHHhcchhHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChh
Confidence            344445555666666666665544321     110 134567777888888888888888887766531           


Q ss_pred             CHhHHHHHHHHHhcCCChHHHHHHHHHHHH----CCC-CCCH-HHHHHHHHHhcccCCHHHHHHHHHH
Q 040394          496 NTVTWSAMIGGYGMQGDGGGSLALFSDMLN----EEV-QPNE-VIFTTILSACSHTGMVGEGWKCFYS  557 (691)
Q Consensus       496 ~~~~~~~li~~~~~~~~~~~A~~~~~~m~~----~g~-~p~~-~~~~~ll~~~~~~g~~~~A~~~~~~  557 (691)
                      .-..++.|...|.+.+++.+|..+|.+...    .|. .|+. .+|..|...|...|+++.|.++.+.
T Consensus       408 ~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~  475 (508)
T KOG1840|consen  408 VGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEK  475 (508)
T ss_pred             hhHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHH
Confidence            122455566666666666666666655332    111 1111 3344444444555555555444443

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.05  E-value=3.2e-08  Score=96.21  Aligned_cols=91  Identities=11%  Similarity=-0.039  Sum_probs=46.2

Q ss_pred             HHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-CHhHHHHHHHHHhc
Q 040394          433 LVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--K-NTVTWSAMIGGYGM  509 (691)
Q Consensus       433 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~li~~~~~  509 (691)
                      |..+...+...|+.+.|...|+...+..  |.++..|+.+...+...|++++|...|+...+  | +...|..+...+..
T Consensus        67 ~~~~g~~~~~~g~~~~A~~~~~~Al~l~--P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~  144 (296)
T PRK11189         67 HYERGVLYDSLGLRALARNDFSQALALR--PDMADAYNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAYLNRGIALYY  144 (296)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            4444444455555555555555555544  44455555555555555555555555555432  2 23444445555555


Q ss_pred             CCChHHHHHHHHHHHH
Q 040394          510 QGDGGGSLALFSDMLN  525 (691)
Q Consensus       510 ~~~~~~A~~~~~~m~~  525 (691)
                      .|++++|++.+++..+
T Consensus       145 ~g~~~eA~~~~~~al~  160 (296)
T PRK11189        145 GGRYELAQDDLLAFYQ  160 (296)
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            5555555555555554

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=99.04  E-value=6.3e-07  Score=91.64  Aligned_cols=252  Identities=12%  Similarity=0.031  Sum_probs=134.2

Q ss_pred             HHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCCh
Q 040394          318 MIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVI  397 (691)
Q Consensus       318 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  397 (691)
                      ...-+-..|+.|.|+.+|...++         |-++++..|-+|+.++|.++-++-     .+..+...+.+.|-..|++
T Consensus       918 WgqYlES~GemdaAl~~Y~~A~D---------~fs~VrI~C~qGk~~kAa~iA~es-----gd~AAcYhlaR~YEn~g~v  983 (1416)
T KOG3617|consen  918 WGQYLESVGEMDAALSFYSSAKD---------YFSMVRIKCIQGKTDKAARIAEES-----GDKAACYHLARMYENDGDV  983 (1416)
T ss_pred             HHHHHhcccchHHHHHHHHHhhh---------hhhheeeEeeccCchHHHHHHHhc-----ccHHHHHHHHHHhhhhHHH
Confidence            33334456777777777765443         455666667777777776654431     1445556677888888888


Q ss_pred             HHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhcc--CcHHHHHHHHHHHHHcCCCCCchhHHHHHHHH
Q 040394          398 ADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASL--GAVQVGSSLHAYSTKQGLLSSNVYVGTALLNF  475 (691)
Q Consensus       398 ~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~--~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~  475 (691)
                      .+|...|.+...     ++..|.....+--     -..|...+...  .+.-.|-++|++.   |      .....-+..
T Consensus       984 ~~Av~FfTrAqa-----fsnAIRlcKEnd~-----~d~L~nlal~s~~~d~v~aArYyEe~---g------~~~~~AVmL 1044 (1416)
T KOG3617|consen  984 VKAVKFFTRAQA-----FSNAIRLCKENDM-----KDRLANLALMSGGSDLVSAARYYEEL---G------GYAHKAVML 1044 (1416)
T ss_pred             HHHHHHHHHHHH-----HHHHHHHHHhcCH-----HHHHHHHHhhcCchhHHHHHHHHHHc---c------hhhhHHHHH
Confidence            888888876541     1111111111000     00111111111  1222333333322   1      111223445


Q ss_pred             HHhcCCHHHHHHHHHhccc--------------CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 040394          476 YAKCGDAQSARMVFDAMRE--------------KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSA  541 (691)
Q Consensus       476 ~~~~g~~~~A~~~~~~~~~--------------~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~  541 (691)
                      |-+.|.+.+|+++-=+-.+              .|+...+.-..-++.+.++++|..++-...+         |.-.++.
T Consensus      1045 YHkAGm~~kALelAF~tqQf~aL~lIa~DLd~~sDp~ll~RcadFF~~~~qyekAV~lL~~ar~---------~~~Alql 1115 (1416)
T KOG3617|consen 1045 YHKAGMIGKALELAFRTQQFSALDLIAKDLDAGSDPKLLRRCADFFENNQQYEKAVNLLCLARE---------FSGALQL 1115 (1416)
T ss_pred             HHhhcchHHHHHHHHhhcccHHHHHHHHhcCCCCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHH---------HHHHHHH
Confidence            7777777777665432222              2566666666777778888888877766554         3333444


Q ss_pred             hcccCCHHHHHHHHHHchhhcCCCCC----hhHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHH
Q 040394          542 CSHTGMVGEGWKCFYSMCRDFKFVPS----MKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFD  617 (691)
Q Consensus       542 ~~~~g~~~~A~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~  617 (691)
                      |. ..++.-..++-+.|.-...-.|+    ......+...|.++|.+..|-+-|...|.+      ...++++.++||.+
T Consensus      1116 C~-~~nv~vtee~aE~mTp~Kd~~~~e~~R~~vLeqvae~c~qQG~Yh~AtKKfTQAGdK------l~AMraLLKSGdt~ 1188 (1416)
T KOG3617|consen 1116 CK-NRNVRVTEEFAELMTPTKDDMPNEQERKQVLEQVAELCLQQGAYHAATKKFTQAGDK------LSAMRALLKSGDTQ 1188 (1416)
T ss_pred             Hh-cCCCchhHHHHHhcCcCcCCCccHHHHHHHHHHHHHHHHhccchHHHHHHHhhhhhH------HHHHHHHHhcCCcc
Confidence            33 33444444555555333223344    345667778888999988888777777533      12344455555544


Q ss_pred             H
Q 040394          618 L  618 (691)
Q Consensus       618 ~  618 (691)
                      +
T Consensus      1189 K 1189 (1416)
T KOG3617|consen 1189 K 1189 (1416)
T ss_pred             e
Confidence            3

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

Probab=99.03  E-value=1.4e-07  Score=82.25  Aligned_cols=200  Identities=11%  Similarity=0.059  Sum_probs=161.6

Q ss_pred             HHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHh
Q 040394          432 TLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYG  508 (691)
Q Consensus       432 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~  508 (691)
                      +...|.-.|...|+...|..-+++..+++  |....++..+...|.+.|+.+.|.+-|+...+   .+-...|....-+|
T Consensus        37 arlqLal~YL~~gd~~~A~~nlekAL~~D--Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~~GdVLNNYG~FLC  114 (250)
T COG3063          37 ARLQLALGYLQQGDYAQAKKNLEKALEHD--PSYYLAHLVRAHYYQKLGENDLADESYRKALSLAPNNGDVLNNYGAFLC  114 (250)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCCccchhhhhhHHHH
Confidence            45667778889999999999999999988  78888899999999999999999999988764   35667888888889


Q ss_pred             cCCChHHHHHHHHHHHHCCCCCC-HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHH
Q 040394          509 MQGDGGGSLALFSDMLNEEVQPN-EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEE  586 (691)
Q Consensus       509 ~~~~~~~A~~~~~~m~~~g~~p~-~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~  586 (691)
                      ..|++++|...|++....-.-|. ..||..+.-+..+.|+.+.|...|++..   ...|+ ..+.-.+.....+.|++..
T Consensus       115 ~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL---~~dp~~~~~~l~~a~~~~~~~~y~~  191 (250)
T COG3063         115 AQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRAL---ELDPQFPPALLELARLHYKAGDYAP  191 (250)
T ss_pred             hCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHH---HhCcCCChHHHHHHHHHHhcccchH
Confidence            99999999999998887433332 3577777777788999999999998553   45666 6677778888889999999


Q ss_pred             HHHHHHhC--CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchh
Q 040394          587 ALEFMENM--PIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACY  636 (691)
Q Consensus       587 A~~~~~~~--~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~  636 (691)
                      |..+++..  +..++..+....+..-...||.+.+...=.++.+..|.+..+
T Consensus       192 Ar~~~~~~~~~~~~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~fP~s~e~  243 (250)
T COG3063         192 ARLYLERYQQRGGAQAESLLLGIRIAKRLGDRAAAQRYQAQLQRLFPYSEEY  243 (250)
T ss_pred             HHHHHHHHHhcccccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCcHHH
Confidence            98888887  445777777777777778899988888888888888886544

>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=99.02  E-value=2e-07  Score=95.78  Aligned_cols=258  Identities=12%  Similarity=0.059  Sum_probs=187.7

Q ss_pred             HHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHH-HHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCc
Q 040394          387 LVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVT-LVSVISACASLGAVQVGSSLHAYSTKQGLLSSN  465 (691)
Q Consensus       387 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~-~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~  465 (691)
                      ....+...|++++|++.++.-..                ..+|..+ .......+.+.|+.++|..++..+.+.+  |.+
T Consensus        10 ~~~il~e~g~~~~AL~~L~~~~~----------------~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN--Pdn   71 (517)
T PF12569_consen   10 KNSILEEAGDYEEALEHLEKNEK----------------QILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN--PDN   71 (517)
T ss_pred             HHHHHHHCCCHHHHHHHHHhhhh----------------hCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCc
Confidence            34567888999999999988654                3455554 4556678889999999999999999999  788


Q ss_pred             hhHHHHHHHHHHhcC-----CHHHHHHHHHhcccC--CHhHHHHHHHHHhcCCCh-HHHHHHHHHHHHCCCCCCHHHHHH
Q 040394          466 VYVGTALLNFYAKCG-----DAQSARMVFDAMREK--NTVTWSAMIGGYGMQGDG-GGSLALFSDMLNEEVQPNEVIFTT  537 (691)
Q Consensus       466 ~~~~~~l~~~~~~~g-----~~~~A~~~~~~~~~~--~~~~~~~li~~~~~~~~~-~~A~~~~~~m~~~g~~p~~~~~~~  537 (691)
                      ...|..+..+..-..     ..+....+++++.+.  .......+.-.+.....+ ..+..++..+...|+++   +|+.
T Consensus        72 ~~Yy~~L~~~~g~~~~~~~~~~~~~~~~y~~l~~~yp~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPs---lF~~  148 (517)
T PF12569_consen   72 YDYYRGLEEALGLQLQLSDEDVEKLLELYDELAEKYPRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPS---LFSN  148 (517)
T ss_pred             HHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHhCccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCch---HHHH
Confidence            888888888874333     567778888877652  222222222222222223 34667778888888665   3444


Q ss_pred             HHHHhcccCCHHHHHHHHHHchhhcC-------------CCCChh--HHHHHHHHHHhcCChHHHHHHHHhC-CCCCC-H
Q 040394          538 ILSACSHTGMVGEGWKCFYSMCRDFK-------------FVPSMK--HYVCMVDLLARAGRLEEALEFMENM-PIEPD-V  600 (691)
Q Consensus       538 ll~~~~~~g~~~~A~~~~~~m~~~~~-------------~~p~~~--~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~-~  600 (691)
                      +-..|....+.+-..+++........             -.|...  ++..+...|-..|++++|++++++. ..+|+ +
T Consensus       149 lk~Ly~d~~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~~  228 (517)
T PF12569_consen  149 LKPLYKDPEKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPTLV  228 (517)
T ss_pred             HHHHHcChhHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCcH
Confidence            44455555555555555555433211             123332  3455667788999999999999987 66776 4


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          601 SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       601 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      ..|..-...+.+.|++++|...++.+.++++.|-.+....+..+.+.|+.++|.+++....+.+.
T Consensus       229 ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~  293 (517)
T PF12569_consen  229 ELYMTKARILKHAGDLKEAAEAMDEARELDLADRYINSKCAKYLLRAGRIEEAEKTASLFTREDV  293 (517)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCC
Confidence            57888888899999999999999999999999999999999999999999999999998887765

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 [], [].

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.00  E-value=1.3e-06  Score=78.88  Aligned_cols=235  Identities=13%  Similarity=0.014  Sum_probs=126.5

Q ss_pred             cCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCC----CChhHHHHHHHHHHhcCCchhHHHH
Q 040394          259 LRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCS----IDLVSWTAMIVGYTQSGYPDKALKL  334 (691)
Q Consensus       259 ~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~----~~~~~~~~li~~~~~~g~~~~a~~~  334 (691)
                      .+++..+..+.++....|   +..+.+.......+.|+.+.|.+-|+...+    .....||.-+. +.+.|+++.|++.
T Consensus       125 e~Dl~g~rsLveQlp~en---~Ad~~in~gCllykegqyEaAvqkFqaAlqvsGyqpllAYniALa-Hy~~~qyasALk~  200 (459)
T KOG4340|consen  125 EGDLPGSRSLVEQLPSEN---EADGQINLGCLLYKEGQYEAAVQKFQAALQVSGYQPLLAYNLALA-HYSSRQYASALKH  200 (459)
T ss_pred             cccCcchHHHHHhccCCC---ccchhccchheeeccccHHHHHHHHHHHHhhcCCCchhHHHHHHH-HHhhhhHHHHHHH
Confidence            344444444444432211   223333333444566666666666665522    23445654443 4456777888888


Q ss_pred             HHHhhHCCCCCcHHHH----HHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCC
Q 040394          335 FTDKKWADFFPNHVTI----ASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEK  410 (691)
Q Consensus       335 ~~~m~~~g~~p~~~t~----~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  410 (691)
                      ..+..++|++-.+..=    ...+.+ ...|+.   ..+....      -...+|.-...+.+.|+.+.|.+.+-.|+.+
T Consensus       201 iSEIieRG~r~HPElgIGm~tegiDv-rsvgNt---~~lh~Sa------l~eAfNLKaAIeyq~~n~eAA~eaLtDmPPR  270 (459)
T KOG4340|consen  201 ISEIIERGIRQHPELGIGMTTEGIDV-RSVGNT---LVLHQSA------LVEAFNLKAAIEYQLRNYEAAQEALTDMPPR  270 (459)
T ss_pred             HHHHHHhhhhcCCccCccceeccCch-hcccch---HHHHHHH------HHHHhhhhhhhhhhcccHHHHHHHhhcCCCc
Confidence            8877777654221100    000000 000000   0000000      1234566667788899999999999999877


Q ss_pred             CchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHH
Q 040394          411 DVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFD  490 (691)
Q Consensus       411 ~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  490 (691)
                      .             ....|++|...+.-.- ..+++-...+-++.+....  |-...++..++-.||+..-++.|-.++.
T Consensus       271 a-------------E~elDPvTLHN~Al~n-~~~~p~~g~~KLqFLL~~n--PfP~ETFANlLllyCKNeyf~lAADvLA  334 (459)
T KOG4340|consen  271 A-------------EEELDPVTLHNQALMN-MDARPTEGFEKLQFLLQQN--PFPPETFANLLLLYCKNEYFDLAADVLA  334 (459)
T ss_pred             c-------------cccCCchhhhHHHHhc-ccCCccccHHHHHHHHhcC--CCChHHHHHHHHHHhhhHHHhHHHHHHh
Confidence            4             3456667765543221 2234444455555566665  6677888889999999999999988887


Q ss_pred             hcccC-----CHhHHHHHHHHHh-cCCChHHHHHHHHHHH
Q 040394          491 AMREK-----NTVTWSAMIGGYG-MQGDGGGSLALFSDML  524 (691)
Q Consensus       491 ~~~~~-----~~~~~~~li~~~~-~~~~~~~A~~~~~~m~  524 (691)
                      +-...     +...|+.| .++. ..-.++++++-++.+.
T Consensus       335 En~~lTyk~L~~Yly~LL-daLIt~qT~pEea~KKL~~La  373 (459)
T KOG4340|consen  335 ENAHLTYKFLTPYLYDLL-DALITCQTAPEEAFKKLDGLA  373 (459)
T ss_pred             hCcchhHHHhhHHHHHHH-HHHHhCCCCHHHHHHHHHHHH
Confidence            65542     33334333 3332 2345566655554443

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=99.00  E-value=2.8e-06  Score=89.19  Aligned_cols=341  Identities=9%  Similarity=-0.008  Sum_probs=193.4

Q ss_pred             HHhhccCchhHHHHHHHHHHhCCCCchhhhHHHHHHhcCCChHHHHHHhccCCCCCc-----chHHHHHHHHHhCCChhH
Q 040394           55 LLGLCKSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPNPDF-----YSFQVMIRWYFLNDLYKD  129 (691)
Q Consensus        55 ll~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-----~~~~~ll~~~~~~~~~~~  129 (691)
                      .++..-+...|...++...+.+...-..+....+.|++..+++.|..+.-...+.+.     ..|....-.|.+.++..+
T Consensus       501 iYrd~~Dm~RA~kCf~KAFeLDatdaeaaaa~adtyae~~~we~a~~I~l~~~qka~a~~~k~nW~~rG~yyLea~n~h~  580 (1238)
T KOG1127|consen  501 IYRDSDDMKRAKKCFDKAFELDATDAEAAAASADTYAEESTWEEAFEICLRAAQKAPAFACKENWVQRGPYYLEAHNLHG  580 (1238)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCchhhhhHHHHHHHhhccccHHHHHHHHHHHhhhchHHHHHhhhhhccccccCccchhh
Confidence            333334555677777776665544444788899999999999999998554433221     234444445678899999


Q ss_pred             HHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCC
Q 040394          130 IVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDK  209 (691)
Q Consensus       130 a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  209 (691)
                      |+.-|+...+.. +-|...|..+..+|...|++..|.++|.......|.+....--.....|..|.+.+|...+..+...
T Consensus       581 aV~~fQsALR~d-PkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~LrP~s~y~~fk~A~~ecd~GkYkeald~l~~ii~~  659 (1238)
T KOG1127|consen  581 AVCEFQSALRTD-PKDYNLWLGLGEAYPESGRYSHALKVFTKASLLRPLSKYGRFKEAVMECDNGKYKEALDALGLIIYA  659 (1238)
T ss_pred             HHHHHHHHhcCC-chhHHHHHHHHHHHHhcCceehHHHhhhhhHhcCcHhHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            999999888763 4477889999999999999999999999998888777777777777788999999999998876331


Q ss_pred             ----------ChhhHHHHHHHHHhCCChhHHHHHHHHHHhC-------CCCCChhhHHHHHHHHHccCChhhHHHHHHHH
Q 040394          210 ----------NVVSWTSMIAGYVQNDCAQEGLVLFNRMREG-------FVEGNQITLGSLVTACAKLRALHQGKWLHGYI  272 (691)
Q Consensus       210 ----------~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-------~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~  272 (691)
                                -..++-.+...+.-.|-..+|.+.++.-.+.       ....+...+..+-          .|..+|-+.
T Consensus       660 ~s~e~~~q~gLaE~~ir~akd~~~~gf~~kavd~~eksie~f~~~l~h~~~~~~~~Wi~as----------dac~~f~q~  729 (1238)
T KOG1127|consen  660 FSLERTGQNGLAESVIRDAKDSAITGFQKKAVDFFEKSIESFIVSLIHSLQSDRLQWIVAS----------DACYIFSQE  729 (1238)
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHhhhhhHHHHHHHh----------HHHHHHHHh
Confidence                      1223444444444455555555555544321       1111111111111          122222222


Q ss_pred             HHHCCCCchHHHHHHHHHHHhcCCH---H---HHHHHHHhc--CCCChhHHHHHHHHHHh----cC----CchhHHHHHH
Q 040394          273 LKIGIEINSHLVTALLDMYVKCGNI---R---DARSVFDEL--CSIDLVSWTAMIVGYTQ----SG----YPDKALKLFT  336 (691)
Q Consensus       273 ~~~g~~~~~~~~~~li~~~~~~g~~---~---~A~~~~~~~--~~~~~~~~~~li~~~~~----~g----~~~~a~~~~~  336 (691)
                      . .. .|+......|..-.-+.+..   |   -+.+.+-.-  ...+..+|..|+..|.+    .|    +...|+..+.
T Consensus       730 e-~~-~vn~h~l~il~~q~e~~~~l~~~d~l~Lg~~c~~~hlsl~~~~~~WyNLGinylr~f~~l~et~~~~~~Ai~c~K  807 (1238)
T KOG1127|consen  730 E-PS-IVNMHYLIILSKQLEKTGALKKNDLLFLGYECGIAHLSLAIHMYPWYNLGINYLRYFLLLGETMKDACTAIRCCK  807 (1238)
T ss_pred             c-cc-chHHHHHHHHHHHHHhcccCcchhHHHHHHHHhhHHHHHhhccchHHHHhHHHHHHHHHcCCcchhHHHHHHHHH
Confidence            2 01 12222222222212222211   1   001111000  00123444444444333    11    1224555555


Q ss_pred             HhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCC
Q 040394          337 DKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEK  410 (691)
Q Consensus       337 ~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  410 (691)
                      ...+. ..-+..+|+.| ......|++.-+...|-......+....+|..+.-.+.+..+++.|...|.....-
T Consensus       808 kaV~L-~ann~~~WnaL-GVlsg~gnva~aQHCfIks~~sep~~~~~W~NlgvL~l~n~d~E~A~~af~~~qSL  879 (1238)
T KOG1127|consen  808 KAVSL-CANNEGLWNAL-GVLSGIGNVACAQHCFIKSRFSEPTCHCQWLNLGVLVLENQDFEHAEPAFSSVQSL  879 (1238)
T ss_pred             HHHHH-hhccHHHHHHH-HHhhccchhhhhhhhhhhhhhccccchhheeccceeEEecccHHHhhHHHHhhhhc
Confidence            54433 12233444433 33355566666666666555555556666777777777777777777777776654

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.00  E-value=2.6e-07  Score=89.90  Aligned_cols=214  Identities=11%  Similarity=0.019  Sum_probs=153.3

Q ss_pred             cHHHHHHHHHHHHHcCCC--CCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-CHhHHHHHHHHHhcCCChHHHHHH
Q 040394          445 AVQVGSSLHAYSTKQGLL--SSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--K-NTVTWSAMIGGYGMQGDGGGSLAL  519 (691)
Q Consensus       445 ~~~~a~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~A~~~  519 (691)
                      ..+.+..-+.++......  +.....+..+...|...|+.++|...|++..+  | +...|+.+...+...|++++|...
T Consensus        41 ~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~~~~~g~~~~A~~~  120 (296)
T PRK11189         41 QQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALRPDMADAYNYLGIYLTQAGNFDAAYEA  120 (296)
T ss_pred             HHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            445555555555543210  12245677888889999999999999998875  3 678999999999999999999999


Q ss_pred             HHHHHHCCCCCC-HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC--CC
Q 040394          520 FSDMLNEEVQPN-EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM--PI  596 (691)
Q Consensus       520 ~~~m~~~g~~p~-~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~--~~  596 (691)
                      |++..+  +.|+ ..++..+..++...|++++|.+.++...   ...|+..........+...++.++|.+.+++.  ..
T Consensus       121 ~~~Al~--l~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al---~~~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~~~  195 (296)
T PRK11189        121 FDSVLE--LDPTYNYAYLNRGIALYYGGRYELAQDDLLAFY---QDDPNDPYRALWLYLAESKLDPKQAKENLKQRYEKL  195 (296)
T ss_pred             HHHHHH--hCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH---HhCCCCHHHHHHHHHHHccCCHHHHHHHHHHHHhhC
Confidence            999998  4565 4567777778889999999999999775   35666432233333345678899999999765  33


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-------hcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCcc
Q 040394          597 EPDVSLFGAFLHGCGLYSRFDLGEVMIKKML-------ELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSK  667 (691)
Q Consensus       597 ~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-------~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~~  667 (691)
                      .|+...+ .+  .....|+...+ +.++.+.       +..|+.+..|..++.++...|++++|...|++..+.++..
T Consensus       196 ~~~~~~~-~~--~~~~lg~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~~~~  269 (296)
T PRK11189        196 DKEQWGW-NI--VEFYLGKISEE-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALANNVYN  269 (296)
T ss_pred             CccccHH-HH--HHHHccCCCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCch
Confidence            3443322 22  22334555443 2444444       4566777899999999999999999999999999876543

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=98.99  E-value=1.3e-06  Score=80.41  Aligned_cols=311  Identities=14%  Similarity=0.101  Sum_probs=193.8

Q ss_pred             hHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHH---HHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHH-HHHH
Q 040394          281 SHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMI---VGYTQSGYPDKALKLFTDKKWADFFPNHVTIAS-VLSA  356 (691)
Q Consensus       281 ~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li---~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~-ll~~  356 (691)
                      +.-.--+...+...|++..|+.-|...++.|+..|.++.   ..|...|+..-|+.=+....+.  +||-..-.. --..
T Consensus        38 vekhlElGk~lla~~Q~sDALt~yHaAve~dp~~Y~aifrRaT~yLAmGksk~al~Dl~rVlel--KpDF~~ARiQRg~v  115 (504)
T KOG0624|consen   38 VEKHLELGKELLARGQLSDALTHYHAAVEGDPNNYQAIFRRATVYLAMGKSKAALQDLSRVLEL--KPDFMAARIQRGVV  115 (504)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhcCCccchhhHHHHHhc--CccHHHHHHHhchh
Confidence            333445566677788899999999988888887777765   3577788888887777776654  666433211 1224


Q ss_pred             HhcCCChhhHHHHHHHHHHhCCC---chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHH
Q 040394          357 SAQLGNLNMGRMVHSLGIRLGLE---DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTL  433 (691)
Q Consensus       357 ~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~  433 (691)
                      +.++|.+++|..-|+.+++..+.   ...++..++-       .++                              ....
T Consensus       116 llK~Gele~A~~DF~~vl~~~~s~~~~~eaqskl~~-------~~e------------------------------~~~l  158 (504)
T KOG0624|consen  116 LLKQGELEQAEADFDQVLQHEPSNGLVLEAQSKLAL-------IQE------------------------------HWVL  158 (504)
T ss_pred             hhhcccHHHHHHHHHHHHhcCCCcchhHHHHHHHHh-------HHH------------------------------HHHH
Confidence            56777777777777777766654   1111111110       000                              1122


Q ss_pred             HHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcc---cCCHhHHHHHHHHHhcC
Q 040394          434 VSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMR---EKNTVTWSAMIGGYGMQ  510 (691)
Q Consensus       434 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~---~~~~~~~~~li~~~~~~  510 (691)
                      ...+..+...|+...++.....+.+..  +.+...+..-..+|...|++..|+.-++...   ..+..+.--+-..+...
T Consensus       159 ~~ql~s~~~~GD~~~ai~~i~~llEi~--~Wda~l~~~Rakc~i~~~e~k~AI~Dlk~askLs~DnTe~~ykis~L~Y~v  236 (504)
T KOG0624|consen  159 VQQLKSASGSGDCQNAIEMITHLLEIQ--PWDASLRQARAKCYIAEGEPKKAIHDLKQASKLSQDNTEGHYKISQLLYTV  236 (504)
T ss_pred             HHHHHHHhcCCchhhHHHHHHHHHhcC--cchhHHHHHHHHHHHhcCcHHHHHHHHHHHHhccccchHHHHHHHHHHHhh
Confidence            334445566788888888888888877  7888999888999999999998877666544   35666666677777888


Q ss_pred             CChHHHHHHHHHHHHCCCCCCHHHHHHHH-------------HHhcccCCHHHHHHHHHHchhhcCCCCC--h---hHHH
Q 040394          511 GDGGGSLALFSDMLNEEVQPNEVIFTTIL-------------SACSHTGMVGEGWKCFYSMCRDFKFVPS--M---KHYV  572 (691)
Q Consensus       511 ~~~~~A~~~~~~m~~~g~~p~~~~~~~ll-------------~~~~~~g~~~~A~~~~~~m~~~~~~~p~--~---~~~~  572 (691)
                      |+.+.++...++..+  +.||.......-             ......+++-++.+..+...+   ..|.  .   ..+.
T Consensus       237 gd~~~sL~~iRECLK--ldpdHK~Cf~~YKklkKv~K~les~e~~ie~~~~t~cle~ge~vlk---~ep~~~~ir~~~~r  311 (504)
T KOG0624|consen  237 GDAENSLKEIRECLK--LDPDHKLCFPFYKKLKKVVKSLESAEQAIEEKHWTECLEAGEKVLK---NEPEETMIRYNGFR  311 (504)
T ss_pred             hhHHHHHHHHHHHHc--cCcchhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHh---cCCcccceeeeeeh
Confidence            888888888888877  567764322111             112234455555555554422   2333  1   1222


Q ss_pred             HHHHHHHhcCChHHHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhH
Q 040394          573 CMVDLLARAGRLEEALEFMENM-PIEPD-VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYY  637 (691)
Q Consensus       573 ~li~~~~~~g~~~~A~~~~~~~-~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~  637 (691)
                      .+-.++...|++-+|+....+. ...|| ..++---..+|....+++.|+.-|+++.+.+|++..+-
T Consensus       312 ~~c~C~~~d~~~~eAiqqC~evL~~d~~dv~~l~dRAeA~l~dE~YD~AI~dye~A~e~n~sn~~~r  378 (504)
T KOG0624|consen  312 VLCTCYREDEQFGEAIQQCKEVLDIDPDDVQVLCDRAEAYLGDEMYDDAIHDYEKALELNESNTRAR  378 (504)
T ss_pred             eeeecccccCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCcccHHHH
Confidence            3344455556666666666555 55554 44555555566666667777777777777666654443

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=98.91  E-value=1.2e-06  Score=86.04  Aligned_cols=354  Identities=14%  Similarity=0.110  Sum_probs=199.5

Q ss_pred             HHHHhcCCHHHHHHHHHhc---CCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCc-HHHHHHHHHHHhcCCChh
Q 040394          289 DMYVKCGNIRDARSVFDEL---CSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPN-HVTIASVLSASAQLGNLN  364 (691)
Q Consensus       289 ~~~~~~g~~~~A~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~  364 (691)
                      ++.+..|+++.|...|-+.   .++|.+.|+.=..+|...|++++|++=-.+-.+  +.|+ ...|+....++.-.|+++
T Consensus        10 naa~s~~d~~~ai~~~t~ai~l~p~nhvlySnrsaa~a~~~~~~~al~da~k~~~--l~p~w~kgy~r~Gaa~~~lg~~~   87 (539)
T KOG0548|consen   10 NAAFSSGDFETAIRLFTEAIMLSPTNHVLYSNRSAAYASLGSYEKALKDATKTRR--LNPDWAKGYSRKGAALFGLGDYE   87 (539)
T ss_pred             HhhcccccHHHHHHHHHHHHccCCCccchhcchHHHHHHHhhHHHHHHHHHHHHh--cCCchhhHHHHhHHHHHhcccHH
Confidence            5567889999999999876   445788899999999999999999876555444  4665 468999999999999999


Q ss_pred             hHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHH------hCCCC-------CchhHHHHHHhhhC-------
Q 040394          365 MGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFE------TTSEK-------DVIAWNSIISGLDD-------  424 (691)
Q Consensus       365 ~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~------~~~~~-------~~~~~~~li~~~~~-------  424 (691)
                      +|..-+.+.++..+.+...++.+.+++...-   ++.+.|.      .....       ....|..++..+.+       
T Consensus        88 eA~~ay~~GL~~d~~n~~L~~gl~~a~~~~~---~~~~~~~~p~~~~~l~~~p~t~~~~~~~~~~~~l~~~~~~p~~l~~  164 (539)
T KOG0548|consen   88 EAILAYSEGLEKDPSNKQLKTGLAQAYLEDY---AADQLFTKPYFHEKLANLPLTNYSLSDPAYVKILEIIQKNPTSLKL  164 (539)
T ss_pred             HHHHHHHHHhhcCCchHHHHHhHHHhhhHHH---HhhhhccCcHHHHHhhcChhhhhhhccHHHHHHHHHhhcCcHhhhc
Confidence            9999999999999999999999998882210   0011111      10000       00112222222211       


Q ss_pred             --------------------------------CCCC------------CH----------HHHHHHHHHHhccCcHHHHH
Q 040394          425 --------------------------------NVSP------------DA----------VTLVSVISACASLGAVQVGS  450 (691)
Q Consensus       425 --------------------------------~~~p------------~~----------~~~~~ll~~~~~~~~~~~a~  450 (691)
                                                      +..|            |.          .-...+.++.-+..+++.+.
T Consensus       165 ~l~d~r~m~a~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~d~~ee~~~k~~a~~ek~lgnaaykkk~f~~a~  244 (539)
T KOG0548|consen  165 YLNDPRLMKADGQLKGVDELLFYASGIEILASMAEPCKQEHNGFPIIEDNTEERRVKEKAHKEKELGNAAYKKKDFETAI  244 (539)
T ss_pred             ccccHHHHHHHHHHhcCccccccccccccCCCCCCcccccCCCCCccchhHHHHHHHHhhhHHHHHHHHHHHhhhHHHHH
Confidence                                            1111            10          11344555556666777777


Q ss_pred             HHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHh----------HHHHHHHHHhcCCChHHHHHHH
Q 040394          451 SLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTV----------TWSAMIGGYGMQGDGGGSLALF  520 (691)
Q Consensus       451 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~----------~~~~li~~~~~~~~~~~A~~~~  520 (691)
                      +-+....+..   .+...++....+|...|.+.++...-+...+.+..          .+..+..+|.+.++++.++..|
T Consensus       245 q~y~~a~el~---~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gre~rad~klIak~~~r~g~a~~k~~~~~~ai~~~  321 (539)
T KOG0548|consen  245 QHYAKALELA---TDITYLNNIAAVYLERGKYAECIELCEKAVEVGRELRADYKLIAKALARLGNAYTKREDYEGAIKYY  321 (539)
T ss_pred             HHHHHHHhHh---hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHHHHHHHHHHHHHHHHhhhhhhhHHhHHHHHHHH
Confidence            7777766653   44555666777777777777776666655443211          1222344666677888888888


Q ss_pred             HHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChh-HHHHHHHHHHhcCChHHHHHHHHhC--CCC
Q 040394          521 SDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMK-HYVCMVDLLARAGRLEEALEFMENM--PIE  597 (691)
Q Consensus       521 ~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~-~~~~li~~~~~~g~~~~A~~~~~~~--~~~  597 (691)
                      .+.......|+..+=.         ...+++....+.   ..-+.|... -...-...+.+.|++..|++.+.++  ..+
T Consensus       322 ~kaLte~Rt~~~ls~l---------k~~Ek~~k~~e~---~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIkr~P  389 (539)
T KOG0548|consen  322 QKALTEHRTPDLLSKL---------KEAEKALKEAER---KAYINPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIKRDP  389 (539)
T ss_pred             HHHhhhhcCHHHHHHH---------HHHHHHHHHHHH---HHhhChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHhcCC
Confidence            8876655455443211         111122111111   111222210 0111133344445555555555444  222


Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          598 PDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       598 p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      -|...|..-..+|.+.|.+..|..-.+..++++|+....|..-+.++....+|++|.+.|++.++
T Consensus       390 ~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL~p~~~kgy~RKg~al~~mk~ydkAleay~eale  454 (539)
T KOG0548|consen  390 EDARLYSNRAACYLKLGEYPEALKDAKKCIELDPNFIKAYLRKGAALRAMKEYDKALEAYQEALE  454 (539)
T ss_pred             chhHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            23344444444445555555555555555555555544554444455555555555555544443

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

Probab=98.90  E-value=6.6e-08  Score=95.39  Aligned_cols=219  Identities=14%  Similarity=0.074  Sum_probs=180.2

Q ss_pred             HhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHH
Q 040394          440 CASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGS  516 (691)
Q Consensus       440 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A  516 (691)
                      +.+.|++.+|.-.|+..++.+  |.+...|.-|.......++-..|+..+.+..+   .|....-.|.-.|...|.-..|
T Consensus       295 lm~nG~L~~A~LafEAAVkqd--P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~NleaLmaLAVSytNeg~q~~A  372 (579)
T KOG1125|consen  295 LMKNGDLSEAALAFEAAVKQD--PQHAEAWQKLGITQAENENEQNAISALRRCLELDPTNLEALMALAVSYTNEGLQNQA  372 (579)
T ss_pred             HHhcCCchHHHHHHHHHHhhC--hHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhHHHH
Confidence            457888999999999999988  88999999999999999998899999988875   3677888889999999999999


Q ss_pred             HHHHHHHHHCCCC-----C---CHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHH
Q 040394          517 LALFSDMLNEEVQ-----P---NEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEAL  588 (691)
Q Consensus       517 ~~~~~~m~~~g~~-----p---~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~  588 (691)
                      +..++.-+....+     +   +...-..  ..+..........++|-++....+..+|+.++..|.-.|--.|++++|+
T Consensus       373 l~~L~~Wi~~~p~y~~l~~a~~~~~~~~~--~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdrai  450 (579)
T KOG1125|consen  373 LKMLDKWIRNKPKYVHLVSAGENEDFENT--KSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAV  450 (579)
T ss_pred             HHHHHHHHHhCccchhccccCccccccCC--cCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHH
Confidence            9999998764311     0   0000000  1222223344566777777677777788889999999999999999999


Q ss_pred             HHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          589 EFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       589 ~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      +.|+.+ ..+| |...||.|...+....+.++|+..|.+++++.|....+.+.|+-.|...|.|++|.+.|-..+.
T Consensus       451 Dcf~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqLqP~yVR~RyNlgIS~mNlG~ykEA~~hlL~AL~  526 (579)
T KOG1125|consen  451 DCFEAALQVKPNDYLLWNRLGATLANGNRSEEAISAYNRALQLQPGYVRVRYNLGISCMNLGAYKEAVKHLLEALS  526 (579)
T ss_pred             HHHHHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhcCCCeeeeehhhhhhhhhhhhHHHHHHHHHHHHH
Confidence            999998 6677 5579999999999999999999999999999999999999999999999999999999877765

>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=98.88  E-value=1.4e-07  Score=90.21  Aligned_cols=156  Identities=13%  Similarity=0.108  Sum_probs=92.3

Q ss_pred             HHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhc----ccCC
Q 040394          472 LLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACS----HTGM  547 (691)
Q Consensus       472 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~----~~g~  547 (691)
                      ....+...|++++|+++++..  .+.......+..|.+.++++.|.+.++.|.+.  ..|. +...+..++.    ..+.
T Consensus       108 ~A~i~~~~~~~~~AL~~l~~~--~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~--~eD~-~l~qLa~awv~l~~g~e~  182 (290)
T PF04733_consen  108 AATILFHEGDYEEALKLLHKG--GSLELLALAVQILLKMNRPDLAEKELKNMQQI--DEDS-ILTQLAEAWVNLATGGEK  182 (290)
T ss_dssp             HHHHHCCCCHHHHHHCCCTTT--TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCC--SCCH-HHHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHcCCHHHHHHHHHcc--CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcH-HHHHHHHHHHHHHhCchh
Confidence            334555667777777776654  45555666677777777777777777777653  3343 2333333222    2235


Q ss_pred             HHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCH-HHHHHHHH
Q 040394          548 VGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRF-DLGEVMIK  624 (691)
Q Consensus       548 ~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~-~~A~~~~~  624 (691)
                      +.+|..+|+++...  ..+++.+.+.+..++...|++++|.+++++. ...| +..+...++-+....|+. +.+.+.+.
T Consensus       183 ~~~A~y~f~El~~~--~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~~~~d~LaNliv~~~~~gk~~~~~~~~l~  260 (290)
T PF04733_consen  183 YQDAFYIFEELSDK--FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDPNDPDTLANLIVCSLHLGKPTEAAERYLS  260 (290)
T ss_dssp             CCHHHHHHHHHHCC--S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHTT-TCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhc--cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCChhHHHHHHH
Confidence            77777777776333  3456666777777777777777777776665 3333 334555555555556655 56667777


Q ss_pred             HHHhcCCCCc
Q 040394          625 KMLELHPDKA  634 (691)
Q Consensus       625 ~~~~~~p~~~  634 (691)
                      ++...+|+++
T Consensus       261 qL~~~~p~h~  270 (290)
T PF04733_consen  261 QLKQSNPNHP  270 (290)
T ss_dssp             HCHHHTTTSH
T ss_pred             HHHHhCCCCh
Confidence            7777777754

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.

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

Probab=98.86  E-value=1.6e-05  Score=80.57  Aligned_cols=194  Identities=11%  Similarity=0.027  Sum_probs=106.0

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHhhHCC-CCCcHHHHHHH-HHHHhcCCChhhHHHHHHHHHHhCCCchhHHHH---HH
Q 040394          314 SWTAMIVGYTQSGYPDKALKLFTDKKWAD-FFPNHVTIASV-LSASAQLGNLNMGRMVHSLGIRLGLEDYTVINA---LV  388 (691)
Q Consensus       314 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~t~~~l-l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~---l~  388 (691)
                      .|..+...+...|+.+.+.+.+....... ..++......+ ...+...|++++|...++...+..|.+...+..   ..
T Consensus         8 a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~~~~~~   87 (355)
T cd05804           8 GHAAAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEALSAWIAGDLPKALALLEQLLDDYPRDLLALKLHLGAF   87 (355)
T ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHhHHHH
Confidence            34444444445555555444444433221 11222111111 123445566666666666666665554433331   11


Q ss_pred             HHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCC-HHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchh
Q 040394          389 DMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPD-AVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVY  467 (691)
Q Consensus       389 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  467 (691)
                      ......+..+.+.+.+....                +..|+ ......+...+...|+++.|...++...+..  |.+..
T Consensus        88 ~~~~~~~~~~~~~~~l~~~~----------------~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~--p~~~~  149 (355)
T cd05804          88 GLGDFSGMRDHVARVLPLWA----------------PENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELN--PDDAW  149 (355)
T ss_pred             HhcccccCchhHHHHHhccC----------------cCCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCCcH
Confidence            22222344455555554422                12233 3344455566777788888888888887776  56666


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhcccC-----CH--hHHHHHHHHHhcCCChHHHHHHHHHHHH
Q 040394          468 VGTALLNFYAKCGDAQSARMVFDAMREK-----NT--VTWSAMIGGYGMQGDGGGSLALFSDMLN  525 (691)
Q Consensus       468 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~~--~~~~~li~~~~~~~~~~~A~~~~~~m~~  525 (691)
                      .+..+...|...|++++|...+++..+.     +.  ..|..+...+...|++++|..++++...
T Consensus       150 ~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~  214 (355)
T cd05804         150 AVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIA  214 (355)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhc
Confidence            7777777777888888888877765531     11  2344566667777777777777777654

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.

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

Probab=98.84  E-value=6.3e-06  Score=83.53  Aligned_cols=299  Identities=8%  Similarity=-0.099  Sum_probs=186.7

Q ss_pred             HHHHHHHHHhcCCChhhHHHHHHHHHHhCCC---chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCC
Q 040394          349 TIASVLSASAQLGNLNMGRMVHSLGIRLGLE---DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDN  425 (691)
Q Consensus       349 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~  425 (691)
                      .+..+...+...|+.+.+...+....+..+.   ...........+...|++++|...+++..+.+              
T Consensus         8 a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~~--------------   73 (355)
T cd05804           8 GHAAAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEALSAWIAGDLPKALALLEQLLDDY--------------   73 (355)
T ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--------------
Confidence            3444445566667777776666666555554   22233334556778899999999999876541              


Q ss_pred             CCCCHHHHHH---HHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhH
Q 040394          426 VSPDAVTLVS---VISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVT  499 (691)
Q Consensus       426 ~~p~~~~~~~---ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~  499 (691)
                       +.|...+..   ........+..+.+.+.+.... ... +........+...+...|++++|...+++..+   .+...
T Consensus        74 -P~~~~a~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~-~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~p~~~~~  150 (355)
T cd05804          74 -PRDLLALKLHLGAFGLGDFSGMRDHVARVLPLWA-PEN-PDYWYLLGMLAFGLEEAGQYDRAEEAARRALELNPDDAWA  150 (355)
T ss_pred             -CCcHHHHHHhHHHHHhcccccCchhHHHHHhccC-cCC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCcHH
Confidence             223333332   1111122455555555555411 111 34445555667788999999999999998875   35667


Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHHCCC-CCCH--HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHH-H--H
Q 040394          500 WSAMIGGYGMQGDGGGSLALFSDMLNEEV-QPNE--VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHY-V--C  573 (691)
Q Consensus       500 ~~~li~~~~~~~~~~~A~~~~~~m~~~g~-~p~~--~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~-~--~  573 (691)
                      +..+...+...|++++|...+++...... .|+.  ..|..+...+...|++++|..++++........+..... +  .
T Consensus       151 ~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~  230 (355)
T cd05804         151 VHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIAPSAESDPALDLLDAAS  230 (355)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHH
Confidence            88899999999999999999999887532 2333  345567778899999999999999873221111222111 1  2


Q ss_pred             HHHHHHhcCChHHHHHH--H-HhC-C---CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC-C---C-----CchhH
Q 040394          574 MVDLLARAGRLEEALEF--M-ENM-P---IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELH-P---D-----KACYY  637 (691)
Q Consensus       574 li~~~~~~g~~~~A~~~--~-~~~-~---~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p---~-----~~~~~  637 (691)
                      ++..+...|....+.++  + ... .   .............++...|+.+.|..+++.+.... .   .     .....
T Consensus       231 ~l~~~~~~g~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~  310 (355)
T cd05804         231 LLWRLELAGHVDVGDRWEDLADYAAWHFPDHGLAFNDLHAALALAGAGDKDALDKLLAALKGRASSADDNKQPARDVGLP  310 (355)
T ss_pred             HHHHHHhcCCCChHHHHHHHHHHHHhhcCcccchHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCchhhhHHhhhHH
Confidence            33333444433322222  1 111 1   11112222356667788999999999999987622 1   1     23445


Q ss_pred             HHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          638 VLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       638 ~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      ...+.++...|++++|.+.+......+
T Consensus       311 ~l~A~~~~~~g~~~~A~~~L~~al~~a  337 (355)
T cd05804         311 LAEALYAFAEGNYATALELLGPVRDDL  337 (355)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            667778889999999999998887644

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.

>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=98.84  E-value=1.9e-07  Score=89.30  Aligned_cols=246  Identities=11%  Similarity=0.016  Sum_probs=164.1

Q ss_pred             HHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhH
Q 040394          389 DMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYV  468 (691)
Q Consensus       389 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  468 (691)
                      +-+.-.|++..++.-.+ ....              .-..+.....-+.+++...|+.+.+.   ..+.+..  +|....
T Consensus         9 rn~fy~G~Y~~~i~e~~-~~~~--------------~~~~~~e~~~~~~Rs~iAlg~~~~vl---~ei~~~~--~~~l~a   68 (290)
T PF04733_consen    9 RNQFYLGNYQQCINEAS-LKSF--------------SPENKLERDFYQYRSYIALGQYDSVL---SEIKKSS--SPELQA   68 (290)
T ss_dssp             HHHHCTT-HHHHCHHHH-CHTS--------------TCHHHHHHHHHHHHHHHHTT-HHHHH---HHS-TTS--SCCCHH
T ss_pred             HHHHHhhhHHHHHHHhh-ccCC--------------CchhHHHHHHHHHHHHHHcCChhHHH---HHhccCC--ChhHHH
Confidence            34455678887775555 2221              11123344556667888888766433   3333333  555666


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhcc-cC----CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhc
Q 040394          469 GTALLNFYAKCGDAQSARMVFDAMR-EK----NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACS  543 (691)
Q Consensus       469 ~~~l~~~~~~~g~~~~A~~~~~~~~-~~----~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~  543 (691)
                      ...+...+...++-+.+..-+++.. ++    +..........+...|++++|++++.+-      .+.......+..+.
T Consensus        69 v~~la~y~~~~~~~e~~l~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~------~~lE~~al~Vqi~L  142 (290)
T PF04733_consen   69 VRLLAEYLSSPSDKESALEELKELLADQAGESNEIVQLLAATILFHEGDYEEALKLLHKG------GSLELLALAVQILL  142 (290)
T ss_dssp             HHHHHHHHCTSTTHHCHHHHHHHCCCTS---CHHHHHHHHHHHHCCCCHHHHHHCCCTTT------TCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCccchHHHHHHHHHHHHhccccccHHHHHHHHHHHHHcCCHHHHHHHHHcc------CcccHHHHHHHHHH
Confidence            5556555544456666766665544 22    2222233345677789999999988642      45666777888999


Q ss_pred             ccCCHHHHHHHHHHchhhcCCCCChh---HHHHHHHHHHhcCChHHHHHHHHhC--CCCCCHHHHHHHHHHHHhcCCHHH
Q 040394          544 HTGMVGEGWKCFYSMCRDFKFVPSMK---HYVCMVDLLARAGRLEEALEFMENM--PIEPDVSLFGAFLHGCGLYSRFDL  618 (691)
Q Consensus       544 ~~g~~~~A~~~~~~m~~~~~~~p~~~---~~~~li~~~~~~g~~~~A~~~~~~~--~~~p~~~~~~~l~~~~~~~g~~~~  618 (691)
                      +.++++.|.+.++.| ++  ...|..   ...+++..+.-.+.+.+|.-+|+++  ...++..+.+.+..++...|++++
T Consensus       143 ~~~R~dlA~k~l~~~-~~--~~eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~~~~t~~~lng~A~~~l~~~~~~e  219 (290)
T PF04733_consen  143 KMNRPDLAEKELKNM-QQ--IDEDSILTQLAEAWVNLATGGEKYQDAFYIFEELSDKFGSTPKLLNGLAVCHLQLGHYEE  219 (290)
T ss_dssp             HTT-HHHHHHHHHHH-HC--CSCCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCCS--SHHHHHHHHHHHHHCT-HHH
T ss_pred             HcCCHHHHHHHHHHH-Hh--cCCcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhCCHHH
Confidence            999999999999999 44  444522   2223333333345799999999999  456788899999999999999999


Q ss_pred             HHHHHHHHHhcCCCCchhHHHHHHHHHhCCCc-HHHHHHHHHHHhC
Q 040394          619 GEVMIKKMLELHPDKACYYVLVSNLYASDGRW-IRVNQVRELMKQR  663 (691)
Q Consensus       619 A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~-~~A~~~~~~~~~~  663 (691)
                      |+..++++++.+|+++.+...++.+....|+. +.+.+++.++...
T Consensus       220 Ae~~L~~al~~~~~~~d~LaNliv~~~~~gk~~~~~~~~l~qL~~~  265 (290)
T PF04733_consen  220 AEELLEEALEKDPNDPDTLANLIVCSLHLGKPTEAAERYLSQLKQS  265 (290)
T ss_dssp             HHHHHHHHCCC-CCHHHHHHHHHHHHHHTT-TCHHHHHHHHHCHHH
T ss_pred             HHHHHHHHHHhccCCHHHHHHHHHHHHHhCCChhHHHHHHHHHHHh
Confidence            99999999999999999999999999999998 6677888887764

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.

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.78  E-value=3.2e-05  Score=70.13  Aligned_cols=311  Identities=11%  Similarity=-0.001  Sum_probs=181.9

Q ss_pred             hhHHHHHHhcCCChHHHHHHhccCCC--C-CcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHH-HHHHcc
Q 040394           83 NTKLVSMYGSFGHVKYARSVFDSMPN--P-DFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKV-LKACCE  158 (691)
Q Consensus        83 ~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~l-l~~~~~  158 (691)
                      ++..+..+.+..++++|.+++..-.+  | +....+.|...|-...++..|-+.|+++-..  .|...-|..- ..++-+
T Consensus        13 ftaviy~lI~d~ry~DaI~~l~s~~Er~p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--~P~~~qYrlY~AQSLY~   90 (459)
T KOG4340|consen   13 FTAVVYRLIRDARYADAIQLLGSELERSPRSRAGLSLLGYCYYRLQEFALAAECYEQLGQL--HPELEQYRLYQAQSLYK   90 (459)
T ss_pred             hHHHHHHHHHHhhHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--ChHHHHHHHHHHHHHHH
Confidence            55666667778888888888766543  2 4456677777777888888888888888764  4444444322 345556


Q ss_pred             cCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCC-CChhhHHHHHHHHHhCCChhHHHHHHHHH
Q 040394          159 LRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLD-KNVVSWTSMIAGYVQNDCAQEGLVLFNRM  237 (691)
Q Consensus       159 ~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~~~~~~~~li~~~~~~g~~~~A~~~~~~m  237 (691)
                      .+.+..|..+...|....--...+...-....-..+|+..+..++++.+. .+..+.+.......+.|+++.|.+-|+..
T Consensus        91 A~i~ADALrV~~~~~D~~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en~Ad~~in~gCllykegqyEaAvqkFqaA  170 (459)
T KOG4340|consen   91 ACIYADALRVAFLLLDNPALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSENEADGQINLGCLLYKEGQYEAAVQKFQAA  170 (459)
T ss_pred             hcccHHHHHHHHHhcCCHHHHHHHHHHHHHHhcccccCcchHHHHHhccCCCccchhccchheeeccccHHHHHHHHHHH
Confidence            77788888887766543100111222222233456777788888888763 55666666666667788888888888877


Q ss_pred             Hh-CCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCC-----
Q 040394          238 RE-GFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSID-----  311 (691)
Q Consensus       238 ~~-~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~-----  311 (691)
                      .+ .|..| ...|+..+.. .+.|+...|.+...+++++|+...+.. +        -|..-+... .+.+..+-     
T Consensus       171 lqvsGyqp-llAYniALaH-y~~~qyasALk~iSEIieRG~r~HPEl-g--------IGm~tegiD-vrsvgNt~~lh~S  238 (459)
T KOG4340|consen  171 LQVSGYQP-LLAYNLALAH-YSSRQYASALKHISEIIERGIRQHPEL-G--------IGMTTEGID-VRSVGNTLVLHQS  238 (459)
T ss_pred             HhhcCCCc-hhHHHHHHHH-HhhhhHHHHHHHHHHHHHhhhhcCCcc-C--------ccceeccCc-hhcccchHHHHHH
Confidence            65 34443 4456655443 456777888888888888775321110 0        000000000 00000010     


Q ss_pred             --hhHHHHHHHHHHhcCCchhHHHHHHHhhHCC-CCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHH
Q 040394          312 --LVSWTAMIVGYTQSGYPDKALKLFTDKKWAD-FFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALV  388 (691)
Q Consensus       312 --~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~  388 (691)
                        +..+|.-...+.+.|+++.|.+-+-+|.-+. -..|++|...+.-. -..+++.....-+..+....|-...++..++
T Consensus       239 al~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~-n~~~~p~~g~~KLqFLL~~nPfP~ETFANlL  317 (459)
T KOG4340|consen  239 ALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALM-NMDARPTEGFEKLQFLLQQNPFPPETFANLL  317 (459)
T ss_pred             HHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHh-cccCCccccHHHHHHHHhcCCCChHHHHHHH
Confidence              1123333444567778888887777775442 34566666544321 1234444444445555555555777777777


Q ss_pred             HHhHhcCChHHHHHHHHhCC
Q 040394          389 DMYAKCHVIADARYIFETTS  408 (691)
Q Consensus       389 ~~~~~~g~~~~a~~~~~~~~  408 (691)
                      -.||+..-++-|-.++.+-.
T Consensus       318 llyCKNeyf~lAADvLAEn~  337 (459)
T KOG4340|consen  318 LLYCKNEYFDLAADVLAENA  337 (459)
T ss_pred             HHHhhhHHHhHHHHHHhhCc
Confidence            77777777777777776544

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=98.77  E-value=4e-05  Score=75.60  Aligned_cols=102  Identities=16%  Similarity=0.139  Sum_probs=51.8

Q ss_pred             cccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCH-HHHHHHHHHHHhcCCHHHH
Q 040394          543 SHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEPDV-SLFGAFLHGCGLYSRFDLG  619 (691)
Q Consensus       543 ~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~-~~~~~l~~~~~~~g~~~~A  619 (691)
                      .+.|++..|+..|.++++.   .|+ ...|....-+|.+.|.+..|++-.+.. ...|+. ..|..=..++....+++.|
T Consensus       369 Fk~gdy~~Av~~YteAIkr---~P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL~p~~~kgy~RKg~al~~mk~ydkA  445 (539)
T KOG0548|consen  369 FKKGDYPEAVKHYTEAIKR---DPEDARLYSNRAACYLKLGEYPEALKDAKKCIELDPNFIKAYLRKGAALRAMKEYDKA  445 (539)
T ss_pred             HhccCHHHHHHHHHHHHhc---CCchhHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444322   232 344444444444555444444443333 223322 2333333344445567777


Q ss_pred             HHHHHHHHhcCCCCchhHHHHHHHHHhC
Q 040394          620 EVMIKKMLELHPDKACYYVLVSNLYASD  647 (691)
Q Consensus       620 ~~~~~~~~~~~p~~~~~~~~l~~~~~~~  647 (691)
                      .+.|++.++.+|++..+...+..+...+
T Consensus       446 leay~eale~dp~~~e~~~~~~rc~~a~  473 (539)
T KOG0548|consen  446 LEAYQEALELDPSNAEAIDGYRRCVEAQ  473 (539)
T ss_pred             HHHHHHHHhcCchhHHHHHHHHHHHHHh
Confidence            7777777777777777777666666543

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=98.74  E-value=0.00017  Score=66.97  Aligned_cols=318  Identities=9%  Similarity=0.034  Sum_probs=190.5

Q ss_pred             ChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHH---HHHHhCCChhHHHHHHHHHHhCCCCCChhhHHH-HHH
Q 040394          179 DSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMI---AGYVQNDCAQEGLVLFNRMREGFVEGNQITLGS-LVT  254 (691)
Q Consensus       179 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li---~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~-li~  254 (691)
                      ++.-..-|...+...|++..|+..|...++-|+..|.++.   ..|...|+...|+.=+.+..+  .+||-..-.. --.
T Consensus        37 dvekhlElGk~lla~~Q~sDALt~yHaAve~dp~~Y~aifrRaT~yLAmGksk~al~Dl~rVle--lKpDF~~ARiQRg~  114 (504)
T KOG0624|consen   37 DVEKHLELGKELLARGQLSDALTHYHAAVEGDPNNYQAIFRRATVYLAMGKSKAALQDLSRVLE--LKPDFMAARIQRGV  114 (504)
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhcCCccchhhHHHHHh--cCccHHHHHHHhch
Confidence            4444555667777788888888888887777777776654   467777887777777777766  4565322111 112


Q ss_pred             HHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHH
Q 040394          255 ACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKL  334 (691)
Q Consensus       255 ~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~  334 (691)
                      .+.+.|.++.|..-|+..++...  +..+   ...+..+.-..++-.            .....+..+...|+...|+.+
T Consensus       115 vllK~Gele~A~~DF~~vl~~~~--s~~~---~~eaqskl~~~~e~~------------~l~~ql~s~~~~GD~~~ai~~  177 (504)
T KOG0624|consen  115 VLLKQGELEQAEADFDQVLQHEP--SNGL---VLEAQSKLALIQEHW------------VLVQQLKSASGSGDCQNAIEM  177 (504)
T ss_pred             hhhhcccHHHHHHHHHHHHhcCC--Ccch---hHHHHHHHHhHHHHH------------HHHHHHHHHhcCCchhhHHHH
Confidence            34456666666666666555421  1100   011111111111111            111234455667888888888


Q ss_pred             HHHhhHCCCCCc-HHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCch
Q 040394          335 FTDKKWADFFPN-HVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVI  413 (691)
Q Consensus       335 ~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  413 (691)
                      ...+.+.  .|- ...+..-..+|...|.+..|+.-++.+.+...++...+.-+-..+...|+.+.++...++..+-   
T Consensus       178 i~~llEi--~~Wda~l~~~Rakc~i~~~e~k~AI~Dlk~askLs~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLKl---  252 (504)
T KOG0624|consen  178 ITHLLEI--QPWDASLRQARAKCYIAEGEPKKAIHDLKQASKLSQDNTEGHYKISQLLYTVGDAENSLKEIRECLKL---  252 (504)
T ss_pred             HHHHHhc--CcchhHHHHHHHHHHHhcCcHHHHHHHHHHHHhccccchHHHHHHHHHHHhhhhHHHHHHHHHHHHcc---
Confidence            8887764  444 4444455568888888888888888888877777777777778888888888888888777653   


Q ss_pred             hHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040394          414 AWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMR  493 (691)
Q Consensus       414 ~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  493 (691)
                                   .||....-..-.      .+....+.++.|                 ......++|.++++..+...
T Consensus       253 -------------dpdHK~Cf~~YK------klkKv~K~les~-----------------e~~ie~~~~t~cle~ge~vl  296 (504)
T KOG0624|consen  253 -------------DPDHKLCFPFYK------KLKKVVKSLESA-----------------EQAIEEKHWTECLEAGEKVL  296 (504)
T ss_pred             -------------CcchhhHHHHHH------HHHHHHHHHHHH-----------------HHHHhhhhHHHHHHHHHHHH
Confidence                         355432211111      111111111111                 11233455666666555544


Q ss_pred             c--CC--Hh---HHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCC-HHHHHHHHHHhcccCCHHHHHHHHHHc
Q 040394          494 E--KN--TV---TWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPN-EVIFTTILSACSHTGMVGEGWKCFYSM  558 (691)
Q Consensus       494 ~--~~--~~---~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~-~~~~~~ll~~~~~~g~~~~A~~~~~~m  558 (691)
                      +  |.  .+   .+..+-.++...+++.+|++...+..+  +.|| ..++.--..+|.-...+|.|+.-|+..
T Consensus       297 k~ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~--~d~~dv~~l~dRAeA~l~dE~YD~AI~dye~A  367 (504)
T KOG0624|consen  297 KNEPEETMIRYNGFRVLCTCYREDEQFGEAIQQCKEVLD--IDPDDVQVLCDRAEAYLGDEMYDDAIHDYEKA  367 (504)
T ss_pred             hcCCcccceeeeeeheeeecccccCCHHHHHHHHHHHHh--cCchHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            3  22  12   334455666778888888888888887  4565 567777777888888888888888865

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.74  E-value=4.7e-05  Score=87.75  Aligned_cols=368  Identities=9%  Similarity=-0.011  Sum_probs=218.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHHhcCCCChhH--HHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCCh
Q 040394          286 ALLDMYVKCGNIRDARSVFDELCSIDLVS--WTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNL  363 (691)
Q Consensus       286 ~li~~~~~~g~~~~A~~~~~~~~~~~~~~--~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~  363 (691)
                      .....+...|++.+|..........+...  ...........|+++.+..+++.+.......+..........+...|++
T Consensus       346 raa~~~~~~g~~~~Al~~a~~a~d~~~~~~ll~~~a~~l~~~g~~~~l~~~l~~lp~~~~~~~~~l~~~~a~~~~~~g~~  425 (903)
T PRK04841        346 AAAEAWLAQGFPSEAIHHALAAGDAQLLRDILLQHGWSLFNQGELSLLEECLNALPWEVLLENPRLVLLQAWLAQSQHRY  425 (903)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHhHHHHHhcCChHHHHHHHHhCCHHHHhcCcchHHHHHHHHHHCCCH
Confidence            33444666677777766666554332211  1112233455677777777776653221111222222333455677888


Q ss_pred             hhHHHHHHHHHHhCCC---------chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCC-CHHHH
Q 040394          364 NMGRMVHSLGIRLGLE---------DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSP-DAVTL  433 (691)
Q Consensus       364 ~~a~~~~~~~~~~~~~---------~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p-~~~~~  433 (691)
                      +++...+......-..         .......+...+...|++++|...+++.......           +..+ .....
T Consensus       426 ~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~~~-----------~~~~~~~~a~  494 (903)
T PRK04841        426 SEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQVAINDGDPEEAERLAELALAELPL-----------TWYYSRIVAT  494 (903)
T ss_pred             HHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCC-----------ccHHHHHHHH
Confidence            8888887766543111         1222233445567789999998888875432000           0000 11234


Q ss_pred             HHHHHHHhccCcHHHHHHHHHHHHHc----CCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc-------C----CHh
Q 040394          434 VSVISACASLGAVQVGSSLHAYSTKQ----GLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE-------K----NTV  498 (691)
Q Consensus       434 ~~ll~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-------~----~~~  498 (691)
                      +.+...+...|+++.|...++.....    +...........+...+...|++++|...+++...       +    ...
T Consensus       495 ~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~  574 (903)
T PRK04841        495 SVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEF  574 (903)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHH
Confidence            55556677889999999888877643    21011123445566778889999999998876543       1    112


Q ss_pred             HHHHHHHHHhcCCChHHHHHHHHHHHHC--CCCCC--HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHH---
Q 040394          499 TWSAMIGGYGMQGDGGGSLALFSDMLNE--EVQPN--EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHY---  571 (691)
Q Consensus       499 ~~~~li~~~~~~~~~~~A~~~~~~m~~~--g~~p~--~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~---  571 (691)
                      .+..+...+...|++++|...+++....  ...+.  ...+..+.......|++++|.+.++..............+   
T Consensus       575 ~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~  654 (903)
T PRK04841        575 LLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLARGDLDNARRYLNRLENLLGNGRYHSDWIAN  654 (903)
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhH
Confidence            3445556677789999999988887653  11222  2333344556778899999998888763321111111111   


Q ss_pred             --HHHHHHHHhcCChHHHHHHHHhCCCC--CCH----HHHHHHHHHHHhcCCHHHHHHHHHHHHhcC------CCCchhH
Q 040394          572 --VCMVDLLARAGRLEEALEFMENMPIE--PDV----SLFGAFLHGCGLYSRFDLGEVMIKKMLELH------PDKACYY  637 (691)
Q Consensus       572 --~~li~~~~~~g~~~~A~~~~~~~~~~--p~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~------p~~~~~~  637 (691)
                        ...+..+...|+.+.|.+++......  ...    ..+..+..++...|++++|...++++....      +.....+
T Consensus       655 ~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~  734 (903)
T PRK04841        655 ADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQILLGQFDEAEIILEELNENARSLRLMSDLNRNL  734 (903)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCchHHHHHHH
Confidence              11223445678999999988776211  111    123456667788899999999999988742      1223466


Q ss_pred             HHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          638 VLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       638 ~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      ..++.++.+.|+.++|.+.+.+..+..
T Consensus       735 ~~la~a~~~~G~~~~A~~~L~~Al~la  761 (903)
T PRK04841        735 ILLNQLYWQQGRKSEAQRVLLEALKLA  761 (903)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            778889999999999999998888744

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.67  E-value=0.0021  Score=74.15  Aligned_cols=408  Identities=8%  Similarity=-0.031  Sum_probs=242.5

Q ss_pred             hHHHHHHHHHHHcCCC--C-C----cchHHHHHHHHccc----CChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCCh
Q 040394          128 KDIVEFYKCMRKRLKE--H-D----NFVFSKVLKACCEL----RDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDI  196 (691)
Q Consensus       128 ~~a~~~~~~m~~~~~~--~-~----~~~~~~ll~~~~~~----~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  196 (691)
                      +.+.++++.+...|.-  + +    ...|+.++..+.+.    .+.++...+              +......+...|++
T Consensus       292 ~~~~~~L~~l~~~~l~~~~~~~~~~~yr~H~L~r~~l~~~l~~~~~~~~~~l--------------h~raa~~~~~~g~~  357 (903)
T PRK04841        292 ENGQMRLEELERQGLFIQRMDDSGEWFRYHPLFASFLRHRCQWELAQELPEL--------------HRAAAEAWLAQGFP  357 (903)
T ss_pred             CcHHHHHHHHHHCCCeeEeecCCCCEEehhHHHHHHHHHHHHhcCchHHHHH--------------HHHHHHHHHHCCCH
Confidence            3456677777766641  1 1    24456666555432    122222233              33334456667777


Q ss_pred             HHHHHHHhccCCCChhh--HHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHH
Q 040394          197 GSSRQVFDETLDKNVVS--WTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILK  274 (691)
Q Consensus       197 ~~A~~~~~~~~~~~~~~--~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~  274 (691)
                      .+|..............  ...........|+++.+...++.+.......+..........+...|+++++..++....+
T Consensus       358 ~~Al~~a~~a~d~~~~~~ll~~~a~~l~~~g~~~~l~~~l~~lp~~~~~~~~~l~~~~a~~~~~~g~~~~a~~~l~~a~~  437 (903)
T PRK04841        358 SEAIHHALAAGDAQLLRDILLQHGWSLFNQGELSLLEECLNALPWEVLLENPRLVLLQAWLAQSQHRYSEVNTLLARAEQ  437 (903)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHhHHHHHhcCChHHHHHHHHhCCHHHHhcCcchHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            77777666654432211  1122234456778887777776653221112222233344455677899999988887755


Q ss_pred             HCC------CCc--hHHHHHHHHHHHhcCCHHHHHHHHHhcCC----CCh----hHHHHHHHHHHhcCCchhHHHHHHHh
Q 040394          275 IGI------EIN--SHLVTALLDMYVKCGNIRDARSVFDELCS----IDL----VSWTAMIVGYTQSGYPDKALKLFTDK  338 (691)
Q Consensus       275 ~g~------~~~--~~~~~~li~~~~~~g~~~~A~~~~~~~~~----~~~----~~~~~li~~~~~~g~~~~a~~~~~~m  338 (691)
                      .--      .+.  ......+...+...|++++|...+++...    .+.    ...+.+...+...|++++|...+++.
T Consensus       438 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~a  517 (903)
T PRK04841        438 ELKDRNIELDGTLQAEFNALRAQVAINDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQT  517 (903)
T ss_pred             hccccCcccchhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            311      111  12223334556788999999998887522    221    24455666778899999999998887


Q ss_pred             hHC----CC-CCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHh----CCC----chhHHHHHHHHhHhcCChHHHHHHHH
Q 040394          339 KWA----DF-FPNHVTIASVLSASAQLGNLNMGRMVHSLGIRL----GLE----DYTVINALVDMYAKCHVIADARYIFE  405 (691)
Q Consensus       339 ~~~----g~-~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~----~~~----~~~~~~~l~~~~~~~g~~~~a~~~~~  405 (691)
                      ...    |- .+...++..+...+...|+++.|...++.....    +..    ....+..+...+...|++++|...+.
T Consensus       518 l~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~  597 (903)
T PRK04841        518 EQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCAR  597 (903)
T ss_pred             HHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHH
Confidence            643    11 111234445566778899999999887776553    221    22334556667788899999998888


Q ss_pred             hCCCCCchhHHHHHHhhhCCCCC--CHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchh-----HHHHHHHHHHh
Q 040394          406 TTSEKDVIAWNSIISGLDDNVSP--DAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVY-----VGTALLNFYAK  478 (691)
Q Consensus       406 ~~~~~~~~~~~~li~~~~~~~~p--~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-----~~~~l~~~~~~  478 (691)
                      +......            ...+  ....+..+.......|+.+.|...+..............     .....+..+..
T Consensus       598 ~al~~~~------------~~~~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  665 (903)
T PRK04841        598 KGLEVLS------------NYQPQQQLQCLAMLAKISLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQM  665 (903)
T ss_pred             HhHHhhh------------ccCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHH
Confidence            7643200            0112  123444556677789999999999888755321011111     11112344556


Q ss_pred             cCCHHHHHHHHHhcccCC---H----hHHHHHHHHHhcCCChHHHHHHHHHHHHC----CCCCCH-HHHHHHHHHhcccC
Q 040394          479 CGDAQSARMVFDAMREKN---T----VTWSAMIGGYGMQGDGGGSLALFSDMLNE----EVQPNE-VIFTTILSACSHTG  546 (691)
Q Consensus       479 ~g~~~~A~~~~~~~~~~~---~----~~~~~li~~~~~~~~~~~A~~~~~~m~~~----g~~p~~-~~~~~ll~~~~~~g  546 (691)
                      .|+.+.|..++.....+.   .    ..+..+..++...|++++|...+++....    |..++. .+...+..++...|
T Consensus       666 ~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G  745 (903)
T PRK04841        666 TGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQILLGQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQG  745 (903)
T ss_pred             CCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcC
Confidence            899999999987766432   1    11345677788899999999999887753    333322 34555556788999


Q ss_pred             CHHHHHHHHHHchhh
Q 040394          547 MVGEGWKCFYSMCRD  561 (691)
Q Consensus       547 ~~~~A~~~~~~m~~~  561 (691)
                      +.++|...+.+....
T Consensus       746 ~~~~A~~~L~~Al~l  760 (903)
T PRK04841        746 RKSEAQRVLLEALKL  760 (903)
T ss_pred             CHHHHHHHHHHHHHH
Confidence            999999998877543

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.66  E-value=2.1e-06  Score=81.11  Aligned_cols=182  Identities=12%  Similarity=-0.002  Sum_probs=124.7

Q ss_pred             CCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--CC-H---hHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHH---
Q 040394          463 SSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--KN-T---VTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEV---  533 (691)
Q Consensus       463 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~-~---~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~---  533 (691)
                      +.....+..+...+...|++++|...|+++..  |+ .   ..+..+..++...|++++|+..++++.+.  .|+..   
T Consensus        30 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~--~p~~~~~~  107 (235)
T TIGR03302        30 EWPAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRL--HPNHPDAD  107 (235)
T ss_pred             cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--CcCCCchH
Confidence            45566777778888889999999999988764  32 2   35677788888899999999999998874  33322   


Q ss_pred             -HHHHHHHHhccc--------CCHHHHHHHHHHchhhcCCCCCh-hHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHH
Q 040394          534 -IFTTILSACSHT--------GMVGEGWKCFYSMCRDFKFVPSM-KHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLF  603 (691)
Q Consensus       534 -~~~~ll~~~~~~--------g~~~~A~~~~~~m~~~~~~~p~~-~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~  603 (691)
                       ++..+-.++...        |++++|.+.++.+...   .|+. ..+..+....    ......           ....
T Consensus       108 ~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~---~p~~~~~~~a~~~~~----~~~~~~-----------~~~~  169 (235)
T TIGR03302       108 YAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRR---YPNSEYAPDAKKRMD----YLRNRL-----------AGKE  169 (235)
T ss_pred             HHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHH---CCCChhHHHHHHHHH----HHHHHH-----------HHHH
Confidence             333333344433        6777888888877533   4442 2222211110    001000           0111


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc---hhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          604 GAFLHGCGLYSRFDLGEVMIKKMLELHPDKA---CYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       604 ~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~---~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      ..+...+.+.|++++|...++++.+..|+++   ..+..++.++...|++++|..+++.+....
T Consensus       170 ~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~~  233 (235)
T TIGR03302       170 LYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGANY  233 (235)
T ss_pred             HHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            2456678899999999999999999877654   688999999999999999999999887653

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).

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

Probab=98.64  E-value=3.5e-06  Score=91.44  Aligned_cols=201  Identities=15%  Similarity=0.181  Sum_probs=168.7

Q ss_pred             CCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC--------CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHH
Q 040394          463 SSNVYVGTALLNFYAKCGDAQSARMVFDAMREK--------NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVI  534 (691)
Q Consensus       463 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--------~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~  534 (691)
                      |.....|-..|......++.+.|.+++++....        -.-.|.++++.....|.-+...++|++..+.  --....
T Consensus      1455 PNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqy--cd~~~V 1532 (1710)
T KOG1070|consen 1455 PNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQY--CDAYTV 1532 (1710)
T ss_pred             CCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHh--cchHHH
Confidence            677778888899999999999999999987641        2347888888888888888899999999873  222356


Q ss_pred             HHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCC---HHHHHHHHHHH
Q 040394          535 FTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PIEPD---VSLFGAFLHGC  610 (691)
Q Consensus       535 ~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~---~~~~~~l~~~~  610 (691)
                      |..|...|.+.+.+++|.++++.|.++++  -....|..++..+.+..+-+.|.++++++ ..-|.   .......++.-
T Consensus      1533 ~~~L~~iy~k~ek~~~A~ell~~m~KKF~--q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~IskfAqLE 1610 (1710)
T KOG1070|consen 1533 HLKLLGIYEKSEKNDEADELLRLMLKKFG--QTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISKFAQLE 1610 (1710)
T ss_pred             HHHHHHHHHHhhcchhHHHHHHHHHHHhc--chhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHHHHHHH
Confidence            78888899999999999999999998876  55678999999999999999999999887 43343   34555566667


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCcc
Q 040394          611 GLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSK  667 (691)
Q Consensus       611 ~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~~  667 (691)
                      .+.||.+.++.+|+..+.-.|.....|..++..-.+.|+.+.++.+|++....++.+
T Consensus      1611 Fk~GDaeRGRtlfEgll~ayPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~ 1667 (1710)
T KOG1070|consen 1611 FKYGDAERGRTLFEGLLSAYPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSI 1667 (1710)
T ss_pred             hhcCCchhhHHHHHHHHhhCccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCCh
Confidence            799999999999999999999999999999999999999999999999999988754

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

Probab=98.59  E-value=3.4e-06  Score=76.12  Aligned_cols=119  Identities=9%  Similarity=0.082  Sum_probs=86.5

Q ss_pred             cCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHH-HhcCC--HHH
Q 040394          545 TGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGC-GLYSR--FDL  618 (691)
Q Consensus       545 ~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~-~~~g~--~~~  618 (691)
                      .++.+++...++...   ...|+ ...|..+...|...|++++|.+.+++. ...| +...+..+..++ ...|+  .++
T Consensus        52 ~~~~~~~i~~l~~~L---~~~P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~~~~~~  128 (198)
T PRK10370         52 QQTPEAQLQALQDKI---RANPQNSEQWALLGEYYLWRNDYDNALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQ  128 (198)
T ss_pred             chhHHHHHHHHHHHH---HHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHH
Confidence            455566666665443   33444 667777888888888888888888877 4445 445666666653 56666  488


Q ss_pred             HHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCc
Q 040394          619 GEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLS  666 (691)
Q Consensus       619 A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~  666 (691)
                      |..+++++++.+|+++..+..++..+.+.|++++|+..++++++...+
T Consensus       129 A~~~l~~al~~dP~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l~~~  176 (198)
T PRK10370        129 TREMIDKALALDANEVTALMLLASDAFMQADYAQAIELWQKVLDLNSP  176 (198)
T ss_pred             HHHHHHHHHHhCCCChhHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            888888888888888888888888888888888888888888876543

>PF12854 PPR_1: PPR repeat

Probab=98.59  E-value=7.7e-08  Score=57.89  Aligned_cols=32  Identities=34%  Similarity=0.580  Sum_probs=23.1

Q ss_pred             CCCCchHHHHHHHHHHHhcCCHHHHHHHHHhc
Q 040394          276 GIEINSHLVTALLDMYVKCGNIRDARSVFDEL  307 (691)
Q Consensus       276 g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~  307 (691)
                      |+.||..+|++||++||+.|++++|.++|++|
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            56677777777777777777777777777766

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

Probab=98.58  E-value=3.1e-06  Score=83.95  Aligned_cols=256  Identities=11%  Similarity=0.073  Sum_probs=157.9

Q ss_pred             HhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHH
Q 040394          357 SAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSV  436 (691)
Q Consensus       357 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~l  436 (691)
                      +.+.|++.+|.-.|+..++..|.+..+|..|.......++-..|+..+.++.+-|               +-|......|
T Consensus       295 lm~nG~L~~A~LafEAAVkqdP~haeAW~~LG~~qaENE~E~~ai~AL~rcl~Ld---------------P~NleaLmaL  359 (579)
T KOG1125|consen  295 LMKNGDLSEAALAFEAAVKQDPQHAEAWQKLGITQAENENEQNAISALRRCLELD---------------PTNLEALMAL  359 (579)
T ss_pred             HHhcCCchHHHHHHHHHHhhChHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcC---------------CccHHHHHHH
Confidence            3455666666666777776666666666666666666666666666666555432               1122333344


Q ss_pred             HHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHH
Q 040394          437 ISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGS  516 (691)
Q Consensus       437 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A  516 (691)
                      .-.|...|.-..|...+...+....  +-....        ..+              ++..+-+.  ..+.........
T Consensus       360 AVSytNeg~q~~Al~~L~~Wi~~~p--~y~~l~--------~a~--------------~~~~~~~~--~s~~~~~~l~~i  413 (579)
T KOG1125|consen  360 AVSYTNEGLQNQALKMLDKWIRNKP--KYVHLV--------SAG--------------ENEDFENT--KSFLDSSHLAHI  413 (579)
T ss_pred             HHHHhhhhhHHHHHHHHHHHHHhCc--cchhcc--------ccC--------------ccccccCC--cCCCCHHHHHHH
Confidence            4444444444444444444443331  110000        000              00000000  011111122333


Q ss_pred             HHHHHHH-HHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC
Q 040394          517 LALFSDM-LNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM  594 (691)
Q Consensus       517 ~~~~~~m-~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~  594 (691)
                      .++|-++ ...+..+|......|--.|--.|.+++|...|+..+   .++|+ ..+||-|...++...+.++|+..|++.
T Consensus       414 ~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdraiDcf~~AL---~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rA  490 (579)
T KOG1125|consen  414 QELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAVDCFEAAL---QVKPNDYLLWNRLGATLANGNRSEEAISAYNRA  490 (579)
T ss_pred             HHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHHHHHHHHH---hcCCchHHHHHHhhHHhcCCcccHHHHHHHHHH
Confidence            4444444 445545777777777777888999999999999664   57887 678999999999999999999999998


Q ss_pred             -CCCCCHH-HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC-----C-----chhHHHHHHHHHhCCCcHHHHHH
Q 040394          595 -PIEPDVS-LFGAFLHGCGLYSRFDLGEVMIKKMLELHPD-----K-----ACYYVLVSNLYASDGRWIRVNQV  656 (691)
Q Consensus       595 -~~~p~~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~-----~-----~~~~~~l~~~~~~~g~~~~A~~~  656 (691)
                       .++|+.+ .+..|.-.|...|.+++|...|-.++.+.+.     .     -.+|..|-.++.-.++.|.+.+.
T Consensus       491 LqLqP~yVR~RyNlgIS~mNlG~ykEA~~hlL~AL~mq~ks~~~~~~~~~se~iw~tLR~als~~~~~D~l~~a  564 (579)
T KOG1125|consen  491 LQLQPGYVRVRYNLGISCMNLGAYKEAVKHLLEALSMQRKSRNHNKAPMASENIWQTLRLALSAMNRSDLLQEA  564 (579)
T ss_pred             HhcCCCeeeeehhhhhhhhhhhhHHHHHHHHHHHHHhhhcccccccCCcchHHHHHHHHHHHHHcCCchHHHHh
Confidence             7888864 7777888999999999999999999885543     1     24677777777777777655443

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=98.55  E-value=0.0021  Score=67.84  Aligned_cols=159  Identities=11%  Similarity=0.034  Sum_probs=97.1

Q ss_pred             HHHHHHHHHhcCCChHH---HHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHH
Q 040394          499 TWSAMIGGYGMQGDGGG---SLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMV  575 (691)
Q Consensus       499 ~~~~li~~~~~~~~~~~---A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li  575 (691)
                      +-+.|+..+.+.++...   |+-+++.-.... +-|..+-..+|+.|+-.|-+..|.++|+.+ .-..+..|..-|- +.
T Consensus       438 av~~Lid~~rktnd~~~l~eaI~LLE~glt~s-~hnf~~KLlLiriY~~lGa~p~a~~~y~tL-dIK~IQ~DTlgh~-~~  514 (932)
T KOG2053|consen  438 AVNHLIDLWRKTNDLTDLFEAITLLENGLTKS-PHNFQTKLLLIRIYSYLGAFPDAYELYKTL-DIKNIQTDTLGHL-IF  514 (932)
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHHHhhcC-CccHHHHHHHHHHHHHhcCChhHHHHHHhc-chHHhhhccchHH-HH
Confidence            45677888888887664   555555555431 345556667788999889999999999988 4446776654443 34


Q ss_pred             HHHHhcCChHHHHHHHHhC-C-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC----chhHHHHHHHHHhCC
Q 040394          576 DLLARAGRLEEALEFMENM-P-IEPD-VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK----ACYYVLVSNLYASDG  648 (691)
Q Consensus       576 ~~~~~~g~~~~A~~~~~~~-~-~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~----~~~~~~l~~~~~~~g  648 (691)
                      ..+...|++..+...++.. . ...+ ..+-..+..+| +.|.+.+..++..-=.++.-..    ..+-..........+
T Consensus       515 ~~~~t~g~~~~~s~~~~~~lkfy~~~~kE~~eyI~~AY-r~g~ySkI~em~~fr~rL~~S~q~~a~~VE~~~l~ll~~~~  593 (932)
T KOG2053|consen  515 RRAETSGRSSFASNTFNEHLKFYDSSLKETPEYIALAY-RRGAYSKIPEMLAFRDRLMHSLQKWACRVENLQLSLLCNAD  593 (932)
T ss_pred             HHHHhcccchhHHHHHHHHHHHHhhhhhhhHHHHHHHH-HcCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            5566677888777766665 1 1111 12233333444 6777777666654433332221    223344556677778


Q ss_pred             CcHHHHHHHHHHH
Q 040394          649 RWIRVNQVRELMK  661 (691)
Q Consensus       649 ~~~~A~~~~~~~~  661 (691)
                      +.++-.+.++-|.
T Consensus       594 ~~~q~~~~~~~~~  606 (932)
T KOG2053|consen  594 RGTQLLKLLESMK  606 (932)
T ss_pred             cHHHHHHHHhccc
Confidence            8877777776665

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.54  E-value=2.3e-06  Score=72.95  Aligned_cols=120  Identities=10%  Similarity=0.066  Sum_probs=79.3

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-C
Q 040394          518 ALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-P  595 (691)
Q Consensus       518 ~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~  595 (691)
                      .++++.++  +.|+.  +.....++...|++++|...|+...   .+.|+ ...+..+..++.+.|++++|+..|++. .
T Consensus        14 ~~~~~al~--~~p~~--~~~~g~~~~~~g~~~~A~~~~~~al---~~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~   86 (144)
T PRK15359         14 DILKQLLS--VDPET--VYASGYASWQEGDYSRAVIDFSWLV---MAQPWSWRAHIALAGTWMMLKEYTTAINFYGHALM   86 (144)
T ss_pred             HHHHHHHH--cCHHH--HHHHHHHHHHcCCHHHHHHHHHHHH---HcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            34444444  34443  3344556667777777777777653   34554 566677777777777777777777776 3


Q ss_pred             CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHH
Q 040394          596 IEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLY  644 (691)
Q Consensus       596 ~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~  644 (691)
                      ..| +...+..+..++...|++++|+..++++++..|+++.++...+.++
T Consensus        87 l~p~~~~a~~~lg~~l~~~g~~~eAi~~~~~Al~~~p~~~~~~~~~~~~~  136 (144)
T PRK15359         87 LDASHPEPVYQTGVCLKMMGEPGLAREAFQTAIKMSYADASWSEIRQNAQ  136 (144)
T ss_pred             cCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHH
Confidence            333 5567777777777777888888888887777777777776666554

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

Probab=98.51  E-value=0.0016  Score=64.71  Aligned_cols=155  Identities=14%  Similarity=0.136  Sum_probs=117.1

Q ss_pred             HHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--CCHh-HHHHHHHHH
Q 040394          431 VTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--KNTV-TWSAMIGGY  507 (691)
Q Consensus       431 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~-~~~~li~~~  507 (691)
                      .+|...|+...+..-+..|..+|.+..+.+..+....++++++..|| .++..-|.++|+--.+  +|.. --...+.-+
T Consensus       367 Lv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~c-skD~~~AfrIFeLGLkkf~d~p~yv~~YldfL  445 (656)
T KOG1914|consen  367 LVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYC-SKDKETAFRIFELGLKKFGDSPEYVLKYLDFL  445 (656)
T ss_pred             eehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHh-cCChhHHHHHHHHHHHhcCCChHHHHHHHHHH
Confidence            46778888888888999999999999998874457888889998776 5788999999987654  3443 345567777


Q ss_pred             hcCCChHHHHHHHHHHHHCCCCCCH--HHHHHHHHHhcccCCHHHHHHHHHHchhhcC--CCCChhHHHHHHHHHHhcCC
Q 040394          508 GMQGDGGGSLALFSDMLNEEVQPNE--VIFTTILSACSHTGMVGEGWKCFYSMCRDFK--FVPSMKHYVCMVDLLARAGR  583 (691)
Q Consensus       508 ~~~~~~~~A~~~~~~m~~~g~~p~~--~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~--~~p~~~~~~~li~~~~~~g~  583 (691)
                      ...++-..+..+|++....++.|+.  ..|..+|.--+.-|++..+.++-+++...+.  ..|....-..+++.|.-.+.
T Consensus       446 ~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~af~~~qe~~~~~~~~~v~RY~~~d~  525 (656)
T KOG1914|consen  446 SHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFTAFPADQEYEGNETALFVDRYGILDL  525 (656)
T ss_pred             HHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHHhcchhhcCCCChHHHHHHHHhhccc
Confidence            8888999999999999998777765  6899999988899999999988887755544  33333344445555555544


Q ss_pred             hHH
Q 040394          584 LEE  586 (691)
Q Consensus       584 ~~~  586 (691)
                      ...
T Consensus       526 ~~c  528 (656)
T KOG1914|consen  526 YPC  528 (656)
T ss_pred             ccc
Confidence            433

>PF12854 PPR_1: PPR repeat

Probab=98.51  E-value=1.3e-07  Score=56.96  Aligned_cols=32  Identities=16%  Similarity=0.144  Sum_probs=24.0

Q ss_pred             CCCCChhhHHHHHHHHHccCChhhHHHHHHHH
Q 040394          241 FVEGNQITLGSLVTACAKLRALHQGKWLHGYI  272 (691)
Q Consensus       241 ~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~  272 (691)
                      |+.||..||+++|+++|+.|++++|.++|++|
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            66777777777777777777777777777766

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.48  E-value=2.8e-06  Score=72.44  Aligned_cols=101  Identities=8%  Similarity=-0.084  Sum_probs=89.1

Q ss_pred             CCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHH
Q 040394          563 KFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLV  640 (691)
Q Consensus       563 ~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l  640 (691)
                      .+.|+.  +..+...+...|++++|.+.|+.. ...| +...|..+..++...|++++|...|+++.+++|+++..+..+
T Consensus        21 ~~~p~~--~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~~~~a~~~l   98 (144)
T PRK15359         21 SVDPET--VYASGYASWQEGDYSRAVIDFSWLVMAQPWSWRAHIALAGTWMMLKEYTTAINFYGHALMLDASHPEPVYQT   98 (144)
T ss_pred             HcCHHH--HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHH
Confidence            345553  556788889999999999999998 5555 667889999999999999999999999999999999999999


Q ss_pred             HHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          641 SNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       641 ~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      +.++...|++++|++.++..++...
T Consensus        99 g~~l~~~g~~~eAi~~~~~Al~~~p  123 (144)
T PRK15359         99 GVCLKMMGEPGLAREAFQTAIKMSY  123 (144)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCC
Confidence            9999999999999999999988553

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.47  E-value=1.6e-05  Score=85.17  Aligned_cols=172  Identities=10%  Similarity=0.023  Sum_probs=104.4

Q ss_pred             CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHH-HHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHH
Q 040394          496 NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEV-IFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVC  573 (691)
Q Consensus       496 ~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~-~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~  573 (691)
                      ++..+-.|.....+.|..++|..+++...+  +.|+.. ....+...+.+.+++++|...+++..   ...|+ ......
T Consensus        85 ~~~~~~~La~i~~~~g~~~ea~~~l~~~~~--~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l---~~~p~~~~~~~~  159 (694)
T PRK15179         85 TELFQVLVARALEAAHRSDEGLAVWRGIHQ--RFPDSSEAFILMLRGVKRQQGIEAGRAEIELYF---SGGSSSAREILL  159 (694)
T ss_pred             cHHHHHHHHHHHHHcCCcHHHHHHHHHHHh--hCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHh---hcCCCCHHHHHH
Confidence            466666677777777777777777777776  466654 34445557777777777777777543   34565 455566


Q ss_pred             HHHHHHhcCChHHHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcH
Q 040394          574 MVDLLARAGRLEEALEFMENM-PIEPD-VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWI  651 (691)
Q Consensus       574 li~~~~~~g~~~~A~~~~~~~-~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~  651 (691)
                      +..++.+.|++++|.++|++. ...|+ ..++..+..++...|+.++|...|+++++...+-...|..+      .++..
T Consensus       160 ~a~~l~~~g~~~~A~~~y~~~~~~~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~~~~~~~~~~~------~~~~~  233 (694)
T PRK15179        160 EAKSWDEIGQSEQADACFERLSRQHPEFENGYVGWAQSLTRRGALWRARDVLQAGLDAIGDGARKLTRR------LVDLN  233 (694)
T ss_pred             HHHHHHHhcchHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhhCcchHHHHHH------HHHHH
Confidence            666777777777777777776 22333 55677777777777777777777777776433323222211      12223


Q ss_pred             HHHHHHHHHHhCCCccCCCeeEEEeCC
Q 040394          652 RVNQVRELMKQRGLSKSPGCSLVDLDI  678 (691)
Q Consensus       652 ~A~~~~~~~~~~g~~~~~~~~~~~~~~  678 (691)
                      .-...++.+.-.++......+.+-++-
T Consensus       234 ~~~~~~~~~~~~~~~~~~~~~~~~~~~  260 (694)
T PRK15179        234 ADLAALRRLGVEGDGRDVPVSILVLEK  260 (694)
T ss_pred             HHHHHHHHcCcccccCCCceeeeeHHH
Confidence            334455555555555555555554443

>PLN02789 farnesyltranstransferase

Probab=98.46  E-value=9.7e-05  Score=71.81  Aligned_cols=223  Identities=11%  Similarity=-0.011  Sum_probs=163.2

Q ss_pred             HHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcC-CHHHHHHHHHhccc---CCHhHHHHHHHHHh
Q 040394          433 LVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCG-DAQSARMVFDAMRE---KNTVTWSAMIGGYG  508 (691)
Q Consensus       433 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~---~~~~~~~~li~~~~  508 (691)
                      +..+-..+...+..+.|.....++++..  |.+..+++.....+...| ++++++..++++.+   ++..+|+.-...+.
T Consensus        40 ~~~~ra~l~~~e~serAL~lt~~aI~ln--P~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npknyqaW~~R~~~l~  117 (320)
T PLN02789         40 MDYFRAVYASDERSPRALDLTADVIRLN--PGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPKNYQIWHHRRWLAE  117 (320)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHHHHC--chhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCcchHHhHHHHHHHH
Confidence            3334444556778899999999999887  677777777777777777 57999999998875   35556776555555


Q ss_pred             cCCCh--HHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCC-ChhHHHHHHHHHHhc---C
Q 040394          509 MQGDG--GGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVP-SMKHYVCMVDLLARA---G  582 (691)
Q Consensus       509 ~~~~~--~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~---g  582 (691)
                      +.|+.  ++++.+++++.+.. +-|...|+....++...|+++++++.++++++.   .| |...|+....++.+.   |
T Consensus       118 ~l~~~~~~~el~~~~kal~~d-pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~---d~~N~sAW~~R~~vl~~~~~l~  193 (320)
T PLN02789        118 KLGPDAANKELEFTRKILSLD-AKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEE---DVRNNSAWNQRYFVITRSPLLG  193 (320)
T ss_pred             HcCchhhHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH---CCCchhHHHHHHHHHHhccccc
Confidence            56653  67899999998853 345677887777888889999999999988644   33 356666665555444   2


Q ss_pred             Ch----HHHHHHHHhC-CCCC-CHHHHHHHHHHHHhc----CCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCC----
Q 040394          583 RL----EEALEFMENM-PIEP-DVSLFGAFLHGCGLY----SRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDG----  648 (691)
Q Consensus       583 ~~----~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~----g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g----  648 (691)
                      ..    ++++++..++ ...| |...|+.+...+...    ++..+|...+.+.....|+++.....|+.+|+...    
T Consensus       194 ~~~~~~e~el~y~~~aI~~~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~~~s~~al~~l~d~~~~~~~~~~  273 (320)
T PLN02789        194 GLEAMRDSELKYTIDAILANPRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKDSNHVFALSDLLDLLCEGLQPTA  273 (320)
T ss_pred             cccccHHHHHHHHHHHHHhCCCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhcccCCcHHHHHHHHHHHHhhhccch
Confidence            22    4667776554 4444 567888888888773    45577999999988899999999999999998643    


Q ss_pred             --------------CcHHHHHHHHHHH
Q 040394          649 --------------RWIRVNQVRELMK  661 (691)
Q Consensus       649 --------------~~~~A~~~~~~~~  661 (691)
                                    ..++|.++++.+.
T Consensus       274 ~~~~~~~~~~~~~~~~~~a~~~~~~l~  300 (320)
T PLN02789        274 EFRDTVDTLAEELSDSTLAQAVCSELE  300 (320)
T ss_pred             hhhhhhhccccccccHHHHHHHHHHHH
Confidence                          3467888888883

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=98.38  E-value=1.9e-05  Score=80.53  Aligned_cols=221  Identities=9%  Similarity=-0.021  Sum_probs=168.3

Q ss_pred             CCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--CCHhHHHH
Q 040394          425 NVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--KNTVTWSA  502 (691)
Q Consensus       425 ~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~~~~  502 (691)
                      +.+|--..-..+...+.+.|=...|..++++...          +..++..|+..|+...|..+..+-.+  |+...|..
T Consensus       393 ~lpp~Wq~q~~laell~slGitksAl~I~Erlem----------w~~vi~CY~~lg~~~kaeei~~q~lek~~d~~lyc~  462 (777)
T KOG1128|consen  393 HLPPIWQLQRLLAELLLSLGITKSALVIFERLEM----------WDPVILCYLLLGQHGKAEEINRQELEKDPDPRLYCL  462 (777)
T ss_pred             CCCCcchHHHHHHHHHHHcchHHHHHHHHHhHHH----------HHHHHHHHHHhcccchHHHHHHHHhcCCCcchhHHH
Confidence            5566655566667777778888888888876543          34567788888888888887766554  57777888


Q ss_pred             HHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhc
Q 040394          503 MIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARA  581 (691)
Q Consensus       503 li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~  581 (691)
                      +.+.....--+++|.++.+..-..       .-..+.......++++++.+.|+.   ...+.|- ..+|-.+..+..+.
T Consensus       463 LGDv~~d~s~yEkawElsn~~sar-------A~r~~~~~~~~~~~fs~~~~hle~---sl~~nplq~~~wf~~G~~ALql  532 (777)
T KOG1128|consen  463 LGDVLHDPSLYEKAWELSNYISAR-------AQRSLALLILSNKDFSEADKHLER---SLEINPLQLGTWFGLGCAALQL  532 (777)
T ss_pred             hhhhccChHHHHHHHHHhhhhhHH-------HHHhhccccccchhHHHHHHHHHH---HhhcCccchhHHHhccHHHHHH
Confidence            877777777777777777654332       111111222346888899888884   3345554 66888888888899


Q ss_pred             CChHHHHHHHHhC-CCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHH
Q 040394          582 GRLEEALEFMENM-PIEPDV-SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVREL  659 (691)
Q Consensus       582 g~~~~A~~~~~~~-~~~p~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~  659 (691)
                      ++++.|.+.|... ...||. ..||.+-.+|.+.|+-.+|...++++++.+-++..+|.....+-.+-|.|++|++.+.+
T Consensus       533 ek~q~av~aF~rcvtL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn~~~w~iWENymlvsvdvge~eda~~A~~r  612 (777)
T KOG1128|consen  533 EKEQAAVKAFHRCVTLEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCNYQHWQIWENYMLVSVDVGEFEDAIKAYHR  612 (777)
T ss_pred             hhhHHHHHHHHHHhhcCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcCCCCCeeeechhhhhhhcccHHHHHHHHHH
Confidence            9999999999887 667765 59999999999999999999999999998888888888888888999999999999999


Q ss_pred             HHhCCC
Q 040394          660 MKQRGL  665 (691)
Q Consensus       660 ~~~~g~  665 (691)
                      +.+...
T Consensus       613 ll~~~~  618 (777)
T KOG1128|consen  613 LLDLRK  618 (777)
T ss_pred             HHHhhh
Confidence            987544

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

Probab=98.37  E-value=0.0011  Score=72.19  Aligned_cols=218  Identities=10%  Similarity=0.068  Sum_probs=135.7

Q ss_pred             hCCCCch--hhhHHHHHHhcCCChHHHHHHhccCCC--CCcc-hHHHHHHHHHhCCChhHHHHH----------------
Q 040394           75 DGLTNDK--CNTKLVSMYGSFGHVKYARSVFDSMPN--PDFY-SFQVMIRWYFLNDLYKDIVEF----------------  133 (691)
Q Consensus        75 ~~~~~~~--~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~-~~~~ll~~~~~~~~~~~a~~~----------------  133 (691)
                      ...+++.  .+..|+..|-+.+++++|.++.+...+  |+.. .|..+.-.+.+.++..++..+                
T Consensus        24 ~~~~p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~P~~i~~yy~~G~l~~q~~~~~~~~lv~~l~~~~~~~~~~~ve  103 (906)
T PRK14720         24 NNYSLSKFKELDDLIDAYKSENLTDEAKDICEEHLKEHKKSISALYISGILSLSRRPLNDSNLLNLIDSFSQNLKWAIVE  103 (906)
T ss_pred             ccCCcchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCcceehHHHHHHHHHhhcchhhhhhhhhhhhcccccchhHHH
Confidence            3344443  677788888788888888887775432  3332 333333345555555555444                


Q ss_pred             --HHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCCCh
Q 040394          134 --YKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNV  211 (691)
Q Consensus       134 --~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  211 (691)
                        +..|...  .-+...+..+..+|-+.|+.++|..+++++++..+.|+.+.|-+.-.|... +.++|++++.+.     
T Consensus       104 ~~~~~i~~~--~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~~n~~aLNn~AY~~ae~-dL~KA~~m~~KA-----  175 (906)
T PRK14720        104 HICDKILLY--GENKLALRTLAEAYAKLNENKKLKGVWERLVKADRDNPEIVKKLATSYEEE-DKEKAITYLKKA-----  175 (906)
T ss_pred             HHHHHHHhh--hhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHh-hHHHHHHHHHHH-----
Confidence              2222221  122246666777777778888888888888888866888888888888888 888887776654     


Q ss_pred             hhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHH-CCCCchHHHHHHHHH
Q 040394          212 VSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKI-GIEINSHLVTALLDM  290 (691)
Q Consensus       212 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~-g~~~~~~~~~~li~~  290 (691)
                            +..+...+++.++.++|.++....  |+               +++.-.++.+.+... |..--+.++-.+-..
T Consensus       176 ------V~~~i~~kq~~~~~e~W~k~~~~~--~~---------------d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~  232 (906)
T PRK14720        176 ------IYRFIKKKQYVGIEEIWSKLVHYN--SD---------------DFDFFLRIERKVLGHREFTRLVGLLEDLYEP  232 (906)
T ss_pred             ------HHHHHhhhcchHHHHHHHHHHhcC--cc---------------cchHHHHHHHHHHhhhccchhHHHHHHHHHH
Confidence                  233666678888888888887643  22               222222333333332 333345556666777


Q ss_pred             HHhcCCHHHHHHHHHhcCC---CChhHHHHHHHHHH
Q 040394          291 YVKCGNIRDARSVFDELCS---IDLVSWTAMIVGYT  323 (691)
Q Consensus       291 ~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~  323 (691)
                      |-+.++++++..+|+.+.+   .|..+..-++..|.
T Consensus       233 y~~~~~~~~~i~iLK~iL~~~~~n~~a~~~l~~~y~  268 (906)
T PRK14720        233 YKALEDWDEVIYILKKILEHDNKNNKAREELIRFYK  268 (906)
T ss_pred             HhhhhhhhHHHHHHHHHHhcCCcchhhHHHHHHHHH
Confidence            8888889999999988833   35556666666655

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

Probab=98.36  E-value=6.7e-05  Score=81.30  Aligned_cols=150  Identities=11%  Similarity=0.122  Sum_probs=78.4

Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 040394          465 NVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSA  541 (691)
Q Consensus       465 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~  541 (691)
                      +...+..+..+|-+.|+.++|..+++++.+   .|+...|.+...|... +.++|.+++.+....               
T Consensus       115 ~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV~~---------------  178 (906)
T PRK14720        115 NKLALRTLAEAYAKLNENKKLKGVWERLVKADRDNPEIVKKLATSYEEE-DKEKAITYLKKAIYR---------------  178 (906)
T ss_pred             hhHHHHHHHHHHHHcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHh-hHHHHHHHHHHHHHH---------------
Confidence            334455555566666666666666665553   2455555555555555 666666655555442               


Q ss_pred             hcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 040394          542 CSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGE  620 (691)
Q Consensus       542 ~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~  620 (691)
                      +...+++..+.++|.+++.   ..|+ ...+-.+.......            .+..--..++.-+-..|...++++++.
T Consensus       179 ~i~~kq~~~~~e~W~k~~~---~~~~d~d~f~~i~~ki~~~------------~~~~~~~~~~~~l~~~y~~~~~~~~~i  243 (906)
T PRK14720        179 FIKKKQYVGIEEIWSKLVH---YNSDDFDFFLRIERKVLGH------------REFTRLVGLLEDLYEPYKALEDWDEVI  243 (906)
T ss_pred             HHhhhcchHHHHHHHHHHh---cCcccchHHHHHHHHHHhh------------hccchhHHHHHHHHHHHhhhhhhhHHH
Confidence            3334455555666665532   2232 11111111111111            111222334444555566666777777


Q ss_pred             HHHHHHHhcCCCCchhHHHHHHHHH
Q 040394          621 VMIKKMLELHPDKACYYVLVSNLYA  645 (691)
Q Consensus       621 ~~~~~~~~~~p~~~~~~~~l~~~~~  645 (691)
                      .+++.+++.+|.|.....-++.+|.
T Consensus       244 ~iLK~iL~~~~~n~~a~~~l~~~y~  268 (906)
T PRK14720        244 YILKKILEHDNKNNKAREELIRFYK  268 (906)
T ss_pred             HHHHHHHhcCCcchhhHHHHHHHHH
Confidence            7777777777777766666666665

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.36  E-value=0.00031  Score=63.22  Aligned_cols=176  Identities=14%  Similarity=0.040  Sum_probs=107.1

Q ss_pred             HHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCC
Q 040394          451 SLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQP  530 (691)
Q Consensus       451 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p  530 (691)
                      ++.+.+..... ..+......-...|+..|++++|.+......  +....-.=+..+.+..+.+-|...+++|.+   --
T Consensus        94 ~l~E~~a~~~~-~sn~i~~l~aa~i~~~~~~~deAl~~~~~~~--~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~---id  167 (299)
T KOG3081|consen   94 SLYELVADSTD-GSNLIDLLLAAIIYMHDGDFDEALKALHLGE--NLEAAALNVQILLKMHRFDLAEKELKKMQQ---ID  167 (299)
T ss_pred             HHHHHHHhhcc-chhHHHHHHhhHHhhcCCChHHHHHHHhccc--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHc---cc
Confidence            33444444332 3333333334456778888888888877733  233332334455666777888888888876   33


Q ss_pred             CHHHHHHHHHHhc----ccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC--CCCCCHHHHH
Q 040394          531 NEVIFTTILSACS----HTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM--PIEPDVSLFG  604 (691)
Q Consensus       531 ~~~~~~~ll~~~~----~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~--~~~p~~~~~~  604 (691)
                      +..|.+-+..++.    ..+.+.+|.-+|++|..+  ..|+..+.+-...++...|++++|..+++..  ....++.+..
T Consensus       168 ed~tLtQLA~awv~la~ggek~qdAfyifeE~s~k--~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~dpetL~  245 (299)
T KOG3081|consen  168 EDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK--TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAKDPETLA  245 (299)
T ss_pred             hHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc--cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCCCHHHHH
Confidence            5556665555443    345677888888887433  5677777777777777788888888877776  3334455554


Q ss_pred             HHHHHHHhcC-CHHHHHHHHHHHHhcCCCCc
Q 040394          605 AFLHGCGLYS-RFDLGEVMIKKMLELHPDKA  634 (691)
Q Consensus       605 ~l~~~~~~~g-~~~~A~~~~~~~~~~~p~~~  634 (691)
                      .++-+-...| +.+-..+.+.+....+|+++
T Consensus       246 Nliv~a~~~Gkd~~~~~r~l~QLk~~~p~h~  276 (299)
T KOG3081|consen  246 NLIVLALHLGKDAEVTERNLSQLKLSHPEHP  276 (299)
T ss_pred             HHHHHHHHhCCChHHHHHHHHHHHhcCCcch
Confidence            4444443444 44555677777777777754

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

Probab=98.35  E-value=0.00014  Score=79.73  Aligned_cols=236  Identities=12%  Similarity=0.110  Sum_probs=158.9

Q ss_pred             HHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCC-----HHHHHHHHHHHhc
Q 040394          368 MVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPD-----AVTLVSVISACAS  442 (691)
Q Consensus       368 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~-----~~~~~~ll~~~~~  442 (691)
                      .-|+......|.+...|-..|......+++++|.+++++....               +.+.     ...|.++++.-..
T Consensus      1445 eDferlvrssPNSSi~WI~YMaf~LelsEiekAR~iaerAL~t---------------IN~REeeEKLNiWiA~lNlEn~ 1509 (1710)
T KOG1070|consen 1445 EDFERLVRSSPNSSILWIRYMAFHLELSEIEKARKIAERALKT---------------INFREEEEKLNIWIAYLNLENA 1509 (1710)
T ss_pred             HHHHHHHhcCCCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhh---------------CCcchhHHHHHHHHHHHhHHHh
Confidence            3355566666667777888888888888888888888887643               2221     1356666666666


Q ss_pred             cCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC---CHhHHHHHHHHHhcCCChHHHHHH
Q 040394          443 LGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK---NTVTWSAMIGGYGMQGDGGGSLAL  519 (691)
Q Consensus       443 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~li~~~~~~~~~~~A~~~  519 (691)
                      .|.-+...++|+++.+..   ....+|..|...|.+.+++++|.++++.|.++   ....|...+..+.++++.+.|..+
T Consensus      1510 yG~eesl~kVFeRAcqyc---d~~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF~q~~~vW~~y~~fLl~~ne~~aa~~l 1586 (1710)
T KOG1070|consen 1510 YGTEESLKKVFERACQYC---DAYTVHLKLLGIYEKSEKNDEADELLRLMLKKFGQTRKVWIMYADFLLRQNEAEAAREL 1586 (1710)
T ss_pred             hCcHHHHHHHHHHHHHhc---chHHHHHHHHHHHHHhhcchhHHHHHHHHHHHhcchhhHHHHHHHHHhcccHHHHHHHH
Confidence            677778888888887754   33556778888888888888888888888753   566888888888888888888888


Q ss_pred             HHHHHHCCCCCCH---HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC--
Q 040394          520 FSDMLNEEVQPNE---VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM--  594 (691)
Q Consensus       520 ~~~m~~~g~~p~~---~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~--  594 (691)
                      +.+..+.  -|..   ....-.++.-.+.|+.+++..+|+..+..+  +--...|+.+++.-.++|+.+.+..+|++.  
T Consensus      1587 L~rAL~~--lPk~eHv~~IskfAqLEFk~GDaeRGRtlfEgll~ay--PKRtDlW~VYid~eik~~~~~~vR~lfeRvi~ 1662 (1710)
T KOG1070|consen 1587 LKRALKS--LPKQEHVEFISKFAQLEFKYGDAERGRTLFEGLLSAY--PKRTDLWSVYIDMEIKHGDIKYVRDLFERVIE 1662 (1710)
T ss_pred             HHHHHhh--cchhhhHHHHHHHHHHHhhcCCchhhHHHHHHHHhhC--ccchhHHHHHHHHHHccCCHHHHHHHHHHHHh
Confidence            8888773  4442   222333344456788888888888775442  222567788888888888888888888776  


Q ss_pred             -CCCCCH--HHHHHHHHHHHhcCCHHHHHHHHHH
Q 040394          595 -PIEPDV--SLFGAFLHGCGLYSRFDLGEVMIKK  625 (691)
Q Consensus       595 -~~~p~~--~~~~~l~~~~~~~g~~~~A~~~~~~  625 (691)
                       +..|-.  ..|...+..-...||-+.++.+=.+
T Consensus      1663 l~l~~kkmKfffKkwLeyEk~~Gde~~vE~VKar 1696 (1710)
T KOG1070|consen 1663 LKLSIKKMKFFFKKWLEYEKSHGDEKNVEYVKAR 1696 (1710)
T ss_pred             cCCChhHhHHHHHHHHHHHHhcCchhhHHHHHHH
Confidence             333322  2444444444445554444444333

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

Probab=98.35  E-value=0.0041  Score=61.90  Aligned_cols=78  Identities=15%  Similarity=0.146  Sum_probs=56.3

Q ss_pred             CCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCC--CChhhHHHHHHH
Q 040394          143 EHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLD--KNVVSWTSMIAG  220 (691)
Q Consensus       143 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~~~~li~~  220 (691)
                      +-|..+|..+|+-+... .++++.+.++++...-+..+..|..-+..-.+..+++..+++|.+-..  -++..|..-|..
T Consensus        17 P~di~sw~~lire~qt~-~~~~~R~~YEq~~~~FP~s~r~W~~yi~~El~skdfe~VEkLF~RCLvkvLnlDLW~lYl~Y   95 (656)
T KOG1914|consen   17 PYDIDSWSQLIREAQTQ-PIDKVRETYEQLVNVFPSSPRAWKLYIERELASKDFESVEKLFSRCLVKVLNLDLWKLYLSY   95 (656)
T ss_pred             CccHHHHHHHHHHHccC-CHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhHhHHHHHHHH
Confidence            45677888888777655 788888888888776555778888888888888888888888877533  256666666654


Q ss_pred             H
Q 040394          221 Y  221 (691)
Q Consensus       221 ~  221 (691)
                      -
T Consensus        96 V   96 (656)
T KOG1914|consen   96 V   96 (656)
T ss_pred             H
Confidence            3

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=98.34  E-value=0.0067  Score=64.19  Aligned_cols=492  Identities=11%  Similarity=0.072  Sum_probs=255.7

Q ss_pred             HhcCCChHHHHHHhccCCC---CCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHH
Q 040394           90 YGSFGHVKYARSVFDSMPN---PDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGM  166 (691)
Q Consensus        90 ~~~~g~~~~A~~~~~~~~~---~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~  166 (691)
                      +.|.|+.++|..+++....   .|..+...+-..|...++.++|..+|+.....  -|+......+..+|.+.+++.+-.
T Consensus        53 l~r~gk~~ea~~~Le~~~~~~~~D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~~--~P~eell~~lFmayvR~~~yk~qQ  130 (932)
T KOG2053|consen   53 LFRLGKGDEALKLLEALYGLKGTDDLTLQFLQNVYRDLGKLDEAVHLYERANQK--YPSEELLYHLFMAYVREKSYKKQQ  130 (932)
T ss_pred             HHHhcCchhHHHHHhhhccCCCCchHHHHHHHHHHHHHhhhhHHHHHHHHHHhh--CCcHHHHHHHHHHHHHHHHHHHHH
Confidence            5678888888888876643   46667888888888888999999999888775  466777777778888877776655


Q ss_pred             HHHHHHHHhCCCChhHHHHHHHHhHhcC-C---------hHHHHHHHhccCCCC--hh---hHHHHHHHHHhCCChhHHH
Q 040394          167 KVHCEIVKVGGPDSFVLTGLVDMYAKCR-D---------IGSSRQVFDETLDKN--VV---SWTSMIAGYVQNDCAQEGL  231 (691)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~---------~~~A~~~~~~~~~~~--~~---~~~~li~~~~~~g~~~~A~  231 (691)
                      ++-=++-+.-+.++..+=++++.+...- .         ..-|.+.++.+.+.+  ..   -.-.-...+...|++++|+
T Consensus       131 kaa~~LyK~~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~LA~~m~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal  210 (932)
T KOG2053|consen  131 KAALQLYKNFPKRAYYFWSVISLILQSIFSENELLDPILLALAEKMVQKLLEKKGKIESEAEIILYLLILELQGKYQEAL  210 (932)
T ss_pred             HHHHHHHHhCCcccchHHHHHHHHHHhccCCcccccchhHHHHHHHHHHHhccCCccchHHHHHHHHHHHHhcccHHHHH
Confidence            4444444443445555555555554431 1         223444555544332  11   1111223345677888888


Q ss_pred             HHHH-HHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHH----------------hc
Q 040394          232 VLFN-RMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYV----------------KC  294 (691)
Q Consensus       232 ~~~~-~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~----------------~~  294 (691)
                      +++. ...+.-...+...-+--+..+...+++.+..++-.++...|.. |   |...++.++                ..
T Consensus       211 ~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~Ll~k~~D-d---y~~~~~sv~klLe~~~~~~a~~~~s~~  286 (932)
T KOG2053|consen  211 EFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRLLEKGND-D---YKIYTDSVFKLLELLNKEPAEAAHSLS  286 (932)
T ss_pred             HHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHHHHhCCc-c---hHHHHHHHHHHHHhcccccchhhhhhh
Confidence            8883 3333333334444455666777888888888888888887643 2   222222211                11


Q ss_pred             CCHHHHHHHHHhcCC-CChhHHHHHHHHHH---hcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHH
Q 040394          295 GNIRDARSVFDELCS-IDLVSWTAMIVGYT---QSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVH  370 (691)
Q Consensus       295 g~~~~A~~~~~~~~~-~~~~~~~~li~~~~---~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~  370 (691)
                      +..+...+..++... .....|-+-+..+.   .-|+.+++.-.|-+  +-|-+|   .|..=+..|...=..+.-..++
T Consensus       287 ~~l~~~~ek~~~~i~~~~Rgp~LA~lel~kr~~~~gd~ee~~~~y~~--kfg~kp---cc~~Dl~~yl~~l~~~q~~~l~  361 (932)
T KOG2053|consen  287 KSLDECIEKAQKNIGSKSRGPYLARLELDKRYKLIGDSEEMLSYYFK--KFGDKP---CCAIDLNHYLGHLNIDQLKSLM  361 (932)
T ss_pred             hhHHHHHHHHHHhhcccccCcHHHHHHHHHHhcccCChHHHHHHHHH--HhCCCc---HhHhhHHHhhccCCHHHHHHHH
Confidence            223333333332211 12222333333333   34666665433322  112222   1111111122111222222222


Q ss_pred             HHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHH-HHHHhhhCC------CCCCHH---------HHH
Q 040394          371 SLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWN-SIISGLDDN------VSPDAV---------TLV  434 (691)
Q Consensus       371 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~-~li~~~~~~------~~p~~~---------~~~  434 (691)
                      ........... .-...+..+.-.-........+..|+.....++. .++..|.+|      .-|+..         +.+
T Consensus       362 ~~l~~~~~~~s-~~~k~l~~h~c~l~~~rl~G~~~~l~ad~i~a~~~kl~~~ye~gls~~K~ll~TE~~~g~~~llLav~  440 (932)
T KOG2053|consen  362 SKLVLADDDSS-GDEKVLQQHLCVLLLLRLLGLYEKLPADSILAYVRKLKLTYEKGLSLSKDLLPTEYSFGDELLLLAVN  440 (932)
T ss_pred             HHhhccCCcch-hhHHHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHhccccccccccccccccHHHHHHHHHH
Confidence            22222211100 0000000000000111222223333333333332 333334333      333433         345


Q ss_pred             HHHHHHhccCcHH---HHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC----CHhHHHHHHHHH
Q 040394          435 SVISACASLGAVQ---VGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK----NTVTWSAMIGGY  507 (691)
Q Consensus       435 ~ll~~~~~~~~~~---~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~~~~~li~~~  507 (691)
                      .|+..+.+.++..   +|.-+++......  +.+..+--.++..|+-.|-+..|.++|+.+.-+    |...|-+ ..-+
T Consensus       441 ~Lid~~rktnd~~~l~eaI~LLE~glt~s--~hnf~~KLlLiriY~~lGa~p~a~~~y~tLdIK~IQ~DTlgh~~-~~~~  517 (932)
T KOG2053|consen  441 HLIDLWRKTNDLTDLFEAITLLENGLTKS--PHNFQTKLLLIRIYSYLGAFPDAYELYKTLDIKNIQTDTLGHLI-FRRA  517 (932)
T ss_pred             HHHHHHHhcCcHHHHHHHHHHHHHHhhcC--CccHHHHHHHHHHHHHhcCChhHHHHHHhcchHHhhhccchHHH-HHHH
Confidence            6778888887754   5666667666666  778888888999999999999999999988744    3333332 3445


Q ss_pred             hcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHH---HHchhhcCCCCChhHHHHHHHHHHhcCCh
Q 040394          508 GMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCF---YSMCRDFKFVPSMKHYVCMVDLLARAGRL  584 (691)
Q Consensus       508 ~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~---~~m~~~~~~~p~~~~~~~li~~~~~~g~~  584 (691)
                      ...|++..+...+....+. +.-+..----+|....+.|.+....+..   +++ ....-.....+-+..++.++..++.
T Consensus       518 ~t~g~~~~~s~~~~~~lkf-y~~~~kE~~eyI~~AYr~g~ySkI~em~~fr~rL-~~S~q~~a~~VE~~~l~ll~~~~~~  595 (932)
T KOG2053|consen  518 ETSGRSSFASNTFNEHLKF-YDSSLKETPEYIALAYRRGAYSKIPEMLAFRDRL-MHSLQKWACRVENLQLSLLCNADRG  595 (932)
T ss_pred             HhcccchhHHHHHHHHHHH-HhhhhhhhHHHHHHHHHcCchhhhHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHhCCcH
Confidence            5567777777776665542 1111111112223223455555544432   222 1111111234556677888889999


Q ss_pred             HHHHHHHHhCCCCC
Q 040394          585 EEALEFMENMPIEP  598 (691)
Q Consensus       585 ~~A~~~~~~~~~~p  598 (691)
                      +.-...+..|..+|
T Consensus       596 ~q~~~~~~~~~l~~  609 (932)
T KOG2053|consen  596 TQLLKLLESMKLPP  609 (932)
T ss_pred             HHHHHHHhccccCc
Confidence            99888888885443

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

Probab=98.33  E-value=7e-05  Score=67.63  Aligned_cols=154  Identities=10%  Similarity=0.162  Sum_probs=113.1

Q ss_pred             HHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHH
Q 040394          473 LNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGW  552 (691)
Q Consensus       473 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~  552 (691)
                      +.+|...|+++.+....+.+..+.        ..+...++.++++..+++..+.. +.|...|..+...|...|++++|.
T Consensus        23 ~~~Y~~~g~~~~v~~~~~~~~~~~--------~~~~~~~~~~~~i~~l~~~L~~~-P~~~~~w~~Lg~~~~~~g~~~~A~   93 (198)
T PRK10370         23 VGSYLLSPKWQAVRAEYQRLADPL--------HQFASQQTPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWRNDYDNAL   93 (198)
T ss_pred             HHHHHHcchHHHHHHHHHHHhCcc--------ccccCchhHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHH
Confidence            456778888877655554333221        11223566777888888877753 556677878888899999999999


Q ss_pred             HHHHHchhhcCCCCC-hhHHHHHHHHH-HhcCC--hHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040394          553 KCFYSMCRDFKFVPS-MKHYVCMVDLL-ARAGR--LEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKM  626 (691)
Q Consensus       553 ~~~~~m~~~~~~~p~-~~~~~~li~~~-~~~g~--~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~  626 (691)
                      ..|++..   .+.|+ ...+..+..++ ...|+  .++|.+++++. ...| +...+..+...+...|++++|+..|+++
T Consensus        94 ~a~~~Al---~l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~~~~al~~LA~~~~~~g~~~~Ai~~~~~a  170 (198)
T PRK10370         94 LAYRQAL---QLRGENAELYAALATVLYYQAGQHMTPQTREMIDKALALDANEVTALMLLASDAFMQADYAQAIELWQKV  170 (198)
T ss_pred             HHHHHHH---HhCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCCChhHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            9999664   45665 67777777764 67677  59999999998 4455 5568888888899999999999999999


Q ss_pred             HhcCCCCchhHH
Q 040394          627 LELHPDKACYYV  638 (691)
Q Consensus       627 ~~~~p~~~~~~~  638 (691)
                      ++..|.+..-+.
T Consensus       171 L~l~~~~~~r~~  182 (198)
T PRK10370        171 LDLNSPRVNRTQ  182 (198)
T ss_pred             HhhCCCCccHHH
Confidence            998887654443

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.31  E-value=6.1e-05  Score=71.07  Aligned_cols=183  Identities=13%  Similarity=0.036  Sum_probs=130.1

Q ss_pred             CCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCch---hHHHHHHHHHHhcCCHHHHHHHHHhccc--CC-Hh--
Q 040394          427 SPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNV---YVGTALLNFYAKCGDAQSARMVFDAMRE--KN-TV--  498 (691)
Q Consensus       427 ~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~-~~--  498 (691)
                      ......+..+...+...|+++.|...++.+.+..  |.++   ..+..+...+.+.|++++|...++++.+  |+ ..  
T Consensus        30 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~  107 (235)
T TIGR03302        30 EWPAEELYEEAKEALDSGDYTEAIKYFEALESRY--PFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDAD  107 (235)
T ss_pred             cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchH
Confidence            4456678888889999999999999999998876  4433   4667788999999999999999999875  32 22  


Q ss_pred             -HHHHHHHHHhcC--------CChHHHHHHHHHHHHCCCCCCHH-HHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCCh
Q 040394          499 -TWSAMIGGYGMQ--------GDGGGSLALFSDMLNEEVQPNEV-IFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSM  568 (691)
Q Consensus       499 -~~~~li~~~~~~--------~~~~~A~~~~~~m~~~g~~p~~~-~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~  568 (691)
                       ++..+..++...        |+.++|.+.++++.+.  .|+.. ....+.....    ..      ... .        
T Consensus       108 ~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~a~~~~~~----~~------~~~-~--------  166 (235)
T TIGR03302       108 YAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRR--YPNSEYAPDAKKRMDY----LR------NRL-A--------  166 (235)
T ss_pred             HHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHH--CCCChhHHHHHHHHHH----HH------HHH-H--------
Confidence             455555556544        7889999999999885  45543 2221111100    00      000 0        


Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhC-CC---CC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040394          569 KHYVCMVDLLARAGRLEEALEFMENM-PI---EP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPD  632 (691)
Q Consensus       569 ~~~~~li~~~~~~g~~~~A~~~~~~~-~~---~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~  632 (691)
                      .....+...|.+.|++++|+..+++. ..   .| ....+..+..++.+.|++++|...++.+....|+
T Consensus       167 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~~~~  235 (235)
T TIGR03302       167 GKELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGANYPD  235 (235)
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            01124667788999999999998887 22   23 3468889999999999999999999888776663

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).

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

Probab=98.28  E-value=1.3e-05  Score=68.01  Aligned_cols=94  Identities=15%  Similarity=0.216  Sum_probs=58.9

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhC
Q 040394          570 HYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASD  647 (691)
Q Consensus       570 ~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~  647 (691)
                      ....+...+...|++++|.+.++.. ...| +...|..+...+...|++++|...++++.+..|+++..+..++.+|...
T Consensus        19 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~   98 (135)
T TIGR02552        19 QIYALAYNLYQQGRYDEALKLFQLLAAYDPYNSRYWLGLAACCQMLKEYEEAIDAYALAAALDPDDPRPYFHAAECLLAL   98 (135)
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHc
Confidence            3444555566666666666666665 2222 4455666666666666666666666666666666666666666666666


Q ss_pred             CCcHHHHHHHHHHHhC
Q 040394          648 GRWIRVNQVRELMKQR  663 (691)
Q Consensus       648 g~~~~A~~~~~~~~~~  663 (691)
                      |++++|...+++..+.
T Consensus        99 g~~~~A~~~~~~al~~  114 (135)
T TIGR02552        99 GEPESALKALDLAIEI  114 (135)
T ss_pred             CCHHHHHHHHHHHHHh
Confidence            7777776666666654

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

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.27  E-value=5.6e-05  Score=67.91  Aligned_cols=160  Identities=11%  Similarity=0.111  Sum_probs=122.8

Q ss_pred             CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHH
Q 040394          496 NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMV  575 (691)
Q Consensus       496 ~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li  575 (691)
                      |... ..+-..+...|+-+....+....... ..-|............+.|++..|...+++.. . .-++|...|+.+.
T Consensus        66 d~~i-~~~a~a~~~~G~a~~~l~~~~~~~~~-~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~-~-l~p~d~~~~~~lg  141 (257)
T COG5010          66 DLSI-AKLATALYLRGDADSSLAVLQKSAIA-YPKDRELLAAQGKNQIRNGNFGEAVSVLRKAA-R-LAPTDWEAWNLLG  141 (257)
T ss_pred             hHHH-HHHHHHHHhcccccchHHHHhhhhcc-CcccHHHHHHHHHHHHHhcchHHHHHHHHHHh-c-cCCCChhhhhHHH
Confidence            3444 55667777788888887777765442 23344455557778888999999999998763 2 2445588999999


Q ss_pred             HHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHH
Q 040394          576 DLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRV  653 (691)
Q Consensus       576 ~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A  653 (691)
                      -+|.+.|+.++|..-|.+. .+.| +....+.|...+.-.||.+.|+.++..+....+.++.+-..|+.+....|++++|
T Consensus       142 aaldq~Gr~~~Ar~ay~qAl~L~~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~ad~~v~~NLAl~~~~~g~~~~A  221 (257)
T COG5010         142 AALDQLGRFDEARRAYRQALELAPNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPAADSRVRQNLALVVGLQGDFREA  221 (257)
T ss_pred             HHHHHccChhHHHHHHHHHHHhccCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCCCchHHHHHHHHHHhhcCChHHH
Confidence            9999999999998877776 4444 4467788888888899999999999998888888888888999999999999999


Q ss_pred             HHHHHH
Q 040394          654 NQVREL  659 (691)
Q Consensus       654 ~~~~~~  659 (691)
                      ..+...
T Consensus       222 ~~i~~~  227 (257)
T COG5010         222 EDIAVQ  227 (257)
T ss_pred             Hhhccc
Confidence            877644

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=98.24  E-value=4.3e-05  Score=78.11  Aligned_cols=188  Identities=14%  Similarity=0.176  Sum_probs=159.0

Q ss_pred             CCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHh
Q 040394          463 SSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSAC  542 (691)
Q Consensus       463 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~  542 (691)
                      ||-...-..+...+...|-..+|..+|+++.     .|.-.+.+|+..|+..+|..+..+-.+  -+||...|..+.+..
T Consensus       395 pp~Wq~q~~laell~slGitksAl~I~Erle-----mw~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~lyc~LGDv~  467 (777)
T KOG1128|consen  395 PPIWQLQRLLAELLLSLGITKSALVIFERLE-----MWDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLYCLLGDVL  467 (777)
T ss_pred             CCcchHHHHHHHHHHHcchHHHHHHHHHhHH-----HHHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhHHHhhhhc
Confidence            6666677788899999999999999999865     677889999999999999999998887  489999999998888


Q ss_pred             cccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHH
Q 040394          543 SHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGE  620 (691)
Q Consensus       543 ~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~  620 (691)
                      ...--++.|.++.+....+        .-..+.....+.++++++.+.|+.- ...| ...+|-.+..+..+.+++..|.
T Consensus       468 ~d~s~yEkawElsn~~sar--------A~r~~~~~~~~~~~fs~~~~hle~sl~~nplq~~~wf~~G~~ALqlek~q~av  539 (777)
T KOG1128|consen  468 HDPSLYEKAWELSNYISAR--------AQRSLALLILSNKDFSEADKHLERSLEINPLQLGTWFGLGCAALQLEKEQAAV  539 (777)
T ss_pred             cChHHHHHHHHHhhhhhHH--------HHHhhccccccchhHHHHHHHHHHHhhcCccchhHHHhccHHHHHHhhhHHHH
Confidence            8888889999998865222        2222333345578999999998875 4444 4568888888888999999999


Q ss_pred             HHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          621 VMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       621 ~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      +.|.....++|++...|+.++.+|.+.|+..+|...+++..+.+.
T Consensus       540 ~aF~rcvtL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn~  584 (777)
T KOG1128|consen  540 KAFHRCVTLEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCNY  584 (777)
T ss_pred             HHHHHHhhcCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcCC
Confidence            999999999999999999999999999999999999999999884

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.21  E-value=0.00019  Score=70.32  Aligned_cols=110  Identities=11%  Similarity=0.144  Sum_probs=58.2

Q ss_pred             hcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHH-HhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChH
Q 040394          508 GMQGDGGGSLALFSDMLNEEVQPNEVIFTTILS-ACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLE  585 (691)
Q Consensus       508 ~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~-~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~  585 (691)
                      ...|++++|+..++.++..  .|+...|..+.. .+.+.++.++|.+.+++++   ...|+ ....-.+..+|.+.|++.
T Consensus       317 ~~~~~~d~A~~~l~~L~~~--~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal---~l~P~~~~l~~~~a~all~~g~~~  391 (484)
T COG4783         317 YLAGQYDEALKLLQPLIAA--QPDNPYYLELAGDILLEANKAKEAIERLKKAL---ALDPNSPLLQLNLAQALLKGGKPQ  391 (484)
T ss_pred             HHhcccchHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHH---hcCCCccHHHHHHHHHHHhcCChH
Confidence            3445555566666655553  444444444333 4555566666666665443   23454 333444555566666666


Q ss_pred             HHHHHHHhC--CCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 040394          586 EALEFMENM--PIEPDVSLFGAFLHGCGLYSRFDLGEVM  622 (691)
Q Consensus       586 ~A~~~~~~~--~~~p~~~~~~~l~~~~~~~g~~~~A~~~  622 (691)
                      +|+.+++..  ..+.|+..|..|.++|...|+..++...
T Consensus       392 eai~~L~~~~~~~p~dp~~w~~LAqay~~~g~~~~a~~A  430 (484)
T COG4783         392 EAIRILNRYLFNDPEDPNGWDLLAQAYAELGNRAEALLA  430 (484)
T ss_pred             HHHHHHHHHhhcCCCCchHHHHHHHHHHHhCchHHHHHH
Confidence            666655555  3334455566666666666655555443

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.21  E-value=0.00018  Score=64.15  Aligned_cols=156  Identities=12%  Similarity=0.088  Sum_probs=77.3

Q ss_pred             HHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHH-HHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcC
Q 040394          504 IGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTIL-SACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAG  582 (691)
Q Consensus       504 i~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll-~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g  582 (691)
                      +-+....|+.+-|..+++++..+ + |.+.-...+= --+...|.+++|.++++.+..+  -+.|..++---+-+.-..|
T Consensus        59 ~IAAld~~~~~lAq~C~~~L~~~-f-p~S~RV~~lkam~lEa~~~~~~A~e~y~~lL~d--dpt~~v~~KRKlAilka~G  134 (289)
T KOG3060|consen   59 FIAALDTGRDDLAQKCINQLRDR-F-PGSKRVGKLKAMLLEATGNYKEAIEYYESLLED--DPTDTVIRKRKLAILKAQG  134 (289)
T ss_pred             HHHHHHhcchHHHHHHHHHHHHh-C-CCChhHHHHHHHHHHHhhchhhHHHHHHHHhcc--CcchhHHHHHHHHHHHHcC
Confidence            33444455555555555555543 2 3332111111 1223345555566655555433  1222444444444444555


Q ss_pred             ChHHHHHHHHhC--CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCC---CcHHHHHHH
Q 040394          583 RLEEALEFMENM--PIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDG---RWIRVNQVR  657 (691)
Q Consensus       583 ~~~~A~~~~~~~--~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g---~~~~A~~~~  657 (691)
                      +.-+|++-+...  .+..|...|..+...|...|++++|.-.+++++=..|-++.++..++.++.-.|   +++-|.++|
T Consensus       135 K~l~aIk~ln~YL~~F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~ll~~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy  214 (289)
T KOG3060|consen  135 KNLEAIKELNEYLDKFMNDQEAWHELAEIYLSEGDFEKAAFCLEELLLIQPFNPLYFQRLAEVLYTQGGAENLELARKYY  214 (289)
T ss_pred             CcHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhHhHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            555555544444  344555566666666666666666666666666666665555555555554443   444455555


Q ss_pred             HHHHhC
Q 040394          658 ELMKQR  663 (691)
Q Consensus       658 ~~~~~~  663 (691)
                      .+.++.
T Consensus       215 ~~alkl  220 (289)
T KOG3060|consen  215 ERALKL  220 (289)
T ss_pred             HHHHHh
Confidence            555543

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=98.20  E-value=2.2e-05  Score=65.54  Aligned_cols=97  Identities=5%  Similarity=-0.017  Sum_probs=84.0

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHH
Q 040394          568 MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYA  645 (691)
Q Consensus       568 ~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~  645 (691)
                      ....-.+...+...|++++|.++|+-. .+.| +..-|-.|..++...|++++|+..|..+..++|+++..+..++.++.
T Consensus        35 l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~ddp~~~~~ag~c~L  114 (157)
T PRK15363         35 LNTLYRYAMQLMEVKEFAGAARLFQLLTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKIDAPQAPWAAAECYL  114 (157)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHHH
Confidence            334445666778999999999999998 4555 45677888888889999999999999999999999999999999999


Q ss_pred             hCCCcHHHHHHHHHHHhCC
Q 040394          646 SDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       646 ~~g~~~~A~~~~~~~~~~g  664 (691)
                      ..|+.+.|++-|+..+...
T Consensus       115 ~lG~~~~A~~aF~~Ai~~~  133 (157)
T PRK15363        115 ACDNVCYAIKALKAVVRIC  133 (157)
T ss_pred             HcCCHHHHHHHHHHHHHHh
Confidence            9999999999999887744

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.16  E-value=0.00015  Score=65.23  Aligned_cols=150  Identities=12%  Similarity=0.011  Sum_probs=84.5

Q ss_pred             HHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHH
Q 040394          355 SASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLV  434 (691)
Q Consensus       355 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~  434 (691)
                      ..+...|+-+....+........+.+..+....+....+.|++..|...+.+....               -++|..+|+
T Consensus        74 ~a~~~~G~a~~~l~~~~~~~~~~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l---------------~p~d~~~~~  138 (257)
T COG5010          74 TALYLRGDADSSLAVLQKSAIAYPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARL---------------APTDWEAWN  138 (257)
T ss_pred             HHHHhcccccchHHHHhhhhccCcccHHHHHHHHHHHHHhcchHHHHHHHHHHhcc---------------CCCChhhhh
Confidence            34444454444444444443333334445555666666666666666666665543               345556666


Q ss_pred             HHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCC
Q 040394          435 SVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQG  511 (691)
Q Consensus       435 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~  511 (691)
                      .+.-+|.+.|+.+.|..-|.+..+..  +.++..++.+...|.-.|+.+.|..++.....   .|...-..+.......|
T Consensus       139 ~lgaaldq~Gr~~~Ar~ay~qAl~L~--~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~ad~~v~~NLAl~~~~~g  216 (257)
T COG5010         139 LLGAALDQLGRFDEARRAYRQALELA--PNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPAADSRVRQNLALVVGLQG  216 (257)
T ss_pred             HHHHHHHHccChhHHHHHHHHHHHhc--cCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCCCchHHHHHHHHHHhhcC
Confidence            66666666666666666666666555  45555566666666666666666666655442   24455555555555666


Q ss_pred             ChHHHHHHHH
Q 040394          512 DGGGSLALFS  521 (691)
Q Consensus       512 ~~~~A~~~~~  521 (691)
                      ++++|..+..
T Consensus       217 ~~~~A~~i~~  226 (257)
T COG5010         217 DFREAEDIAV  226 (257)
T ss_pred             ChHHHHhhcc
Confidence            6666655544

>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=98.16  E-value=3.8e-05  Score=76.09  Aligned_cols=122  Identities=16%  Similarity=0.116  Sum_probs=92.2

Q ss_pred             HHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHh
Q 040394          535 FTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGL  612 (691)
Q Consensus       535 ~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~  612 (691)
                      ...++..+...++++.|..+++++.+.   .|+  ....++..+...++..+|++++++. . .+.|...+..-...|.+
T Consensus       172 v~~Ll~~l~~t~~~~~ai~lle~L~~~---~pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d~~LL~~Qa~fLl~  246 (395)
T PF09295_consen  172 VDTLLKYLSLTQRYDEAIELLEKLRER---DPE--VAVLLARVYLLMNEEVEAIRLLNEALKENPQDSELLNLQAEFLLS  246 (395)
T ss_pred             HHHHHHHHhhcccHHHHHHHHHHHHhc---CCc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHh
Confidence            344555666677788888888877433   244  3345677777777778888887777 3 33355556555666788


Q ss_pred             cCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHH
Q 040394          613 YSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMK  661 (691)
Q Consensus       613 ~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  661 (691)
                      .++++.|..+.+++.+..|++..+|..|+.+|...|++++|.-.++.+.
T Consensus       247 k~~~~lAL~iAk~av~lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  247 KKKYELALEIAKKAVELSPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             cCCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            9999999999999999999999999999999999999999998888765

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>PLN02789 farnesyltranstransferase

Probab=98.16  E-value=0.0013  Score=63.99  Aligned_cols=233  Identities=12%  Similarity=0.052  Sum_probs=158.8

Q ss_pred             HHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCH-HHHHHHHHHHhccC-cHHHHHHHHHHHHHcCCC
Q 040394          385 NALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDA-VTLVSVISACASLG-AVQVGSSLHAYSTKQGLL  462 (691)
Q Consensus       385 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~-~~~~~ll~~~~~~~-~~~~a~~~~~~~~~~~~~  462 (691)
                      ..+-..+...+..++|+.+..++...                .|+. .+|..--..+...| +++++...++.+.+..  
T Consensus        41 ~~~ra~l~~~e~serAL~lt~~aI~l----------------nP~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~n--  102 (320)
T PLN02789         41 DYFRAVYASDERSPRALDLTADVIRL----------------NPGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDN--  102 (320)
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHHHHH----------------CchhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHC--
Confidence            44445566677888888888887653                3443 34555555555666 6799999999999887  


Q ss_pred             CCchhHHHHHHHHHHhcCCH--HHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHH
Q 040394          463 SSNVYVGTALLNFYAKCGDA--QSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTT  537 (691)
Q Consensus       463 ~~~~~~~~~l~~~~~~~g~~--~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~  537 (691)
                      |.+..+++.....+.+.|+.  +++..+++.+.+   .|..+|+.....+...|+++++++.++++++.+.. |...|+.
T Consensus       103 pknyqaW~~R~~~l~~l~~~~~~~el~~~~kal~~dpkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~-N~sAW~~  181 (320)
T PLN02789        103 PKNYQIWHHRRWLAEKLGPDAANKELEFTRKILSLDAKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVR-NNSAWNQ  181 (320)
T ss_pred             CcchHHhHHHHHHHHHcCchhhHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCC-chhHHHH
Confidence            67777777666666666763  677888877775   47788998888889999999999999999997633 3444554


Q ss_pred             HHHHhccc---CC----HHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhc----CChHHHHHHHHhC-CCCC-CHHHH
Q 040394          538 ILSACSHT---GM----VGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARA----GRLEEALEFMENM-PIEP-DVSLF  603 (691)
Q Consensus       538 ll~~~~~~---g~----~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~----g~~~~A~~~~~~~-~~~p-~~~~~  603 (691)
                      ....+.+.   |.    .+++.++..+++   ...|+ ...|+.+..++...    ++..+|.+++.+. ...| +....
T Consensus       182 R~~vl~~~~~l~~~~~~~e~el~y~~~aI---~~~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~~~s~~al  258 (320)
T PLN02789        182 RYFVITRSPLLGGLEAMRDSELKYTIDAI---LANPRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKDSNHVFAL  258 (320)
T ss_pred             HHHHHHhccccccccccHHHHHHHHHHHH---HhCCCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhcccCCcHHHH
Confidence            44444333   22    245667765543   34565 77888888888773    3456788887776 3333 56678


Q ss_pred             HHHHHHHHhcC------------------CHHHHHHHHHHHHhcCCCCchhHHH
Q 040394          604 GAFLHGCGLYS------------------RFDLGEVMIKKMLELHPDKACYYVL  639 (691)
Q Consensus       604 ~~l~~~~~~~g------------------~~~~A~~~~~~~~~~~p~~~~~~~~  639 (691)
                      ..|+..|+...                  ..++|..+++.+.+.+|=-..+|..
T Consensus       259 ~~l~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~l~~~d~ir~~yw~~  312 (320)
T PLN02789        259 SDLLDLLCEGLQPTAEFRDTVDTLAEELSDSTLAQAVCSELEVADPMRRNYWAW  312 (320)
T ss_pred             HHHHHHHHhhhccchhhhhhhhccccccccHHHHHHHHHHHHhhCcHHHHHHHH
Confidence            88888887532                  2366777777775566654455543

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.15  E-value=0.00066  Score=61.16  Aligned_cols=161  Identities=12%  Similarity=0.063  Sum_probs=106.1

Q ss_pred             HHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCC
Q 040394          232 VLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSID  311 (691)
Q Consensus       232 ~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~  311 (691)
                      ++.+.+.......+......-...|++.+++++|.+.....    .  +......=+..+.+..+++-|...+++|.+-|
T Consensus        94 ~l~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~----~--~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~id  167 (299)
T KOG3081|consen   94 SLYELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLG----E--NLEAAALNVQILLKMHRFDLAEKELKKMQQID  167 (299)
T ss_pred             HHHHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhcc----c--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Confidence            34444444444444344444455677778888887776552    1  22333333445667778888888888886643


Q ss_pred             -hhHHHHHHHHHHh----cCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHH
Q 040394          312 -LVSWTAMIVGYTQ----SGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINA  386 (691)
Q Consensus       312 -~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  386 (691)
                       -.+.+.|..++.+    .+.+.+|.-+|++|-++ ..|+..+.+....++...|++++|..+++........++.+...
T Consensus       168 ed~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~dpetL~N  246 (299)
T KOG3081|consen  168 EDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAKDPETLAN  246 (299)
T ss_pred             hHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCCCHHHHHH
Confidence             3455555555543    45678888888888764 67888888888888888888888888888888888876666666


Q ss_pred             HHHHhHhcCChHH
Q 040394          387 LVDMYAKCHVIAD  399 (691)
Q Consensus       387 l~~~~~~~g~~~~  399 (691)
                      ++-+-...|...+
T Consensus       247 liv~a~~~Gkd~~  259 (299)
T KOG3081|consen  247 LIVLALHLGKDAE  259 (299)
T ss_pred             HHHHHHHhCCChH
Confidence            6655555554433

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.11  E-value=0.0004  Score=68.14  Aligned_cols=175  Identities=14%  Similarity=0.051  Sum_probs=121.9

Q ss_pred             CHHHHHHHHHhccc------CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHH
Q 040394          481 DAQSARMVFDAMRE------KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKC  554 (691)
Q Consensus       481 ~~~~A~~~~~~~~~------~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~  554 (691)
                      ++.++...-+.++.      ++...+...+.+......-..+..++.+-.+.  .-...-|..-+ .+...|.+++|+..
T Consensus       252 RIa~lr~ra~q~p~~~~~d~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~--~~~aa~YG~A~-~~~~~~~~d~A~~~  328 (484)
T COG4783         252 RIADLRNRAEQSPPYNKLDSPDFQLARARIRAKYEALPNQQAADLLAKRSKR--GGLAAQYGRAL-QTYLAGQYDEALKL  328 (484)
T ss_pred             HHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhccccccchHHHHHHHhCc--cchHHHHHHHH-HHHHhcccchHHHH
Confidence            44555555566553      24445555555444333323333222222221  11122233333 34567899999999


Q ss_pred             HHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC
Q 040394          555 FYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEPD-VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHP  631 (691)
Q Consensus       555 ~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p  631 (691)
                      ++.+...   .|+ +.......+.+.+.++.++|.+.++++ ...|+ ...+..+..++.+.|+..+|+.++++....+|
T Consensus       329 l~~L~~~---~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~~p  405 (484)
T COG4783         329 LQPLIAA---QPDNPYYLELAGDILLEANKAKEAIERLKKALALDPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFNDP  405 (484)
T ss_pred             HHHHHHh---CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCCccHHHHHHHHHHHhcCChHHHHHHHHHHhhcCC
Confidence            9988644   566 556667788999999999999999998 66777 56778888999999999999999999999999


Q ss_pred             CCchhHHHHHHHHHhCCCcHHHHHHHHHHH
Q 040394          632 DKACYYVLVSNLYASDGRWIRVNQVRELMK  661 (691)
Q Consensus       632 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  661 (691)
                      +++..|..|+..|...|+..+|.....+..
T Consensus       406 ~dp~~w~~LAqay~~~g~~~~a~~A~AE~~  435 (484)
T COG4783         406 EDPNGWDLLAQAYAELGNRAEALLARAEGY  435 (484)
T ss_pred             CCchHHHHHHHHHHHhCchHHHHHHHHHHH
Confidence            999999999999998887777766655543

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.09  E-value=0.00036  Score=75.07  Aligned_cols=129  Identities=7%  Similarity=0.017  Sum_probs=103.0

Q ss_pred             CcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCC-cchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHH
Q 040394          110 DFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHD-NFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVD  188 (691)
Q Consensus       110 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  188 (691)
                      +...+-.|..+..+.|++++|..+|+...+.  .|+ ......+...+.+.+++++|....++.....+.+......+..
T Consensus        85 ~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~--~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~p~~~~~~~~~a~  162 (694)
T PRK15179         85 TELFQVLVARALEAAHRSDEGLAVWRGIHQR--FPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGGSSSAREILLEAK  162 (694)
T ss_pred             cHHHHHHHHHHHHHcCCcHHHHHHHHHHHhh--CCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcCCCCHHHHHHHHH
Confidence            4677888888888888888888888888875  454 4566777788888888888888888888888888888888888


Q ss_pred             HhHhcCChHHHHHHHhccCCCC---hhhHHHHHHHHHhCCChhHHHHHHHHHHhC
Q 040394          189 MYAKCRDIGSSRQVFDETLDKN---VVSWTSMIAGYVQNDCAQEGLVLFNRMREG  240 (691)
Q Consensus       189 ~~~~~g~~~~A~~~~~~~~~~~---~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  240 (691)
                      ++.+.|++++|..+|++...++   ..++..+...+-..|+.++|...|++..+.
T Consensus       163 ~l~~~g~~~~A~~~y~~~~~~~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~  217 (694)
T PRK15179        163 SWDEIGQSEQADACFERLSRQHPEFENGYVGWAQSLTRRGALWRARDVLQAGLDA  217 (694)
T ss_pred             HHHHhcchHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            8888888888888888876442   457777777888888888888888887653

>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=98.09  E-value=5.2e-05  Score=75.13  Aligned_cols=120  Identities=10%  Similarity=0.112  Sum_probs=52.9

Q ss_pred             HHHHHhcCCChHHHHHHhccCCCCCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHH
Q 040394           86 LVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEG  165 (691)
Q Consensus        86 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a  165 (691)
                      |+..+...++++.|..+|+++.+.+......+++.+...++-.+|++++++..+. .+.+...+..-.+.+.+.++.+.|
T Consensus       175 Ll~~l~~t~~~~~ai~lle~L~~~~pev~~~LA~v~l~~~~E~~AI~ll~~aL~~-~p~d~~LL~~Qa~fLl~k~~~~lA  253 (395)
T PF09295_consen  175 LLKYLSLTQRYDEAIELLEKLRERDPEVAVLLARVYLLMNEEVEAIRLLNEALKE-NPQDSELLNLQAEFLLSKKKYELA  253 (395)
T ss_pred             HHHHHhhcccHHHHHHHHHHHHhcCCcHHHHHHHHHHhcCcHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHhcCCHHHH
Confidence            3344444444444444444444433333444444444444444444444444433 122223333333334444444444


Q ss_pred             HHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhcc
Q 040394          166 MKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDET  206 (691)
Q Consensus       166 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  206 (691)
                      .++.+++.+..|.+-.+|..|..+|.+.|++++|+..++.+
T Consensus       254 L~iAk~av~lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~  294 (395)
T PF09295_consen  254 LEIAKKAVELSPSEFETWYQLAECYIQLGDFENALLALNSC  294 (395)
T ss_pred             HHHHHHHHHhCchhHHHHHHHHHHHHhcCCHHHHHHHHhcC
Confidence            44444444444444444444444444444444444444443

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.07  E-value=6.5e-06  Score=50.50  Aligned_cols=33  Identities=27%  Similarity=0.474  Sum_probs=26.6

Q ss_pred             hHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCC
Q 040394          213 SWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGN  245 (691)
Q Consensus       213 ~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~  245 (691)
                      +||++|.+|++.|++++|.++|++|.+.|+.||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            678888888888888888888888888887776

This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=98.03  E-value=6.6e-06  Score=62.78  Aligned_cols=78  Identities=15%  Similarity=0.297  Sum_probs=60.6

Q ss_pred             cCChHHHHHHHHhC-CCCC---CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHH
Q 040394          581 AGRLEEALEFMENM-PIEP---DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQV  656 (691)
Q Consensus       581 ~g~~~~A~~~~~~~-~~~p---~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~  656 (691)
                      .|++++|+.+++++ ...|   +...+..+..++.+.|++++|..++++ .+.+|.+......++.+|.+.|++++|+++
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~~~~~~~~~l~a~~~~~l~~y~eAi~~   80 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLDPSNPDIHYLLARCLLKLGKYEEAIKA   80 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHHHCHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCCCCCHHHHHHHHHHHHHhCCHHHHHHH
Confidence            46778888888877 2223   445666688888999999999999988 777787777888889999999999999998


Q ss_pred             HHH
Q 040394          657 REL  659 (691)
Q Consensus       657 ~~~  659 (691)
                      +++
T Consensus        81 l~~   83 (84)
T PF12895_consen   81 LEK   83 (84)
T ss_dssp             HHH
T ss_pred             Hhc
Confidence            875

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=98.03  E-value=0.00015  Score=62.17  Aligned_cols=115  Identities=13%  Similarity=0.103  Sum_probs=63.5

Q ss_pred             cCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCH----HHHHHHHHHHHhcCCHHH
Q 040394          545 TGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEPDV----SLFGAFLHGCGLYSRFDL  618 (691)
Q Consensus       545 ~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~----~~~~~l~~~~~~~g~~~~  618 (691)
                      .++...+.+.++.+...++-.|- ....-.+...+...|++++|.+.|+.. ...||.    .....|...+...|++++
T Consensus        24 ~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d~  103 (145)
T PF09976_consen   24 AGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQYDE  103 (145)
T ss_pred             CCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHH
Confidence            45555555556655444222211 122233445566666666666666666 222332    233445556666777777


Q ss_pred             HHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHH
Q 040394          619 GEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELM  660 (691)
Q Consensus       619 A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  660 (691)
                      |...++.. ...+-.+..+...+.+|.+.|++++|+..|+..
T Consensus       104 Al~~L~~~-~~~~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~A  144 (145)
T PF09976_consen  104 ALATLQQI-PDEAFKALAAELLGDIYLAQGDYDEARAAYQKA  144 (145)
T ss_pred             HHHHHHhc-cCcchHHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence            77777552 222333556667777777777777777777653

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

Probab=98.00  E-value=0.00019  Score=60.85  Aligned_cols=114  Identities=12%  Similarity=0.154  Sum_probs=86.7

Q ss_pred             HHHHHHHCCCCCCH-HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCC-ChhHHHHHHHHHHhcCChHHHHHHHHhC-C
Q 040394          519 LFSDMLNEEVQPNE-VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVP-SMKHYVCMVDLLARAGRLEEALEFMENM-P  595 (691)
Q Consensus       519 ~~~~m~~~g~~p~~-~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~~-~  595 (691)
                      ++++...  ..|+. .....+...+...|++++|.+.++.+..   ..| +...+..+...+.+.|++++|.+.+++. .
T Consensus         5 ~~~~~l~--~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~---~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~   79 (135)
T TIGR02552         5 TLKDLLG--LDSEQLEQIYALAYNLYQQGRYDEALKLFQLLAA---YDPYNSRYWLGLAACCQMLKEYEEAIDAYALAAA   79 (135)
T ss_pred             hHHHHHc--CChhhHHHHHHHHHHHHHcccHHHHHHHHHHHHH---hCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3445554  34543 3455556677888999999999987743   234 4677888888899999999999988887 3


Q ss_pred             CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhH
Q 040394          596 IEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYY  637 (691)
Q Consensus       596 ~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~  637 (691)
                      ..| +...+..+...+...|++++|...++++++..|++....
T Consensus        80 ~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~  122 (135)
T TIGR02552        80 LDPDDPRPYFHAAECLLALGEPESALKALDLAIEICGENPEYS  122 (135)
T ss_pred             cCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccchHH
Confidence            344 567788888889999999999999999999999976544

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

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.00  E-value=1e-05  Score=49.66  Aligned_cols=33  Identities=30%  Similarity=0.624  Sum_probs=29.1

Q ss_pred             HHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCC
Q 040394          499 TWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPN  531 (691)
Q Consensus       499 ~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~  531 (691)
                      +||+++.+|++.|++++|.++|++|.+.|+.||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            688888999999999999999999988888887

This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.96  E-value=0.00011  Score=60.71  Aligned_cols=94  Identities=10%  Similarity=0.043  Sum_probs=53.3

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhC-CCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC---chhHHHHHH
Q 040394          571 YVCMVDLLARAGRLEEALEFMENM-PIEPD----VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK---ACYYVLVSN  642 (691)
Q Consensus       571 ~~~li~~~~~~g~~~~A~~~~~~~-~~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~---~~~~~~l~~  642 (691)
                      +..++..+.+.|++++|.+.++.+ ...|+    ...+..+...+.+.|+++.|...++++....|++   +.++..++.
T Consensus         5 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~   84 (119)
T TIGR02795         5 YYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGM   84 (119)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHH
Confidence            334445555566666666665555 22222    2344445556666666666666666666665554   344556666


Q ss_pred             HHHhCCCcHHHHHHHHHHHhCC
Q 040394          643 LYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       643 ~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      ++.+.|++++|...++++.+..
T Consensus        85 ~~~~~~~~~~A~~~~~~~~~~~  106 (119)
T TIGR02795        85 SLQELGDKEKAKATLQQVIKRY  106 (119)
T ss_pred             HHHHhCChHHHHHHHHHHHHHC
Confidence            6666666666666666666543

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.

>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=97.95  E-value=2.8e-05  Score=56.70  Aligned_cols=65  Identities=14%  Similarity=0.074  Sum_probs=60.3

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCC-CcHHHHHHHHHHHhC
Q 040394          599 DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDG-RWIRVNQVRELMKQR  663 (691)
Q Consensus       599 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~  663 (691)
                      +..+|..+...+...|++++|+..|+++++.+|+++..+..++.+|...| ++++|++.+++.++.
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l   67 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKL   67 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHc
Confidence            45788889999999999999999999999999999999999999999999 799999999988763

...

>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=97.95  E-value=8.7e-05  Score=58.25  Aligned_cols=94  Identities=20%  Similarity=0.290  Sum_probs=77.6

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCC
Q 040394          571 YVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDG  648 (691)
Q Consensus       571 ~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g  648 (691)
                      +..+...+...|++++|.+.+++. ...| +...+..+...+...|++++|...+++..+..|.+...+..++.++...|
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPDNAKAYYNLGLAYYKLG   82 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHHHHHHHH
Confidence            455667778889999999888887 3344 34677778888888899999999999999999998888999999999999


Q ss_pred             CcHHHHHHHHHHHhCC
Q 040394          649 RWIRVNQVRELMKQRG  664 (691)
Q Consensus       649 ~~~~A~~~~~~~~~~g  664 (691)
                      ++++|...++...+.+
T Consensus        83 ~~~~a~~~~~~~~~~~   98 (100)
T cd00189          83 KYEEALEAYEKALELD   98 (100)
T ss_pred             hHHHHHHHHHHHHccC
Confidence            9999999998877643

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=97.95  E-value=1.5e-05  Score=48.36  Aligned_cols=33  Identities=18%  Similarity=0.341  Sum_probs=21.0

Q ss_pred             hhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCC
Q 040394          212 VSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEG  244 (691)
Q Consensus       212 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p  244 (691)
                      .+|+.+|.+|++.|+++.|.++|++|.+.|++|
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            456666666666666666666666666666655

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=97.92  E-value=1.7e-05  Score=48.13  Aligned_cols=33  Identities=30%  Similarity=0.579  Sum_probs=26.7

Q ss_pred             hHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCC
Q 040394          498 VTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQP  530 (691)
Q Consensus       498 ~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p  530 (691)
                      .+|++++.+|++.|+++.|.++|++|.+.|++|
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            478888888888888888888888888888776

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.92  E-value=0.0046  Score=55.50  Aligned_cols=151  Identities=12%  Similarity=0.003  Sum_probs=87.9

Q ss_pred             CCchhHHHHHHHhhHC---C-CCCcHHH-HHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHH
Q 040394          326 GYPDKALKLFTDKKWA---D-FFPNHVT-IASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADA  400 (691)
Q Consensus       326 g~~~~a~~~~~~m~~~---g-~~p~~~t-~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a  400 (691)
                      .+.++.++++.+++..   | ..|+..+ |-.+.-+....|+.+.|...++.+.+.-+.+..+-..-...+-..|++++|
T Consensus        26 rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~fp~S~RV~~lkam~lEa~~~~~~A  105 (289)
T KOG3060|consen   26 RNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRFPGSKRVGKLKAMLLEATGNYKEA  105 (289)
T ss_pred             cCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhchhhH
Confidence            4556666666665432   3 4455544 333444566667777777777776666555666555555566667777888


Q ss_pred             HHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcC
Q 040394          401 RYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCG  480 (691)
Q Consensus       401 ~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  480 (691)
                      .++++.+.+.|               +.|.+++-.-+...-..|+.-+|.+-+....+.-  ..|...|.-+...|...|
T Consensus       106 ~e~y~~lL~dd---------------pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~F--~~D~EAW~eLaeiY~~~~  168 (289)
T KOG3060|consen  106 IEYYESLLEDD---------------PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDKF--MNDQEAWHELAEIYLSEG  168 (289)
T ss_pred             HHHHHHHhccC---------------cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHHh--cCcHHHHHHHHHHHHhHh
Confidence            88887777664               3444555544444444555555555555544443  455556666666666666


Q ss_pred             CHHHHHHHHHhcc
Q 040394          481 DAQSARMVFDAMR  493 (691)
Q Consensus       481 ~~~~A~~~~~~~~  493 (691)
                      +++.|.-.++++.
T Consensus       169 ~f~kA~fClEE~l  181 (289)
T KOG3060|consen  169 DFEKAAFCLEELL  181 (289)
T ss_pred             HHHHHHHHHHHHH
Confidence            6666655555544

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.90  E-value=3.5e-05  Score=55.37  Aligned_cols=59  Identities=14%  Similarity=0.160  Sum_probs=51.5

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          606 FLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       606 l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      +...+...|++++|+..++++++..|+++..+..++.++...|++++|...++++++..
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~   61 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQDPDNPEAWYLLGRILYQQGRYDEALAYYERALELD   61 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            45677889999999999999999999999999999999999999999999999987643

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=97.87  E-value=0.028  Score=53.79  Aligned_cols=243  Identities=17%  Similarity=0.177  Sum_probs=167.7

Q ss_pred             HhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCH--HHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHH
Q 040394          392 AKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDA--VTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVG  469 (691)
Q Consensus       392 ~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~--~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  469 (691)
                      .-.|+.+.|.+-|+.|...                 |..  .-+..|.-...+.|+.+.|..+-+..-..-  +.-....
T Consensus       131 l~eG~~~~Ar~kfeAMl~d-----------------PEtRllGLRgLyleAqr~GareaAr~yAe~Aa~~A--p~l~WA~  191 (531)
T COG3898         131 LLEGDYEDARKKFEAMLDD-----------------PETRLLGLRGLYLEAQRLGAREAARHYAERAAEKA--PQLPWAA  191 (531)
T ss_pred             HhcCchHHHHHHHHHHhcC-----------------hHHHHHhHHHHHHHHHhcccHHHHHHHHHHHHhhc--cCCchHH
Confidence            3468888888888888753                 322  234455555567889999998888887766  6778888


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhccc-----CCHh--HHHHHHHHHh---cCCChHHHHHHHHHHHHCCCCCCHHHHH-HH
Q 040394          470 TALLNFYAKCGDAQSARMVFDAMRE-----KNTV--TWSAMIGGYG---MQGDGGGSLALFSDMLNEEVQPNEVIFT-TI  538 (691)
Q Consensus       470 ~~l~~~~~~~g~~~~A~~~~~~~~~-----~~~~--~~~~li~~~~---~~~~~~~A~~~~~~m~~~g~~p~~~~~~-~l  538 (691)
                      .+.+...+..|+|+.|+++.+.-..     +++.  .--.|+.+-.   -.-|...|...-.+..+  +.||..--. ..
T Consensus       192 ~AtLe~r~~~gdWd~AlkLvd~~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp~~Ar~~A~~a~K--L~pdlvPaav~A  269 (531)
T COG3898         192 RATLEARCAAGDWDGALKLVDAQRAAKVIEKDVAERSRAVLLTAKAMSLLDADPASARDDALEANK--LAPDLVPAAVVA  269 (531)
T ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHHHhhchhhHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHhh--cCCccchHHHHH
Confidence            9999999999999999999987553     3432  1122222211   12345566665555544  577765433 33


Q ss_pred             HHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC----CCCCC-HHHHHHHHHHHHhc
Q 040394          539 LSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM----PIEPD-VSLFGAFLHGCGLY  613 (691)
Q Consensus       539 l~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~----~~~p~-~~~~~~l~~~~~~~  613 (691)
                      ..++.+.|+..++-.+++.+-   +..|.+.++..  ..+.+.|+..  +.-+++.    ..+|| ..+...+..+-...
T Consensus       270 Aralf~d~~~rKg~~ilE~aW---K~ePHP~ia~l--Y~~ar~gdta--~dRlkRa~~L~slk~nnaes~~~va~aAlda  342 (531)
T COG3898         270 ARALFRDGNLRKGSKILETAW---KAEPHPDIALL--YVRARSGDTA--LDRLKRAKKLESLKPNNAESSLAVAEAALDA  342 (531)
T ss_pred             HHHHHhccchhhhhhHHHHHH---hcCCChHHHHH--HHHhcCCCcH--HHHHHHHHHHHhcCccchHHHHHHHHHHHhc
Confidence            458899999999999999763   34666555433  2345566543  2222222    34454 45677778888899


Q ss_pred             CCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhC-CCcHHHHHHHHHHHhC
Q 040394          614 SRFDLGEVMIKKMLELHPDKACYYVLVSNLYASD-GRWIRVNQVRELMKQR  663 (691)
Q Consensus       614 g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~-g~~~~A~~~~~~~~~~  663 (691)
                      |++..|..--+.+....|. ..+|.+++.+-... |+-.++...+-+.++.
T Consensus       343 ~e~~~ARa~Aeaa~r~~pr-es~~lLlAdIeeAetGDqg~vR~wlAqav~A  392 (531)
T COG3898         343 GEFSAARAKAEAAAREAPR-ESAYLLLADIEEAETGDQGKVRQWLAQAVKA  392 (531)
T ss_pred             cchHHHHHHHHHHhhhCch-hhHHHHHHHHHhhccCchHHHHHHHHHHhcC
Confidence            9999999999999999999 77888888887766 9999998888776664

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=97.84  E-value=9e-05  Score=68.51  Aligned_cols=112  Identities=13%  Similarity=0.147  Sum_probs=93.6

Q ss_pred             CCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHh---cCCHHHHHHHHHHHHhcCCCCchhH
Q 040394          564 FVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGL---YSRFDLGEVMIKKMLELHPDKACYY  637 (691)
Q Consensus       564 ~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~---~g~~~~A~~~~~~~~~~~p~~~~~~  637 (691)
                      -.|+ ...|..|...|.+.|+...|..-|.+. ...| +...+..+..++..   ..+..++..++++++..+|++....
T Consensus       151 ~nP~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D~~~iral  230 (287)
T COG4235         151 QNPGDAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALLRQALALDPANIRAL  230 (287)
T ss_pred             hCCCCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcCCccHHHH
Confidence            3454 889999999999999999999999998 4444 44556666665543   3467899999999999999999999


Q ss_pred             HHHHHHHHhCCCcHHHHHHHHHHHhCCCccCCCeeEEE
Q 040394          638 VLVSNLYASDGRWIRVNQVRELMKQRGLSKSPGCSLVD  675 (691)
Q Consensus       638 ~~l~~~~~~~g~~~~A~~~~~~~~~~g~~~~~~~~~~~  675 (691)
                      +.|+..+...|++.+|...++.|++.....+|..+.++
T Consensus       231 ~lLA~~afe~g~~~~A~~~Wq~lL~~lp~~~~rr~~ie  268 (287)
T COG4235         231 SLLAFAAFEQGDYAEAAAAWQMLLDLLPADDPRRSLIE  268 (287)
T ss_pred             HHHHHHHHHcccHHHHHHHHHHHHhcCCCCCchHHHHH
Confidence            99999999999999999999999999888888766543

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.83  E-value=0.00014  Score=66.68  Aligned_cols=71  Identities=23%  Similarity=0.348  Sum_probs=32.8

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhC-CCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHH
Q 040394          571 YVCMVDLLARAGRLEEALEFMENM-PIEPDV-SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVS  641 (691)
Q Consensus       571 ~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~  641 (691)
                      |..-..+|.+.|.++.|++-.+.. .+.|.. .+|..|..+|...|++++|++.|+++++++|++..+...|-
T Consensus       118 ycNRAAAy~~Lg~~~~AVkDce~Al~iDp~yskay~RLG~A~~~~gk~~~A~~aykKaLeldP~Ne~~K~nL~  190 (304)
T KOG0553|consen  118 YCNRAAAYSKLGEYEDAVKDCESALSIDPHYSKAYGRLGLAYLALGKYEEAIEAYKKALELDPDNESYKSNLK  190 (304)
T ss_pred             HHHHHHHHHHhcchHHHHHHHHHHHhcChHHHHHHHHHHHHHHccCcHHHHHHHHHhhhccCCCcHHHHHHHH
Confidence            333444444444444444444433 333332 24555555555555555555555555555555444444443

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.82  E-value=0.0003  Score=58.03  Aligned_cols=105  Identities=6%  Similarity=0.051  Sum_probs=71.8

Q ss_pred             HHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCC----HHHHHHHH
Q 040394          534 IFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEPD----VSLFGAFL  607 (691)
Q Consensus       534 ~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~----~~~~~~l~  607 (691)
                      ++......+...|++++|.+.++.+.....-.|. ...+..+..++.+.|++++|.+.++.+ ...|+    ..++..+.
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~   83 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLG   83 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHH
Confidence            3444555666677777777777776543211111 335556777788888888888888876 32333    45677777


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCchhHH
Q 040394          608 HGCGLYSRFDLGEVMIKKMLELHPDKACYYV  638 (691)
Q Consensus       608 ~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~  638 (691)
                      .++.+.|+.++|...++++++..|+++....
T Consensus        84 ~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~  114 (119)
T TIGR02795        84 MSLQELGDKEKAKATLQQVIKRYPGSSAAKL  114 (119)
T ss_pred             HHHHHhCChHHHHHHHHHHHHHCcCChhHHH
Confidence            8888899999999999999999998765443

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.

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=97.81  E-value=0.0011  Score=56.70  Aligned_cols=124  Identities=12%  Similarity=0.102  Sum_probs=75.8

Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCH---HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC--hhHHHHH
Q 040394          500 WSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNE---VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS--MKHYVCM  574 (691)
Q Consensus       500 ~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~---~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~--~~~~~~l  574 (691)
                      |..++..+ ..++...+...++.+.+.. +.+.   ...-.+...+...|++++|...|+..... ...|+  ....-.|
T Consensus        15 y~~~~~~~-~~~~~~~~~~~~~~l~~~~-~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~-~~d~~l~~~a~l~L   91 (145)
T PF09976_consen   15 YEQALQAL-QAGDPAKAEAAAEQLAKDY-PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALAN-APDPELKPLARLRL   91 (145)
T ss_pred             HHHHHHHH-HCCCHHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhh-CCCHHHHHHHHHHH
Confidence            33334444 3667777777777777652 2221   22223334666778888888888777443 22222  1233446


Q ss_pred             HHHHHhcCChHHHHHHHHhCC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040394          575 VDLLARAGRLEEALEFMENMP-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKM  626 (691)
Q Consensus       575 i~~~~~~g~~~~A~~~~~~~~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~  626 (691)
                      ...+...|++++|+..++... .......+......+...|++++|...|+++
T Consensus        92 A~~~~~~~~~d~Al~~L~~~~~~~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~A  144 (145)
T PF09976_consen   92 ARILLQQGQYDEALATLQQIPDEAFKALAAELLGDIYLAQGDYDEARAAYQKA  144 (145)
T ss_pred             HHHHHHcCCHHHHHHHHHhccCcchHHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence            677778888888888887752 2234456666777788888888888888765

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.71  E-value=0.00044  Score=61.29  Aligned_cols=97  Identities=16%  Similarity=0.112  Sum_probs=70.5

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHH
Q 040394          568 MKHYVCMVDLLARAGRLEEALEFMENM-PIEPD----VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSN  642 (691)
Q Consensus       568 ~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~  642 (691)
                      ...+..+...+...|++++|...+++. ...|+    ...+..+...+.+.|++++|...++++++..|+++..+..++.
T Consensus        35 a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~  114 (172)
T PRK02603         35 AFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNPKQPSALNNIAV  114 (172)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHH
Confidence            334566667777778888888877776 22222    3567777788888888888888888888888888888888888


Q ss_pred             HHHhCCC--------------cHHHHHHHHHHHhCC
Q 040394          643 LYASDGR--------------WIRVNQVRELMKQRG  664 (691)
Q Consensus       643 ~~~~~g~--------------~~~A~~~~~~~~~~g  664 (691)
                      ++...|+              +++|.+.+++..+.+
T Consensus       115 ~~~~~g~~~~a~~~~~~A~~~~~~A~~~~~~a~~~~  150 (172)
T PRK02603        115 IYHKRGEKAEEAGDQDEAEALFDKAAEYWKQAIRLA  150 (172)
T ss_pred             HHHHcCChHhHhhCHHHHHHHHHHHHHHHHHHHhhC
Confidence            8887776              456666666665543

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.67  E-value=0.00043  Score=69.14  Aligned_cols=105  Identities=10%  Similarity=0.122  Sum_probs=87.9

Q ss_pred             HHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCC
Q 040394          539 LSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSR  615 (691)
Q Consensus       539 l~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~  615 (691)
                      ...+...|++++|++.|++.++   ..|+ ...|..+..+|.+.|++++|+..++++ ...| +...|..+..+|...|+
T Consensus         9 a~~a~~~~~~~~Ai~~~~~Al~---~~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~~~a~~~lg~~~~~lg~   85 (356)
T PLN03088          9 AKEAFVDDDFALAVDLYTQAID---LDPNNAELYADRAQANIKLGNFTEAVADANKAIELDPSLAKAYLRKGTACMKLEE   85 (356)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCC
Confidence            3456678999999999998753   4665 677888899999999999999999998 5555 55688889999999999


Q ss_pred             HHHHHHHHHHHHhcCCCCchhHHHHHHHHHh
Q 040394          616 FDLGEVMIKKMLELHPDKACYYVLVSNLYAS  646 (691)
Q Consensus       616 ~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~  646 (691)
                      +++|+..+++++++.|+++.....+..+..+
T Consensus        86 ~~eA~~~~~~al~l~P~~~~~~~~l~~~~~k  116 (356)
T PLN03088         86 YQTAKAALEKGASLAPGDSRFTKLIKECDEK  116 (356)
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            9999999999999999999888777665433

>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=97.66  E-value=6.9e-05  Score=54.43  Aligned_cols=54  Identities=17%  Similarity=0.292  Sum_probs=42.4

Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          611 GLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       611 ~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      .+.|++++|+..++++.+.+|++..++..++.+|.+.|++++|.++++++....
T Consensus         2 l~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~   55 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRNPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQD   55 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGG
T ss_pred             hhccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            467788888888888888888888888888888888888888888887766543

...

>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat

Probab=97.65  E-value=6.2e-05  Score=44.48  Aligned_cols=29  Identities=34%  Similarity=0.587  Sum_probs=19.6

Q ss_pred             hHHHHHHHHHhCCChhHHHHHHHHHHhCC
Q 040394          213 SWTSMIAGYVQNDCAQEGLVLFNRMREGF  241 (691)
Q Consensus       213 ~~~~li~~~~~~g~~~~A~~~~~~m~~~~  241 (691)
                      +||.+|++|++.|++++|.++|++|.+.|
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            56666666666677777777766666655

Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=97.61  E-value=0.0002  Score=52.92  Aligned_cols=59  Identities=14%  Similarity=0.092  Sum_probs=52.2

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          607 LHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       607 ~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      ...+.+.+++++|...++++++.+|+++..+...+.++...|++++|.+.+++..+.+.
T Consensus         2 ~~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~p   60 (73)
T PF13371_consen    2 KQIYLQQEDYEEALEVLERALELDPDDPELWLQRARCLFQLGRYEEALEDLERALELSP   60 (73)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhccHHHHHHHHHHHHHHCC
Confidence            35678889999999999999999999999999999999999999999999999987654

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.61  E-value=0.00066  Score=59.95  Aligned_cols=93  Identities=12%  Similarity=-0.086  Sum_probs=74.2

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHH
Q 040394          568 MKHYVCMVDLLARAGRLEEALEFMENM-PIEPD----VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSN  642 (691)
Q Consensus       568 ~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~  642 (691)
                      ...+..++..+...|++++|+..+++. ...|+    ..+|..+...+...|++++|+..++++++..|.....+..++.
T Consensus        35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~~~~~~~~~~la~  114 (168)
T CHL00033         35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERNPFLPQALNNMAV  114 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHH
Confidence            455666777788889999999988887 33332    3478888899999999999999999999999999888888888


Q ss_pred             HHH-------hCCCcHHHHHHHHHH
Q 040394          643 LYA-------SDGRWIRVNQVRELM  660 (691)
Q Consensus       643 ~~~-------~~g~~~~A~~~~~~~  660 (691)
                      ++.       ..|++++|...+++.
T Consensus       115 i~~~~~~~~~~~g~~~~A~~~~~~a  139 (168)
T CHL00033        115 ICHYRGEQAIEQGDSEIAEAWFDQA  139 (168)
T ss_pred             HHHHhhHHHHHcccHHHHHHHHHHH
Confidence            888       888888665555443

>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends

Probab=97.61  E-value=0.001  Score=51.54  Aligned_cols=82  Identities=13%  Similarity=0.041  Sum_probs=69.1

Q ss_pred             hHHHHHHHHHhCCChhHHHHHHHHHHhCCC-CCChhhHHHHHHHHHccC--------ChhhHHHHHHHHHHHCCCCchHH
Q 040394          213 SWTSMIAGYVQNDCAQEGLVLFNRMREGFV-EGNQITLGSLVTACAKLR--------ALHQGKWLHGYILKIGIEINSHL  283 (691)
Q Consensus       213 ~~~~li~~~~~~g~~~~A~~~~~~m~~~~~-~p~~~t~~~li~~~~~~~--------~~~~a~~~~~~~~~~g~~~~~~~  283 (691)
                      +-...|..+...+++.....+|+.++++|+ .|+..+|+.++.+.++..        ++.....+++.|+..++.|+..+
T Consensus        27 t~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~et  106 (120)
T PF08579_consen   27 TQIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDET  106 (120)
T ss_pred             HHHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHH
Confidence            445566777778999999999999999999 999999999999987543        34566788999999999999999


Q ss_pred             HHHHHHHHHhc
Q 040394          284 VTALLDMYVKC  294 (691)
Q Consensus       284 ~~~li~~~~~~  294 (691)
                      |+.++..+.+.
T Consensus       107 Ynivl~~Llkg  117 (120)
T PF08579_consen  107 YNIVLGSLLKG  117 (120)
T ss_pred             HHHHHHHHHHh
Confidence            99999887653

Rpm2 is a protein subunit of the yeast mitochondrial RNase P. It has the ability to act as a transcriptional activator in the nucleus, where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components. Rpm2p is also involved in maturation of Rpm1 and in translation of mitochondrial mRNAs [, , ].

>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat

Probab=97.58  E-value=8.6e-05  Score=43.83  Aligned_cols=30  Identities=27%  Similarity=0.548  Sum_probs=23.0

Q ss_pred             HHHHHHHHHhcCCChHHHHHHHHHHHHCCC
Q 040394          499 TWSAMIGGYGMQGDGGGSLALFSDMLNEEV  528 (691)
Q Consensus       499 ~~~~li~~~~~~~~~~~A~~~~~~m~~~g~  528 (691)
                      +|++++++|++.|++++|.++|++|.+.|+
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            677778888888888888888888777663

Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=97.55  E-value=0.097  Score=51.00  Aligned_cols=78  Identities=13%  Similarity=0.151  Sum_probs=35.5

Q ss_pred             HHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHH
Q 040394          473 LNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGW  552 (691)
Q Consensus       473 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~  552 (691)
                      +.-+...|+...|.++-.+..-|+...|-..+.+++..++|++-..+...    .  -++..|-.++.+|.+.|...+|.
T Consensus       184 i~~li~~~~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~s----k--KsPIGyepFv~~~~~~~~~~eA~  257 (319)
T PF04840_consen  184 IRKLIEMGQEKQAEKLKKEFKVPDKRFWWLKIKALAENKDWDELEKFAKS----K--KSPIGYEPFVEACLKYGNKKEAS  257 (319)
T ss_pred             HHHHHHCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHhC----C--CCCCChHHHHHHHHHCCCHHHHH
Confidence            33344445555555555555445555555555555555555444433221    1  11234444444444455555554


Q ss_pred             HHHH
Q 040394          553 KCFY  556 (691)
Q Consensus       553 ~~~~  556 (691)
                      .+..
T Consensus       258 ~yI~  261 (319)
T PF04840_consen  258 KYIP  261 (319)
T ss_pred             HHHH
Confidence            4444

Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.51  E-value=0.00035  Score=64.27  Aligned_cols=88  Identities=10%  Similarity=0.140  Sum_probs=77.7

Q ss_pred             HHHHhcCChHHHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHH
Q 040394          576 DLLARAGRLEEALEFMENM-PIEPD-VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRV  653 (691)
Q Consensus       576 ~~~~~~g~~~~A~~~~~~~-~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A  653 (691)
                      .-+.+.+++++|+..|.+. .+.|. .+.|..=..+|.+.|.++.|++-.+.++.++|..+..|..|+.+|...|++++|
T Consensus        89 N~~m~~~~Y~eAv~kY~~AI~l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp~yskay~RLG~A~~~~gk~~~A  168 (304)
T KOG0553|consen   89 NKLMKNKDYQEAVDKYTEAIELDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSIDPHYSKAYGRLGLAYLALGKYEEA  168 (304)
T ss_pred             HHHHHhhhHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcChHHHHHHHHHHHHHHccCcHHHH
Confidence            4567889999999999988 66764 556666677899999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhC
Q 040394          654 NQVRELMKQR  663 (691)
Q Consensus       654 ~~~~~~~~~~  663 (691)
                      ++.|++.++.
T Consensus       169 ~~aykKaLel  178 (304)
T KOG0553|consen  169 IEAYKKALEL  178 (304)
T ss_pred             HHHHHhhhcc
Confidence            9999887764

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.51  E-value=0.00031  Score=50.37  Aligned_cols=61  Identities=21%  Similarity=0.293  Sum_probs=50.7

Q ss_pred             HHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040394          574 MVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKA  634 (691)
Q Consensus       574 li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~  634 (691)
                      +...+.+.|++++|++.|++. ...| +...+..+..++...|++++|...++++++..|+++
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~P~~p   65 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQDPDNPEAWYLLGRILYQQGRYDEALAYYERALELDPDNP   65 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-H
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCC
Confidence            456788899999999999998 5556 456888899999999999999999999999999864

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=97.51  E-value=0.016  Score=49.47  Aligned_cols=133  Identities=11%  Similarity=0.092  Sum_probs=99.1

Q ss_pred             CCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCC---HHHH
Q 040394          528 VQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PIEPD---VSLF  603 (691)
Q Consensus       528 ~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~---~~~~  603 (691)
                      ..|+...-..+..+....|+..+|...|++. -.--+.-|..+.-.+..+....+++..|...+++. ...|+   +.+.
T Consensus        85 ~ApTvqnr~rLa~al~elGr~~EA~~hy~qa-lsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~  163 (251)
T COG4700          85 IAPTVQNRYRLANALAELGRYHEAVPHYQQA-LSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGH  163 (251)
T ss_pred             hchhHHHHHHHHHHHHHhhhhhhhHHHHHHH-hccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCch
Confidence            4677766667778888889999999888876 33224445667777788888888999998888887 22232   2234


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          604 GAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       604 ~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      ..+.+.+...|.+.+|+..|+.+....|+ +......+..+.++|+..+|..-+..+.+
T Consensus       164 Ll~aR~laa~g~~a~Aesafe~a~~~ypg-~~ar~~Y~e~La~qgr~~ea~aq~~~v~d  221 (251)
T COG4700         164 LLFARTLAAQGKYADAESAFEVAISYYPG-PQARIYYAEMLAKQGRLREANAQYVAVVD  221 (251)
T ss_pred             HHHHHHHHhcCCchhHHHHHHHHHHhCCC-HHHHHHHHHHHHHhcchhHHHHHHHHHHH
Confidence            55778888899999999999999998888 66666667788999988888766655544

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=97.48  E-value=0.13  Score=50.69  Aligned_cols=126  Identities=15%  Similarity=0.144  Sum_probs=72.7

Q ss_pred             HHhcCC-HHHHHHHHHhccc---CCHhHHHHHH----HHHhc---CCChHHHHHHHHHHHHCCCCCCHH----HHHHHHH
Q 040394          476 YAKCGD-AQSARMVFDAMRE---KNTVTWSAMI----GGYGM---QGDGGGSLALFSDMLNEEVQPNEV----IFTTILS  540 (691)
Q Consensus       476 ~~~~g~-~~~A~~~~~~~~~---~~~~~~~~li----~~~~~---~~~~~~A~~~~~~m~~~g~~p~~~----~~~~ll~  540 (691)
                      +-+.|. -+.|+.+++.+.+   -|...-|.+.    .+|.+   .....+-+.+-+-..+.|+.|-..    .-|.+.+
T Consensus       389 lW~~g~~dekalnLLk~il~ft~yD~ec~n~v~~fvKq~Y~qaLs~~~~~rLlkLe~fi~e~gl~~i~i~e~eian~LaD  468 (549)
T PF07079_consen  389 LWEIGQCDEKALNLLKLILQFTNYDIECENIVFLFVKQAYKQALSMHAIPRLLKLEDFITEVGLTPITISEEEIANFLAD  468 (549)
T ss_pred             HHhcCCccHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCCcccccHHHHHHHHHH
Confidence            344454 6667777777664   2444333322    22221   233444444444455667666432    3333333


Q ss_pred             --HhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHHH
Q 040394          541 --ACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAF  606 (691)
Q Consensus       541 --~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l  606 (691)
                        -+...|++.++.-.-..+.   .+.|++.+|..+.-.+....++++|.+++...+  |+..++++-
T Consensus       469 AEyLysqgey~kc~~ys~WL~---~iaPS~~~~RLlGl~l~e~k~Y~eA~~~l~~LP--~n~~~~dsk  531 (549)
T PF07079_consen  469 AEYLYSQGEYHKCYLYSSWLT---KIAPSPQAYRLLGLCLMENKRYQEAWEYLQKLP--PNERMRDSK  531 (549)
T ss_pred             HHHHHhcccHHHHHHHHHHHH---HhCCcHHHHHHHHHHHHHHhhHHHHHHHHHhCC--CchhhHHHH
Confidence              2345677777776655552   367888888888777778888888888888764  455555443

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.47  E-value=0.0013  Score=65.71  Aligned_cols=101  Identities=15%  Similarity=0.136  Sum_probs=80.6

Q ss_pred             HHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcC
Q 040394          504 IGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAG  582 (691)
Q Consensus       504 i~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g  582 (691)
                      ...+...|++++|+..|++.++.. +-+...|..+..++...|++++|+..++..+   .+.|+ ...|..+..+|...|
T Consensus         9 a~~a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al---~l~P~~~~a~~~lg~~~~~lg   84 (356)
T PLN03088          9 AKEAFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAI---ELDPSLAKAYLRKGTACMKLE   84 (356)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH---HhCcCCHHHHHHHHHHHHHhC
Confidence            566778899999999999999853 3345677777789999999999999999775   35665 678888999999999


Q ss_pred             ChHHHHHHHHhC-CCCCCHHHHHHHHH
Q 040394          583 RLEEALEFMENM-PIEPDVSLFGAFLH  608 (691)
Q Consensus       583 ~~~~A~~~~~~~-~~~p~~~~~~~l~~  608 (691)
                      ++++|+..|++. ...|+.......+.
T Consensus        85 ~~~eA~~~~~~al~l~P~~~~~~~~l~  111 (356)
T PLN03088         85 EYQTAKAALEKGASLAPGDSRFTKLIK  111 (356)
T ss_pred             CHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence            999999999997 66666554444433

>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=97.47  E-value=0.00018  Score=52.20  Aligned_cols=63  Identities=21%  Similarity=0.363  Sum_probs=41.4

Q ss_pred             HhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHH
Q 040394          579 ARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVS  641 (691)
Q Consensus       579 ~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~  641 (691)
                      ...|++++|++.|+++ ...| +...+..+..+|.+.|++++|..+++++....|+++.++..++
T Consensus         2 l~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~l~a   66 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRNPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQDPDNPEYQQLLA   66 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTTHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCHHHHHHHHh
Confidence            3566777777777776 2233 5556666777777777777777777777777777665555554

...

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.46  E-value=0.0072  Score=58.16  Aligned_cols=86  Identities=15%  Similarity=0.105  Sum_probs=52.2

Q ss_pred             HHhcCChHHHHHHHHhC-CCCCC-----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcH
Q 040394          578 LARAGRLEEALEFMENM-PIEPD-----VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWI  651 (691)
Q Consensus       578 ~~~~g~~~~A~~~~~~~-~~~p~-----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~  651 (691)
                      ..+.|++.+|.+.+.+. ++.|+     ...|........+.|+.++|+.-.+.+++++|.-...+..-++++...++|+
T Consensus       259 ~fk~G~y~~A~E~Yteal~idP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al~iD~syikall~ra~c~l~le~~e  338 (486)
T KOG0550|consen  259 AFKNGNYRKAYECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEALKIDSSYIKALLRRANCHLALEKWE  338 (486)
T ss_pred             HhhccchhHHHHHHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhhhhhcCHHHHHHHHHHHHHHHHHHHHH
Confidence            34566666666666665 33333     3334333444456666777777666666666666666666666666667777


Q ss_pred             HHHHHHHHHHhC
Q 040394          652 RVNQVRELMKQR  663 (691)
Q Consensus       652 ~A~~~~~~~~~~  663 (691)
                      +|.+.+++..+.
T Consensus       339 ~AV~d~~~a~q~  350 (486)
T KOG0550|consen  339 EAVEDYEKAMQL  350 (486)
T ss_pred             HHHHHHHHHHhh
Confidence            776666666553

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=97.45  E-value=0.14  Score=50.38  Aligned_cols=70  Identities=9%  Similarity=0.142  Sum_probs=50.1

Q ss_pred             HHHhCCCCC----CHHHHHHHHHH--HHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHH
Q 040394          590 FMENMPIEP----DVSLFGAFLHG--CGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELM  660 (691)
Q Consensus       590 ~~~~~~~~p----~~~~~~~l~~~--~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  660 (691)
                      ++++.|++|    +...-|.|..+  +..+|++.++.-.-.-..++.| ++.+|..++.++....+|++|.+++..+
T Consensus       446 fi~e~gl~~i~i~e~eian~LaDAEyLysqgey~kc~~ys~WL~~iaP-S~~~~RLlGl~l~e~k~Y~eA~~~l~~L  521 (549)
T PF07079_consen  446 FITEVGLTPITISEEEIANFLADAEYLYSQGEYHKCYLYSSWLTKIAP-SPQAYRLLGLCLMENKRYQEAWEYLQKL  521 (549)
T ss_pred             HHHhcCCCcccccHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCC-cHHHHHHHHHHHHHHhhHHHHHHHHHhC
Confidence            344445555    33355555555  4578888888877777777888 4888888888888888888888888654

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=97.44  E-value=0.00036  Score=53.15  Aligned_cols=79  Identities=20%  Similarity=0.331  Sum_probs=34.9

Q ss_pred             CCChHHHHHHHHHHHHCCCC-CCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHH
Q 040394          510 QGDGGGSLALFSDMLNEEVQ-PNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEA  587 (691)
Q Consensus       510 ~~~~~~A~~~~~~m~~~g~~-p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A  587 (691)
                      .|+++.|+.+++++.+.... |+...+..+..++.+.|++++|..+++..    +..|+ ....-.+..++.+.|++++|
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~~----~~~~~~~~~~~l~a~~~~~l~~y~eA   77 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQKL----KLDPSNPDIHYLLARCLLKLGKYEEA   77 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHCH----THHHCHHHHHHHHHHHHHHTT-HHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHHh----CCCCCCHHHHHHHHHHHHHhCCHHHH
Confidence            35555555555555553211 12233333444555555555555555541    12222 12222334445555555555


Q ss_pred             HHHHH
Q 040394          588 LEFME  592 (691)
Q Consensus       588 ~~~~~  592 (691)
                      ++.++
T Consensus        78 i~~l~   82 (84)
T PF12895_consen   78 IKALE   82 (84)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            55544

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.43  E-value=0.0045  Score=64.68  Aligned_cols=139  Identities=9%  Similarity=0.005  Sum_probs=69.0

Q ss_pred             CCHhHHHHHHHHHhc--C---CChHHHHHHHHHHHHCCCCCCHH-HHHHHHHHhccc--------CCHHHHHHHHHHchh
Q 040394          495 KNTVTWSAMIGGYGM--Q---GDGGGSLALFSDMLNEEVQPNEV-IFTTILSACSHT--------GMVGEGWKCFYSMCR  560 (691)
Q Consensus       495 ~~~~~~~~li~~~~~--~---~~~~~A~~~~~~m~~~g~~p~~~-~~~~ll~~~~~~--------g~~~~A~~~~~~m~~  560 (691)
                      .|...|..++++...  .   ++...|..+|++..+  ..|+.. .+..+..++...        +++..+.+..+....
T Consensus       335 ~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~--ldP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~a  412 (517)
T PRK10153        335 HQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILK--SEPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIVA  412 (517)
T ss_pred             CCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH--hCCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhhh
Confidence            466677777766433  2   225567777777777  356653 333322222111        011222222222111


Q ss_pred             hcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCch
Q 040394          561 DFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKAC  635 (691)
Q Consensus       561 ~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~  635 (691)
                      ......+...|..+.-.+...|++++|...++++ ...|+...|..+...+...|+.++|.+.++++..++|.+++
T Consensus       413 l~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L~P~~pt  488 (517)
T PRK10153        413 LPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLEMSWLNYVLLGKVYELKGDNRLAADAYSTAFNLRPGENT  488 (517)
T ss_pred             cccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCch
Confidence            0011222344555544444556666666666665 44455555666666666666666666666666666666553

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.40  E-value=0.0064  Score=63.57  Aligned_cols=135  Identities=11%  Similarity=0.031  Sum_probs=88.3

Q ss_pred             CCCCHHHHHHHHHHhcc--c---CCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhc--------CChHHHHHHHHh
Q 040394          528 VQPNEVIFTTILSACSH--T---GMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARA--------GRLEEALEFMEN  593 (691)
Q Consensus       528 ~~p~~~~~~~ll~~~~~--~---g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~--------g~~~~A~~~~~~  593 (691)
                      .+.|...|..++++...  .   ++...|..+|++.+   ...|+ ...+..+..++...        ++...+.+..++
T Consensus       333 ~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai---~ldP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~  409 (517)
T PRK10153        333 LPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEIL---KSEPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDN  409 (517)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH---HhCCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHH
Confidence            46666777777775432  2   23667888887654   46777 44444443333221        123455555554


Q ss_pred             C----CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCc
Q 040394          594 M----PIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLS  666 (691)
Q Consensus       594 ~----~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~  666 (691)
                      .    ....+...|..+.......|++++|...++++++++|+ ...|..++.++...|+.++|.+.+++.......
T Consensus       410 a~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~ps-~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L~P~  485 (517)
T PRK10153        410 IVALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLEMS-WLNYVLLGKVYELKGDNRLAADAYSTAFNLRPG  485 (517)
T ss_pred             hhhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC
Confidence            3    13334566776666666778888888888888888885 778888888888888888888888888775543

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

Probab=97.37  E-value=0.0059  Score=58.74  Aligned_cols=133  Identities=12%  Similarity=0.164  Sum_probs=77.9

Q ss_pred             HHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHH-hcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHH
Q 040394          499 TWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSA-CSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDL  577 (691)
Q Consensus       499 ~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~-~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~  577 (691)
                      +|..++....+.+..+.|..+|.+..+.+ ..+...|...... +...++.+.|.++|+...+.  +..+...|...++.
T Consensus         3 v~i~~m~~~~r~~g~~~aR~vF~~a~~~~-~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~--f~~~~~~~~~Y~~~   79 (280)
T PF05843_consen    3 VWIQYMRFMRRTEGIEAARKVFKRARKDK-RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKK--FPSDPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH--HTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCChHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHH
Confidence            45566666666666666777777666432 2223333333322 22345566677777776555  33345556666777


Q ss_pred             HHhcCChHHHHHHHHhC-CCCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040394          578 LARAGRLEEALEFMENM-PIEPDV----SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKA  634 (691)
Q Consensus       578 ~~~~g~~~~A~~~~~~~-~~~p~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~  634 (691)
                      +.+.|+.+.|..+|++. ..-|..    ..|...+.--.+.|+.+.+..+.+++.+..|++.
T Consensus        80 l~~~~d~~~aR~lfer~i~~l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~~~~~~  141 (280)
T PF05843_consen   80 LIKLNDINNARALFERAISSLPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEELFPEDN  141 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHCCTSSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHTTTS-
T ss_pred             HHHhCcHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhhh
Confidence            77777777777777776 222222    3777777777777888888888888777776643

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.

>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.33  E-value=0.0039  Score=62.36  Aligned_cols=122  Identities=9%  Similarity=0.049  Sum_probs=99.6

Q ss_pred             CCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCC-CCchhHHHHHHHHHHhcCCHHHHHHHHHhccc----CCHh
Q 040394          424 DNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLL-SSNVYVGTALLNFYAKCGDAQSARMVFDAMRE----KNTV  498 (691)
Q Consensus       424 ~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----~~~~  498 (691)
                      ++.+.+...+..+++.+....+++.+..++......... ...+.+..++++.|.+.|..+++..++..=..    ||..
T Consensus        60 ~~~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~  139 (429)
T PF10037_consen   60 RKKPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNF  139 (429)
T ss_pred             cCCCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChh
Confidence            356667788888999999999999999998888765210 23455667999999999999999999887554    7999


Q ss_pred             HHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhccc
Q 040394          499 TWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHT  545 (691)
Q Consensus       499 ~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~  545 (691)
                      ++|.||..+.+.|++..|.++..+|..++...+..|+...+.+|.+-
T Consensus       140 s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  140 SFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             hHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            99999999999999999999999999888788888877777766554

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of small ribosomal proteins possessing one of three conserved sequence blocks found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins. This leaves open the possibility that they may be functional partners of GTP-binding ribosomal proteins [].

>PRK15331 chaperone protein SicA; Provisional

Probab=97.32  E-value=0.0025  Score=53.79  Aligned_cols=88  Identities=15%  Similarity=0.089  Sum_probs=68.5

Q ss_pred             HHHHHhcCChHHHHHHHHhC-CC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHH
Q 040394          575 VDLLARAGRLEEALEFMENM-PI-EPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIR  652 (691)
Q Consensus       575 i~~~~~~g~~~~A~~~~~~~-~~-~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  652 (691)
                      ..-+...|++++|..+|+-+ -. .-+..-|..|..++...+++++|...|..+..+.++|+......+.+|...|+.+.
T Consensus        44 Ay~~y~~Gk~~eA~~~F~~L~~~d~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~dp~p~f~agqC~l~l~~~~~  123 (165)
T PRK15331         44 AYEFYNQGRLDEAETFFRFLCIYDFYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKNDYRPVFFTGQCQLLMRKAAK  123 (165)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCCccchHHHHHHHhCCHHH
Confidence            33455778888888888776 22 23445567777777778888899988888888888888888888888888899888


Q ss_pred             HHHHHHHHHh
Q 040394          653 VNQVRELMKQ  662 (691)
Q Consensus       653 A~~~~~~~~~  662 (691)
                      |+.-|+...+
T Consensus       124 A~~~f~~a~~  133 (165)
T PRK15331        124 ARQCFELVNE  133 (165)
T ss_pred             HHHHHHHHHh
Confidence            8888887776

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.32  E-value=0.004  Score=50.42  Aligned_cols=105  Identities=10%  Similarity=-0.030  Sum_probs=63.7

Q ss_pred             HHHHHHhCCChhHHHHHHHHHHHcCCCCC--cchHHHHHHHHcccCChhHHHHHHHHHHHhCCC---ChhHHHHHHHHhH
Q 040394          117 MIRWYFLNDLYKDIVEFYKCMRKRLKEHD--NFVFSKVLKACCELRDIDEGMKVHCEIVKVGGP---DSFVLTGLVDMYA  191 (691)
Q Consensus       117 ll~~~~~~~~~~~a~~~~~~m~~~~~~~~--~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~l~~~~~  191 (691)
                      +..++-..|+.++|+.+|++....|....  ...+..+...+...|++++|..+++......+.   +......+..++.
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L~   86 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAALRVFLALALY   86 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHH
Confidence            34455667777888888887777765543  235556666777777777777777777765443   3344444455566


Q ss_pred             hcCChHHHHHHHhccCCCChhhHHHHHHHH
Q 040394          192 KCRDIGSSRQVFDETLDKNVVSWTSMIAGY  221 (691)
Q Consensus       192 ~~g~~~~A~~~~~~~~~~~~~~~~~li~~~  221 (691)
                      ..|+.++|...+-....++...|.--|..|
T Consensus        87 ~~gr~~eAl~~~l~~la~~~~~y~ra~~~y  116 (120)
T PF12688_consen   87 NLGRPKEALEWLLEALAETLPRYRRAIRFY  116 (120)
T ss_pred             HCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            666666666665544333333444444433

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.30  E-value=0.0034  Score=55.61  Aligned_cols=129  Identities=9%  Similarity=0.040  Sum_probs=80.7

Q ss_pred             chHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCC--cchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHH
Q 040394          112 YSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHD--NFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDM  189 (691)
Q Consensus       112 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~--~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  189 (691)
                      ..|..+...+...|++++|...|++..+....+.  ...+..+...+.+.|+.++|...++...+..+.+...+..+...
T Consensus        36 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~  115 (172)
T PRK02603         36 FVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNPKQPSALNNIAVI  115 (172)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHH
Confidence            3566666777777888888888887776532222  24667777777788888888888888887766677777777777


Q ss_pred             hHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCC
Q 040394          190 YAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRA  261 (691)
Q Consensus       190 ~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~  261 (691)
                      +...|+...+..-++..                 ...+++|.+++++....  .|+  .|..++..+...|+
T Consensus       116 ~~~~g~~~~a~~~~~~A-----------------~~~~~~A~~~~~~a~~~--~p~--~~~~~~~~~~~~~~  166 (172)
T PRK02603        116 YHKRGEKAEEAGDQDEA-----------------EALFDKAAEYWKQAIRL--APN--NYIEAQNWLKTTGR  166 (172)
T ss_pred             HHHcCChHhHhhCHHHH-----------------HHHHHHHHHHHHHHHhh--Cch--hHHHHHHHHHhcCc
Confidence            77777655544322211                 01245566666666542  222  35555555554443

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=97.30  E-value=0.054  Score=50.72  Aligned_cols=174  Identities=10%  Similarity=0.012  Sum_probs=103.4

Q ss_pred             HHHHHHhcCCHHHHHHHHHhccc--CCH-hH---HHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcc-
Q 040394          472 LLNFYAKCGDAQSARMVFDAMRE--KNT-VT---WSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSH-  544 (691)
Q Consensus       472 l~~~~~~~g~~~~A~~~~~~~~~--~~~-~~---~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~-  544 (691)
                      ....+...|++++|...|+.+..  |+. ..   .-.++.++.+.+++++|...+++..+....-...-+...+.+.+. 
T Consensus        38 ~A~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~g~~~~  117 (243)
T PRK10866         38 TAQQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGLTNM  117 (243)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHHhhh
Confidence            44445667888888888888764  321 22   234567777888888888888888875322112233333333221 


Q ss_pred             -c---------------CCH---HHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHH
Q 040394          545 -T---------------GMV---GEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGA  605 (691)
Q Consensus       545 -~---------------g~~---~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~  605 (691)
                       .               .|.   ..|...|+.+                +.-|-...-..+|...+..+...--..- ..
T Consensus       118 ~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~l----------------i~~yP~S~ya~~A~~rl~~l~~~la~~e-~~  180 (243)
T PRK10866        118 ALDDSALQGFFGVDRSDRDPQHARAAFRDFSKL----------------VRGYPNSQYTTDATKRLVFLKDRLAKYE-LS  180 (243)
T ss_pred             hcchhhhhhccCCCccccCHHHHHHHHHHHHHH----------------HHHCcCChhHHHHHHHHHHHHHHHHHHH-HH
Confidence             0               111   2233333333                3333333334444443333311111111 13


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCc---hhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          606 FLHGCGLYSRFDLGEVMIKKMLELHPDKA---CYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       606 l~~~~~~~g~~~~A~~~~~~~~~~~p~~~---~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      +..-|.+.|.+..|..-++.+++..|+.+   .....+...|...|..++|..+...+..
T Consensus       181 ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~~  240 (243)
T PRK10866        181 VAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIAA  240 (243)
T ss_pred             HHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHhc
Confidence            45567889999999999999999888765   4567788899999999999998876643

>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=97.30  E-value=0.0013  Score=51.33  Aligned_cols=91  Identities=11%  Similarity=0.154  Sum_probs=45.6

Q ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhc
Q 040394          114 FQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKC  193 (691)
Q Consensus       114 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~  193 (691)
                      |..+...+...|++++|...+++..+.. +.+...+..+...+...+++++|...++...+..+.+..++..+...+...
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPDNAKAYYNLGLAYYKL   81 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHHHHHHH
Confidence            3344445555555666666555555432 222234444445555555555555555555554444444444555555555


Q ss_pred             CChHHHHHHHhc
Q 040394          194 RDIGSSRQVFDE  205 (691)
Q Consensus       194 g~~~~A~~~~~~  205 (691)
                      |++++|...++.
T Consensus        82 ~~~~~a~~~~~~   93 (100)
T cd00189          82 GKYEEALEAYEK   93 (100)
T ss_pred             HhHHHHHHHHHH
Confidence            555555544443

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

Probab=97.29  E-value=0.21  Score=49.06  Aligned_cols=131  Identities=15%  Similarity=0.167  Sum_probs=83.5

Q ss_pred             HHHHHHHHHhcCCChHHHHHHHHHHHHCC-CCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHH-HHHHH
Q 040394          499 TWSAMIGGYGMQGDGGGSLALFSDMLNEE-VQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHY-VCMVD  576 (691)
Q Consensus       499 ~~~~li~~~~~~~~~~~A~~~~~~m~~~g-~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~-~~li~  576 (691)
                      .|..++..-.+..-.+.|..+|.+..+.| +.++...+++++.-++ .|+...|..+|+.=...   -||...| +-.+.
T Consensus       399 v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~---f~d~~~y~~kyl~  474 (660)
T COG5107         399 VFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLK---FPDSTLYKEKYLL  474 (660)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHh---CCCchHHHHHHHH
Confidence            45556666666666777777777777777 5566667777766544 46667777777643333   3443332 33455


Q ss_pred             HHHhcCChHHHHHHHHhC--CCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC
Q 040394          577 LLARAGRLEEALEFMENM--PIEPD--VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK  633 (691)
Q Consensus       577 ~~~~~g~~~~A~~~~~~~--~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~  633 (691)
                      .+.+-++-+.|..+|+..  .+..+  ..+|..++..-...|+...+..+-+++.+..|..
T Consensus       475 fLi~inde~naraLFetsv~r~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~~pQe  535 (660)
T COG5107         475 FLIRINDEENARALFETSVERLEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFRELVPQE  535 (660)
T ss_pred             HHHHhCcHHHHHHHHHHhHHHHHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHHcCcH
Confidence            666777777777777754  22222  4577777777777777777777777777777773

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=97.28  E-value=0.0054  Score=58.79  Aligned_cols=128  Identities=9%  Similarity=0.025  Sum_probs=70.7

Q ss_pred             HHHHHHHhcccCCHHHHHHHHHH---chhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-------C-CCCCHHH
Q 040394          535 FTTILSACSHTGMVGEGWKCFYS---MCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-------P-IEPDVSL  602 (691)
Q Consensus       535 ~~~ll~~~~~~g~~~~A~~~~~~---m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-------~-~~p~~~~  602 (691)
                      |..+-..|.-.|+++.|+...+.   +.+.+|-... ...+..+.+++.-.|+++.|.+.++..       + -.....+
T Consensus       198 ~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~tl~LAielg~r~vEAQs  277 (639)
T KOG1130|consen  198 YGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLTLNLAIELGNRTVEAQS  277 (639)
T ss_pred             hcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHHHHHHHHhcchhHHHHH
Confidence            33333444445666666554432   1123332222 345566666677777777777666654       1 1122335


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhc----C--CCCchhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          603 FGAFLHGCGLYSRFDLGEVMIKKMLEL----H--PDKACYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       603 ~~~l~~~~~~~g~~~~A~~~~~~~~~~----~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      ..+|...|.-..++++|+.+..+-+.+    +  ......++.|++.|...|..++|..+.+.-++
T Consensus       278 cYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~alg~h~kAl~fae~hl~  343 (639)
T KOG1130|consen  278 CYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNALGEHRKALYFAELHLR  343 (639)
T ss_pred             HHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence            556666666666777777766654431    1  12245666777777777777777666555544

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.26  E-value=0.0023  Score=60.27  Aligned_cols=93  Identities=13%  Similarity=0.098  Sum_probs=50.4

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhC-CCCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc---hhHHHHHH
Q 040394          571 YVCMVDLLARAGRLEEALEFMENM-PIEPDV----SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKA---CYYVLVSN  642 (691)
Q Consensus       571 ~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~---~~~~~l~~  642 (691)
                      |..-+..+.+.|++++|+..|+.+ ...|+.    ..+..+...|...|++++|...|+++.+..|+++   ..+..++.
T Consensus       146 Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg~  225 (263)
T PRK10803        146 YNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVGV  225 (263)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHHH
Confidence            333333334455666665555555 222221    2444455666666666666666666666555543   34444555


Q ss_pred             HHHhCCCcHHHHHHHHHHHhC
Q 040394          643 LYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       643 ~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      ++...|++++|.++++.+++.
T Consensus       226 ~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        226 IMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             HHHHcCCHHHHHHHHHHHHHH
Confidence            666666666666666666553

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=97.25  E-value=0.033  Score=54.58  Aligned_cols=161  Identities=14%  Similarity=0.146  Sum_probs=94.2

Q ss_pred             HHHHHHHhcCCHHHHHHHHHhcccC-------CHhHHHHHHHHHhc---CCChHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 040394          471 ALLNFYAKCGDAQSARMVFDAMREK-------NTVTWSAMIGGYGM---QGDGGGSLALFSDMLNEEVQPNEVIFTTILS  540 (691)
Q Consensus       471 ~l~~~~~~~g~~~~A~~~~~~~~~~-------~~~~~~~li~~~~~---~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~  540 (691)
                      .++-.|-...+++...++.+.+...       ....-....-++.+   .|+.++|+.++..+....-.++..+|..+-+
T Consensus       146 ~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL~GR  225 (374)
T PF13281_consen  146 NLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLGLLGR  225 (374)
T ss_pred             HHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHHHHH
Confidence            3444566666666666666666542       11111123344445   6777777777777555555666667666555


Q ss_pred             Hhc---------ccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCCh----HHHHHHH---HhC-------CCC
Q 040394          541 ACS---------HTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRL----EEALEFM---ENM-------PIE  597 (691)
Q Consensus       541 ~~~---------~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~----~~A~~~~---~~~-------~~~  597 (691)
                      .|-         .....+.|+..|.   +.+.+.|+...--.++..+.-.|..    .+..++-   ...       ...
T Consensus       226 IyKD~~~~s~~~d~~~ldkAi~~Y~---kgFe~~~~~Y~GIN~AtLL~~~g~~~~~~~el~~i~~~l~~llg~kg~~~~~  302 (374)
T PF13281_consen  226 IYKDLFLESNFTDRESLDKAIEWYR---KGFEIEPDYYSGINAATLLMLAGHDFETSEELRKIGVKLSSLLGRKGSLEKM  302 (374)
T ss_pred             HHHHHHHHcCccchHHHHHHHHHHH---HHHcCCccccchHHHHHHHHHcCCcccchHHHHHHHHHHHHHHHhhcccccc
Confidence            442         1224677887777   5556667643322333333333321    1222221   111       233


Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040394          598 PDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKA  634 (691)
Q Consensus       598 p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~  634 (691)
                      .|-..+.+++.++.-.||+++|.+.++++.+..|+..
T Consensus       303 ~dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l~~~~W  339 (374)
T PF13281_consen  303 QDYWDVATLLEASVLAGDYEKAIQAAEKAFKLKPPAW  339 (374)
T ss_pred             ccHHHHHHHHHHHHHcCCHHHHHHHHHHHhhcCCcch
Confidence            4666778888999999999999999999999988743

>PF06239 ECSIT: Evolutionarily conserved signalling intermediate in Toll pathway; InterPro: IPR010418 Activation of NF-kappaB as a consequence of signalling through the Toll and IL-1 receptors is a major element of innate immune responses

Probab=97.24  E-value=0.0041  Score=54.81  Aligned_cols=89  Identities=11%  Similarity=0.151  Sum_probs=67.9

Q ss_pred             cCCHhHHHHHHHHHhc-----CCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccC----------------CHHHHH
Q 040394          494 EKNTVTWSAMIGGYGM-----QGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTG----------------MVGEGW  552 (691)
Q Consensus       494 ~~~~~~~~~li~~~~~-----~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g----------------~~~~A~  552 (691)
                      .++-.+|..++..+.+     .|..+=....++.|.+-|+.-|..+|+.||+.+=+..                +-+-|+
T Consensus        44 ~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i  123 (228)
T PF06239_consen   44 AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAI  123 (228)
T ss_pred             cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHH
Confidence            4566677777777654     4777778888899999999999999999998876522                345677


Q ss_pred             HHHHHchhhcCCCCChhHHHHHHHHHHhcCC
Q 040394          553 KCFYSMCRDFKFVPSMKHYVCMVDLLARAGR  583 (691)
Q Consensus       553 ~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~  583 (691)
                      +++++| +.+|+.||..++..+++.+++.+.
T Consensus       124 ~lL~qM-E~~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  124 DLLEQM-ENNGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             HHHHHH-HHcCCCCcHHHHHHHHHHhccccH
Confidence            888888 777888888888888888776654

ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=97.23  E-value=0.00025  Score=42.57  Aligned_cols=34  Identities=32%  Similarity=0.495  Sum_probs=31.2

Q ss_pred             HHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHH
Q 040394          622 MIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQ  655 (691)
Q Consensus       622 ~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~  655 (691)
                      +++++++++|+++..|..++.+|...|++++|++
T Consensus         1 ~y~kAie~~P~n~~a~~nla~~~~~~g~~~~A~~   34 (34)
T PF13431_consen    1 CYKKAIELNPNNAEAYNNLANLYLNQGDYEEAIA   34 (34)
T ss_pred             ChHHHHHHCCCCHHHHHHHHHHHHHCcCHHhhcC
Confidence            3688999999999999999999999999999863

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.21  E-value=0.033  Score=53.84  Aligned_cols=124  Identities=11%  Similarity=0.171  Sum_probs=67.3

Q ss_pred             HHHHHhc-CCHHHHHHHHHhcC-----CCC----hhHHHHHHHHHHhcCCchhHHHHHHHhhHCCC-----CCcHH-HHH
Q 040394          288 LDMYVKC-GNIRDARSVFDELC-----SID----LVSWTAMIVGYTQSGYPDKALKLFTDKKWADF-----FPNHV-TIA  351 (691)
Q Consensus       288 i~~~~~~-g~~~~A~~~~~~~~-----~~~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~-----~p~~~-t~~  351 (691)
                      ...|... |++++|.+.|++..     ...    ..++..+...+.+.|++++|.++|++....-.     +.+.. .|.
T Consensus       121 A~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l  200 (282)
T PF14938_consen  121 AEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFL  200 (282)
T ss_dssp             HHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHH
Confidence            3344444 56666666665541     111    12455566677888888888888887665422     22222 223


Q ss_pred             HHHHHHhcCCChhhHHHHHHHHHHhCCC-----chhHHHHHHHHhHh--cCChHHHHHHHHhCCCCC
Q 040394          352 SVLSASAQLGNLNMGRMVHSLGIRLGLE-----DYTVINALVDMYAK--CHVIADARYIFETTSEKD  411 (691)
Q Consensus       352 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~-----~~~~~~~l~~~~~~--~g~~~~a~~~~~~~~~~~  411 (691)
                      ..+-++...|+...|...++......+.     ...+...|+.++-.  ...++.++.-|+.+..-|
T Consensus       201 ~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~~~~D~e~f~~av~~~d~~~~ld  267 (282)
T PF14938_consen  201 KAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAYEEGDVEAFTEAVAEYDSISRLD  267 (282)
T ss_dssp             HHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHHHTT-CCCHHHHCHHHTTSS---
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHhCCHHHHHHHHHHHcccCccH
Confidence            3333555567888888888877766543     23445556666654  345677777777776544

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=97.19  E-value=0.26  Score=48.10  Aligned_cols=111  Identities=15%  Similarity=0.099  Sum_probs=82.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCC
Q 040394          283 LVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGN  362 (691)
Q Consensus       283 ~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~  362 (691)
                      +.+..|.-+...|+...|.++..+..-|+...|-..+.+++..++|++..++...      +-++.-|-.++.+|...|+
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~s------kKsPIGyepFv~~~~~~~~  252 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEFKVPDKRFWWLKIKALAENKDWDELEKFAKS------KKSPIGYEPFVEACLKYGN  252 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHhC------CCCCCChHHHHHHHHHCCC
Confidence            3445566677788888888888888888888888889999999998887776432      1234667778888888888


Q ss_pred             hhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCC
Q 040394          363 LNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTS  408 (691)
Q Consensus       363 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  408 (691)
                      ..+|..+...+.         +..-+..|.++|++.+|.+.--+..
T Consensus       253 ~~eA~~yI~k~~---------~~~rv~~y~~~~~~~~A~~~A~~~k  289 (319)
T PF04840_consen  253 KKEASKYIPKIP---------DEERVEMYLKCGDYKEAAQEAFKEK  289 (319)
T ss_pred             HHHHHHHHHhCC---------hHHHHHHHHHCCCHHHHHHHHHHcC
Confidence            888887776622         2567788888888888877655443

Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm

>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.16  E-value=0.0089  Score=59.85  Aligned_cols=123  Identities=10%  Similarity=-0.049  Sum_probs=99.7

Q ss_pred             CCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhC--CC-chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHH
Q 040394          342 DFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLG--LE-DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSI  418 (691)
Q Consensus       342 g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~--~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~l  418 (691)
                      +...+...+..+++.+....+++.+..++.......  .. -+.+..++|+.|.+.|..+.++.+++.=...        
T Consensus        61 ~~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~y--------  132 (429)
T PF10037_consen   61 KKPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQY--------  132 (429)
T ss_pred             CCCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhc--------
Confidence            445577778888888888888888888876665542  22 4455569999999999999999999887766        


Q ss_pred             HHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhc
Q 040394          419 ISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKC  479 (691)
Q Consensus       419 i~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  479 (691)
                            |+-||..|++.||..+.+.|++..|.++...|..++. ..++.++..-+.+|.+.
T Consensus       133 ------GiF~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~-~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  133 ------GIFPDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQEE-FDNPSTQALALYSCYKY  186 (429)
T ss_pred             ------ccCCChhhHHHHHHHHhhcccHHHHHHHHHHHHHhhc-cCCchHHHHHHHHHHHh
Confidence                  8999999999999999999999999999999998886 66677776666666655

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of small ribosomal proteins possessing one of three conserved sequence blocks found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins. This leaves open the possibility that they may be functional partners of GTP-binding ribosomal proteins [].

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.16  E-value=0.0094  Score=48.28  Aligned_cols=88  Identities=17%  Similarity=0.107  Sum_probs=59.0

Q ss_pred             HHHHHHhcCChHHHHHHHHhC---CCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC---CchhHHHHHHHHH
Q 040394          574 MVDLLARAGRLEEALEFMENM---PIEPD--VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPD---KACYYVLVSNLYA  645 (691)
Q Consensus       574 li~~~~~~g~~~~A~~~~~~~---~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~---~~~~~~~l~~~~~  645 (691)
                      +..++-..|+.++|+.+|++.   +....  ...+..+...+...|++++|..++++.....|+   +......++.++.
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L~   86 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAALRVFLALALY   86 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHH
Confidence            344556677777777777766   22222  235556666777778888888888887777777   5556666677777


Q ss_pred             hCCCcHHHHHHHHHHH
Q 040394          646 SDGRWIRVNQVRELMK  661 (691)
Q Consensus       646 ~~g~~~~A~~~~~~~~  661 (691)
                      ..|+.++|.+.+-...
T Consensus        87 ~~gr~~eAl~~~l~~l  102 (120)
T PF12688_consen   87 NLGRPKEALEWLLEAL  102 (120)
T ss_pred             HCCCHHHHHHHHHHHH
Confidence            8888888877765443

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.13  E-value=0.16  Score=49.33  Aligned_cols=225  Identities=16%  Similarity=0.047  Sum_probs=135.3

Q ss_pred             CCHHHHHHHH-HHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHh--------
Q 040394          428 PDAVTLVSVI-SACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTV--------  498 (691)
Q Consensus       428 p~~~~~~~ll-~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~--------  498 (691)
                      |.-.++..+- .++.-.|+.+.|.++--...+..  +.+....-.-..++.-.++.+.|...|++...-|+.        
T Consensus       166 pac~~a~~lka~cl~~~~~~~~a~~ea~~ilkld--~~n~~al~vrg~~~yy~~~~~ka~~hf~qal~ldpdh~~sk~~~  243 (486)
T KOG0550|consen  166 PACFKAKLLKAECLAFLGDYDEAQSEAIDILKLD--ATNAEALYVRGLCLYYNDNADKAINHFQQALRLDPDHQKSKSAS  243 (486)
T ss_pred             chhhHHHHhhhhhhhhcccchhHHHHHHHHHhcc--cchhHHHHhcccccccccchHHHHHHHhhhhccChhhhhHHhHh
Confidence            4444554443 34557789999988888877766  333333222223344567788888888887753322        


Q ss_pred             -------HHHHHHHHHhcCCChHHHHHHHHHHHHC---CCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-
Q 040394          499 -------TWSAMIGGYGMQGDGGGSLALFSDMLNE---EVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-  567 (691)
Q Consensus       499 -------~~~~li~~~~~~~~~~~A~~~~~~m~~~---g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-  567 (691)
                             .|..=..-..+.|++..|.+.|.+.+..   +..|+...|.....+..+.|+.++|+.-.+...   .+.|. 
T Consensus       244 ~~~k~le~~k~~gN~~fk~G~y~~A~E~Yteal~idP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al---~iD~sy  320 (486)
T KOG0550|consen  244 MMPKKLEVKKERGNDAFKNGNYRKAYECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEAL---KIDSSY  320 (486)
T ss_pred             hhHHHHHHHHhhhhhHhhccchhHHHHHHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhhhh---hcCHHH
Confidence                   1222234456889999999999999873   344556667777778889999999998887542   34444 


Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCC---HHHHHHHHHHHHhcCC---------------HHHHHHHHHHHHh
Q 040394          568 MKHYVCMVDLLARAGRLEEALEFMENM-PIEPD---VSLFGAFLHGCGLYSR---------------FDLGEVMIKKMLE  628 (691)
Q Consensus       568 ~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~---~~~~~~l~~~~~~~g~---------------~~~A~~~~~~~~~  628 (691)
                      +..|-.-..++...++|++|.+-+++. ....+   ..++.....++.++.+               .+--...-+.++.
T Consensus       321 ikall~ra~c~l~le~~e~AV~d~~~a~q~~~s~e~r~~l~~A~~aLkkSkRkd~ykilGi~~~as~~eikkayrk~AL~  400 (486)
T KOG0550|consen  321 IKALLRRANCHLALEKWEEAVEDYEKAMQLEKDCEIRRTLREAQLALKKSKRKDWYKILGISRNASDDEIKKAYRKLALV  400 (486)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhhhhhHHHHhhhhhhcccchhhhHHHHHHHH
Confidence            334444445566678899998888886 32222   2344444333432221               1111111222334


Q ss_pred             cCCCCch--------hHHHHHHHHHhCCCcHHHHHHH
Q 040394          629 LHPDKAC--------YYVLVSNLYASDGRWIRVNQVR  657 (691)
Q Consensus       629 ~~p~~~~--------~~~~l~~~~~~~g~~~~A~~~~  657 (691)
                      .+|+...        -+.-++..|...++..+..++.
T Consensus       401 ~Hpd~~agsq~eaE~kFkevgeAy~il~d~~kr~r~d  437 (486)
T KOG0550|consen  401 HHPDKNAGSQKEAEAKFKEVGEAYTILSDPMKRVRFD  437 (486)
T ss_pred             hCCCcCcchhHHHHHHHHHHHHHHHHhcCHHHHhhcc
Confidence            5665321        2345777888888888877764

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

Probab=97.12  E-value=0.0098  Score=57.24  Aligned_cols=127  Identities=13%  Similarity=0.090  Sum_probs=96.1

Q ss_pred             HHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHh-cCCHHHHHHHHHhccc---CCHhHHHHHHHH
Q 040394          431 VTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAK-CGDAQSARMVFDAMRE---KNTVTWSAMIGG  506 (691)
Q Consensus       431 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~~~A~~~~~~~~~---~~~~~~~~li~~  506 (691)
                      .+|..+++.+.+.+..+.|..+|.+..+.+  ..+..+|......-.+ .++.+.|.++|+...+   .+...|...+.-
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~--~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~f~~~~~~~~~Y~~~   79 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDK--RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKKFPSDPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCC--CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence            468888899999999999999999998665  4455666555555333 5677779999998875   477888888999


Q ss_pred             HhcCCChHHHHHHHHHHHHCCCCCCH---HHHHHHHHHhcccCCHHHHHHHHHHchh
Q 040394          507 YGMQGDGGGSLALFSDMLNEEVQPNE---VIFTTILSACSHTGMVGEGWKCFYSMCR  560 (691)
Q Consensus       507 ~~~~~~~~~A~~~~~~m~~~g~~p~~---~~~~~ll~~~~~~g~~~~A~~~~~~m~~  560 (691)
                      +...++.+.|..+|++.... +.++.   ..|...+.--.+.|+++.+.++.+++.+
T Consensus        80 l~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~  135 (280)
T PF05843_consen   80 LIKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEE  135 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHH
T ss_pred             HHHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            99999999999999998875 33333   4788888887888999999888887743

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.

>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends

Probab=97.09  E-value=0.0062  Score=47.34  Aligned_cols=80  Identities=11%  Similarity=0.145  Sum_probs=61.3

Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHHCCC-CCCHHHHHHHHHHhcccC--------CHHHHHHHHHHchhhcCCCCChhH
Q 040394          500 WSAMIGGYGMQGDGGGSLALFSDMLNEEV-QPNEVIFTTILSACSHTG--------MVGEGWKCFYSMCRDFKFVPSMKH  570 (691)
Q Consensus       500 ~~~li~~~~~~~~~~~A~~~~~~m~~~g~-~p~~~~~~~ll~~~~~~g--------~~~~A~~~~~~m~~~~~~~p~~~~  570 (691)
                      -...|..+...+++.....+|+.+...|+ .|+..+|+.++.+.++..        ++-..+.+|+.|. ..+++|+..+
T Consensus        28 ~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL-~~~lKP~~et  106 (120)
T PF08579_consen   28 QIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDIL-SNKLKPNDET  106 (120)
T ss_pred             HHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHH-HhccCCcHHH
Confidence            34456666667999999999999999999 899999999998776532        2345677888885 4478888888


Q ss_pred             HHHHHHHHHh
Q 040394          571 YVCMVDLLAR  580 (691)
Q Consensus       571 ~~~li~~~~~  580 (691)
                      |+.++..+.+
T Consensus       107 Ynivl~~Llk  116 (120)
T PF08579_consen  107 YNIVLGSLLK  116 (120)
T ss_pred             HHHHHHHHHH
Confidence            8888877654

Rpm2 is a protein subunit of the yeast mitochondrial RNase P. It has the ability to act as a transcriptional activator in the nucleus, where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components. Rpm2p is also involved in maturation of Rpm1 and in translation of mitochondrial mRNAs [, , ].

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.08  E-value=0.0086  Score=52.83  Aligned_cols=80  Identities=4%  Similarity=-0.027  Sum_probs=50.9

Q ss_pred             chHHHHHHHHHhCCChhHHHHHHHHHHHcCCCC--CcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHH
Q 040394          112 YSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEH--DNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDM  189 (691)
Q Consensus       112 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~--~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  189 (691)
                      ..|..+...+...|++++|+..|++.......|  ...++..+...+...|+.++|...++...+..+.....+..+...
T Consensus        36 ~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~~~~~~~~~~la~i  115 (168)
T CHL00033         36 FTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERNPFLPQALNNMAVI  115 (168)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHH
Confidence            345666666667777777777777776542222  123566666777777777777777777776654455555555555


Q ss_pred             hH
Q 040394          190 YA  191 (691)
Q Consensus       190 ~~  191 (691)
                      +.
T Consensus       116 ~~  117 (168)
T CHL00033        116 CH  117 (168)
T ss_pred             HH
Confidence            55

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.06  E-value=0.011  Score=49.75  Aligned_cols=85  Identities=6%  Similarity=0.000  Sum_probs=47.2

Q ss_pred             HHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhcc--CC-CChhhHHHHHHHHHhCCChhHHH
Q 040394          155 ACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDET--LD-KNVVSWTSMIAGYVQNDCAQEGL  231 (691)
Q Consensus       155 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~--~~-~~~~~~~~li~~~~~~g~~~~A~  231 (691)
                      .+...|++++|+.+|+.+...++.+...|..|..++-..|++++|+..|...  .+ .|...+-.+..++...|+.+.|.
T Consensus        44 ~ly~~G~l~~A~~~f~~L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~ddp~~~~~ag~c~L~lG~~~~A~  123 (157)
T PRK15363         44 QLMEVKEFAGAARLFQLLTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKIDAPQAPWAAAECYLACDNVCYAI  123 (157)
T ss_pred             HHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHcCCHHHHH
Confidence            3345555555555555555555555555555555555556666665555543  12 24455555555566666666666


Q ss_pred             HHHHHHHh
Q 040394          232 VLFNRMRE  239 (691)
Q Consensus       232 ~~~~~m~~  239 (691)
                      +.|+....
T Consensus       124 ~aF~~Ai~  131 (157)
T PRK15363        124 KALKAVVR  131 (157)
T ss_pred             HHHHHHHH
Confidence            66655443

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.03  E-value=0.023  Score=54.95  Aligned_cols=123  Identities=11%  Similarity=0.165  Sum_probs=50.3

Q ss_pred             HHHHHHHhCCChhHHHHHHHHHHHcCC----CC-CcchHHHHHHHHcccCChhHHHHHHHHHHH----hCCC--ChhHHH
Q 040394          116 VMIRWYFLNDLYKDIVEFYKCMRKRLK----EH-DNFVFSKVLKACCELRDIDEGMKVHCEIVK----VGGP--DSFVLT  184 (691)
Q Consensus       116 ~ll~~~~~~~~~~~a~~~~~~m~~~~~----~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~----~~~~--~~~~~~  184 (691)
                      .....|...|++++|.+.|.+..+...    +. -...|......+. ..++++|...++...+    .|.+  -...+.
T Consensus        40 ~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~k-~~~~~~Ai~~~~~A~~~y~~~G~~~~aA~~~~  118 (282)
T PF14938_consen   40 KAANCFKLAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEEAANCYK-KGDPDEAIECYEKAIEIYREAGRFSQAAKCLK  118 (282)
T ss_dssp             HHHHHHHHTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH-HTTHHHHHHHHHHHHHHHHHCT-HHHHHHHHH
T ss_pred             HHHHHHHHHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH-hhCHHHHHHHHHHHHHHHHhcCcHHHHHHHHH
Confidence            344455555555555555554432110    00 0112333333332 2255555555554443    1211  122333


Q ss_pred             HHHHHhHhc-CChHHHHHHHhccCC-----CC----hhhHHHHHHHHHhCCChhHHHHHHHHHHh
Q 040394          185 GLVDMYAKC-RDIGSSRQVFDETLD-----KN----VVSWTSMIAGYVQNDCAQEGLVLFNRMRE  239 (691)
Q Consensus       185 ~l~~~~~~~-g~~~~A~~~~~~~~~-----~~----~~~~~~li~~~~~~g~~~~A~~~~~~m~~  239 (691)
                      .+...|... |++++|.+.|++..+     ..    ..++..+...+.+.|++++|.++|++...
T Consensus       119 ~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~  183 (282)
T PF14938_consen  119 ELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAK  183 (282)
T ss_dssp             HHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            444445554 555555555544311     01    12334444555555555555555555543

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=97.00  E-value=0.0032  Score=62.33  Aligned_cols=62  Identities=15%  Similarity=0.095  Sum_probs=39.5

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCHH----HHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 040394          568 MKHYVCMVDLLARAGRLEEALEFMENM-PIEPDVS----LFGAFLHGCGLYSRFDLGEVMIKKMLEL  629 (691)
Q Consensus       568 ~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~~----~~~~l~~~~~~~g~~~~A~~~~~~~~~~  629 (691)
                      ...++.+..+|...|++++|+..|++. ...|+..    +|..+..+|...|+.++|+..++++++.
T Consensus        75 a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         75 AEDAVNLGLSLFSKGRVKDALAQFETALELNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            455666666666666666666666664 5555532    3666666666666666666666666665

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=96.98  E-value=0.0019  Score=46.84  Aligned_cols=64  Identities=17%  Similarity=0.317  Sum_probs=52.4

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcC-CHHHHHHHHHHHHhcCC
Q 040394          568 MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYS-RFDLGEVMIKKMLELHP  631 (691)
Q Consensus       568 ~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~p  631 (691)
                      ...|..+...+...|++++|+..|++. ...| +...|..+..++...| ++++|+..++++++++|
T Consensus         3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l~P   69 (69)
T PF13414_consen    3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKLDP   69 (69)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHcCc
Confidence            456777888888889999998888887 4445 4568888888888888 79999999999998887

...

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=96.98  E-value=0.12  Score=52.89  Aligned_cols=220  Identities=10%  Similarity=0.067  Sum_probs=109.6

Q ss_pred             cCchhHHHHHHH--HHHhCCCCchhhhHHHHHHhcCCChHHHHHHhccCCCCCcchHHHHHHHHHhCCChhHHHHHHHHH
Q 040394           60 KSTGSLKAFHAL--LIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCM  137 (691)
Q Consensus        60 ~~~~~a~~~~~~--~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m  137 (691)
                      +++...+-+++.  +.+.|-.|+.+.  +...++-+|++.+|-++|.                  +.|.-.+|+++|..|
T Consensus       612 Rdl~~L~li~EL~~~k~rge~P~~iL--lA~~~Ay~gKF~EAAklFk------------------~~G~enRAlEmyTDl  671 (1081)
T KOG1538|consen  612 RDLRYLELISELEERKKRGETPNDLL--LADVFAYQGKFHEAAKLFK------------------RSGHENRALEMYTDL  671 (1081)
T ss_pred             hccHHHHHHHHHHHHHhcCCCchHHH--HHHHHHhhhhHHHHHHHHH------------------HcCchhhHHHHHHHH
Confidence            444444444443  333444344422  4556677788888888774                  567777888888877


Q ss_pred             HHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHH
Q 040394          138 RKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSM  217 (691)
Q Consensus       138 ~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~l  217 (691)
                      +-.          -..+-+...|+.++-..+.+.-.+-.. +..--.+-...+...|+.++|..+.-             
T Consensus       672 RMF----------D~aQE~~~~g~~~eKKmL~RKRA~WAr-~~kePkaAAEmLiSaGe~~KAi~i~~-------------  727 (1081)
T KOG1538|consen  672 RMF----------DYAQEFLGSGDPKEKKMLIRKRADWAR-NIKEPKAAAEMLISAGEHVKAIEICG-------------  727 (1081)
T ss_pred             HHH----------HHHHHHhhcCChHHHHHHHHHHHHHhh-hcCCcHHHHHHhhcccchhhhhhhhh-------------
Confidence            643          123445556666655555443222110 11111223344455566655544332             


Q ss_pred             HHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCH
Q 040394          218 IAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNI  297 (691)
Q Consensus       218 i~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~  297 (691)
                           .+|-.+-+.++-.++-.    .+..+...+..-+.+...+..|-++|..|-+.         ..+++.+...+++
T Consensus       728 -----d~gW~d~lidI~rkld~----~ere~l~~~a~ylk~l~~~gLAaeIF~k~gD~---------ksiVqlHve~~~W  789 (1081)
T KOG1538|consen  728 -----DHGWVDMLIDIARKLDK----AEREPLLLCATYLKKLDSPGLAAEIFLKMGDL---------KSLVQLHVETQRW  789 (1081)
T ss_pred             -----cccHHHHHHHHHhhcch----hhhhHHHHHHHHHhhccccchHHHHHHHhccH---------HHHhhheeecccc
Confidence                 22222333333333211    12333444444444555566666666655322         2355566667777


Q ss_pred             HHHHHHHHhcCCCChhHHHHHH-------------HHHHhcCCchhHHHHHHHhhHC
Q 040394          298 RDARSVFDELCSIDLVSWTAMI-------------VGYTQSGYPDKALKLFTDKKWA  341 (691)
Q Consensus       298 ~~A~~~~~~~~~~~~~~~~~li-------------~~~~~~g~~~~a~~~~~~m~~~  341 (691)
                      ++|..+-++.++--...|-.-.             ++|.+.|+-.+|.++++++...
T Consensus       790 ~eAFalAe~hPe~~~dVy~pyaqwLAE~DrFeEAqkAfhkAGr~~EA~~vLeQLtnn  846 (1081)
T KOG1538|consen  790 DEAFALAEKHPEFKDDVYMPYAQWLAENDRFEEAQKAFHKAGRQREAVQVLEQLTNN  846 (1081)
T ss_pred             hHhHhhhhhCccccccccchHHHHhhhhhhHHHHHHHHHHhcchHHHHHHHHHhhhh
Confidence            7777777666442222222222             3445556666666666655443

>PF06239 ECSIT: Evolutionarily conserved signalling intermediate in Toll pathway; InterPro: IPR010418 Activation of NF-kappaB as a consequence of signalling through the Toll and IL-1 receptors is a major element of innate immune responses

Probab=96.97  E-value=0.0058  Score=53.89  Aligned_cols=89  Identities=15%  Similarity=0.094  Sum_probs=63.0

Q ss_pred             CCChhhHHHHHHHHHhC-----CChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHcc----------------CChhhHH
Q 040394          208 DKNVVSWTSMIAGYVQN-----DCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKL----------------RALHQGK  266 (691)
Q Consensus       208 ~~~~~~~~~li~~~~~~-----g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~----------------~~~~~a~  266 (691)
                      .++..+|..++..|.+.     |..+=....++.|.+-|+.-|..+|+.|++.+=+.                .+-+-|.
T Consensus        44 ~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i  123 (228)
T PF06239_consen   44 AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAI  123 (228)
T ss_pred             cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHH
Confidence            34556666666666543     55555666777777777777888888877776432                2456778


Q ss_pred             HHHHHHHHHCCCCchHHHHHHHHHHHhcCC
Q 040394          267 WLHGYILKIGIEINSHLVTALLDMYVKCGN  296 (691)
Q Consensus       267 ~~~~~~~~~g~~~~~~~~~~li~~~~~~g~  296 (691)
                      +++++|...|+-||..++..+++.+++.+.
T Consensus       124 ~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  124 DLLEQMENNGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             HHHHHHHHcCCCCcHHHHHHHHHHhccccH
Confidence            888888888888888888888888866553

ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=96.96  E-value=0.0017  Score=41.90  Aligned_cols=42  Identities=17%  Similarity=0.263  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHH
Q 040394          601 SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSN  642 (691)
Q Consensus       601 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~  642 (691)
                      .+|..+...|...|++++|+++++++++..|+++..+..++.
T Consensus         2 ~~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~~~a~~~La~   43 (44)
T PF13428_consen    2 AAWLALARAYRRLGQPDEAERLLRRALALDPDDPEAWRALAQ   43 (44)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCHHHHHHhhh
Confidence            357788899999999999999999999999999998887764

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=96.93  E-value=0.2  Score=46.91  Aligned_cols=67  Identities=6%  Similarity=0.040  Sum_probs=43.4

Q ss_pred             CcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCc-chH---HHHHHHHcccCChhHHHHHHHHHHHhCCC
Q 040394          110 DFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDN-FVF---SKVLKACCELRDIDEGMKVHCEIVKVGGP  178 (691)
Q Consensus       110 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~---~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  178 (691)
                      +...+......+...|++++|++.|+++...-  |+. ...   -.+..++-+.++.++|...+++.++..|.
T Consensus        31 ~~~~~Y~~A~~~~~~g~y~~Ai~~f~~l~~~y--P~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~  101 (243)
T PRK10866         31 PPSEIYATAQQKLQDGNWKQAITQLEALDNRY--PFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPT  101 (243)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcC
Confidence            33334344555566788888888888887752  322 221   33446667788888888888888887765

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=96.90  E-value=0.049  Score=46.54  Aligned_cols=96  Identities=10%  Similarity=0.053  Sum_probs=45.1

Q ss_pred             CCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCC-ChhHHHHHHHHhHhcCChHHHHHHHhccCC-----CChhhHHHH
Q 040394          144 HDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGP-DSFVLTGLVDMYAKCRDIGSSRQVFDETLD-----KNVVSWTSM  217 (691)
Q Consensus       144 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~~~~~~~l  217 (691)
                      |++..-..+..++...|+..+|...|++...--+. |....-.+.++....+++..|...++++.+     +.+.+.-.+
T Consensus        87 pTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~Ll~  166 (251)
T COG4700          87 PTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGHLLF  166 (251)
T ss_pred             hhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCchHHH
Confidence            33333344444444555555555555544432222 444444455555555555555555544422     122333344


Q ss_pred             HHHHHhCCChhHHHHHHHHHHh
Q 040394          218 IAGYVQNDCAQEGLVLFNRMRE  239 (691)
Q Consensus       218 i~~~~~~g~~~~A~~~~~~m~~  239 (691)
                      .+.+...|++.+|..-|+....
T Consensus       167 aR~laa~g~~a~Aesafe~a~~  188 (251)
T COG4700         167 ARTLAAQGKYADAESAFEVAIS  188 (251)
T ss_pred             HHHHHhcCCchhHHHHHHHHHH
Confidence            4555555555555555555544

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=96.87  E-value=0.15  Score=52.29  Aligned_cols=41  Identities=12%  Similarity=0.109  Sum_probs=28.2

Q ss_pred             chhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHH
Q 040394          328 PDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHS  371 (691)
Q Consensus       328 ~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~  371 (691)
                      +-+.+.-+++|+++|-.|+....   ...|+-.|++.+|.++|.
T Consensus       616 ~L~li~EL~~~k~rge~P~~iLl---A~~~Ay~gKF~EAAklFk  656 (1081)
T KOG1538|consen  616 YLELISELEERKKRGETPNDLLL---ADVFAYQGKFHEAAKLFK  656 (1081)
T ss_pred             HHHHHHHHHHHHhcCCCchHHHH---HHHHHhhhhHHHHHHHHH
Confidence            44556667888999988988644   334566777777766654

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.85  E-value=0.075  Score=48.18  Aligned_cols=129  Identities=16%  Similarity=0.129  Sum_probs=91.7

Q ss_pred             hHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCC------ChhHHHHH
Q 040394          113 SFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGP------DSFVLTGL  186 (691)
Q Consensus       113 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~------~~~~~~~l  186 (691)
                      .-+.+++.+...+.+.-..+++++.++...+.++.....+.+.-.+.||.+.|...|++..+....      ...+....
T Consensus       179 Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~  258 (366)
T KOG2796|consen  179 VMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNS  258 (366)
T ss_pred             HHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhh
Confidence            456677777778888888888888888766667777777888888888998888888877654321      33333444


Q ss_pred             HHHhHhcCChHHHHHHHhccCCC---ChhhHHHHHHHHHhCCChhHHHHHHHHHHhCC
Q 040394          187 VDMYAKCRDIGSSRQVFDETLDK---NVVSWTSMIAGYVQNDCAQEGLVLFNRMREGF  241 (691)
Q Consensus       187 ~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~  241 (691)
                      ...|.-.+++.+|...+++++..   |+..-|.-.-+..-.|+..+|++.++.|++..
T Consensus       259 a~i~lg~nn~a~a~r~~~~i~~~D~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~~  316 (366)
T KOG2796|consen  259 AFLHLGQNNFAEAHRFFTEILRMDPRNAVANNNKALCLLYLGKLKDALKQLEAMVQQD  316 (366)
T ss_pred             hhheecccchHHHHHHHhhccccCCCchhhhchHHHHHHHHHHHHHHHHHHHHHhccC
Confidence            45566678888888888877653   44455554445555788888888888887743

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.83  E-value=0.41  Score=50.97  Aligned_cols=175  Identities=13%  Similarity=0.080  Sum_probs=116.3

Q ss_pred             hhhHHHHHHhcCCChHHHHHHhccCCCCCcchHHHHH----HHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHc
Q 040394           82 CNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMI----RWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACC  157 (691)
Q Consensus        82 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~ll----~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~  157 (691)
                      ....-+.++.+...++.|..+-..-.. +...-..+.    +-+.+.|++++|...|-+-+.. +.|     ..+++-|.
T Consensus       336 ~le~kL~iL~kK~ly~~Ai~LAk~~~~-d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~-le~-----s~Vi~kfL  408 (933)
T KOG2114|consen  336 DLETKLDILFKKNLYKVAINLAKSQHL-DEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGF-LEP-----SEVIKKFL  408 (933)
T ss_pred             cHHHHHHHHHHhhhHHHHHHHHHhcCC-CHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHccc-CCh-----HHHHHHhc
Confidence            345567888888888888888765433 222223333    3346789999999988777654 233     34567777


Q ss_pred             ccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCCChh--hHHHHHHHHHhCCChhHHHHHHH
Q 040394          158 ELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVV--SWTSMIAGYVQNDCAQEGLVLFN  235 (691)
Q Consensus       158 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~--~~~~li~~~~~~g~~~~A~~~~~  235 (691)
                      ...++..-...++.+.+.|..+..--..|+.+|.+.++.+.-.+..+.... ...  -....+..+.+.+-.++|..+-.
T Consensus       409 daq~IknLt~YLe~L~~~gla~~dhttlLLncYiKlkd~~kL~efI~~~~~-g~~~fd~e~al~Ilr~snyl~~a~~LA~  487 (933)
T KOG2114|consen  409 DAQRIKNLTSYLEALHKKGLANSDHTTLLLNCYIKLKDVEKLTEFISKCDK-GEWFFDVETALEILRKSNYLDEAELLAT  487 (933)
T ss_pred             CHHHHHHHHHHHHHHHHcccccchhHHHHHHHHHHhcchHHHHHHHhcCCC-cceeeeHHHHHHHHHHhChHHHHHHHHH
Confidence            777888888889999999988888888999999999999998888877652 222  23455566666666666665555


Q ss_pred             HHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHH
Q 040394          236 RMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYI  272 (691)
Q Consensus       236 ~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~  272 (691)
                      ....     +......++   -..+++++|.++++.+
T Consensus       488 k~~~-----he~vl~ill---e~~~ny~eAl~yi~sl  516 (933)
T KOG2114|consen  488 KFKK-----HEWVLDILL---EDLHNYEEALRYISSL  516 (933)
T ss_pred             Hhcc-----CHHHHHHHH---HHhcCHHHHHHHHhcC
Confidence            4432     222223232   3456677777666554

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=96.83  E-value=0.032  Score=52.72  Aligned_cols=103  Identities=6%  Similarity=0.037  Sum_probs=74.2

Q ss_pred             HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCC----HHHHHHH
Q 040394          533 VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEPD----VSLFGAF  606 (691)
Q Consensus       533 ~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~----~~~~~~l  606 (691)
                      ..|...+....+.|++++|...|+.+.+.+.-.+- ...+-.+...|...|++++|...|+.+ ...|+    ...+..+
T Consensus       144 ~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~kl  223 (263)
T PRK10803        144 TDYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKV  223 (263)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHH
Confidence            34555554445668888888888888655322111 246667888889999999999988888 22232    3455566


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCch
Q 040394          607 LHGCGLYSRFDLGEVMIKKMLELHPDKAC  635 (691)
Q Consensus       607 ~~~~~~~g~~~~A~~~~~~~~~~~p~~~~  635 (691)
                      ...+...|+.++|...++++++..|++..
T Consensus       224 g~~~~~~g~~~~A~~~~~~vi~~yP~s~~  252 (263)
T PRK10803        224 GVIMQDKGDTAKAKAVYQQVIKKYPGTDG  252 (263)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHCcCCHH
Confidence            77788899999999999999999999653

>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=96.80  E-value=0.0024  Score=47.72  Aligned_cols=62  Identities=13%  Similarity=0.103  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhc----CCC---CchhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          601 SLFGAFLHGCGLYSRFDLGEVMIKKMLEL----HPD---KACYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       601 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~p~---~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      .+++.+...|...|++++|+..+++++++    .++   ...++..++.+|...|++++|.+.+++..+
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~   74 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALD   74 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            46677777888888888888888888762    222   245677888888888888888888887654

...

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.76  E-value=0.006  Score=44.84  Aligned_cols=65  Identities=25%  Similarity=0.304  Sum_probs=52.8

Q ss_pred             HHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHH
Q 040394          576 DLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLV  640 (691)
Q Consensus       576 ~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l  640 (691)
                      ..|.+.+++++|++.++.+ ...| +...|......+.+.|++++|...++++++..|+++......
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~p~~~~~~~~~   69 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELDPDDPELWLQRARCLFQLGRYEEALEDLERALELSPDDPDARALR   69 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhccHHHHHHHHHHHHHHCCCcHHHHHHH
Confidence            5678889999999999988 4444 456777788889999999999999999999999876655443

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

Probab=96.76  E-value=0.84  Score=47.01  Aligned_cols=414  Identities=10%  Similarity=0.073  Sum_probs=222.9

Q ss_pred             hHHHHHHHHHccCChhhHHHHHHHHHHHCCCCc-hHHHHHHHHHHHhcCCHHHHHHHHHhcC---CCChhHHHHHHHHHH
Q 040394          248 TLGSLVTACAKLRALHQGKWLHGYILKIGIEIN-SHLVTALLDMYVKCGNIRDARSVFDELC---SIDLVSWTAMIVGYT  323 (691)
Q Consensus       248 t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~~~---~~~~~~~~~li~~~~  323 (691)
                      .+..+|.---...+.+.+...+..++..  -|. ..-|......=.+.|..+.+.++|++..   ..++..|.....-+.
T Consensus        47 ~wt~li~~~~~~~~~~~~r~~y~~fL~k--yPl~~gyW~kfA~~E~klg~~~~s~~Vfergv~aip~SvdlW~~Y~~f~~  124 (577)
T KOG1258|consen   47 AWTTLIQENDSIEDVDALREVYDIFLSK--YPLCYGYWKKFADYEYKLGNAENSVKVFERGVQAIPLSVDLWLSYLAFLK  124 (577)
T ss_pred             chHHHHhccCchhHHHHHHHHHHHHHhh--CccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHh
Confidence            3444444433344455555666666543  233 2345566666667788888888888762   235555655554333


Q ss_pred             -hcCCchhHHHHHHHhhHC-CCCC-cHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCC-chhHHHHHHHHhHh-----c
Q 040394          324 -QSGYPDKALKLFTDKKWA-DFFP-NHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLE-DYTVINALVDMYAK-----C  394 (691)
Q Consensus       324 -~~g~~~~a~~~~~~m~~~-g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~-----~  394 (691)
                       ..|+.+...+.|+..+.. |..- ...-|...|.--..+++......+++..++.... -...|.......-.     .
T Consensus       125 n~~~d~~~lr~~fe~A~~~vG~dF~S~~lWdkyie~en~qks~k~v~~iyeRileiP~~~~~~~f~~f~~~l~~~~~~~l  204 (577)
T KOG1258|consen  125 NNNGDPETLRDLFERAKSYVGLDFLSDPLWDKYIEFENGQKSWKRVANIYERILEIPLHQLNRHFDRFKQLLNQNEEKIL  204 (577)
T ss_pred             ccCCCHHHHHHHHHHHHHhcccchhccHHHHHHHHHHhccccHHHHHHHHHHHHhhhhhHhHHHHHHHHHHHhcCChhhh
Confidence             345666666666665543 3222 2344555666556667777777777777665544 22223322222222     1


Q ss_pred             CChHHHHHHHHhCCCC--------CchhHHHHHHhhhCCCCCCHHH--HHHHHHHHh-------ccCcHHHHHHHHHHHH
Q 040394          395 HVIADARYIFETTSEK--------DVIAWNSIISGLDDNVSPDAVT--LVSVISACA-------SLGAVQVGSSLHAYST  457 (691)
Q Consensus       395 g~~~~a~~~~~~~~~~--------~~~~~~~li~~~~~~~~p~~~~--~~~ll~~~~-------~~~~~~~a~~~~~~~~  457 (691)
                      -..+++.++-.....+        ....+..-+...  +-+.+..+  .+.+-..+.       ...........++.-+
T Consensus       205 ~~~d~~~~l~~~~~~~~~~~~~~~~~e~~~~~v~~~--~~~s~~l~~~~~~l~~~~~~~~~~~~~s~~~~~kr~~fE~~I  282 (577)
T KOG1258|consen  205 LSIDELIQLRSDVAERSKITHSQEPLEELEIGVKDS--TDPSKSLTEEKTILKRIVSIHEKVYQKSEEEEEKRWGFEEGI  282 (577)
T ss_pred             cCHHHHHHHhhhHHhhhhcccccChhHHHHHHHhhc--cCccchhhHHHHHHHHHHHHHHHHHHhhHhHHHHHHhhhhhc
Confidence            2223332222221110        000011100000  00111111  111111111       1111111222222222


Q ss_pred             HcC------CCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC---CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCC
Q 040394          458 KQG------LLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK---NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEV  528 (691)
Q Consensus       458 ~~~------~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~  528 (691)
                      +.-      ..+.....|...+..-.+.|+.+.+.-+|+....|   -...|--.+.-....|+.+-|..++....+-..
T Consensus       283 krpYfhvkpl~~aql~nw~~yLdf~i~~g~~~~~~~l~ercli~cA~Y~efWiky~~~m~~~~~~~~~~~~~~~~~~i~~  362 (577)
T KOG1258|consen  283 KRPYFHVKPLDQAQLKNWRYYLDFEITLGDFSRVFILFERCLIPCALYDEFWIKYARWMESSGDVSLANNVLARACKIHV  362 (577)
T ss_pred             cccccccCcccHHHHHHHHHHhhhhhhcccHHHHHHHHHHHHhHHhhhHHHHHHHHHHHHHcCchhHHHHHHHhhhhhcC
Confidence            211      11334567778888888999999999999998865   234555555555556898888888877666433


Q ss_pred             C--CCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHH---HHHHhC-CCCCCHH
Q 040394          529 Q--PNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEAL---EFMENM-PIEPDVS  601 (691)
Q Consensus       529 ~--p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~---~~~~~~-~~~p~~~  601 (691)
                      +  |....+.+.  -+-..|+.+.|..+++.+..+  + |+ ...-..-+....+.|+.+.+.   +++... ..+.+..
T Consensus       363 k~~~~i~L~~a~--f~e~~~n~~~A~~~lq~i~~e--~-pg~v~~~l~~~~~e~r~~~~~~~~~~~~l~s~~~~~~~~~~  437 (577)
T KOG1258|consen  363 KKTPIIHLLEAR--FEESNGNFDDAKVILQRIESE--Y-PGLVEVVLRKINWERRKGNLEDANYKNELYSSIYEGKENNG  437 (577)
T ss_pred             CCCcHHHHHHHH--HHHhhccHHHHHHHHHHHHhh--C-CchhhhHHHHHhHHHHhcchhhhhHHHHHHHHhcccccCcc
Confidence            3  333333332  344578999999999999655  3 66 333334456677889998888   555554 3333333


Q ss_pred             HHHHHHHH-----HHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHH---HHHHHHHHHhCCCccCCC
Q 040394          602 LFGAFLHG-----CGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIR---VNQVRELMKQRGLSKSPG  670 (691)
Q Consensus       602 ~~~~l~~~-----~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~---A~~~~~~~~~~g~~~~~~  670 (691)
                      +...+.--     +...++.+.|..++.++.+..|++...|..+......++...+   -.-+...+....+.++.+
T Consensus       438 i~~~l~~~~~r~~~~i~~d~~~a~~~l~~~~~~~~~~k~~~~~~~~~~~~~~~~~e~d~~e~~~~~~~~~~~~~~~~  514 (577)
T KOG1258|consen  438 ILEKLYVKFARLRYKIREDADLARIILLEANDILPDCKVLYLELIRFELIQPSGREYDLLEPIDWKELKMLIDFDDS  514 (577)
T ss_pred             hhHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhcCCccHHHHHHHHHHHHhCCcchhhhhhhhHHHHHHhhhcccccc
Confidence            33333322     3356899999999999999999999999888888776663322   233344444444444333

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=96.55  E-value=1.3  Score=46.35  Aligned_cols=152  Identities=11%  Similarity=0.033  Sum_probs=82.6

Q ss_pred             cCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCC-----ChhHHHHHHHHHHhcCCchhHHH
Q 040394          259 LRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSI-----DLVSWTAMIVGYTQSGYPDKALK  333 (691)
Q Consensus       259 ~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~-----~~~~~~~li~~~~~~g~~~~a~~  333 (691)
                      -|++++|++++-+|-++.         .-|..+.+.|++-...++++.-...     -..+|+.+...+.....+++|.+
T Consensus       747 ~g~feeaek~yld~drrD---------LAielr~klgDwfrV~qL~r~g~~d~dD~~~e~A~r~ig~~fa~~~~We~A~~  817 (1189)
T KOG2041|consen  747 YGEFEEAEKLYLDADRRD---------LAIELRKKLGDWFRVYQLIRNGGSDDDDEGKEDAFRNIGETFAEMMEWEEAAK  817 (1189)
T ss_pred             hcchhHhhhhhhccchhh---------hhHHHHHhhhhHHHHHHHHHccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            466677776666554432         2345566667776666666554221     12366777777777777777777


Q ss_pred             HHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCch
Q 040394          334 LFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVI  413 (691)
Q Consensus       334 ~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  413 (691)
                      .|..-..      .   ...+.++.....+++-+.    ....-+++....-.+.+++.+.|.-++|.+.|-+...+   
T Consensus       818 yY~~~~~------~---e~~~ecly~le~f~~LE~----la~~Lpe~s~llp~~a~mf~svGMC~qAV~a~Lr~s~p---  881 (1189)
T KOG2041|consen  818 YYSYCGD------T---ENQIECLYRLELFGELEV----LARTLPEDSELLPVMADMFTSVGMCDQAVEAYLRRSLP---  881 (1189)
T ss_pred             HHHhccc------h---HhHHHHHHHHHhhhhHHH----HHHhcCcccchHHHHHHHHHhhchHHHHHHHHHhccCc---
Confidence            6654211      1   112233333333332222    12222336666677777888888888877766554322   


Q ss_pred             hHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHH
Q 040394          414 AWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAY  455 (691)
Q Consensus       414 ~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~  455 (691)
                                          ...+..|...+++.+|.++-+.
T Consensus       882 --------------------kaAv~tCv~LnQW~~avelaq~  903 (1189)
T KOG2041|consen  882 --------------------KAAVHTCVELNQWGEAVELAQR  903 (1189)
T ss_pred             --------------------HHHHHHHHHHHHHHHHHHHHHh
Confidence                                2334566666666666665543

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=96.54  E-value=0.027  Score=52.56  Aligned_cols=97  Identities=11%  Similarity=0.133  Sum_probs=51.4

Q ss_pred             CCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcC---ChHHHHHHHhccCC--C-ChhhHHHH
Q 040394          144 HDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCR---DIGSSRQVFDETLD--K-NVVSWTSM  217 (691)
Q Consensus       144 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~~--~-~~~~~~~l  217 (691)
                      -|...|-.|-..|...|+.+.|..-|....+..++++..+..+..++....   +..++..+|++...  | |+.+-..|
T Consensus       154 ~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D~~~iral~lL  233 (287)
T COG4235         154 GDAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALLRQALALDPANIRALSLL  233 (287)
T ss_pred             CCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcCCccHHHHHHH
Confidence            344555555555555555555555555555555555555555555444332   23445555555432  2 34444445


Q ss_pred             HHHHHhCCChhHHHHHHHHHHhC
Q 040394          218 IAGYVQNDCAQEGLVLFNRMREG  240 (691)
Q Consensus       218 i~~~~~~g~~~~A~~~~~~m~~~  240 (691)
                      ...+...|++.+|...|+.|.+.
T Consensus       234 A~~afe~g~~~~A~~~Wq~lL~~  256 (287)
T COG4235         234 AFAAFEQGDYAEAAAAWQMLLDL  256 (287)
T ss_pred             HHHHHHcccHHHHHHHHHHHHhc
Confidence            55555666666666666666553

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=96.52  E-value=0.2  Score=40.24  Aligned_cols=140  Identities=12%  Similarity=0.108  Sum_probs=84.8

Q ss_pred             hcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHH
Q 040394          508 GMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEA  587 (691)
Q Consensus       508 ~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A  587 (691)
                      .-.|..++..+++.+....   .+..-+|.+|--....-+-+-..++++.+    |--.|.          ..+|+....
T Consensus        13 ildG~V~qGveii~k~v~S---sni~E~NWvICNiiDaa~C~yvv~~LdsI----GkiFDi----------s~C~NlKrV   75 (161)
T PF09205_consen   13 ILDGDVKQGVEIIEKTVNS---SNIKEYNWVICNIIDAADCDYVVETLDSI----GKIFDI----------SKCGNLKRV   75 (161)
T ss_dssp             HHTT-HHHHHHHHHHHHHH---S-HHHHTHHHHHHHHH--HHHHHHHHHHH----GGGS-G----------GG-S-THHH
T ss_pred             HHhchHHHHHHHHHHHcCc---CCccccceeeeecchhhchhHHHHHHHHH----hhhcCc----------hhhcchHHH
Confidence            3467777888888777752   34444555544333333334444555544    333332          235566666


Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCc
Q 040394          588 LEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLS  666 (691)
Q Consensus       588 ~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~  666 (691)
                      ...+-.++  .+....+..+..+..+|+-++-.+++..+.+.+..+|.....++.+|.+.|+..++.+++++.-+.|++
T Consensus        76 i~C~~~~n--~~se~vD~ALd~lv~~~kkDqLdki~~~l~kn~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~k  152 (161)
T PF09205_consen   76 IECYAKRN--KLSEYVDLALDILVKQGKKDQLDKIYNELKKNEEINPEFLVKIANAYKKLGNTREANELLKEACEKGLK  152 (161)
T ss_dssp             HHHHHHTT-----HHHHHHHHHHHHTT-HHHHHHHHHHH-----S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             HHHHHHhc--chHHHHHHHHHHHHHhccHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhchH
Confidence            66655554  234455667788889999999999999988655555899999999999999999999999999999985

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.47  E-value=0.021  Score=52.60  Aligned_cols=83  Identities=8%  Similarity=0.091  Sum_probs=53.4

Q ss_pred             HhcCChHHHHHHHHhC-------CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC---chhHHHHHHHHHhCC
Q 040394          579 ARAGRLEEALEFMENM-------PIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK---ACYYVLVSNLYASDG  648 (691)
Q Consensus       579 ~~~g~~~~A~~~~~~~-------~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~---~~~~~~l~~~~~~~g  648 (691)
                      .+.|++.+|...|...       ...||..-|  |..++...|+++.|...|..+.+-.|++   |..+..|+.+..+.|
T Consensus       152 ~ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yW--LGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg~~~~~l~  229 (262)
T COG1729         152 YKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYW--LGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLGVSLGRLG  229 (262)
T ss_pred             HHcCCHHHHHHHHHHHHHcCCCCcccchhHHH--HHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHhc
Confidence            3455566666666555       133444444  6677777777777777777777755544   355667777777777


Q ss_pred             CcHHHHHHHHHHHhC
Q 040394          649 RWIRVNQVRELMKQR  663 (691)
Q Consensus       649 ~~~~A~~~~~~~~~~  663 (691)
                      +.++|..+|+++.++
T Consensus       230 ~~d~A~atl~qv~k~  244 (262)
T COG1729         230 NTDEACATLQQVIKR  244 (262)
T ss_pred             CHHHHHHHHHHHHHH
Confidence            777777777777654

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=96.44  E-value=0.073  Score=44.03  Aligned_cols=89  Identities=13%  Similarity=0.115  Sum_probs=63.3

Q ss_pred             HHHHHhcCChHHHHHHHHhC--CCC---CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCch---hHHHHHHHHHh
Q 040394          575 VDLLARAGRLEEALEFMENM--PIE---PDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKAC---YYVLVSNLYAS  646 (691)
Q Consensus       575 i~~~~~~g~~~~A~~~~~~~--~~~---p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~---~~~~l~~~~~~  646 (691)
                      .....+.|++++|.+.|+.+  ..+   -....-..|+.++.+.+++++|...+++.++++|.++.   .++..+.++.+
T Consensus        17 a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y~~gL~~~~   96 (142)
T PF13512_consen   17 AQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYYMRGLSYYE   96 (142)
T ss_pred             HHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHHHHHHHHHHH
Confidence            34456788899998888888  111   23346667888999999999999999999999988763   45555555555


Q ss_pred             CCC---------------cHHHHHHHHHHHhC
Q 040394          647 DGR---------------WIRVNQVRELMKQR  663 (691)
Q Consensus       647 ~g~---------------~~~A~~~~~~~~~~  663 (691)
                      +..               ..+|...|+.+++.
T Consensus        97 ~~~~~~~~~~~~drD~~~~~~A~~~f~~lv~~  128 (142)
T PF13512_consen   97 QDEGSLQSFFRSDRDPTPARQAFRDFEQLVRR  128 (142)
T ss_pred             HhhhHHhhhcccccCcHHHHHHHHHHHHHHHH
Confidence            544               55666666666653

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=96.34  E-value=0.38  Score=43.84  Aligned_cols=64  Identities=9%  Similarity=0.039  Sum_probs=39.3

Q ss_pred             HHHHHHHHhCCChhHHHHHHHHHHHcCCC--CCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCC
Q 040394          115 QVMIRWYFLNDLYKDIVEFYKCMRKRLKE--HDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGP  178 (691)
Q Consensus       115 ~~ll~~~~~~~~~~~a~~~~~~m~~~~~~--~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  178 (691)
                      -.....+...|++.+|+..|+.+...-..  -.....-.+..++-+.|+.+.|...++.+++..|.
T Consensus         9 Y~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~   74 (203)
T PF13525_consen    9 YQKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPN   74 (203)
T ss_dssp             HHHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC
Confidence            33444556778888888888887765211  11234455566777778888888888887776655

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=96.33  E-value=1.1  Score=43.38  Aligned_cols=113  Identities=13%  Similarity=0.051  Sum_probs=74.2

Q ss_pred             cCCHHHHHHHHHhc---CCCChhHHHHHHHH--HHhcCCchhHHHHHHHhhHCCCCCcHHH--HHHHHHHHhcCCChhhH
Q 040394          294 CGNIRDARSVFDEL---CSIDLVSWTAMIVG--YTQSGYPDKALKLFTDKKWADFFPNHVT--IASVLSASAQLGNLNMG  366 (691)
Q Consensus       294 ~g~~~~A~~~~~~~---~~~~~~~~~~li~~--~~~~g~~~~a~~~~~~m~~~g~~p~~~t--~~~ll~~~~~~~~~~~a  366 (691)
                      .|+-..|.+.-.+-   ...|....-.++.+  -.-.|+++.|.+-|+.|...   |....  ...|.-...+.|+.+.|
T Consensus        97 AGda~lARkmt~~~~~llssDqepLIhlLeAQaal~eG~~~~Ar~kfeAMl~d---PEtRllGLRgLyleAqr~GareaA  173 (531)
T COG3898          97 AGDASLARKMTARASKLLSSDQEPLIHLLEAQAALLEGDYEDARKKFEAMLDD---PETRLLGLRGLYLEAQRLGAREAA  173 (531)
T ss_pred             cCchHHHHHHHHHHHhhhhccchHHHHHHHHHHHHhcCchHHHHHHHHHHhcC---hHHHHHhHHHHHHHHHhcccHHHH
Confidence            45556665555443   23344444444432  34468888888888888752   22221  22223334467888888


Q ss_pred             HHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCC
Q 040394          367 RMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSE  409 (691)
Q Consensus       367 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  409 (691)
                      .++-+.....-+.-.......+...+..|+++.|+++.+.-..
T Consensus       174 r~yAe~Aa~~Ap~l~WA~~AtLe~r~~~gdWd~AlkLvd~~~~  216 (531)
T COG3898         174 RHYAERAAEKAPQLPWAARATLEARCAAGDWDGALKLVDAQRA  216 (531)
T ss_pred             HHHHHHHHhhccCCchHHHHHHHHHHhcCChHHHHHHHHHHHH
Confidence            8888888887777777788889999999999999999886554

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.29  E-value=1.9  Score=45.61  Aligned_cols=111  Identities=13%  Similarity=0.087  Sum_probs=76.7

Q ss_pred             CCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHHHHHH
Q 040394          530 PNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHG  609 (691)
Q Consensus       530 p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~  609 (691)
                      -...+.+--+.-+...|+..+|.++-.+.     --||...|..-+.+++..+++++-+++-+++..   +.-|.-++.+
T Consensus       682 f~dlSl~dTv~~li~~g~~k~a~ql~~~F-----kipdKr~~wLk~~aLa~~~kweeLekfAkskks---PIGy~PFVe~  753 (829)
T KOG2280|consen  682 FVDLSLHDTVTTLILIGQNKRAEQLKSDF-----KIPDKRLWWLKLTALADIKKWEELEKFAKSKKS---PIGYLPFVEA  753 (829)
T ss_pred             cccCcHHHHHHHHHHccchHHHHHHHHhc-----CCcchhhHHHHHHHHHhhhhHHHHHHHHhccCC---CCCchhHHHH
Confidence            33344555556666778888888877665     247777888888888888888887777776642   3456667788


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHH
Q 040394          610 CGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQV  656 (691)
Q Consensus       610 ~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~  656 (691)
                      |.+.|+.++|..++-+.-.+.        -...+|.+.|++.+|.+.
T Consensus       754 c~~~~n~~EA~KYiprv~~l~--------ekv~ay~~~~~~~eAad~  792 (829)
T KOG2280|consen  754 CLKQGNKDEAKKYIPRVGGLQ--------EKVKAYLRVGDVKEAADL  792 (829)
T ss_pred             HHhcccHHHHhhhhhccCChH--------HHHHHHHHhccHHHHHHH
Confidence            888888888887776532221        345677788888887655

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=96.26  E-value=0.027  Score=54.28  Aligned_cols=129  Identities=13%  Similarity=0.008  Sum_probs=87.4

Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhccc---------CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHC----C-CCCC
Q 040394          466 VYVGTALLNFYAKCGDAQSARMVFDAMRE---------KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNE----E-VQPN  531 (691)
Q Consensus       466 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---------~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~----g-~~p~  531 (691)
                      ...|..|.+.|.-.|+++.|+..-+.-..         .....+..+..++.-.|+++.|.+.|+.-...    | -...
T Consensus       195 GRa~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~tl~LAielg~r~vE  274 (639)
T KOG1130|consen  195 GRAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLTLNLAIELGNRTVE  274 (639)
T ss_pred             cchhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHHHHHHHHhcchhHH
Confidence            45667777788888999998876654221         13346778888899999999999888775432    2 1223


Q ss_pred             HHHHHHHHHHhcccCCHHHHHHHHHHchh---hcC-CCCChhHHHHHHHHHHhcCChHHHHHHHHhC
Q 040394          532 EVIFTTILSACSHTGMVGEGWKCFYSMCR---DFK-FVPSMKHYVCMVDLLARAGRLEEALEFMENM  594 (691)
Q Consensus       532 ~~~~~~ll~~~~~~g~~~~A~~~~~~m~~---~~~-~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~  594 (691)
                      ..+..++-..|.-..+++.|+.++.+-..   +.+ ..-....+.+|..+|...|..++|+.+.+..
T Consensus       275 AQscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~alg~h~kAl~fae~h  341 (639)
T KOG1130|consen  275 AQSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNALGEHRKALYFAELH  341 (639)
T ss_pred             HHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence            34555666677777788888888764321   111 1122567888899999999999988776554

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=96.25  E-value=0.044  Score=53.24  Aligned_cols=137  Identities=11%  Similarity=-0.029  Sum_probs=96.4

Q ss_pred             HHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCC
Q 040394          504 IGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGR  583 (691)
Q Consensus       504 i~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~  583 (691)
                      ...|.+.|++..|..-|++....  -.           +...-+.++......         .-...+..|.-+|.+.++
T Consensus       215 Gn~~fK~gk~~~A~~~Yerav~~--l~-----------~~~~~~~ee~~~~~~---------~k~~~~lNlA~c~lKl~~  272 (397)
T KOG0543|consen  215 GNVLFKEGKFKLAKKRYERAVSF--LE-----------YRRSFDEEEQKKAEA---------LKLACHLNLAACYLKLKE  272 (397)
T ss_pred             hhHHHhhchHHHHHHHHHHHHHH--hh-----------ccccCCHHHHHHHHH---------HHHHHhhHHHHHHHhhhh
Confidence            45677777888887777776541  00           011111122111111         112356677788889999


Q ss_pred             hHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHH-HHHHHHH
Q 040394          584 LEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRV-NQVRELM  660 (691)
Q Consensus       584 ~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A-~~~~~~~  660 (691)
                      +.+|++...+. . .++|....-.=..+|...|+++.|+..|++++++.|+|..+..-|+.+-.+...+.+. .++|..|
T Consensus       273 ~~~Ai~~c~kvLe~~~~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~~P~Nka~~~el~~l~~k~~~~~~kekk~y~~m  352 (397)
T KOG0543|consen  273 YKEAIESCNKVLELDPNNVKALYRRGQALLALGEYDLARDDFQKALKLEPSNKAARAELIKLKQKIREYEEKEKKMYANM  352 (397)
T ss_pred             HHHHHHHHHHHHhcCCCchhHHHHHHHHHHhhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999888887 3 3456667777788999999999999999999999999999988888877776666555 7888888


Q ss_pred             Hh
Q 040394          661 KQ  662 (691)
Q Consensus       661 ~~  662 (691)
                      ..
T Consensus       353 F~  354 (397)
T KOG0543|consen  353 FA  354 (397)
T ss_pred             hh
Confidence            75

>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=96.22  E-value=0.0053  Score=45.85  Aligned_cols=61  Identities=18%  Similarity=0.297  Sum_probs=41.4

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhC-------C-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 040394          569 KHYVCMVDLLARAGRLEEALEFMENM-------P-IEPD-VSLFGAFLHGCGLYSRFDLGEVMIKKMLEL  629 (691)
Q Consensus       569 ~~~~~li~~~~~~g~~~~A~~~~~~~-------~-~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  629 (691)
                      .+++.+...|.+.|++++|++.+++.       + ..|+ ..++..+...+...|++++|++.+++++++
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~i   75 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALDI   75 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            35666666777777777776666665       1 1122 346777888888888888888888887753

...

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.22  E-value=0.7  Score=41.75  Aligned_cols=200  Identities=11%  Similarity=0.069  Sum_probs=119.5

Q ss_pred             HHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCC--HhHHHHHHHHHhc
Q 040394          432 TLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKN--TVTWSAMIGGYGM  509 (691)
Q Consensus       432 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~li~~~~~  509 (691)
                      .|.....+|....+++.|...+.+..+.-  ..+...|.       ....++.|..+.+++.+-+  +..|+--...|..
T Consensus        33 ~yekAAvafRnAk~feKakdcLlkA~~~y--Ennrslfh-------AAKayEqaamLake~~klsEvvdl~eKAs~lY~E  103 (308)
T KOG1585|consen   33 LYEKAAVAFRNAKKFEKAKDCLLKASKGY--ENNRSLFH-------AAKAYEQAAMLAKELSKLSEVVDLYEKASELYVE  103 (308)
T ss_pred             HHHHHHHHHHhhccHHHHHHHHHHHHHHH--HhcccHHH-------HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence            45555667778888999888887776432  22222211       1233455556666665432  2355666778888


Q ss_pred             CCChHHHHHHHHHHHH--CCCCCCHH--HHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChH
Q 040394          510 QGDGGGSLALFSDMLN--EEVQPNEV--IFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLE  585 (691)
Q Consensus       510 ~~~~~~A~~~~~~m~~--~g~~p~~~--~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~  585 (691)
                      +|.++.|-..+++.-+  .++.|+..  .|.--+......++...|.+                .+......|.+..+++
T Consensus       104 ~GspdtAAmaleKAak~lenv~Pd~AlqlYqralavve~~dr~~ma~e----------------l~gk~sr~lVrl~kf~  167 (308)
T KOG1585|consen  104 CGSPDTAAMALEKAAKALENVKPDDALQLYQRALAVVEEDDRDQMAFE----------------LYGKCSRVLVRLEKFT  167 (308)
T ss_pred             hCCcchHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHhccchHHHHHH----------------HHHHhhhHhhhhHHhh
Confidence            8888887777766543  22445432  23222222223333333333                3344456677888888


Q ss_pred             HHHHHHHhCC-------CCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHh----cCCCCchhHHHHHHHHHhCCCcHHH
Q 040394          586 EALEFMENMP-------IEPDV-SLFGAFLHGCGLYSRFDLGEVMIKKMLE----LHPDKACYYVLVSNLYASDGRWIRV  653 (691)
Q Consensus       586 ~A~~~~~~~~-------~~p~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~----~~p~~~~~~~~l~~~~~~~g~~~~A  653 (691)
                      +|-..+.+-+       ..|+. ..+...+-.+....|+..|...++.-.+    ..|++..+...|...| ..|+.+++
T Consensus       168 Eaa~a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ay-d~gD~E~~  246 (308)
T KOG1585|consen  168 EAATAFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAY-DEGDIEEI  246 (308)
T ss_pred             HHHHHHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHh-ccCCHHHH
Confidence            8766655541       22333 3455666666777799999999988555    5677777888887664 67888888


Q ss_pred             HHHH
Q 040394          654 NQVR  657 (691)
Q Consensus       654 ~~~~  657 (691)
                      ..++
T Consensus       247 ~kvl  250 (308)
T KOG1585|consen  247 KKVL  250 (308)
T ss_pred             HHHH
Confidence            6664

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.20  E-value=0.43  Score=43.50  Aligned_cols=137  Identities=8%  Similarity=-0.059  Sum_probs=93.2

Q ss_pred             HHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHH-----H
Q 040394          499 TWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYV-----C  573 (691)
Q Consensus       499 ~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~-----~  573 (691)
                      .-+.++..+.-.|.+.-.+..+.+.++...+-++.....+.+.-.+.||.+.|..+|+...+.. -..|....+     .
T Consensus       179 Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~-~kL~~~q~~~~V~~n  257 (366)
T KOG2796|consen  179 VMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVT-QKLDGLQGKIMVLMN  257 (366)
T ss_pred             HHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHH-hhhhccchhHHHHhh
Confidence            3445666667778888888888888887656667777777778888999999999999774332 233333333     3


Q ss_pred             HHHHHHhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchh
Q 040394          574 MVDLLARAGRLEEALEFMENMP--IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACY  636 (691)
Q Consensus       574 li~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~  636 (691)
                      ....|.-++++.+|...+.+..  .+.|+...|.=.-+..-.|+...|.+.++.+.+..|.....
T Consensus       258 ~a~i~lg~nn~a~a~r~~~~i~~~D~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~~P~~~l~  322 (366)
T KOG2796|consen  258 SAFLHLGQNNFAEAHRFFTEILRMDPRNAVANNNKALCLLYLGKLKDALKQLEAMVQQDPRHYLH  322 (366)
T ss_pred             hhhheecccchHHHHHHHhhccccCCCchhhhchHHHHHHHHHHHHHHHHHHHHHhccCCccchh
Confidence            3345667788888888888872  22233333333333344678999999999999999884433

>PRK11906 transcriptional regulator; Provisional

Probab=96.17  E-value=0.093  Score=52.42  Aligned_cols=142  Identities=12%  Similarity=0.091  Sum_probs=75.1

Q ss_pred             ChHHHHHHHHHHHH-CCCCCCHH-HHHHHHHHhcc---------cCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHH
Q 040394          512 DGGGSLALFSDMLN-EEVQPNEV-IFTTILSACSH---------TGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLA  579 (691)
Q Consensus       512 ~~~~A~~~~~~m~~-~g~~p~~~-~~~~ll~~~~~---------~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~  579 (691)
                      ..+.|+.+|.+... ....|+.. .|..+..++..         ..+..+|.+..+..   ..+.|+ ......+..++.
T Consensus       273 ~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h~~~~~~g~~~~~~~~~~a~~~A~rA---veld~~Da~a~~~~g~~~~  349 (458)
T PRK11906        273 SIYRAMTIFDRLQNKSDIQTLKTECYCLLAECHMSLALHGKSELELAAQKALELLDYV---SDITTVDGKILAIMGLITG  349 (458)
T ss_pred             HHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHH---HhcCCCCHHHHHHHHHHHH
Confidence            34557777777772 22456543 34433333321         11223344444433   234444 445555555556


Q ss_pred             hcCChHHHHHHHHhC-CCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHH--HHHHHHHhCCCcHHHHH
Q 040394          580 RAGRLEEALEFMENM-PIEPDV-SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYV--LVSNLYASDGRWIRVNQ  655 (691)
Q Consensus       580 ~~g~~~~A~~~~~~~-~~~p~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~--~l~~~~~~~g~~~~A~~  655 (691)
                      -.++.+.|..+|++. ...||. .+|......+.-.|+.++|.+.++++++++|.....-.  .....|+..+ .++|++
T Consensus       350 ~~~~~~~a~~~f~rA~~L~Pn~A~~~~~~~~~~~~~G~~~~a~~~i~~alrLsP~~~~~~~~~~~~~~~~~~~-~~~~~~  428 (458)
T PRK11906        350 LSGQAKVSHILFEQAKIHSTDIASLYYYRALVHFHNEKIEEARICIDKSLQLEPRRRKAVVIKECVDMYVPNP-LKNNIK  428 (458)
T ss_pred             hhcchhhHHHHHHHHhhcCCccHHHHHHHHHHHHHcCCHHHHHHHHHHHhccCchhhHHHHHHHHHHHHcCCc-hhhhHH
Confidence            666677777777776 455543 35555555666677777777777777777776543322  2223444443 344554


Q ss_pred             HH
Q 040394          656 VR  657 (691)
Q Consensus       656 ~~  657 (691)
                      ++
T Consensus       429 ~~  430 (458)
T PRK11906        429 LY  430 (458)
T ss_pred             HH
Confidence            43

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

Probab=96.07  E-value=1.7  Score=43.02  Aligned_cols=125  Identities=18%  Similarity=0.223  Sum_probs=68.6

Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHhccc-----CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCH-HHHHHHHH
Q 040394          467 YVGTALLNFYAKCGDAQSARMVFDAMRE-----KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNE-VIFTTILS  540 (691)
Q Consensus       467 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~-~~~~~ll~  540 (691)
                      .++...++...+....+.|..+|-+..+     +++..+++++.-++. |+...|..+|+--...  -||. .-.+..+.
T Consensus       398 ~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~-~d~~ta~~ifelGl~~--f~d~~~y~~kyl~  474 (660)
T COG5107         398 FVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYAT-GDRATAYNIFELGLLK--FPDSTLYKEKYLL  474 (660)
T ss_pred             hHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhc-CCcchHHHHHHHHHHh--CCCchHHHHHHHH
Confidence            3444555555666666667777766553     355566666665553 4556666666654332  2333 33334455


Q ss_pred             HhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC
Q 040394          541 ACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM  594 (691)
Q Consensus       541 ~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~  594 (691)
                      -+...++-..|..+|+..+.+..-.--..+|..+|+--..-|+...|..+=++|
T Consensus       475 fLi~inde~naraLFetsv~r~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf  528 (660)
T COG5107         475 FLIRINDEENARALFETSVERLEKTQLKRIYDKMIEYESMVGSLNNVYSLEERF  528 (660)
T ss_pred             HHHHhCcHHHHHHHHHHhHHHHHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHH
Confidence            555666666677777644333211111455666666556666666665555555

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

Probab=95.97  E-value=2.4  Score=43.84  Aligned_cols=126  Identities=12%  Similarity=0.085  Sum_probs=59.0

Q ss_pred             chHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcc-hHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHh
Q 040394          112 YSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNF-VFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMY  190 (691)
Q Consensus       112 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~  190 (691)
                      ..|..++.---+....+.+..++..+...  -|... -|.....-=.+.|..+.+.++|++-+..-+-+...|...+..+
T Consensus        46 ~~wt~li~~~~~~~~~~~~r~~y~~fL~k--yPl~~gyW~kfA~~E~klg~~~~s~~Vfergv~aip~SvdlW~~Y~~f~  123 (577)
T KOG1258|consen   46 DAWTTLIQENDSIEDVDALREVYDIFLSK--YPLCYGYWKKFADYEYKLGNAENSVKVFERGVQAIPLSVDLWLSYLAFL  123 (577)
T ss_pred             cchHHHHhccCchhHHHHHHHHHHHHHhh--CccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence            34444444333333334445555555433  22222 1222222223455566666666655543222555555554444


Q ss_pred             Hh-cCChHHHHHHHhccCC------CChhhHHHHHHHHHhCCChhHHHHHHHHHHh
Q 040394          191 AK-CRDIGSSRQVFDETLD------KNVVSWTSMIAGYVQNDCAQEGLVLFNRMRE  239 (691)
Q Consensus       191 ~~-~g~~~~A~~~~~~~~~------~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  239 (691)
                      +. .|+.+...+.|+....      .....|...|.--..++++.....+|++.++
T Consensus       124 ~n~~~d~~~lr~~fe~A~~~vG~dF~S~~lWdkyie~en~qks~k~v~~iyeRile  179 (577)
T KOG1258|consen  124 KNNNGDPETLRDLFERAKSYVGLDFLSDPLWDKYIEFENGQKSWKRVANIYERILE  179 (577)
T ss_pred             hccCCCHHHHHHHHHHHHHhcccchhccHHHHHHHHHHhccccHHHHHHHHHHHHh
Confidence            43 2445555555554322      1334455555555556666666666666654

>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=95.93  E-value=0.038  Score=47.31  Aligned_cols=68  Identities=19%  Similarity=0.265  Sum_probs=52.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHh-----CCCccCC
Q 040394          602 LFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQ-----RGLSKSP  669 (691)
Q Consensus       602 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~g~~~~~  669 (691)
                      ....++..+...|++++|...+++++..+|-+...+..+..+|...|+..+|.++|+++.+     -|+.|+|
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~  136 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALDPYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSP  136 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----H
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCH
Confidence            4556677778899999999999999999999999999999999999999999999887743     4665554

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []

Probab=95.92  E-value=1.4  Score=42.54  Aligned_cols=156  Identities=10%  Similarity=0.129  Sum_probs=80.3

Q ss_pred             hcCCChHHHHHHhccCCC------CCc------chHHHHHHHHHhCCChhHHHHHHHHHHHc--------CCCCCc----
Q 040394           91 GSFGHVKYARSVFDSMPN------PDF------YSFQVMIRWYFLNDLYKDIVEFYKCMRKR--------LKEHDN----  146 (691)
Q Consensus        91 ~~~g~~~~A~~~~~~~~~------~~~------~~~~~ll~~~~~~~~~~~a~~~~~~m~~~--------~~~~~~----  146 (691)
                      .++|+++.|..++.+...      |+.      ..||.-...+.+..+++.|...+++..+.        ...|+.    
T Consensus         4 ~~~~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~yn~G~~l~~~~~~~~~a~~wL~~a~~~l~~~~~~~~~~~~~~elr   83 (278)
T PF08631_consen    4 WKQGDLDLAEHMYSKAKDLLNSLDPDMAEELARVCYNIGKSLLSKKDKYEEAVKWLQRAYDILEKPGKMDKLSPDGSELR   83 (278)
T ss_pred             hhhCCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhhhccccCCcHHHHH
Confidence            466777778777777643      211      12333333333333777777777665432        122222    


Q ss_pred             -chHHHHHHHHcccCChh---HHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCC---ChhhHHHHHH
Q 040394          147 -FVFSKVLKACCELRDID---EGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDK---NVVSWTSMIA  219 (691)
Q Consensus       147 -~~~~~ll~~~~~~~~~~---~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~li~  219 (691)
                       .++..++.++...+..+   +|..+++.+....+..+.++..-+..+.+.++.+++.+++.+|...   ....+..++.
T Consensus        84 ~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~~~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~~~~~e~~~~~~l~  163 (278)
T PF08631_consen   84 LSILRLLANAYLEWDTYESVEKALNALRLLESEYGNKPEVFLLKLEILLKSFDEEEYEEILMRMIRSVDHSESNFDSILH  163 (278)
T ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHhccCChhHHHHHHHHHHHhcccccchHHHHHH
Confidence             23444555555555433   3555555554444445666666666666677777777777766442   2233444443


Q ss_pred             HHH--hCCChhHHHHHHHHHHhCCCCCCh
Q 040394          220 GYV--QNDCAQEGLVLFNRMREGFVEGNQ  246 (691)
Q Consensus       220 ~~~--~~g~~~~A~~~~~~m~~~~~~p~~  246 (691)
                      .+.  .......+...+..+....+.|..
T Consensus       164 ~i~~l~~~~~~~a~~~ld~~l~~r~~~~~  192 (278)
T PF08631_consen  164 HIKQLAEKSPELAAFCLDYLLLNRFKSSE  192 (278)
T ss_pred             HHHHHHhhCcHHHHHHHHHHHHHHhCCCh
Confidence            331  122334555555555444444443

It is also involved in sporulation [].

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=95.91  E-value=1.5  Score=40.88  Aligned_cols=216  Identities=19%  Similarity=0.120  Sum_probs=141.0

Q ss_pred             CcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc-----CCHhHHHHHHHHHhcCCChHHHHH
Q 040394          444 GAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE-----KNTVTWSAMIGGYGMQGDGGGSLA  518 (691)
Q Consensus       444 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~~~~~~~li~~~~~~~~~~~A~~  518 (691)
                      +....+...+...............+......+...+.+..+...+.....     .....+......+...++...+..
T Consensus        37 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  116 (291)
T COG0457          37 GELAEALELLEEALELLPNSDLAGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEALE  116 (291)
T ss_pred             hhHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHHH
Confidence            344445555555554442001356666677777778888887777776542     244556666667777777888888


Q ss_pred             HHHHHHHCCCCCCHHHHHHHHH-HhcccCCHHHHHHHHHHchhhcCCCC----ChhHHHHHHHHHHhcCChHHHHHHHHh
Q 040394          519 LFSDMLNEEVQPNEVIFTTILS-ACSHTGMVGEGWKCFYSMCRDFKFVP----SMKHYVCMVDLLARAGRLEEALEFMEN  593 (691)
Q Consensus       519 ~~~~m~~~g~~p~~~~~~~ll~-~~~~~g~~~~A~~~~~~m~~~~~~~p----~~~~~~~li~~~~~~g~~~~A~~~~~~  593 (691)
                      .+.........+. ........ .+...|+++.|...+.....   ..|    ....+......+...++.++|...+.+
T Consensus       117 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~  192 (291)
T COG0457         117 LLEKALALDPDPD-LAEALLALGALYELGDYEEALELYEKALE---LDPELNELAEALLALGALLEALGRYEEALELLEK  192 (291)
T ss_pred             HHHHHHcCCCCcc-hHHHHHHHHHHHHcCCHHHHHHHHHHHHh---cCCCccchHHHHHHhhhHHHHhcCHHHHHHHHHH
Confidence            8888776433331 12222222 67778888888888887632   233    233344444446677888888888887


Q ss_pred             C-CCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          594 M-PIEPD--VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       594 ~-~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      . ...++  ...+..+...+...++++.|...+..+....|.....+..++..+...|+++++...+++..+.
T Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (291)
T COG0457         193 ALKLNPDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPDNAEALYNLALLLLELGRYEEALEALEKALEL  265 (291)
T ss_pred             HHhhCcccchHHHHHhhHHHHHcccHHHHHHHHHHHHhhCcccHHHHhhHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            7 33333  5677777777888888888888888888888876666666666666777788888888777664

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=95.89  E-value=1.3  Score=40.26  Aligned_cols=83  Identities=14%  Similarity=0.119  Sum_probs=49.3

Q ss_pred             HHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCC---chhHHHHHHHHh
Q 040394          315 WTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLE---DYTVINALVDMY  391 (691)
Q Consensus       315 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~l~~~~  391 (691)
                      +..++.-|-......+|...+..+...   . ...-..+...|.+.|.+..|..-++.+++.-+.   .......++.+|
T Consensus       113 ~~~li~~yP~S~y~~~A~~~l~~l~~~---l-a~~e~~ia~~Y~~~~~y~aA~~r~~~v~~~yp~t~~~~~al~~l~~~y  188 (203)
T PF13525_consen  113 FEELIKRYPNSEYAEEAKKRLAELRNR---L-AEHELYIARFYYKRGKYKAAIIRFQYVIENYPDTPAAEEALARLAEAY  188 (203)
T ss_dssp             HHHHHHH-TTSTTHHHHHHHHHHHHHH---H-HHHHHHHHHHHHCTT-HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCchHHHHHHHHHHHHHHH---H-HHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHH
Confidence            444555666666666666555554432   0 111123455677888888888888888877666   445567777888


Q ss_pred             HhcCChHHHH
Q 040394          392 AKCHVIADAR  401 (691)
Q Consensus       392 ~~~g~~~~a~  401 (691)
                      .+.|..+.+.
T Consensus       189 ~~l~~~~~a~  198 (203)
T PF13525_consen  189 YKLGLKQAAD  198 (203)
T ss_dssp             HHTT-HHHHH
T ss_pred             HHhCChHHHH
Confidence            8888777543

>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase

Probab=95.80  E-value=0.11  Score=42.63  Aligned_cols=49  Identities=10%  Similarity=0.198  Sum_probs=27.5

Q ss_pred             CCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHH
Q 040394          528 VQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVD  576 (691)
Q Consensus       528 ~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~  576 (691)
                      ..|+..+..+++.+|+..|++..|.++.+...+.++++-+..+|..|+.
T Consensus        48 l~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~   96 (126)
T PF12921_consen   48 LYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLE   96 (126)
T ss_pred             CCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            3455555555555555556666666665555555555555555555444

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.77  E-value=3.6  Score=44.32  Aligned_cols=119  Identities=12%  Similarity=0.025  Sum_probs=73.5

Q ss_pred             HHHHHHHhHhcCChHHHHHHHhccCCCChh---hHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHcc
Q 040394          183 LTGLVDMYAKCRDIGSSRQVFDETLDKNVV---SWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKL  259 (691)
Q Consensus       183 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~---~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~  259 (691)
                      ...-++.+++...++-|..+.+.-..+...   ....-.+.+.+.|++++|...|-+-... +.|     ..+|.-+...
T Consensus       337 le~kL~iL~kK~ly~~Ai~LAk~~~~d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~-le~-----s~Vi~kfLda  410 (933)
T KOG2114|consen  337 LETKLDILFKKNLYKVAINLAKSQHLDEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGF-LEP-----SEVIKKFLDA  410 (933)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHccc-CCh-----HHHHHHhcCH
Confidence            444566667777777777776653322111   2223334456778888888877765432 222     2345555555


Q ss_pred             CChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcC
Q 040394          260 RALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELC  308 (691)
Q Consensus       260 ~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~  308 (691)
                      .+...-..+++.+.+.|+. +...-+.|+.+|.+.++.++-.++.+...
T Consensus       411 q~IknLt~YLe~L~~~gla-~~dhttlLLncYiKlkd~~kL~efI~~~~  458 (933)
T KOG2114|consen  411 QRIKNLTSYLEALHKKGLA-NSDHTTLLLNCYIKLKDVEKLTEFISKCD  458 (933)
T ss_pred             HHHHHHHHHHHHHHHcccc-cchhHHHHHHHHHHhcchHHHHHHHhcCC
Confidence            6666666777777777765 44445678888888888887777776654

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=95.76  E-value=3.2  Score=43.61  Aligned_cols=151  Identities=11%  Similarity=0.074  Sum_probs=80.5

Q ss_pred             CChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCC-----ChhhHHHHHHHHHhCCChhHHHHHH
Q 040394          160 RDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDK-----NVVSWTSMIAGYVQNDCAQEGLVLF  234 (691)
Q Consensus       160 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~~~~~~~li~~~~~~g~~~~A~~~~  234 (691)
                      |++++|++++-++-+.+        .-+..+.+.|||-...++++.-..-     -..+|+.+...+.....|++|.+.|
T Consensus       748 g~feeaek~yld~drrD--------LAielr~klgDwfrV~qL~r~g~~d~dD~~~e~A~r~ig~~fa~~~~We~A~~yY  819 (1189)
T KOG2041|consen  748 GEFEEAEKLYLDADRRD--------LAIELRKKLGDWFRVYQLIRNGGSDDDDEGKEDAFRNIGETFAEMMEWEEAAKYY  819 (1189)
T ss_pred             cchhHhhhhhhccchhh--------hhHHHHHhhhhHHHHHHHHHccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56666666665554432        2344555566666666666543221     1235666666666666666666666


Q ss_pred             HHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhH
Q 040394          235 NRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVS  314 (691)
Q Consensus       235 ~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~  314 (691)
                      ..-...         ...+.++.+..++++-+.+-..     ++-+....-.+.+++.+.|.-++|.+.|-+-..|..  
T Consensus       820 ~~~~~~---------e~~~ecly~le~f~~LE~la~~-----Lpe~s~llp~~a~mf~svGMC~qAV~a~Lr~s~pka--  883 (1189)
T KOG2041|consen  820 SYCGDT---------ENQIECLYRLELFGELEVLART-----LPEDSELLPVMADMFTSVGMCDQAVEAYLRRSLPKA--  883 (1189)
T ss_pred             Hhccch---------HhHHHHHHHHHhhhhHHHHHHh-----cCcccchHHHHHHHHHhhchHHHHHHHHHhccCcHH--
Confidence            553210         1233444444443333332222     234555556666777777777777766655544322  


Q ss_pred             HHHHHHHHHhcCCchhHHHHHHH
Q 040394          315 WTAMIVGYTQSGYPDKALKLFTD  337 (691)
Q Consensus       315 ~~~li~~~~~~g~~~~a~~~~~~  337 (691)
                         -+..|...+++.+|.++-+.
T Consensus       884 ---Av~tCv~LnQW~~avelaq~  903 (1189)
T KOG2041|consen  884 ---AVHTCVELNQWGEAVELAQR  903 (1189)
T ss_pred             ---HHHHHHHHHHHHHHHHHHHh
Confidence               23455566666667666554

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=95.55  E-value=0.11  Score=51.90  Aligned_cols=65  Identities=11%  Similarity=-0.088  Sum_probs=37.4

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCch---hHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          599 DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKAC---YYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       599 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~---~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      +...|+.+..+|.+.|++++|+..++++++++|++..   .|+.++.+|...|+.++|++.+++.++.
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALELNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            3445555555555666666666666666666666553   2555556666666666666665555553

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=95.54  E-value=2.8  Score=41.51  Aligned_cols=78  Identities=12%  Similarity=0.022  Sum_probs=46.7

Q ss_pred             ChhHHHHHHHHhHhcCChHHHHHHHhccCCC---C----hhhHHHHHHHHHh---CCChhHHHHHHHHHHhCCCCCChhh
Q 040394          179 DSFVLTGLVDMYAKCRDIGSSRQVFDETLDK---N----VVSWTSMIAGYVQ---NDCAQEGLVLFNRMREGFVEGNQIT  248 (691)
Q Consensus       179 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~----~~~~~~li~~~~~---~g~~~~A~~~~~~m~~~~~~p~~~t  248 (691)
                      +..+-..++-.|....+++...++++.+...   +    ...--...-++.+   .|+.++|++++..+....-.++..|
T Consensus       140 s~div~~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~  219 (374)
T PF13281_consen  140 SPDIVINLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDT  219 (374)
T ss_pred             ChhHHHHHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHH
Confidence            3444445555677777777777777776543   1    1111123334445   6777888888777666556667777


Q ss_pred             HHHHHHHH
Q 040394          249 LGSLVTAC  256 (691)
Q Consensus       249 ~~~li~~~  256 (691)
                      |..+.+.|
T Consensus       220 ~gL~GRIy  227 (374)
T PF13281_consen  220 LGLLGRIY  227 (374)
T ss_pred             HHHHHHHH
Confidence            76666654

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=95.49  E-value=0.16  Score=40.60  Aligned_cols=89  Identities=25%  Similarity=0.156  Sum_probs=51.6

Q ss_pred             HHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc----hhHHHHHHHHHhCCCc
Q 040394          577 LLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKA----CYYVLVSNLYASDGRW  650 (691)
Q Consensus       577 ~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~----~~~~~l~~~~~~~g~~  650 (691)
                      ++...|+.+.|++.|.+. . .+.....||.-.+++.-+|+.++|.+-+++++++.-+..    ..|..-+.+|...|+.
T Consensus        52 alaE~g~Ld~AlE~F~qal~l~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~trtacqa~vQRg~lyRl~g~d  131 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCLAPERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQTRTACQAFVQRGLLYRLLGND  131 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHhcccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHhCch
Confidence            345566666666666655 2 223455666666666666666666666666666432211    2344555566666666


Q ss_pred             HHHHHHHHHHHhCCC
Q 040394          651 IRVNQVRELMKQRGL  665 (691)
Q Consensus       651 ~~A~~~~~~~~~~g~  665 (691)
                      +.|..-|+..-+-|.
T Consensus       132 d~AR~DFe~AA~LGS  146 (175)
T KOG4555|consen  132 DAARADFEAAAQLGS  146 (175)
T ss_pred             HHHHHhHHHHHHhCC
Confidence            666666666655543

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=95.27  E-value=0.067  Score=52.02  Aligned_cols=89  Identities=11%  Similarity=0.060  Sum_probs=71.5

Q ss_pred             HHHHhcCChHHHHHHHHhC--------CCC---------CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHH
Q 040394          576 DLLARAGRLEEALEFMENM--------PIE---------PDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYV  638 (691)
Q Consensus       576 ~~~~~~g~~~~A~~~~~~~--------~~~---------p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~  638 (691)
                      +.|.+.|++..|...|++.        +.+         .-..+++.+..++.+.+++..|+....+.++.+|+|.-..+
T Consensus       216 n~~fK~gk~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~~~N~KALy  295 (397)
T KOG0543|consen  216 NVLFKEGKFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLACHLNLAACYLKLKEYKEAIESCNKVLELDPNNVKALY  295 (397)
T ss_pred             hHHHhhchHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhcCCCchhHHH
Confidence            3456666666666665553        111         12345677788889999999999999999999999999999


Q ss_pred             HHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          639 LVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       639 ~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      .-+.+|...|+++.|+..|+++++..
T Consensus       296 RrG~A~l~~~e~~~A~~df~ka~k~~  321 (397)
T KOG0543|consen  296 RRGQALLALGEYDLARDDFQKALKLE  321 (397)
T ss_pred             HHHHHHHhhccHHHHHHHHHHHHHhC
Confidence            99999999999999999999998853

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=95.26  E-value=1.1  Score=46.66  Aligned_cols=114  Identities=14%  Similarity=0.075  Sum_probs=70.7

Q ss_pred             CCHHHHHHHHHHchhhcCCCCChhHHHH-HHHHHHhcCChHHHHHHHHhCC-CC-----CCHHHHHHHHHHHHhcCCHHH
Q 040394          546 GMVGEGWKCFYSMCRDFKFVPSMKHYVC-MVDLLARAGRLEEALEFMENMP-IE-----PDVSLFGAFLHGCGLYSRFDL  618 (691)
Q Consensus       546 g~~~~A~~~~~~m~~~~~~~p~~~~~~~-li~~~~~~g~~~~A~~~~~~~~-~~-----p~~~~~~~l~~~~~~~g~~~~  618 (691)
                      .+.+.|.++++.+.+.   -|+...|.. -.+.+...|++++|++.|++.- .+     .....+--+.+.+...+++++
T Consensus       247 ~~~~~a~~lL~~~~~~---yP~s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~  323 (468)
T PF10300_consen  247 VPLEEAEELLEEMLKR---YPNSALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEE  323 (468)
T ss_pred             CCHHHHHHHHHHHHHh---CCCcHHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHH
Confidence            4555666666655332   355443332 2334455666677766666541 11     122345556677778889999


Q ss_pred             HHHHHHHHHhcCCCCch-hHHHHHHHHHhCCCc-------HHHHHHHHHHHh
Q 040394          619 GEVMIKKMLELHPDKAC-YYVLVSNLYASDGRW-------IRVNQVRELMKQ  662 (691)
Q Consensus       619 A~~~~~~~~~~~p~~~~-~~~~l~~~~~~~g~~-------~~A~~~~~~~~~  662 (691)
                      |...+.++.+.+.-+.. +++..+-++...|+.       ++|.+.+++...
T Consensus       324 A~~~f~~L~~~s~WSka~Y~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp~  375 (468)
T PF10300_consen  324 AAEYFLRLLKESKWSKAFYAYLAAACLLMLGREEEAKEHKKEAEELFRKVPK  375 (468)
T ss_pred             HHHHHHHHHhccccHHHHHHHHHHHHHHhhccchhhhhhHHHHHHHHHHHHH
Confidence            99999998887666444 445666677788888       888888777654

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=95.21  E-value=1.2  Score=44.96  Aligned_cols=101  Identities=14%  Similarity=0.193  Sum_probs=66.0

Q ss_pred             HHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhCC-C-CCCH--HHHHHHHHHHH
Q 040394          536 TTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMP-I-EPDV--SLFGAFLHGCG  611 (691)
Q Consensus       536 ~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~~-~-~p~~--~~~~~l~~~~~  611 (691)
                      ..+..++.+.|+.++|++.+++|.+.....-+..+...|+..+...+.+.++..++.+.. + -|..  ..|...+-.+.
T Consensus       263 rRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YTaALLkaR  342 (539)
T PF04184_consen  263 RRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYTAALLKAR  342 (539)
T ss_pred             HHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHHHHHHHHH
Confidence            345556678888888888888886654322234566678888888889998888888873 1 2332  34555443333


Q ss_pred             hcCC---------------HHHHHHHHHHHHhcCCCCchh
Q 040394          612 LYSR---------------FDLGEVMIKKMLELHPDKACY  636 (691)
Q Consensus       612 ~~g~---------------~~~A~~~~~~~~~~~p~~~~~  636 (691)
                      ..+|               -..|.+.+.++.+.+|.-+.+
T Consensus       343 av~d~fs~e~a~rRGls~ae~~aveAi~RAvefNPHVp~Y  382 (539)
T PF04184_consen  343 AVGDKFSPEAASRRGLSPAEMNAVEAIHRAVEFNPHVPKY  382 (539)
T ss_pred             hhccccCchhhhhcCCChhHHHHHHHHHHHHHhCCCCchh
Confidence            3333               234668888888888775444

The molecular function of this protein is uncertain.

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=95.09  E-value=0.21  Score=45.89  Aligned_cols=98  Identities=11%  Similarity=0.094  Sum_probs=74.8

Q ss_pred             HHHHHhcc--cCCHhHHHHHHHHHhc-----CCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCC-----------
Q 040394          486 RMVFDAMR--EKNTVTWSAMIGGYGM-----QGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGM-----------  547 (691)
Q Consensus       486 ~~~~~~~~--~~~~~~~~~li~~~~~-----~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~-----------  547 (691)
                      +..|....  +.|-.+|-..+..+..     .++++-....++.|.+.|+.-|..+|+.||..+-+..-           
T Consensus        54 e~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~  133 (406)
T KOG3941|consen   54 EKQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFL  133 (406)
T ss_pred             hhhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHh
Confidence            44455554  4566677777766653     45677777788899999999999999999988765432           


Q ss_pred             -----HHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCCh
Q 040394          548 -----VGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRL  584 (691)
Q Consensus       548 -----~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~  584 (691)
                           -+=++.++++| +.+|+.||..+-..|+.++.+.+-.
T Consensus       134 HYP~QQ~C~I~vLeqM-E~hGVmPdkE~e~~lvn~FGr~~~p  174 (406)
T KOG3941|consen  134 HYPQQQNCAIKVLEQM-EWHGVMPDKEIEDILVNAFGRWNFP  174 (406)
T ss_pred             hCchhhhHHHHHHHHH-HHcCCCCchHHHHHHHHHhcccccc
Confidence                 23468899999 8889999999999999999988864

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.03  E-value=1.6  Score=36.93  Aligned_cols=84  Identities=14%  Similarity=0.148  Sum_probs=37.8

Q ss_pred             HHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHH
Q 040394          151 KVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEG  230 (691)
Q Consensus       151 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A  230 (691)
                      .++..+...+........++.+...+..+...++.++..|++.+ ..+....++.  ..+......+++.|.+.+.++++
T Consensus        12 ~vv~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~li~ly~~~~-~~~ll~~l~~--~~~~yd~~~~~~~c~~~~l~~~~   88 (140)
T smart00299       12 EVVELFEKRNLLEELIPYLESALKLNSENPALQTKLIELYAKYD-PQKEIERLDN--KSNHYDIEKVGKLCEKAKLYEEA   88 (140)
T ss_pred             HHHHHHHhCCcHHHHHHHHHHHHccCccchhHHHHHHHHHHHHC-HHHHHHHHHh--ccccCCHHHHHHHHHHcCcHHHH
Confidence            44444444455555555555555544335555555555555432 2222233331  12222333344444445555555


Q ss_pred             HHHHHHH
Q 040394          231 LVLFNRM  237 (691)
Q Consensus       231 ~~~~~~m  237 (691)
                      .-++.++
T Consensus        89 ~~l~~k~   95 (140)
T smart00299       89 VELYKKD   95 (140)
T ss_pred             HHHHHhh
Confidence            5555444

>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase

Probab=95.02  E-value=0.3  Score=40.05  Aligned_cols=93  Identities=17%  Similarity=0.090  Sum_probs=54.0

Q ss_pred             ChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhc--CCCChhHHHHHHHHH
Q 040394          245 NQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDEL--CSIDLVSWTAMIVGY  322 (691)
Q Consensus       245 ~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~--~~~~~~~~~~li~~~  322 (691)
                      |..++..+|.++++.|+++....+++..-  |+.++...         ..+.       +..-  ..|+..+..+++.+|
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~W--gI~~~~~~---------~~~~-------~~~~spl~Pt~~lL~AIv~sf   62 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVW--GIDVNGKK---------KEGD-------YPPSSPLYPTSRLLIAIVHSF   62 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhc--CCCCCCcc---------ccCc-------cCCCCCCCCCHHHHHHHHHHH
Confidence            45566677777777777776666665443  22211100         0000       1000  235666777777777


Q ss_pred             HhcCCchhHHHHHHHhhHC-CCCCcHHHHHHHHH
Q 040394          323 TQSGYPDKALKLFTDKKWA-DFFPNHVTIASVLS  355 (691)
Q Consensus       323 ~~~g~~~~a~~~~~~m~~~-g~~p~~~t~~~ll~  355 (691)
                      +.+|++..|+++++...+. +++.+..+|..|+.
T Consensus        63 ~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~   96 (126)
T PF12921_consen   63 GYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLE   96 (126)
T ss_pred             HhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            7777777777777776554 56666777777776

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=95.01  E-value=0.18  Score=46.24  Aligned_cols=97  Identities=11%  Similarity=0.092  Sum_probs=70.4

Q ss_pred             HHHHhccC--CCChhhHHHHHHHHHhC-----CChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccC------------
Q 040394          200 RQVFDETL--DKNVVSWTSMIAGYVQN-----DCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLR------------  260 (691)
Q Consensus       200 ~~~~~~~~--~~~~~~~~~li~~~~~~-----g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~------------  260 (691)
                      ++.|....  ++|..+|-..+..+...     +.++-....++.|.+.|+.-|..+|+.|+..+-+..            
T Consensus        54 e~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~  133 (406)
T KOG3941|consen   54 EKQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFL  133 (406)
T ss_pred             hhhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHh
Confidence            34444444  45677777777766543     455666667888888999999999999888765432            


Q ss_pred             ----ChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCC
Q 040394          261 ----ALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGN  296 (691)
Q Consensus       261 ----~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~  296 (691)
                          +-+-+..++++|...|+.||..+-..|++++.+.+-
T Consensus       134 HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~  173 (406)
T KOG3941|consen  134 HYPQQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNF  173 (406)
T ss_pred             hCchhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhccccc
Confidence                334577888888888888888888888888877664

>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=94.96  E-value=0.13  Score=44.09  Aligned_cols=69  Identities=13%  Similarity=0.240  Sum_probs=49.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhc---CCCChhHHHHHHHHHHhcCCchhHHHHHHHhhH-----CCCCCcHHHH
Q 040394          282 HLVTALLDMYVKCGNIRDARSVFDEL---CSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKW-----ADFFPNHVTI  350 (691)
Q Consensus       282 ~~~~~li~~~~~~g~~~~A~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~t~  350 (691)
                      .+...++..+...|++++|..+.+.+   .+-+...|..+|.+|...|+...|.+.|+.+..     .|+.|+..+-
T Consensus        63 ~~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~  139 (146)
T PF03704_consen   63 DALERLAEALLEAGDYEEALRLLQRALALDPYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETR  139 (146)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHH
T ss_pred             HHHHHHHHHHHhccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHH
Confidence            34566777788899999999999888   334667899999999999999999999988743     4888888765

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_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=94.90  E-value=0.079  Score=31.60  Aligned_cols=32  Identities=16%  Similarity=0.190  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC
Q 040394          602 LFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK  633 (691)
Q Consensus       602 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~  633 (691)
                      .|..+...+...|++++|++.++++++++|++
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            45666777777788888888888877777764

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 ....

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=94.74  E-value=1  Score=46.25  Aligned_cols=158  Identities=5%  Similarity=0.037  Sum_probs=102.2

Q ss_pred             HHHHhCCChhHHHHHHH--HHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCCh
Q 040394          119 RWYFLNDLYKDIVEFYK--CMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDI  196 (691)
Q Consensus       119 ~~~~~~~~~~~a~~~~~--~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  196 (691)
                      +...-+++++++.++..  ++... +  +..-.+.+++-+-+.|..+.|.++...-.           .-.....+.|++
T Consensus       269 k~av~~~d~~~v~~~i~~~~ll~~-i--~~~~~~~i~~fL~~~G~~e~AL~~~~D~~-----------~rFeLAl~lg~L  334 (443)
T PF04053_consen  269 KTAVLRGDFEEVLRMIAASNLLPN-I--PKDQGQSIARFLEKKGYPELALQFVTDPD-----------HRFELALQLGNL  334 (443)
T ss_dssp             HHHHHTT-HHH-----HHHHTGGG-----HHHHHHHHHHHHHTT-HHHHHHHSS-HH-----------HHHHHHHHCT-H
T ss_pred             HHHHHcCChhhhhhhhhhhhhccc-C--ChhHHHHHHHHHHHCCCHHHHHhhcCChH-----------HHhHHHHhcCCH
Confidence            34455788888776664  22211 1  24457788888888999998888755432           235566788999


Q ss_pred             HHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHC
Q 040394          197 GSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIG  276 (691)
Q Consensus       197 ~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g  276 (691)
                      +.|.++.++..  +...|..|.....+.|+++-|.+.|.+...         |..++-.|.-.|+.+...++.+.....|
T Consensus       335 ~~A~~~a~~~~--~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~kl~~~a~~~~  403 (443)
T PF04053_consen  335 DIALEIAKELD--DPEKWKQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSKLAKIAEERG  403 (443)
T ss_dssp             HHHHHHCCCCS--THHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhcC--cHHHHHHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHHHHHHHHHcc
Confidence            99999988876  566999999999999999999999998753         5667777778888887777777766665


Q ss_pred             CCCchHHHHHHHHHHHhcCCHHHHHHHHHhc
Q 040394          277 IEINSHLVTALLDMYVKCGNIRDARSVFDEL  307 (691)
Q Consensus       277 ~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~  307 (691)
                      -      ++....++.-.|+.++..+++.+-
T Consensus       404 ~------~n~af~~~~~lgd~~~cv~lL~~~  428 (443)
T PF04053_consen  404 D------INIAFQAALLLGDVEECVDLLIET  428 (443)
T ss_dssp             -------HHHHHHHHHHHT-HHHHHHHHHHT
T ss_pred             C------HHHHHHHHHHcCCHHHHHHHHHHc
Confidence            2      344444455557777666666543

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 WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=94.72  E-value=0.91  Score=37.75  Aligned_cols=20  Identities=5%  Similarity=0.021  Sum_probs=16.2

Q ss_pred             HHHHHHHHHHHHhcCCCCch
Q 040394          616 FDLGEVMIKKMLELHPDKAC  635 (691)
Q Consensus       616 ~~~A~~~~~~~~~~~p~~~~  635 (691)
                      ...|..-|++.++..|++..
T Consensus       115 ~~~A~~~f~~lv~~yP~S~y  134 (142)
T PF13512_consen  115 ARQAFRDFEQLVRRYPNSEY  134 (142)
T ss_pred             HHHHHHHHHHHHHHCcCChh
Confidence            66888889999999999643

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=94.70  E-value=0.071  Score=31.87  Aligned_cols=32  Identities=16%  Similarity=0.206  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040394          601 SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPD  632 (691)
Q Consensus       601 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~  632 (691)
                      .+|..+...+...|++++|+..++++++++|+
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~   33 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALELDPD   33 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHCcC
Confidence            45677777888888888888888888888876

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 ....

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=94.63  E-value=3.7  Score=37.91  Aligned_cols=57  Identities=11%  Similarity=0.047  Sum_probs=43.5

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCch---hHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          606 FLHGCGLYSRFDLGEVMIKKMLELHPDKAC---YYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       606 l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~---~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      +.+-|.+.|.+..|..-++++++..|+.+.   .+..+..+|...|..++|...-+-+..
T Consensus       173 IaryY~kr~~~~AA~nR~~~v~e~y~~t~~~~eaL~~l~eaY~~lgl~~~a~~~~~vl~~  232 (254)
T COG4105         173 IARYYLKRGAYVAAINRFEEVLENYPDTSAVREALARLEEAYYALGLTDEAKKTAKVLGA  232 (254)
T ss_pred             HHHHHHHhcChHHHHHHHHHHHhccccccchHHHHHHHHHHHHHhCChHHHHHHHHHHHh
Confidence            445678889999999999999987766554   455667788899999999877655544

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=94.36  E-value=2.8  Score=35.40  Aligned_cols=125  Identities=10%  Similarity=0.002  Sum_probs=70.1

Q ss_pred             HHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHh
Q 040394          501 SAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLAR  580 (691)
Q Consensus       501 ~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~  580 (691)
                      ..++..+...+.+.....+++.+...+ ..+...++.++..|++.+ ..+..+.++.       .++.......+..|.+
T Consensus        11 ~~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~~-~~~ll~~l~~-------~~~~yd~~~~~~~c~~   81 (140)
T smart00299       11 SEVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKYD-PQKEIERLDN-------KSNHYDIEKVGKLCEK   81 (140)
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHHC-HHHHHHHHHh-------ccccCCHHHHHHHHHH
Confidence            345556666667777777777777665 355566677777666542 3333444431       1223333446666677


Q ss_pred             cCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhc-CCHHHHHHHHHHHHhcCCCCchhHHHHHHHHH
Q 040394          581 AGRLEEALEFMENMPIEPDVSLFGAFLHGCGLY-SRFDLGEVMIKKMLELHPDKACYYVLVSNLYA  645 (691)
Q Consensus       581 ~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~-g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~  645 (691)
                      .+.++++.-++.+++..      ...+..+... ++++.|.+++++     ++++..|..++..+.
T Consensus        82 ~~l~~~~~~l~~k~~~~------~~Al~~~l~~~~d~~~a~~~~~~-----~~~~~lw~~~~~~~l  136 (140)
T smart00299       82 AKLYEEAVELYKKDGNF------KDAIVTLIEHLGNYEKAIEYFVK-----QNNPELWAEVLKALL  136 (140)
T ss_pred             cCcHHHHHHHHHhhcCH------HHHHHHHHHcccCHHHHHHHHHh-----CCCHHHHHHHHHHHH
Confidence            77777777777776522      2222233333 677777776665     334556665555443

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=94.32  E-value=1.6  Score=41.00  Aligned_cols=139  Identities=5%  Similarity=-0.044  Sum_probs=59.5

Q ss_pred             HHhcCCChHHHHHHhccCCC---CCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHH
Q 040394           89 MYGSFGHVKYARSVFDSMPN---PDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEG  165 (691)
Q Consensus        89 ~~~~~g~~~~A~~~~~~~~~---~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a  165 (691)
                      .....|++.+|..+|+....   .+...--.+...|...|+++.|..++..+...--.........-|..+.+.....+.
T Consensus       143 ~~~~~e~~~~a~~~~~~al~~~~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll~qaa~~~~~  222 (304)
T COG3118         143 ELIEAEDFGEAAPLLKQALQAAPENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELLEQAAATPEI  222 (304)
T ss_pred             hhhhccchhhHHHHHHHHHHhCcccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHhcCCCH
Confidence            34445555555555544321   223344444555555555555555555544331111111111122223233333322


Q ss_pred             HHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCC-----ChhhHHHHHHHHHhCCChh
Q 040394          166 MKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDK-----NVVSWTSMIAGYVQNDCAQ  228 (691)
Q Consensus       166 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~~~~~~~li~~~~~~g~~~  228 (691)
                      ..+-++. ...+.|......+...+...|+.++|.+.+-.+.++     |...-..|+..+.--|.-+
T Consensus       223 ~~l~~~~-aadPdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~~d~~~Rk~lle~f~~~g~~D  289 (304)
T COG3118         223 QDLQRRL-AADPDDVEAALALADQLHLVGRNEAALEHLLALLRRDRGFEDGEARKTLLELFEAFGPAD  289 (304)
T ss_pred             HHHHHHH-HhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccCcHHHHHHHHHHHhcCCCC
Confidence            2222222 223345555555555555556665555554444332     3344455555555444333

>PRK11619 lytic murein transglycosylase; Provisional

Probab=94.28  E-value=9.9  Score=41.47  Aligned_cols=115  Identities=8%  Similarity=0.006  Sum_probs=60.8

Q ss_pred             CCChHHHHHHHHHHHHCC-CCCCHH--HHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHH
Q 040394          510 QGDGGGSLALFSDMLNEE-VQPNEV--IFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEE  586 (691)
Q Consensus       510 ~~~~~~A~~~~~~m~~~g-~~p~~~--~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~  586 (691)
                      ..+.+.|..++....... +.+...  ....+.......+..++|...++...   ....+......-+..-.+.++++.
T Consensus       254 r~d~~~A~~~~~~~~~~~~~~~~~~~~~~~~lA~~~a~~~~~~~a~~w~~~~~---~~~~~~~~~e~r~r~Al~~~dw~~  330 (644)
T PRK11619        254 RQDAENARLMIPSLVRAQKLNEDQRQELRDIVAWRLMGNDVTDEQAKWRDDVI---MRSQSTSLLERRVRMALGTGDRRG  330 (644)
T ss_pred             HhCHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHhcc---cccCCcHHHHHHHHHHHHccCHHH
Confidence            455677777777764432 333322  22222222222222445555555431   112234444445555557788888


Q ss_pred             HHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 040394          587 ALEFMENMP--IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKML  627 (691)
Q Consensus       587 A~~~~~~~~--~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  627 (691)
                      +...+..|+  ..-...-.--+.+++...|+.++|...|+++.
T Consensus       331 ~~~~i~~L~~~~~~~~rw~YW~aRa~~~~g~~~~A~~~~~~~a  373 (644)
T PRK11619        331 LNTWLARLPMEAKEKDEWRYWQADLLLEQGRKAEAEEILRQLM  373 (644)
T ss_pred             HHHHHHhcCHhhccCHhhHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            877777772  12222223335566666788888888888763

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=94.28  E-value=4.9  Score=37.90  Aligned_cols=123  Identities=12%  Similarity=0.038  Sum_probs=74.9

Q ss_pred             HHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHH
Q 040394          355 SASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLV  434 (691)
Q Consensus       355 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~  434 (691)
                      ......|++.++...++......+.+..+--.++.+|...|+.+.|..++..++....              ........
T Consensus       142 ~~~~~~e~~~~a~~~~~~al~~~~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~--------------~~~~~~l~  207 (304)
T COG3118         142 KELIEAEDFGEAAPLLKQALQAAPENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQ--------------DKAAHGLQ  207 (304)
T ss_pred             hhhhhccchhhHHHHHHHHHHhCcccchHHHHHHHHHHHcCChHHHHHHHHhCcccch--------------hhHHHHHH
Confidence            3456678888888888888888888777788899999999999999999999876521              01111111


Q ss_pred             HHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc
Q 040394          435 SVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE  494 (691)
Q Consensus       435 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  494 (691)
                      .-+..+.+.........+-+..-. +  |.+...-..+...+...|+.++|.+.+-.+.+
T Consensus       208 a~i~ll~qaa~~~~~~~l~~~~aa-d--Pdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~  264 (304)
T COG3118         208 AQIELLEQAAATPEIQDLQRRLAA-D--PDDVEAALALADQLHLVGRNEAALEHLLALLR  264 (304)
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHHh-C--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            122222222222222222222222 1  44666666666667777777777666555443

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=94.26  E-value=1.5  Score=37.32  Aligned_cols=110  Identities=15%  Similarity=0.089  Sum_probs=67.6

Q ss_pred             HhcccCCHHHHHHHHHHchhhcCCCCChh-HHHHHHHHHHhcCChHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCCHHH
Q 040394          541 ACSHTGMVGEGWKCFYSMCRDFKFVPSMK-HYVCMVDLLARAGRLEEALEFMENM-PIEPDVSLFGAFLHGCGLYSRFDL  618 (691)
Q Consensus       541 ~~~~~g~~~~A~~~~~~m~~~~~~~p~~~-~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~~~~~~l~~~~~~~g~~~~  618 (691)
                      .-...++.+++..+++.+ +.  +.|... .-..-...+.+.|++.+|+.+|+.+ ...|....-..|+..|....+-..
T Consensus        19 ~al~~~~~~D~e~lL~AL-rv--LRP~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~~~~~p~~kALlA~CL~~~~D~~   95 (160)
T PF09613_consen   19 VALRLGDPDDAEALLDAL-RV--LRPEFPELDLFDGWLHIVRGDWDDALRLLRELEERAPGFPYAKALLALCLYALGDPS   95 (160)
T ss_pred             HHHccCChHHHHHHHHHH-HH--hCCCchHHHHHHHHHHHHhCCHHHHHHHHHHHhccCCCChHHHHHHHHHHHHcCChH
Confidence            335667888888888877 33  566632 2222344567889999999999998 445555666667766666555455


Q ss_pred             HHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHH
Q 040394          619 GEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQ  655 (691)
Q Consensus       619 A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~  655 (691)
                      -...-+++++..|+ +.+...+..+ ........|.+
T Consensus        96 Wr~~A~evle~~~d-~~a~~Lv~~L-l~~~~~~~a~~  130 (160)
T PF09613_consen   96 WRRYADEVLESGAD-PDARALVRAL-LARADLEPAHE  130 (160)
T ss_pred             HHHHHHHHHhcCCC-hHHHHHHHHH-HHhccccchhh
Confidence            56666666666665 5555555333 33334444433

>PRK15331 chaperone protein SicA; Provisional

Probab=94.22  E-value=0.79  Score=39.09  Aligned_cols=84  Identities=10%  Similarity=-0.017  Sum_probs=62.5

Q ss_pred             HcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhcc---CCCChhhHHHHHHHHHhCCChhHHHH
Q 040394          156 CCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDET---LDKNVVSWTSMIAGYVQNDCAQEGLV  232 (691)
Q Consensus       156 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~A~~  232 (691)
                      +-..|++++|..+|+.+...++.+..-+..|..++-..+++++|...|...   ...|+..+--+..++...|+.+.|..
T Consensus        47 ~y~~Gk~~eA~~~F~~L~~~d~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~dp~p~f~agqC~l~l~~~~~A~~  126 (165)
T PRK15331         47 FYNQGRLDEAETFFRFLCIYDFYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKNDYRPVFFTGQCQLLMRKAAKARQ  126 (165)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCCccchHHHHHHHhCCHHHHHH
Confidence            346788888888888888877777777888888888888888888877642   23455555566677777888888888


Q ss_pred             HHHHHHh
Q 040394          233 LFNRMRE  239 (691)
Q Consensus       233 ~~~~m~~  239 (691)
                      .|....+
T Consensus       127 ~f~~a~~  133 (165)
T PRK15331        127 CFELVNE  133 (165)
T ss_pred             HHHHHHh
Confidence            8777765

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=94.21  E-value=2.5  Score=44.17  Aligned_cols=158  Identities=13%  Similarity=0.054  Sum_probs=102.3

Q ss_pred             HHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCH-----HHHHHHHHHHhc----cCcHHHHHHHHHH
Q 040394          385 NALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDA-----VTLVSVISACAS----LGAVQVGSSLHAY  455 (691)
Q Consensus       385 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~-----~~~~~ll~~~~~----~~~~~~a~~~~~~  455 (691)
                      ..++....-.|+-+.+++.+.+..+.+             ++.-..     .+|..++..++.    ..+.+.+.++++.
T Consensus       192 ~kll~~vGF~gdR~~GL~~L~~~~~~~-------------~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~  258 (468)
T PF10300_consen  192 LKLLSFVGFSGDRELGLRLLWEASKSE-------------NIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEE  258 (468)
T ss_pred             HHHHhhcCcCCcHHHHHHHHHHHhccC-------------CcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHH
Confidence            445555566677777766666654432             111111     234444443333    4578899999999


Q ss_pred             HHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC-------CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCC
Q 040394          456 STKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK-------NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEV  528 (691)
Q Consensus       456 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-------~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~  528 (691)
                      +.+.-  |......-.-.+.+...|++++|.+.|+.....       ....+--+...+.-..++++|...|.++.+.. 
T Consensus       259 ~~~~y--P~s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s-  335 (468)
T PF10300_consen  259 MLKRY--PNSALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKES-  335 (468)
T ss_pred             HHHhC--CCcHHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcc-
Confidence            98875  444444444567788899999999999975531       22345556677888899999999999999853 


Q ss_pred             CCCHHHHHHHHHHh-cccCCH-------HHHHHHHHHc
Q 040394          529 QPNEVIFTTILSAC-SHTGMV-------GEGWKCFYSM  558 (691)
Q Consensus       529 ~p~~~~~~~ll~~~-~~~g~~-------~~A~~~~~~m  558 (691)
                      ..+..+|..+..+| ...|+.       ++|.++|.+.
T Consensus       336 ~WSka~Y~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~v  373 (468)
T PF10300_consen  336 KWSKAFYAYLAAACLLMLGREEEAKEHKKEAEELFRKV  373 (468)
T ss_pred             ccHHHHHHHHHHHHHHhhccchhhhhhHHHHHHHHHHH
Confidence            34445555555433 456666       7788887765

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.13  E-value=1.1  Score=41.69  Aligned_cols=103  Identities=14%  Similarity=0.207  Sum_probs=71.4

Q ss_pred             HHHHHHHHhcccCCHHHHHHHHHHchhhcCCCC-ChhHHHHHHHHHHhcCChHHHHHHHHhC----CCCC-CHHHHHHHH
Q 040394          534 IFTTILSACSHTGMVGEGWKCFYSMCRDFKFVP-SMKHYVCMVDLLARAGRLEEALEFMENM----PIEP-DVSLFGAFL  607 (691)
Q Consensus       534 ~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~~----~~~p-~~~~~~~l~  607 (691)
                      .|+..+.. .+.|++..|...|...++.+.-.+ ....+-.|...+...|++++|...|..+    +..| -+..+--|.
T Consensus       144 ~Y~~A~~~-~ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg  222 (262)
T COG1729         144 LYNAALDL-YKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLG  222 (262)
T ss_pred             HHHHHHHH-HHcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHH
Confidence            45555543 455678888888887766542111 1345556788888888888888887777    2222 235666677


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCchhH
Q 040394          608 HGCGLYSRFDLGEVMIKKMLELHPDKACYY  637 (691)
Q Consensus       608 ~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~  637 (691)
                      .+..+.|+.++|...|++..+..|+.+..-
T Consensus       223 ~~~~~l~~~d~A~atl~qv~k~YP~t~aA~  252 (262)
T COG1729         223 VSLGRLGNTDEACATLQQVIKRYPGTDAAK  252 (262)
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHCCCCHHHH
Confidence            778888999999999999999999865443

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=93.97  E-value=0.15  Score=32.67  Aligned_cols=40  Identities=15%  Similarity=0.158  Sum_probs=24.4

Q ss_pred             hHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHH
Q 040394          148 VFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLV  187 (691)
Q Consensus       148 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~  187 (691)
                      ++..+...+...|++++|++++++.++..|.|...+..+.
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~~~a~~~La   42 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALALDPDDPEAWRALA   42 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCHHHHHHhh
Confidence            3445556666666666666666666666666666555543

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.94  E-value=0.59  Score=44.23  Aligned_cols=160  Identities=11%  Similarity=0.052  Sum_probs=117.2

Q ss_pred             hcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHH----HHHHHHHhcCC
Q 040394          508 GMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYV----CMVDLLARAGR  583 (691)
Q Consensus       508 ~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~----~li~~~~~~g~  583 (691)
                      --.|+..+|-..++++.+. .+.|...+...-.+|...|+.+.-...++++...  ..||...|.    .+.-++..+|-
T Consensus       114 ~~~g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~--wn~dlp~~sYv~GmyaFgL~E~g~  190 (491)
T KOG2610|consen  114 WGRGKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPK--WNADLPCYSYVHGMYAFGLEECGI  190 (491)
T ss_pred             hccccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhccchhhhhhHHHHhccc--cCCCCcHHHHHHHHHHhhHHHhcc
Confidence            3478888888899999886 5777788888888999999999988888877543  345543333    33345568999


Q ss_pred             hHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC----chhHHHHHHHHHhCCCcHHHHHHH
Q 040394          584 LEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK----ACYYVLVSNLYASDGRWIRVNQVR  657 (691)
Q Consensus       584 ~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~----~~~~~~l~~~~~~~g~~~~A~~~~  657 (691)
                      +++|.+.-++. .+.| |.....+....+.-.|+.+++.+++++-...-...    ..-|.+.+..+.+.+.++.|.++|
T Consensus       191 y~dAEk~A~ralqiN~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~Al~~iE~aeye~aleIy  270 (491)
T KOG2610|consen  191 YDDAEKQADRALQINRFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALFHIEGAEYEKALEIY  270 (491)
T ss_pred             chhHHHHHHhhccCCCcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHhhhcccchhHHHHHH
Confidence            99999998887 4444 45566666677778899999999988755432221    244667788889999999999999


Q ss_pred             HHHHhCCCccCCC
Q 040394          658 ELMKQRGLSKSPG  670 (691)
Q Consensus       658 ~~~~~~g~~~~~~  670 (691)
                      ++=.-....++.+
T Consensus       271 D~ei~k~l~k~Da  283 (491)
T KOG2610|consen  271 DREIWKRLEKDDA  283 (491)
T ss_pred             HHHHHHHhhccch
Confidence            8765544555544

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=93.93  E-value=7.8  Score=38.96  Aligned_cols=150  Identities=11%  Similarity=-0.031  Sum_probs=80.0

Q ss_pred             CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCC---CHHHHHHHHHHhcccCCHHHHHHHHHHchh-hcCCCCChhHH
Q 040394          496 NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQP---NEVIFTTILSACSHTGMVGEGWKCFYSMCR-DFKFVPSMKHY  571 (691)
Q Consensus       496 ~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p---~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~-~~~~~p~~~~~  571 (691)
                      ...+|..++..+.+.|+++.|...+.++...+..+   .+.............|+..+|...++.... ...-..+....
T Consensus       145 ~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~~~~~~~~~~~~~~~  224 (352)
T PF02259_consen  145 LAETWLKFAKLARKAGNFQLALSALNRLFQLNPSSESLLPRVFLEYAKLLWAQGEQEEAIQKLRELLKCRLSKNIDSISN  224 (352)
T ss_pred             HHHHHHHHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcchHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhccccccH
Confidence            44577778888888888888888888877643221   233344445566677888888888777654 11111111111


Q ss_pred             HHHHHHHHhcCChHHHHHH-HHhCCCCCCHHHHHHHHHHHHhc------CCHHHHHHHHHHHHhcCCCCchhHHHHHHHH
Q 040394          572 VCMVDLLARAGRLEEALEF-MENMPIEPDVSLFGAFLHGCGLY------SRFDLGEVMIKKMLELHPDKACYYVLVSNLY  644 (691)
Q Consensus       572 ~~li~~~~~~g~~~~A~~~-~~~~~~~p~~~~~~~l~~~~~~~------g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~  644 (691)
                      ..+...+..  ..+..... ........-...+..+...+...      ++.+.+...|+++.+..|+....+..++..+
T Consensus       225 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~a~~~l~~a~w~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~k~~~~~a~~~  302 (352)
T PF02259_consen  225 AELKSGLLE--SLEVISSTNLDKESKELKAKAFLLLAKWLDELYSKLSSESSDEILKYYKEATKLDPSWEKAWHSWALFN  302 (352)
T ss_pred             HHHhhcccc--ccccccccchhhhhHHHHHHHHHHHHHHHHhhccccccccHHHHHHHHHHHHHhChhHHHHHHHHHHHH
Confidence            111111000  00000000 00000000012233333333333      7889999999999999998888888777766


Q ss_pred             HhC
Q 040394          645 ASD  647 (691)
Q Consensus       645 ~~~  647 (691)
                      .+.
T Consensus       303 ~~~  305 (352)
T PF02259_consen  303 DKL  305 (352)
T ss_pred             HHH
Confidence            543

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 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=93.78  E-value=1.1  Score=46.07  Aligned_cols=157  Identities=10%  Similarity=-0.040  Sum_probs=94.8

Q ss_pred             HHHHHhcCCHHHHHHHHH--hcc-cCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHH
Q 040394          473 LNFYAKCGDAQSARMVFD--AMR-EKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVG  549 (691)
Q Consensus       473 ~~~~~~~g~~~~A~~~~~--~~~-~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~  549 (691)
                      .....-.++++++.+...  ++. .-+..-.+.++.-+-+.|.++.|+++.+         |..+   -.....+.|+++
T Consensus       268 fk~av~~~d~~~v~~~i~~~~ll~~i~~~~~~~i~~fL~~~G~~e~AL~~~~---------D~~~---rFeLAl~lg~L~  335 (443)
T PF04053_consen  268 FKTAVLRGDFEEVLRMIAASNLLPNIPKDQGQSIARFLEKKGYPELALQFVT---------DPDH---RFELALQLGNLD  335 (443)
T ss_dssp             HHHHHHTT-HHH-----HHHHTGGG--HHHHHHHHHHHHHTT-HHHHHHHSS----------HHH---HHHHHHHCT-HH
T ss_pred             HHHHHHcCChhhhhhhhhhhhhcccCChhHHHHHHHHHHHCCCHHHHHhhcC---------ChHH---HhHHHHhcCCHH
Confidence            344455788888766665  222 1134457778888888888888888643         3222   123345678888


Q ss_pred             HHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 040394          550 EGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLEL  629 (691)
Q Consensus       550 ~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  629 (691)
                      .|.++.++.       ++...|..|.+...+.|+++-|.+.+++.+      -+..|+-.|...|+.+.-.++.+.+...
T Consensus       336 ~A~~~a~~~-------~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~------d~~~L~lLy~~~g~~~~L~kl~~~a~~~  402 (443)
T PF04053_consen  336 IALEIAKEL-------DDPEKWKQLGDEALRQGNIELAEECYQKAK------DFSGLLLLYSSTGDREKLSKLAKIAEER  402 (443)
T ss_dssp             HHHHHCCCC-------STHHHHHHHHHHHHHTTBHHHHHHHHHHCT-------HHHHHHHHHHCT-HHHHHHHHHHHHHT
T ss_pred             HHHHHHHhc-------CcHHHHHHHHHHHHHcCCHHHHHHHHHhhc------CccccHHHHHHhCCHHHHHHHHHHHHHc
Confidence            888775533       367789999999999999999999998885      3566677778888887777776665543


Q ss_pred             CCCCchhHHHHHHHHHhCCCcHHHHHHHHH
Q 040394          630 HPDKACYYVLVSNLYASDGRWIRVNQVREL  659 (691)
Q Consensus       630 ~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~  659 (691)
                      .-.+     ....++.-.|+.++-.+++..
T Consensus       403 ~~~n-----~af~~~~~lgd~~~cv~lL~~  427 (443)
T PF04053_consen  403 GDIN-----IAFQAALLLGDVEECVDLLIE  427 (443)
T ss_dssp             T-HH-----HHHHHHHHHT-HHHHHHHHHH
T ss_pred             cCHH-----HHHHHHHHcCCHHHHHHHHHH
Confidence            3322     222334455788877777643

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 WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=93.70  E-value=1.2  Score=42.71  Aligned_cols=218  Identities=12%  Similarity=0.044  Sum_probs=129.5

Q ss_pred             CcHHHHHHHHHHHHHcC-CCCCchhHHHHHHHHHHhcCCHHHHHHHHHh----ccc---C--CHhHHHHHHHHHhcCCCh
Q 040394          444 GAVQVGSSLHAYSTKQG-LLSSNVYVGTALLNFYAKCGDAQSARMVFDA----MRE---K--NTVTWSAMIGGYGMQGDG  513 (691)
Q Consensus       444 ~~~~~a~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~----~~~---~--~~~~~~~li~~~~~~~~~  513 (691)
                      .+.+.+...|......- -......++..+..+.+..|.+++++..--.    ..+   .  -...|-.+.+++.+.-++
T Consensus        20 ~~~~~al~~w~~~L~~l~~~~~Rf~~lG~l~~a~s~~g~y~~mL~~a~sqi~~a~~~~ds~~~~ea~lnlar~~e~l~~f   99 (518)
T KOG1941|consen   20 NQTEKALQVWTKVLEKLSDLMGRFRVLGCLVTAHSEMGRYKEMLKFAVSQIDTARELEDSDFLLEAYLNLARSNEKLCEF   99 (518)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44455555554433221 0012334556677777888887776554321    111   1  123555566666666666


Q ss_pred             HHHHHHHHHHHH-CCCCCCH---HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC----hhHHHHHHHHHHhcCChH
Q 040394          514 GGSLALFSDMLN-EEVQPNE---VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS----MKHYVCMVDLLARAGRLE  585 (691)
Q Consensus       514 ~~A~~~~~~m~~-~g~~p~~---~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~g~~~  585 (691)
                      .+++.+-+.-.. .|..|..   ....++-.++...+.++++++.|+...+-..-.-|    ..++..|...|.+..+++
T Consensus       100 ~kt~~y~k~~l~lpgt~~~~~~gq~~l~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~l~D~~  179 (518)
T KOG1941|consen  100 HKTISYCKTCLGLPGTRAGQLGGQVSLSMGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQLKDYE  179 (518)
T ss_pred             hhHHHHHHHHhcCCCCCcccccchhhhhHHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHHHHhhh
Confidence            666665544333 2233311   22334555777778888999888866333222222    357888899999999999


Q ss_pred             HHHHHHHhC-------CCCCC-----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhc--CCCC----chhHHHHHHHHHhC
Q 040394          586 EALEFMENM-------PIEPD-----VSLFGAFLHGCGLYSRFDLGEVMIKKMLEL--HPDK----ACYYVLVSNLYASD  647 (691)
Q Consensus       586 ~A~~~~~~~-------~~~p~-----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~p~~----~~~~~~l~~~~~~~  647 (691)
                      +|.-+..+.       +++-=     ..+...|.-++...|....|.+..+++.++  .-.|    ......++.+|...
T Consensus       180 Kal~f~~kA~~lv~s~~l~d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~~aDIyR~~  259 (518)
T KOG1941|consen  180 KALFFPCKAAELVNSYGLKDWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLCFADIYRSR  259 (518)
T ss_pred             HHhhhhHhHHHHHHhcCcCchhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHHHHHHHHhc
Confidence            887665554       32211     123344556778899999999999988773  2222    33446788999999


Q ss_pred             CCcHHHHHHHHHHH
Q 040394          648 GRWIRVNQVRELMK  661 (691)
Q Consensus       648 g~~~~A~~~~~~~~  661 (691)
                      |+.+.|..-|+...
T Consensus       260 gd~e~af~rYe~Am  273 (518)
T KOG1941|consen  260 GDLERAFRRYEQAM  273 (518)
T ss_pred             ccHhHHHHHHHHHH
Confidence            99999988776543

>PRK11906 transcriptional regulator; Provisional

Probab=93.58  E-value=3.7  Score=41.53  Aligned_cols=140  Identities=11%  Similarity=0.064  Sum_probs=90.4

Q ss_pred             CHHHHHHHHHhcc---cCC---HhHHHHHHHHHhc---------CCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhccc
Q 040394          481 DAQSARMVFDAMR---EKN---TVTWSAMIGGYGM---------QGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHT  545 (691)
Q Consensus       481 ~~~~A~~~~~~~~---~~~---~~~~~~li~~~~~---------~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~  545 (691)
                      ..+.|..+|.+..   +-|   ...|..+..++..         ..+..+|.++-++..+.+ +-|......+-.+....
T Consensus       273 ~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h~~~~~~g~~~~~~~~~~a~~~A~rAveld-~~Da~a~~~~g~~~~~~  351 (458)
T PRK11906        273 SIYRAMTIFDRLQNKSDIQTLKTECYCLLAECHMSLALHGKSELELAAQKALELLDYVSDIT-TVDGKILAIMGLITGLS  351 (458)
T ss_pred             HHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHhh
Confidence            3567888888877   333   5566666554432         223455677777777754 44566666666666777


Q ss_pred             CCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHh-CCCCCCHH---HHHHHHHHHHhcCCHHHHH
Q 040394          546 GMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMEN-MPIEPDVS---LFGAFLHGCGLYSRFDLGE  620 (691)
Q Consensus       546 g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~-~~~~p~~~---~~~~l~~~~~~~g~~~~A~  620 (691)
                      ++++.|...|++.   ..+.|| ..+|......+.-+|+.++|.+.+++ +...|...   .....+..|+.+ ..+.|+
T Consensus       352 ~~~~~a~~~f~rA---~~L~Pn~A~~~~~~~~~~~~~G~~~~a~~~i~~alrLsP~~~~~~~~~~~~~~~~~~-~~~~~~  427 (458)
T PRK11906        352 GQAKVSHILFEQA---KIHSTDIASLYYYRALVHFHNEKIEEARICIDKSLQLEPRRRKAVVIKECVDMYVPN-PLKNNI  427 (458)
T ss_pred             cchhhHHHHHHHH---hhcCCccHHHHHHHHHHHHHcCCHHHHHHHHHHHhccCchhhHHHHHHHHHHHHcCC-chhhhH
Confidence            7888999888854   367888 45566666666778899999988888 46666543   333333344443 566777


Q ss_pred             HHHHH
Q 040394          621 VMIKK  625 (691)
Q Consensus       621 ~~~~~  625 (691)
                      .++-+
T Consensus       428 ~~~~~  432 (458)
T PRK11906        428 KLYYK  432 (458)
T ss_pred             HHHhh
Confidence            77665

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=93.54  E-value=0.28  Score=42.71  Aligned_cols=99  Identities=15%  Similarity=0.135  Sum_probs=63.8

Q ss_pred             HhcccCCHHHHHHHHHHchhhcCCCCC------hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCH-HHHHHHHHHHHh
Q 040394          541 ACSHTGMVGEGWKCFYSMCRDFKFVPS------MKHYVCMVDLLARAGRLEEALEFMENM-PIEPDV-SLFGAFLHGCGL  612 (691)
Q Consensus       541 ~~~~~g~~~~A~~~~~~m~~~~~~~p~------~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~-~~~~~l~~~~~~  612 (691)
                      -+.+.|++++|..-|...+..   .|.      ...|..-..++.+.+.++.|++-..+. .+.|.. .....-..+|.+
T Consensus       104 ~~F~ngdyeeA~skY~~Ale~---cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKaiel~pty~kAl~RRAeayek  180 (271)
T KOG4234|consen  104 ELFKNGDYEEANSKYQEALES---CPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKAIELNPTYEKALERRAEAYEK  180 (271)
T ss_pred             HhhhcccHHHHHHHHHHHHHh---CccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhhHhcCchhHHHHHHHHHHHHh
Confidence            456788888888888866433   333      234445556677788888887766665 444432 233333446667


Q ss_pred             cCCHHHHHHHHHHHHhcCCCCchhHHHHHH
Q 040394          613 YSRFDLGEVMIKKMLELHPDKACYYVLVSN  642 (691)
Q Consensus       613 ~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~  642 (691)
                      ...++.|+.-|+++++.+|.........+.
T Consensus       181 ~ek~eealeDyKki~E~dPs~~ear~~i~r  210 (271)
T KOG4234|consen  181 MEKYEEALEDYKKILESDPSRREAREAIAR  210 (271)
T ss_pred             hhhHHHHHHHHHHHHHhCcchHHHHHHHHh
Confidence            778888888888888888886655444443

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=93.53  E-value=0.52  Score=39.16  Aligned_cols=86  Identities=9%  Similarity=0.058  Sum_probs=47.5

Q ss_pred             hcCChHHHHHHHHhC-CCCCCHHHHH-HHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHH
Q 040394          580 RAGRLEEALEFMENM-PIEPDVSLFG-AFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVR  657 (691)
Q Consensus       580 ~~g~~~~A~~~~~~~-~~~p~~~~~~-~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~  657 (691)
                      ..++++++..++..+ -..|+..-.. .-.+.+...|++++|..++++..+-.|..+..--.++.++...|+.+- ..+-
T Consensus        22 ~~~d~~D~e~lLdALrvLrP~~~e~d~~dg~l~i~rg~w~eA~rvlr~l~~~~~~~p~~kAL~A~CL~al~Dp~W-r~~A  100 (153)
T TIGR02561        22 RSADPYDAQAMLDALRVLRPNLKELDMFDGWLLIARGNYDEAARILRELLSSAGAPPYGKALLALCLNAKGDAEW-HVHA  100 (153)
T ss_pred             hcCCHHHHHHHHHHHHHhCCCccccchhHHHHHHHcCCHHHHHHHHHhhhccCCCchHHHHHHHHHHHhcCChHH-HHHH
Confidence            466777777777776 2334332211 123345567777777777777766666655555566666666665432 2223


Q ss_pred             HHHHhCCCc
Q 040394          658 ELMKQRGLS  666 (691)
Q Consensus       658 ~~~~~~g~~  666 (691)
                      +.+++.|-.
T Consensus       101 ~~~le~~~~  109 (153)
T TIGR02561       101 DEVLARDAD  109 (153)
T ss_pred             HHHHHhCCC
Confidence            344444443

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=93.35  E-value=0.66  Score=39.35  Aligned_cols=96  Identities=11%  Similarity=0.105  Sum_probs=65.0

Q ss_pred             hHHHHHHHHH---HhcCChHHHHHHHHhC-CCCCCHHHHHH-HHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHH
Q 040394          569 KHYVCMVDLL---ARAGRLEEALEFMENM-PIEPDVSLFGA-FLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNL  643 (691)
Q Consensus       569 ~~~~~li~~~---~~~g~~~~A~~~~~~~-~~~p~~~~~~~-l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~  643 (691)
                      .+.+.|+..+   .+.++.+++..++..+ -..|....... -.+.+...|++.+|..+++++.+..|..+..--.++.+
T Consensus         8 ~iv~gLie~~~~al~~~~~~D~e~lL~ALrvLRP~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~~~~~p~~kALlA~C   87 (160)
T PF09613_consen    8 EIVGGLIEVLSVALRLGDPDDAEALLDALRVLRPEFPELDLFDGWLHIVRGDWDDALRLLRELEERAPGFPYAKALLALC   87 (160)
T ss_pred             HHHHHHHHHHHHHHccCChHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhCCHHHHHHHHHHHhccCCCChHHHHHHHHH
Confidence            3445555544   4678899999998888 35555543322 23456788999999999999888888877777777777


Q ss_pred             HHhCCCcHHHHHHHHHHHhCCC
Q 040394          644 YASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       644 ~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      +...|+.+ =..+-+++.+.+-
T Consensus        88 L~~~~D~~-Wr~~A~evle~~~  108 (160)
T PF09613_consen   88 LYALGDPS-WRRYADEVLESGA  108 (160)
T ss_pred             HHHcCChH-HHHHHHHHHhcCC
Confidence            77777653 2333455556554

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.27  E-value=3  Score=39.71  Aligned_cols=155  Identities=11%  Similarity=0.042  Sum_probs=108.7

Q ss_pred             HHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHH----HHHHHhcccCCH
Q 040394          476 YAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFT----TILSACSHTGMV  548 (691)
Q Consensus       476 ~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~----~ll~~~~~~g~~  548 (691)
                      ..-.|+..+|...++++.+   .|...++-.-.+|...|+...-...+++..-. ..||...|.    .+.-++...|-+
T Consensus       113 ~~~~g~~h~a~~~wdklL~d~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~-wn~dlp~~sYv~GmyaFgL~E~g~y  191 (491)
T KOG2610|consen  113 LWGRGKHHEAAIEWDKLLDDYPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPK-WNADLPCYSYVHGMYAFGLEECGIY  191 (491)
T ss_pred             hhccccccHHHHHHHHHHHhCchhhhhhhhhhhHHHhccchhhhhhHHHHhccc-cCCCCcHHHHHHHHHHhhHHHhccc
Confidence            3456888888888888876   37788888889999999999999999888764 345553332    233355688999


Q ss_pred             HHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhCCCCCC------HHHHHHHHHHHHhcCCHHHHHH
Q 040394          549 GEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENMPIEPD------VSLFGAFLHGCGLYSRFDLGEV  621 (691)
Q Consensus       549 ~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~------~~~~~~l~~~~~~~g~~~~A~~  621 (691)
                      ++|++.-++.   ..+.|+ .-.-.++.+.+.-.|++.++.+++.+-...-+      ...|-...-.+...+.++.|++
T Consensus       192 ~dAEk~A~ra---lqiN~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~Al~~iE~aeye~ale  268 (491)
T KOG2610|consen  192 DDAEKQADRA---LQINRFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALFHIEGAEYEKALE  268 (491)
T ss_pred             hhHHHHHHhh---ccCCCcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHhhhcccchhHHHH
Confidence            9999988754   244544 34455677888899999999999998731111      1123333344567799999999


Q ss_pred             HHHHHH--hcCCCCc
Q 040394          622 MIKKML--ELHPDKA  634 (691)
Q Consensus       622 ~~~~~~--~~~p~~~  634 (691)
                      +|++-.  ++..++.
T Consensus       269 IyD~ei~k~l~k~Da  283 (491)
T KOG2610|consen  269 IYDREIWKRLEKDDA  283 (491)
T ss_pred             HHHHHHHHHhhccch
Confidence            998643  3555655

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=93.27  E-value=0.16  Score=30.89  Aligned_cols=26  Identities=12%  Similarity=0.155  Sum_probs=20.1

Q ss_pred             hHHHHHHHHHhCCCcHHHHHHHHHHH
Q 040394          636 YYVLVSNLYASDGRWIRVNQVRELMK  661 (691)
Q Consensus       636 ~~~~l~~~~~~~g~~~~A~~~~~~~~  661 (691)
                      ++..|+.+|.+.|+|++|++++++.+
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL   26 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQAL   26 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            35678888888888888888888855

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

Probab=93.18  E-value=11  Score=38.34  Aligned_cols=79  Identities=16%  Similarity=0.167  Sum_probs=50.2

Q ss_pred             HHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcC-ChHHHHHHHhccC
Q 040394          129 DIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCR-DIGSSRQVFDETL  207 (691)
Q Consensus       129 ~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~  207 (691)
                      +...+|.....+ +.-|+..|..-+.-+-+.+.+.+...+|.+|....|.++..|-.-..-....+ .++.|..+|.+-.
T Consensus        89 rIv~lyr~at~r-f~~D~~lW~~yi~f~kk~~~~~~v~ki~~~~l~~Hp~~~dLWI~aA~wefe~n~ni~saRalflrgL  167 (568)
T KOG2396|consen   89 RIVFLYRRATNR-FNGDVKLWLSYIAFCKKKKTYGEVKKIFAAMLAKHPNNPDLWIYAAKWEFEINLNIESARALFLRGL  167 (568)
T ss_pred             HHHHHHHHHHHh-cCCCHHHHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCchhHHhhhhhHHhhccchHHHHHHHHHHh
Confidence            334445544443 44477777777777777777888888888888877776666654443333333 3777777777654


Q ss_pred             C
Q 040394          208 D  208 (691)
Q Consensus       208 ~  208 (691)
                      +
T Consensus       168 R  168 (568)
T KOG2396|consen  168 R  168 (568)
T ss_pred             h
Confidence            4

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=93.13  E-value=2.2  Score=43.16  Aligned_cols=54  Identities=11%  Similarity=0.217  Sum_probs=28.1

Q ss_pred             HHHHHHhcCChHHHHHHHHhC-C-CCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 040394          574 MVDLLARAGRLEEALEFMENM-P-IEP--DVSLFGAFLHGCGLYSRFDLGEVMIKKML  627 (691)
Q Consensus       574 li~~~~~~g~~~~A~~~~~~~-~-~~p--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  627 (691)
                      +...+.+.|+.++|++.++++ . .++  +..+...|+.++...+.+.++..++.+--
T Consensus       265 LAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYd  322 (539)
T PF04184_consen  265 LAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYD  322 (539)
T ss_pred             HHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhc
Confidence            444444556666666655555 2 111  12345555555666666666666655543

The molecular function of this protein is uncertain.

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=93.08  E-value=0.24  Score=39.75  Aligned_cols=59  Identities=14%  Similarity=0.017  Sum_probs=53.6

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHh-CCCc
Q 040394          608 HGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQ-RGLS  666 (691)
Q Consensus       608 ~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~g~~  666 (691)
                      -++...|+.+.|++.|.+++.+-|..+..|..-+..+.-+|+.++|.+-+++.++ .|.+
T Consensus        51 valaE~g~Ld~AlE~F~qal~l~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~  110 (175)
T KOG4555|consen   51 IALAEAGDLDGALELFGQALCLAPERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQ  110 (175)
T ss_pred             HHHHhccchHHHHHHHHHHHHhcccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCcc
Confidence            3567899999999999999999999999999999999999999999999999987 4444

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=92.38  E-value=7.8  Score=34.64  Aligned_cols=29  Identities=17%  Similarity=0.173  Sum_probs=18.3

Q ss_pred             hhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          635 CYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       635 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      .+|..|+..+...|+.++|..+++.....
T Consensus       238 EtyFYL~K~~l~~G~~~~A~~LfKLaian  266 (297)
T COG4785         238 ETYFYLGKYYLSLGDLDEATALFKLAVAN  266 (297)
T ss_pred             HHHHHHHHHHhccccHHHHHHHHHHHHHH
Confidence            45566666666777777776666655543

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=92.26  E-value=0.78  Score=43.24  Aligned_cols=59  Identities=12%  Similarity=0.228  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhC-CCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040394          570 HYVCMVDLLARAGRLEEALEFMENM-PIE-PDVSLFGAFLHGCGLYSRFDLGEVMIKKMLE  628 (691)
Q Consensus       570 ~~~~li~~~~~~g~~~~A~~~~~~~-~~~-p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  628 (691)
                      ++..++..+...|+.+.+.+.+++. ... -+...|..++.+|.+.|+...|+..|+++.+
T Consensus       155 ~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~  215 (280)
T COG3629         155 ALTKLAEALIACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKK  215 (280)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchHHHHHHHHHHH
Confidence            3444444455555555555554444 222 2444555555555555555555555554443

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=92.14  E-value=9.8  Score=35.23  Aligned_cols=49  Identities=22%  Similarity=0.173  Sum_probs=22.2

Q ss_pred             hcCCHHHHHHHHHhcCC--C----ChhHHHHHHHHHHhcCCchhHHHHHHHhhHC
Q 040394          293 KCGNIRDARSVFDELCS--I----DLVSWTAMIVGYTQSGYPDKALKLFTDKKWA  341 (691)
Q Consensus       293 ~~g~~~~A~~~~~~~~~--~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  341 (691)
                      +.|++++|.+.|+.+..  |    ...+--.++.++.+.++++.|+..+++....
T Consensus        46 ~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~l  100 (254)
T COG4105          46 QKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRL  100 (254)
T ss_pred             hcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHh
Confidence            44555555555555521  1    1122333444445555555555555554443

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=92.04  E-value=0.28  Score=29.74  Aligned_cols=27  Identities=4%  Similarity=-0.039  Sum_probs=21.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040394          602 LFGAFLHGCGLYSRFDLGEVMIKKMLE  628 (691)
Q Consensus       602 ~~~~l~~~~~~~g~~~~A~~~~~~~~~  628 (691)
                      +|..|...|.+.|++++|+.++++++.
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL~   27 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQALA   27 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            467788889999999999999998664

>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=91.83  E-value=0.34  Score=28.77  Aligned_cols=31  Identities=19%  Similarity=0.226  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040394          602 LFGAFLHGCGLYSRFDLGEVMIKKMLELHPD  632 (691)
Q Consensus       602 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~  632 (691)
                      +|..+...+...|++++|...|++++++.|+
T Consensus         3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~~~~~   33 (34)
T PF13181_consen    3 AYYNLGKIYEQLGDYEEALEYFEKALELNPD   33 (34)
T ss_dssp             HHHHHHHHHHHTTSHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            4555666666777777777777777776664

...

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=91.79  E-value=0.26  Score=29.41  Aligned_cols=32  Identities=9%  Similarity=0.158  Sum_probs=24.8

Q ss_pred             HHHHHHhCCCChhHHHHHHHHhHhcCChHHHH
Q 040394          169 HCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSR  200 (691)
Q Consensus       169 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  200 (691)
                      |++.++..|.+..+|+.|...|...|++++|+
T Consensus         2 y~kAie~~P~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen    2 YKKAIELNPNNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             hHHHHHHCCCCHHHHHHHHHHHHHCcCHHhhc
Confidence            45666677778888888888888888888875

>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []

Probab=91.61  E-value=13  Score=35.72  Aligned_cols=101  Identities=9%  Similarity=-0.010  Sum_probs=60.3

Q ss_pred             HHHHHHHHHHhccCcHH---HHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC---CHhHHHHHH
Q 040394          431 VTLVSVISACASLGAVQ---VGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK---NTVTWSAMI  504 (691)
Q Consensus       431 ~~~~~ll~~~~~~~~~~---~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~li  504 (691)
                      .++..++.++...+..+   .|..+++.+....  +..+.++..-+..+.+.++.+++.+.+.+|...   ....+...+
T Consensus        85 ~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~--~~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~~~~~e~~~~~~l  162 (278)
T PF08631_consen   85 SILRLLANAYLEWDTYESVEKALNALRLLESEY--GNKPEVFLLKLEILLKSFDEEEYEEILMRMIRSVDHSESNFDSIL  162 (278)
T ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhC--CCCcHHHHHHHHHHhccCChhHHHHHHHHHHHhcccccchHHHHH
Confidence            45667777777776654   4555555554443  445666666677777788888888888888742   233444444


Q ss_pred             HHHh--cCCChHHHHHHHHHHHHCCCCCCHH
Q 040394          505 GGYG--MQGDGGGSLALFSDMLNEEVQPNEV  533 (691)
Q Consensus       505 ~~~~--~~~~~~~A~~~~~~m~~~g~~p~~~  533 (691)
                      ..+.  .......|...+..+....+.|...
T Consensus       163 ~~i~~l~~~~~~~a~~~ld~~l~~r~~~~~~  193 (278)
T PF08631_consen  163 HHIKQLAEKSPELAAFCLDYLLLNRFKSSED  193 (278)
T ss_pred             HHHHHHHhhCcHHHHHHHHHHHHHHhCCChh
Confidence            4441  1233455666666666555555543

It is also involved in sporulation [].

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.59  E-value=6.2  Score=33.86  Aligned_cols=93  Identities=18%  Similarity=0.050  Sum_probs=46.5

Q ss_pred             HHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHH-HHHHHH--HHHhccCcHHHHHHHHHHHHHcCCCC
Q 040394          387 LVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAV-TLVSVI--SACASLGAVQVGSSLHAYSTKQGLLS  463 (691)
Q Consensus       387 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~-~~~~ll--~~~~~~~~~~~a~~~~~~~~~~~~~~  463 (691)
                      ........|+...|...|+++-...              ..|-.. -...|=  -.+...|.++....-.+.+...+. +
T Consensus       100 ~at~~a~kgdta~AV~aFdeia~dt--------------~~P~~~rd~ARlraa~lLvD~gsy~dV~srvepLa~d~n-~  164 (221)
T COG4649         100 AATLLAQKGDTAAAVAAFDEIAADT--------------SIPQIGRDLARLRAAYLLVDNGSYDDVSSRVEPLAGDGN-P  164 (221)
T ss_pred             HHHHHhhcccHHHHHHHHHHHhccC--------------CCcchhhHHHHHHHHHHHhccccHHHHHHHhhhccCCCC-h
Confidence            3444556677777777777765431              122221 111111  123455555555555555544443 3


Q ss_pred             CchhHHHHHHHHHHhcCCHHHHHHHHHhccc
Q 040394          464 SNVYVGTALLNFYAKCGDAQSARMVFDAMRE  494 (691)
Q Consensus       464 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  494 (691)
                      -....-..|.-+-.+.|++..|.++|..+..
T Consensus       165 mR~sArEALglAa~kagd~a~A~~~F~qia~  195 (221)
T COG4649         165 MRHSAREALGLAAYKAGDFAKAKSWFVQIAN  195 (221)
T ss_pred             hHHHHHHHHhHHHHhccchHHHHHHHHHHHc
Confidence            3344444555555566666666666665543

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=91.50  E-value=5.7  Score=36.19  Aligned_cols=162  Identities=15%  Similarity=0.131  Sum_probs=91.4

Q ss_pred             HHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHC
Q 040394          447 QVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNE  526 (691)
Q Consensus       447 ~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~  526 (691)
                      +.|.-+.+++.+.   +.-...|+--..+|..+|..+.|-..+++.-+            .....+++.|+++|++...-
T Consensus        75 EqaamLake~~kl---sEvvdl~eKAs~lY~E~GspdtAAmaleKAak------------~lenv~Pd~AlqlYqralav  139 (308)
T KOG1585|consen   75 EQAAMLAKELSKL---SEVVDLYEKASELYVECGSPDTAAMALEKAAK------------ALENVKPDDALQLYQRALAV  139 (308)
T ss_pred             HHHHHHHHHHHHh---HHHHHHHHHHHHHHHHhCCcchHHHHHHHHHH------------HhhcCCHHHHHHHHHHHHHH
Confidence            4444444444432   33445566666778888887777766665432            22344566666666665431


Q ss_pred             CCCCC------HHHHHHHHHHhcccCCHHHHHHHHHHch---hhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC--
Q 040394          527 EVQPN------EVIFTTILSACSHTGMVGEGWKCFYSMC---RDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM--  594 (691)
Q Consensus       527 g~~p~------~~~~~~ll~~~~~~g~~~~A~~~~~~m~---~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~--  594 (691)
                       +..+      ...+...-..+.+...+++|-..+.+-.   ....--|+ -..|-..|-.+.-..++..|...++.-  
T Consensus       140 -ve~~dr~~ma~el~gk~sr~lVrl~kf~Eaa~a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~q  218 (308)
T KOG1585|consen  140 -VEEDDRDQMAFELYGKCSRVLVRLEKFTEAATAFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQ  218 (308)
T ss_pred             -HhccchHHHHHHHHHHhhhHhhhhHHhhHHHHHHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhc
Confidence             1111      1223333445566666666655554220   00011122 233555666777788999999999884  


Q ss_pred             -C---CCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 040394          595 -P---IEPDVSLFGAFLHGCGLYSRFDLGEVMIKK  625 (691)
Q Consensus       595 -~---~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~  625 (691)
                       +   ...+..+...|+.+| ..||.+++..++..
T Consensus       219 ip~f~~sed~r~lenLL~ay-d~gD~E~~~kvl~s  252 (308)
T KOG1585|consen  219 IPAFLKSEDSRSLENLLTAY-DEGDIEEIKKVLSS  252 (308)
T ss_pred             CccccChHHHHHHHHHHHHh-ccCCHHHHHHHHcC
Confidence             2   223456778888777 77888888777653

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=91.05  E-value=2.2  Score=41.10  Aligned_cols=185  Identities=10%  Similarity=-0.029  Sum_probs=120.5

Q ss_pred             hcCCHHHHHHHHHhcccC------CHhHHHHHHHHHhcCCChHHHHHHH----HHHHHCC-CCCCHHHHHHHHHHhcccC
Q 040394          478 KCGDAQSARMVFDAMREK------NTVTWSAMIGGYGMQGDGGGSLALF----SDMLNEE-VQPNEVIFTTILSACSHTG  546 (691)
Q Consensus       478 ~~g~~~~A~~~~~~~~~~------~~~~~~~li~~~~~~~~~~~A~~~~----~~m~~~g-~~p~~~~~~~ll~~~~~~g  546 (691)
                      ...+.++|+..+.....+      ...+|..+..+.++.|.+++++..-    +-..+.. -..-...|..+.+++.+..
T Consensus        18 ~s~~~~~al~~w~~~L~~l~~~~~Rf~~lG~l~~a~s~~g~y~~mL~~a~sqi~~a~~~~ds~~~~ea~lnlar~~e~l~   97 (518)
T KOG1941|consen   18 QSNQTEKALQVWTKVLEKLSDLMGRFRVLGCLVTAHSEMGRYKEMLKFAVSQIDTARELEDSDFLLEAYLNLARSNEKLC   97 (518)
T ss_pred             cCchHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445667777776655532      2346777888888999888876432    2121110 0011134555556666666


Q ss_pred             CHHHHHHHHHHchhhcCCCCC---hhHHHHHHHHHHhcCChHHHHHHHHhC-C-----CCC--CHHHHHHHHHHHHhcCC
Q 040394          547 MVGEGWKCFYSMCRDFKFVPS---MKHYVCMVDLLARAGRLEEALEFMENM-P-----IEP--DVSLFGAFLHGCGLYSR  615 (691)
Q Consensus       547 ~~~~A~~~~~~m~~~~~~~p~---~~~~~~li~~~~~~g~~~~A~~~~~~~-~-----~~p--~~~~~~~l~~~~~~~g~  615 (691)
                      ++.+++.+-..-....|..|.   .....++..++...+.++++++.|+.. .     ..|  ....+..|...|.+..|
T Consensus        98 ~f~kt~~y~k~~l~lpgt~~~~~~gq~~l~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~l~D  177 (518)
T KOG1941|consen   98 EFHKTISYCKTCLGLPGTRAGQLGGQVSLSMGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQLKD  177 (518)
T ss_pred             HhhhHHHHHHHHhcCCCCCcccccchhhhhHHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHHHHh
Confidence            666777766654444444552   223445667777788899999999887 1     222  23478888899999999


Q ss_pred             HHHHHHHHHHHHhcC----CCC------chhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          616 FDLGEVMIKKMLELH----PDK------ACYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       616 ~~~A~~~~~~~~~~~----p~~------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      +++|.-+..++.++.    -++      ....+.++..+...|+..+|.+..++..+
T Consensus       178 ~~Kal~f~~kA~~lv~s~~l~d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~k  234 (518)
T KOG1941|consen  178 YEKALFFPCKAAELVNSYGLKDWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMK  234 (518)
T ss_pred             hhHHhhhhHhHHHHHHhcCcCchhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHH
Confidence            999999999988732    222      23456788889999999999988877654

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=90.80  E-value=35  Score=38.97  Aligned_cols=156  Identities=14%  Similarity=0.090  Sum_probs=83.9

Q ss_pred             CCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHH----HhcCCChhhHHHHH
Q 040394          295 GNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSA----SAQLGNLNMGRMVH  370 (691)
Q Consensus       295 g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~----~~~~~~~~~a~~~~  370 (691)
                      ++++.|+.-+.++.   ...|.-.+..--++|.+++|+.++        +|+...+..+..+    +.....+++|.-+|
T Consensus       894 ~ry~~AL~hLs~~~---~~~~~e~~n~I~kh~Ly~~aL~ly--------~~~~e~~k~i~~~ya~hL~~~~~~~~Aal~Y  962 (1265)
T KOG1920|consen  894 KRYEDALSHLSECG---ETYFPECKNYIKKHGLYDEALALY--------KPDSEKQKVIYEAYADHLREELMSDEAALMY  962 (1265)
T ss_pred             HHHHHHHHHHHHcC---ccccHHHHHHHHhcccchhhhhee--------ccCHHHHHHHHHHHHHHHHHhccccHHHHHH
Confidence            45666666666653   223444444445677777777775        4565555444433    33445555554444


Q ss_pred             HHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHH--HHHHHHHHhccCcHHH
Q 040394          371 SLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVT--LVSVISACASLGAVQV  448 (691)
Q Consensus       371 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~--~~~ll~~~~~~~~~~~  448 (691)
                      +..-+.        .-.+.+|..+|++.+|+.+-.++...                 -|...  -..|..-+...++.-+
T Consensus       963 e~~Gkl--------ekAl~a~~~~~dWr~~l~~a~ql~~~-----------------~de~~~~a~~L~s~L~e~~kh~e 1017 (1265)
T KOG1920|consen  963 ERCGKL--------EKALKAYKECGDWREALSLAAQLSEG-----------------KDELVILAEELVSRLVEQRKHYE 1017 (1265)
T ss_pred             HHhccH--------HHHHHHHHHhccHHHHHHHHHhhcCC-----------------HHHHHHHHHHHHHHHHHcccchh
Confidence            332211        23445566666666666666665422                 12211  1345556666666666


Q ss_pred             HHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC
Q 040394          449 GSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK  495 (691)
Q Consensus       449 a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  495 (691)
                      |-++..+....    +     .-.+..|++...|++|..+-......
T Consensus      1018 Aa~il~e~~sd----~-----~~av~ll~ka~~~~eAlrva~~~~~~ 1055 (1265)
T KOG1920|consen 1018 AAKILLEYLSD----P-----EEAVALLCKAKEWEEALRVASKAKRD 1055 (1265)
T ss_pred             HHHHHHHHhcC----H-----HHHHHHHhhHhHHHHHHHHHHhcccc
Confidence            66665544321    1     12344567777788887777665543

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=90.56  E-value=8.5  Score=37.28  Aligned_cols=128  Identities=13%  Similarity=0.152  Sum_probs=80.6

Q ss_pred             HHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHh--c----CCHHHHHHHHHhcccC-------CHhHHHHHHHHHhcCCC
Q 040394          446 VQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAK--C----GDAQSARMVFDAMREK-------NTVTWSAMIGGYGMQGD  512 (691)
Q Consensus       446 ~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~----g~~~~A~~~~~~~~~~-------~~~~~~~li~~~~~~~~  512 (691)
                      ++....+++.+.+.|. ..+..+|-+..-....  .    .....|..+|+.|++.       +-..+..|+..  ..++
T Consensus        78 ~~~~~~~y~~L~~~gF-k~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~  154 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGF-KRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSED  154 (297)
T ss_pred             HHHHHHHHHHHHHhcc-CccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--cccc
Confidence            4566788899999988 6666655543332222  2    2355688999999862       44455555444  3333


Q ss_pred             h----HHHHHHHHHHHHCCCCCCHH--HHHHHHHHhcccCC--HHHHHHHHHHchhhcCCCCChhHHHHHHHH
Q 040394          513 G----GGSLALFSDMLNEEVQPNEV--IFTTILSACSHTGM--VGEGWKCFYSMCRDFKFVPSMKHYVCMVDL  577 (691)
Q Consensus       513 ~----~~A~~~~~~m~~~g~~p~~~--~~~~ll~~~~~~g~--~~~A~~~~~~m~~~~~~~p~~~~~~~li~~  577 (691)
                      +    +.+..+|+.+.+.|+..+..  ....++..+.....  ..++.++++.+ ++.|+++....|..+.-.
T Consensus       155 ~e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l-~~~~~kik~~~yp~lGlL  226 (297)
T PF13170_consen  155 VEELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNAL-KKNGVKIKYMHYPTLGLL  226 (297)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHH-HHcCCccccccccHHHHH
Confidence            3    45678888898888887654  33333333322222  44778888888 666999887777765443

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=90.27  E-value=0.5  Score=27.98  Aligned_cols=29  Identities=10%  Similarity=0.036  Sum_probs=25.1

Q ss_pred             hhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          635 CYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       635 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      .++..++.++...|++++|++.+++.++.
T Consensus         2 ~~~~~lg~~~~~~~~~~~A~~~~~~al~l   30 (34)
T PF07719_consen    2 EAWYYLGQAYYQLGNYEEAIEYFEKALEL   30 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            46788999999999999999999998764

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 ....

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=90.07  E-value=7  Score=32.76  Aligned_cols=66  Identities=5%  Similarity=-0.100  Sum_probs=41.5

Q ss_pred             ccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCCC-hhhHHHHHHHHHh
Q 040394          158 ELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKN-VVSWTSMIAGYVQ  223 (691)
Q Consensus       158 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~li~~~~~  223 (691)
                      ..++++++..+++.|.-..|.....-..-...+...|++++|.++|+++.+.. ...|..-+.++|-
T Consensus        22 ~~~d~~D~e~lLdALrvLrP~~~e~d~~dg~l~i~rg~w~eA~rvlr~l~~~~~~~p~~kAL~A~CL   88 (153)
T TIGR02561        22 RSADPYDAQAMLDALRVLRPNLKELDMFDGWLLIARGNYDEAARILRELLSSAGAPPYGKALLALCL   88 (153)
T ss_pred             hcCCHHHHHHHHHHHHHhCCCccccchhHHHHHHHcCCHHHHHHHHHhhhccCCCchHHHHHHHHHH
Confidence            46677777777777777666655555555556677777777777777776543 2344444444443

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=89.90  E-value=0.72  Score=43.75  Aligned_cols=96  Identities=11%  Similarity=0.073  Sum_probs=70.0

Q ss_pred             HHHhcccCCHHHHHHHHHHchhhcCCCC-ChhHHHHHHHHHHhcCChHHHHHHHHhC-CCC-CCHHHHHHHHHHHHhcCC
Q 040394          539 LSACSHTGMVGEGWKCFYSMCRDFKFVP-SMKHYVCMVDLLARAGRLEEALEFMENM-PIE-PDVSLFGAFLHGCGLYSR  615 (691)
Q Consensus       539 l~~~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~-p~~~~~~~l~~~~~~~g~  615 (691)
                      -.-|.+.|.+++|+..|..-   ..+.| |.+++..-..+|.+..++..|..-.... ... .=...|..-+.+-...|+
T Consensus       104 GN~yFKQgKy~EAIDCYs~~---ia~~P~NpV~~~NRA~AYlk~K~FA~AE~DC~~AiaLd~~Y~KAYSRR~~AR~~Lg~  180 (536)
T KOG4648|consen  104 GNTYFKQGKYEEAIDCYSTA---IAVYPHNPVYHINRALAYLKQKSFAQAEEDCEAAIALDKLYVKAYSRRMQARESLGN  180 (536)
T ss_pred             hhhhhhccchhHHHHHhhhh---hccCCCCccchhhHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHHHHHHHHHhh
Confidence            34678899999999999844   36777 7888888888999999888777655554 211 112345555555556788


Q ss_pred             HHHHHHHHHHHHhcCCCCchhH
Q 040394          616 FDLGEVMIKKMLELHPDKACYY  637 (691)
Q Consensus       616 ~~~A~~~~~~~~~~~p~~~~~~  637 (691)
                      .++|.+-++..+++.|++...-
T Consensus       181 ~~EAKkD~E~vL~LEP~~~ELk  202 (536)
T KOG4648|consen  181 NMEAKKDCETVLALEPKNIELK  202 (536)
T ss_pred             HHHHHHhHHHHHhhCcccHHHH
Confidence            8999999999999999965443

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=89.82  E-value=5.7  Score=38.41  Aligned_cols=51  Identities=14%  Similarity=0.252  Sum_probs=36.3

Q ss_pred             hhHHHHHHHHHHHcCCCCCcchHHHHHHHHcc--cC----ChhHHHHHHHHHHHhCC
Q 040394          127 YKDIVEFYKCMRKRLKEHDNFVFSKVLKACCE--LR----DIDEGMKVHCEIVKVGG  177 (691)
Q Consensus       127 ~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~--~~----~~~~a~~~~~~~~~~~~  177 (691)
                      +++.+.+++.|.+.|+.-+..+|.+..-....  ..    ....|.++|+.|++..+
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~  134 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHP  134 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCc
Confidence            45667788999999999888777664443332  22    34568899999988774

>KOG1550 consensus Extracellular protein SEL-1 and related proteins [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=89.75  E-value=32  Score=37.01  Aligned_cols=212  Identities=8%  Similarity=0.036  Sum_probs=125.9

Q ss_pred             cHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHh-cCCHHHHHHHHHhcccC-CHhHHHHHHHHH----hcCCChHHHHH
Q 040394          445 AVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAK-CGDAQSARMVFDAMREK-NTVTWSAMIGGY----GMQGDGGGSLA  518 (691)
Q Consensus       445 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~~~A~~~~~~~~~~-~~~~~~~li~~~----~~~~~~~~A~~  518 (691)
                      +.+.|..++....+.|  .|+.......+..... ..+...|.++|....+. .+..+-.+...|    ....+...|..
T Consensus       308 d~~~A~~~~~~aA~~g--~~~a~~~lg~~~~~g~~~~d~~~A~~yy~~Aa~~G~~~A~~~la~~y~~G~gv~r~~~~A~~  385 (552)
T KOG1550|consen  308 DYEKALKLYTKAAELG--NPDAQYLLGVLYETGTKERDYRRAFEYYSLAAKAGHILAIYRLALCYELGLGVERNLELAFA  385 (552)
T ss_pred             cHHHHHHHHHHHHhcC--CchHHHHHHHHHHcCCccccHHHHHHHHHHHHHcCChHHHHHHHHHHHhCCCcCCCHHHHHH
Confidence            6778999999999988  5666655444433333 34678999999887754 333333333222    23567888999


Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHH---Hh----cCChHHHHHHH
Q 040394          519 LFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLL---AR----AGRLEEALEFM  591 (691)
Q Consensus       519 ~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~---~~----~g~~~~A~~~~  591 (691)
                      ++++..+.| .|....-...+..+.. +.++.+.-.+..+ ...+..-....-..++...   ..    ..+.+.+...+
T Consensus       386 ~~k~aA~~g-~~~A~~~~~~~~~~g~-~~~~~~~~~~~~~-a~~g~~~~q~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~  462 (552)
T KOG1550|consen  386 YYKKAAEKG-NPSAAYLLGAFYEYGV-GRYDTALALYLYL-AELGYEVAQSNAAYLLDQSEEDLFSRGVISTLERAFSLY  462 (552)
T ss_pred             HHHHHHHcc-ChhhHHHHHHHHHHcc-ccccHHHHHHHHH-HHhhhhHHhhHHHHHHHhccccccccccccchhHHHHHH
Confidence            999999988 4443333333444444 6666666665555 4434332211111111111   11    22556666777


Q ss_pred             HhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhC-C--CcHHHHHHHHHHHhCC
Q 040394          592 ENMPIEPDVSLFGAFLHGCGL----YSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASD-G--RWIRVNQVRELMKQRG  664 (691)
Q Consensus       592 ~~~~~~p~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~-g--~~~~A~~~~~~~~~~g  664 (691)
                      .+...+-+......+...|..    ..+.+.|...+..+....   ......++.++..- |  .+..|.++++...+.+
T Consensus       463 ~~a~~~g~~~a~~~lgd~y~~g~g~~~d~~~a~~~y~~a~~~~---~~~~~nlg~~~e~g~g~~~~~~a~~~~~~~~~~~  539 (552)
T KOG1550|consen  463 SRAAAQGNADAILKLGDYYYYGLGTGRDPEKAAAQYARASEQG---AQALFNLGYMHEHGEGIKVLHLAKRYYDQASEED  539 (552)
T ss_pred             HHHHhccCHHHHhhhcceeeecCCCCCChHHHHHHHHHHHHhh---hHHHhhhhhHHhcCcCcchhHHHHHHHHHHHhcC
Confidence            776545555666666665543    246888888888877766   55666666666533 1  2678888888777644

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=89.31  E-value=14  Score=32.07  Aligned_cols=100  Identities=11%  Similarity=0.036  Sum_probs=56.3

Q ss_pred             HHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcC--CHHHHHHHHHhcC
Q 040394          231 LVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCG--NIRDARSVFDELC  308 (691)
Q Consensus       231 ~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g--~~~~A~~~~~~~~  308 (691)
                      .+.++.+.+.+++|+...+..++..+.+.|++..    +.+++..++-+|.......+-.+....  -..-|.+.+.++.
T Consensus        14 lEYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~----L~qllq~~Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL~   89 (167)
T PF07035_consen   14 LEYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQ----LHQLLQYHVIPDSKPLACQLLSLGNQYPPAYQLGLDMLKRLG   89 (167)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHH----HHHHHhhcccCCcHHHHHHHHHhHccChHHHHHHHHHHHHhh
Confidence            3455666667777777777777777777776543    344445555555544443332222211  1223344444332


Q ss_pred             CCChhHHHHHHHHHHhcCCchhHHHHHHHh
Q 040394          309 SIDLVSWTAMIVGYTQSGYPDKALKLFTDK  338 (691)
Q Consensus       309 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  338 (691)
                          ..+..++..+...|++-+|+++.+..
T Consensus        90 ----~~~~~iievLL~~g~vl~ALr~ar~~  115 (167)
T PF07035_consen   90 ----TAYEEIIEVLLSKGQVLEALRYARQY  115 (167)
T ss_pred             ----hhHHHHHHHHHhCCCHHHHHHHHHHc
Confidence                23455566677777777777777654

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=89.14  E-value=3.8  Score=38.80  Aligned_cols=76  Identities=16%  Similarity=0.218  Sum_probs=63.6

Q ss_pred             hHHHHHHHHHHHhcCCHHHHHHHHHhcCC---CChhHHHHHHHHHHhcCCchhHHHHHHHhhH-----CCCCCcHHHHHH
Q 040394          281 SHLVTALLDMYVKCGNIRDARSVFDELCS---IDLVSWTAMIVGYTQSGYPDKALKLFTDKKW-----ADFFPNHVTIAS  352 (691)
Q Consensus       281 ~~~~~~li~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~t~~~  352 (691)
                      ..++..++..+..+|+.+.+.+.++++..   -+...|..+|.+|.+.|+...|+..|+.+.+     .|+.|...+...
T Consensus       153 ~~~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~  232 (280)
T COG3629         153 IKALTKLAEALIACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRAL  232 (280)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHH
Confidence            45678888999999999999999998833   3667899999999999999999999988765     589998888766


Q ss_pred             HHHH
Q 040394          353 VLSA  356 (691)
Q Consensus       353 ll~~  356 (691)
                      ....
T Consensus       233 y~~~  236 (280)
T COG3629         233 YEEI  236 (280)
T ss_pred             HHHH
Confidence            6655

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=89.14  E-value=11  Score=30.78  Aligned_cols=140  Identities=14%  Similarity=0.113  Sum_probs=77.0

Q ss_pred             HhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHH
Q 040394          222 VQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDAR  301 (691)
Q Consensus       222 ~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~  301 (691)
                      .-.|..++..++..+...+   .+..-||.+|--....-+-+...+.++.+   |---|..          .+|++....
T Consensus        13 ildG~V~qGveii~k~v~S---sni~E~NWvICNiiDaa~C~yvv~~LdsI---GkiFDis----------~C~NlKrVi   76 (161)
T PF09205_consen   13 ILDGDVKQGVEIIEKTVNS---SNIKEYNWVICNIIDAADCDYVVETLDSI---GKIFDIS----------KCGNLKRVI   76 (161)
T ss_dssp             HHTT-HHHHHHHHHHHHHH---S-HHHHTHHHHHHHHH--HHHHHHHHHHH---GGGS-GG----------G-S-THHHH
T ss_pred             HHhchHHHHHHHHHHHcCc---CCccccceeeeecchhhchhHHHHHHHHH---hhhcCch----------hhcchHHHH
Confidence            4467777888887777654   35556666666555554444444444433   2222221          223333333


Q ss_pred             HHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCC
Q 040394          302 SVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLE  379 (691)
Q Consensus       302 ~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  379 (691)
                      ..+-.+. .+......-+..+...|+-|+-.+++.++.. +-.+++.....+..+|.+.|+..++..++.++.+.|..
T Consensus        77 ~C~~~~n-~~se~vD~ALd~lv~~~kkDqLdki~~~l~k-n~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~k  152 (161)
T PF09205_consen   77 ECYAKRN-KLSEYVDLALDILVKQGKKDQLDKIYNELKK-NEEINPEFLVKIANAYKKLGNTREANELLKEACEKGLK  152 (161)
T ss_dssp             HHHHHTT----HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             HHHHHhc-chHHHHHHHHHHHHHhccHHHHHHHHHHHhh-ccCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhchH
Confidence            3332221 1233445556777888888888888888765 34677777888888999999988888888888777754

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=89.13  E-value=0.77  Score=26.86  Aligned_cols=28  Identities=11%  Similarity=0.179  Sum_probs=17.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040394          605 AFLHGCGLYSRFDLGEVMIKKMLELHPD  632 (691)
Q Consensus       605 ~l~~~~~~~g~~~~A~~~~~~~~~~~p~  632 (691)
                      .+..++.+.|++++|...++++++..|+
T Consensus         5 ~~a~~~~~~g~~~~A~~~~~~~~~~~P~   32 (33)
T PF13174_consen    5 RLARCYYKLGDYDEAIEYFQRLIKRYPD   32 (33)
T ss_dssp             HHHHHHHHHCHHHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHHCcC
Confidence            3445555666667777777666666665

>KOG0403 consensus Neoplastic transformation suppressor Pdcd4/MA-3, contains MA3 domain [Signal transduction mechanisms]

Probab=89.10  E-value=26  Score=35.10  Aligned_cols=75  Identities=15%  Similarity=0.036  Sum_probs=58.5

Q ss_pred             HHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhC
Q 040394          350 IASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDD  424 (691)
Q Consensus       350 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~  424 (691)
                      ...|+.-|...|+..+|.+..+++--.-.....++.+++.+.-+.|+-.....+++..-..+.++.+.|-.++.+
T Consensus       512 I~~LLeEY~~~GdisEA~~CikeLgmPfFhHEvVkkAlVm~mEkk~d~t~~ldLLk~cf~sglIT~nQMtkGf~R  586 (645)
T KOG0403|consen  512 IDMLLEEYELSGDISEACHCIKELGMPFFHHEVVKKALVMVMEKKGDSTMILDLLKECFKSGLITTNQMTKGFER  586 (645)
T ss_pred             HHHHHHHHHhccchHHHHHHHHHhCCCcchHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcCceeHHHhhhhhhh
Confidence            456788899999999998876554222222677889999999999998888999998888887877777777765

>KOG0403 consensus Neoplastic transformation suppressor Pdcd4/MA-3, contains MA3 domain [Signal transduction mechanisms]

Probab=88.90  E-value=27  Score=35.00  Aligned_cols=58  Identities=21%  Similarity=0.240  Sum_probs=39.9

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhcccC---CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCC
Q 040394          470 TALLNFYAKCGDAQSARMVFDAMREK---NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEE  527 (691)
Q Consensus       470 ~~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g  527 (691)
                      ..|+.-|...|+..+|.+.++++--|   ..+.+.+++.+.-+.|+-...+.++++.-..|
T Consensus       513 ~~LLeEY~~~GdisEA~~CikeLgmPfFhHEvVkkAlVm~mEkk~d~t~~ldLLk~cf~sg  573 (645)
T KOG0403|consen  513 DMLLEEYELSGDISEACHCIKELGMPFFHHEVVKKALVMVMEKKGDSTMILDLLKECFKSG  573 (645)
T ss_pred             HHHHHHHHhccchHHHHHHHHHhCCCcchHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcC
Confidence            34666677777777777777776654   45567777777777777666666666665554

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=88.77  E-value=15  Score=31.72  Aligned_cols=121  Identities=13%  Similarity=0.147  Sum_probs=74.7

Q ss_pred             HhcCCChHHHHHHHHHHHHCCCCCCHHHHH-HHHHHhcccCCHHHHHHHHHHchhhcCCCCChh-HHHHH--HHHHHhcC
Q 040394          507 YGMQGDGGGSLALFSDMLNEEVQPNEVIFT-TILSACSHTGMVGEGWKCFYSMCRDFKFVPSMK-HYVCM--VDLLARAG  582 (691)
Q Consensus       507 ~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~-~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~-~~~~l--i~~~~~~g  582 (691)
                      +++.+..++|+.-|..+.+.|...-+..-. .+.......|+...|...|+++-.. .-.|-+. -...|  .-.+...|
T Consensus        68 lA~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~d-t~~P~~~rd~ARlraa~lLvD~g  146 (221)
T COG4649          68 LAQENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAAD-TSIPQIGRDLARLRAAYLLVDNG  146 (221)
T ss_pred             HHHcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhcc-CCCcchhhHHHHHHHHHHHhccc
Confidence            345667777777777777766443322111 1122446778888888888877433 2222211 11111  22356788


Q ss_pred             ChHHHHHHHHhCCCCC---CHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040394          583 RLEEALEFMENMPIEP---DVSLFGAFLHGCGLYSRFDLGEVMIKKMLE  628 (691)
Q Consensus       583 ~~~~A~~~~~~~~~~p---~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  628 (691)
                      .+++.....+.+..+-   ....-..|.-+-.+.|++.+|...|+++..
T Consensus       147 sy~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~  195 (221)
T COG4649         147 SYDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIAN  195 (221)
T ss_pred             cHHHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHc
Confidence            8888888888773222   234556777777889999999999998776

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=88.75  E-value=16  Score=36.68  Aligned_cols=69  Identities=14%  Similarity=0.117  Sum_probs=56.4

Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC----CCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCc
Q 040394          598 PDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHP----DKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLS  666 (691)
Q Consensus       598 p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p----~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~  666 (691)
                      ....+|..+...+.+.|.++.|...+.++....+    ..+.+...-+.++...|+.++|...++...+..+.
T Consensus       144 ~~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~~~~~~~  216 (352)
T PF02259_consen  144 ELAETWLKFAKLARKAGNFQLALSALNRLFQLNPSSESLLPRVFLEYAKLLWAQGEQEEAIQKLRELLKCRLS  216 (352)
T ss_pred             HHHHHHHHHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcchHHHHHHHHHHcCCHHHHHHHHHHHHHHHhh
Confidence            3456899999999999999999999999988542    23566666788999999999999999998884443

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=88.69  E-value=43  Score=37.02  Aligned_cols=84  Identities=18%  Similarity=0.033  Sum_probs=40.5

Q ss_pred             hccCcHHHHHHHHHHHHHcCCCCCchh-------HHHHHH-HHHHhcCCHHHHHHHHHhccc--------CCHhHHHHHH
Q 040394          441 ASLGAVQVGSSLHAYSTKQGLLSSNVY-------VGTALL-NFYAKCGDAQSARMVFDAMRE--------KNTVTWSAMI  504 (691)
Q Consensus       441 ~~~~~~~~a~~~~~~~~~~~~~~~~~~-------~~~~l~-~~~~~~g~~~~A~~~~~~~~~--------~~~~~~~~li  504 (691)
                      ....++++|..+..+....-. .++..       .++.+- ......|+++.|.++.+...+        ..+..+..+.
T Consensus       426 ~s~~r~~ea~~li~~l~~~l~-~~~~~~~~~l~ae~~aL~a~val~~~~~e~a~~lar~al~~L~~~~~~~r~~~~sv~~  504 (894)
T COG2909         426 ASQHRLAEAETLIARLEHFLK-APMHSRQGDLLAEFQALRAQVALNRGDPEEAEDLARLALVQLPEAAYRSRIVALSVLG  504 (894)
T ss_pred             HHccChHHHHHHHHHHHHHhC-cCcccchhhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhcccccchhhhhhhhhhh
Confidence            345566666666666554321 21111       112211 112234556666555554432        2344555555


Q ss_pred             HHHhcCCChHHHHHHHHHHHH
Q 040394          505 GGYGMQGDGGGSLALFSDMLN  525 (691)
Q Consensus       505 ~~~~~~~~~~~A~~~~~~m~~  525 (691)
                      .+..-.|++++|..+.++..+
T Consensus       505 ~a~~~~G~~~~Al~~~~~a~~  525 (894)
T COG2909         505 EAAHIRGELTQALALMQQAEQ  525 (894)
T ss_pred             HHHHHhchHHHHHHHHHHHHH
Confidence            555566666666665555444

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.65  E-value=3.8  Score=38.69  Aligned_cols=98  Identities=10%  Similarity=0.192  Sum_probs=73.6

Q ss_pred             cCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc-C--------CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCC
Q 040394          459 QGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE-K--------NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQ  529 (691)
Q Consensus       459 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~--------~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~  529 (691)
                      .|. +....+...++..-....+++.+...+-+++. |        ..++|-.+   + -.=++++++.++..=++.|+-
T Consensus        58 ~g~-~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~~irl---l-lky~pq~~i~~l~npIqYGiF  132 (418)
T KOG4570|consen   58 RGL-PVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHTWIRL---L-LKYDPQKAIYTLVNPIQYGIF  132 (418)
T ss_pred             cCC-CcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHHHHHHH---H-HccChHHHHHHHhCcchhccc
Confidence            444 55566666667666677888888888877764 2        22333332   2 233677999999999999999


Q ss_pred             CCHHHHHHHHHHhcccCCHHHHHHHHHHchhh
Q 040394          530 PNEVIFTTILSACSHTGMVGEGWKCFYSMCRD  561 (691)
Q Consensus       530 p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~  561 (691)
                      ||..+++.+++.+.+.+++.+|.++.-.|+..
T Consensus       133 ~dqf~~c~l~D~flk~~n~~~aa~vvt~~~~q  164 (418)
T KOG4570|consen  133 PDQFTFCLLMDSFLKKENYKDAASVVTEVMMQ  164 (418)
T ss_pred             cchhhHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            99999999999999999999999888777554

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.00  E-value=44  Score=36.29  Aligned_cols=29  Identities=17%  Similarity=0.259  Sum_probs=22.6

Q ss_pred             hHHHHHHHHhHhcCChHHHHHHHHhCCCC
Q 040394          382 TVINALVDMYAKCHVIADARYIFETTSEK  410 (691)
Q Consensus       382 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  410 (691)
                      .....|+..|...+++..|..++-...+.
T Consensus       506 ~L~e~La~LYl~d~~Y~~Al~~ylklk~~  534 (846)
T KOG2066|consen  506 ALLEVLAHLYLYDNKYEKALPIYLKLQDK  534 (846)
T ss_pred             hHHHHHHHHHHHccChHHHHHHHHhccCh
Confidence            34455888888899999999888887655

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=87.92  E-value=0.94  Score=26.83  Aligned_cols=29  Identities=14%  Similarity=0.062  Sum_probs=25.3

Q ss_pred             hhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          635 CYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       635 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      ..|..++.+|...|++++|++.+++.++.
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~   30 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALEL   30 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHH
Confidence            46889999999999999999999998874

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 ....

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=87.60  E-value=59  Score=37.30  Aligned_cols=115  Identities=14%  Similarity=0.068  Sum_probs=63.8

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHH
Q 040394          470 TALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVG  549 (691)
Q Consensus       470 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~  549 (691)
                      .-.++.--+.|-+.+|+.++..-.+.-...|.+...-+...+.+++|.-.|+..-+         ....+.+|...|+|.
T Consensus       912 ~e~~n~I~kh~Ly~~aL~ly~~~~e~~k~i~~~ya~hL~~~~~~~~Aal~Ye~~Gk---------lekAl~a~~~~~dWr  982 (1265)
T KOG1920|consen  912 PECKNYIKKHGLYDEALALYKPDSEKQKVIYEAYADHLREELMSDEAALMYERCGK---------LEKALKAYKECGDWR  982 (1265)
T ss_pred             HHHHHHHHhcccchhhhheeccCHHHHHHHHHHHHHHHHHhccccHHHHHHHHhcc---------HHHHHHHHHHhccHH
Confidence            33444444555555555554433333334555555555566666666666554322         123455666777777


Q ss_pred             HHHHHHHHchhhcCCCCC--hhHHHHHHHHHHhcCChHHHHHHHHhCCCC
Q 040394          550 EGWKCFYSMCRDFKFVPS--MKHYVCMVDLLARAGRLEEALEFMENMPIE  597 (691)
Q Consensus       550 ~A~~~~~~m~~~~~~~p~--~~~~~~li~~~~~~g~~~~A~~~~~~~~~~  597 (691)
                      +|..+..++.    ..-+  ..+-..|+.-+...+++-+|-++..+....
T Consensus       983 ~~l~~a~ql~----~~~de~~~~a~~L~s~L~e~~kh~eAa~il~e~~sd 1028 (1265)
T KOG1920|consen  983 EALSLAAQLS----EGKDELVILAEELVSRLVEQRKHYEAAKILLEYLSD 1028 (1265)
T ss_pred             HHHHHHHhhc----CCHHHHHHHHHHHHHHHHHcccchhHHHHHHHHhcC
Confidence            7777776551    1222  122245666777777777777777776433

>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=87.53  E-value=10  Score=33.49  Aligned_cols=59  Identities=8%  Similarity=0.003  Sum_probs=26.0

Q ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHhCCCCCC--hhhHHHHHHHHHccCChhhHHHHHHHH
Q 040394          214 WTSMIAGYVQNDCAQEGLVLFNRMREGFVEGN--QITLGSLVTACAKLRALHQGKWLHGYI  272 (691)
Q Consensus       214 ~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~--~~t~~~li~~~~~~~~~~~a~~~~~~~  272 (691)
                      +..+...|++.|+.+.|++.|.++.+....|.  ...+-.+|+.....+++..+.......
T Consensus        39 ~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka   99 (177)
T PF10602_consen   39 LEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKA   99 (177)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            34444444455555555555555444322222  122334444444445555444444443

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.

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=87.00  E-value=1.5  Score=27.31  Aligned_cols=27  Identities=11%  Similarity=0.246  Sum_probs=14.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040394          602 LFGAFLHGCGLYSRFDLGEVMIKKMLE  628 (691)
Q Consensus       602 ~~~~l~~~~~~~g~~~~A~~~~~~~~~  628 (691)
                      +++.|...|...|++++|..+++++++
T Consensus         4 ~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    4 ALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            445555555555666666555555554

>PRK09687 putative lyase; Provisional

Probab=86.92  E-value=30  Score=33.28  Aligned_cols=58  Identities=16%  Similarity=0.169  Sum_probs=24.4

Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHH
Q 040394          465 NVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLN  525 (691)
Q Consensus       465 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~  525 (691)
                      +..+....+.++++.|+.+-...+.+.+..++  .....+.++...|+. +|+..+.++.+
T Consensus       205 ~~~VR~~A~~aLg~~~~~~av~~Li~~L~~~~--~~~~a~~ALg~ig~~-~a~p~L~~l~~  262 (280)
T PRK09687        205 NEEIRIEAIIGLALRKDKRVLSVLIKELKKGT--VGDLIIEAAGELGDK-TLLPVLDTLLY  262 (280)
T ss_pred             ChHHHHHHHHHHHccCChhHHHHHHHHHcCCc--hHHHHHHHHHhcCCH-hHHHHHHHHHh
Confidence            44444445555555555332222222322222  122344455555553 35555555444

>PRK09687 putative lyase; Provisional

Probab=86.88  E-value=30  Score=33.27  Aligned_cols=121  Identities=7%  Similarity=-0.105  Sum_probs=54.2

Q ss_pred             chHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcC-CchhHHHHHHHhhHCCCCCcHHHHHHHHHHHh
Q 040394          280 NSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSG-YPDKALKLFTDKKWADFFPNHVTIASVLSASA  358 (691)
Q Consensus       280 ~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g-~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~  358 (691)
                      +..+-...+.++++.++.+....+..-+..++...-...+.++.+.+ ....+...+..+..   .++...-...+.++.
T Consensus       141 ~~~VR~~a~~aLg~~~~~~ai~~L~~~L~d~~~~VR~~A~~aLg~~~~~~~~~~~~L~~~L~---D~~~~VR~~A~~aLg  217 (280)
T PRK09687        141 STNVRFAVAFALSVINDEAAIPLLINLLKDPNGDVRNWAAFALNSNKYDNPDIREAFVAMLQ---DKNEEIRIEAIIGLA  217 (280)
T ss_pred             CHHHHHHHHHHHhccCCHHHHHHHHHHhcCCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhc---CCChHHHHHHHHHHH
Confidence            44444455555555554332222233334444444444444444432 12344444444442   344555555555555


Q ss_pred             cCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCC
Q 040394          359 QLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSE  409 (691)
Q Consensus       359 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  409 (691)
                      +.++.. +...+-...+.+.    +....+.++...|.. +|...+..+..
T Consensus       218 ~~~~~~-av~~Li~~L~~~~----~~~~a~~ALg~ig~~-~a~p~L~~l~~  262 (280)
T PRK09687        218 LRKDKR-VLSVLIKELKKGT----VGDLIIEAAGELGDK-TLLPVLDTLLY  262 (280)
T ss_pred             ccCChh-HHHHHHHHHcCCc----hHHHHHHHHHhcCCH-hHHHHHHHHHh
Confidence            555532 3322222222221    223455666666664 46666666553

>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function

Probab=86.84  E-value=4.2  Score=37.16  Aligned_cols=68  Identities=13%  Similarity=0.040  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHH-------hc--CCC----CchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCcc
Q 040394          601 SLFGAFLHGCGLYSRFDLGEVMIKKML-------EL--HPD----KACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSK  667 (691)
Q Consensus       601 ~~~~~l~~~~~~~g~~~~A~~~~~~~~-------~~--~p~----~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~~  667 (691)
                      ..+..+.+.|...|+.+....+++++.       +.  .|.    .....++++.+..+.|++++|.+.+.++...+-.+
T Consensus       119 ~l~LrlAWlyR~~~~~~~E~~fl~~Al~~y~~a~~~e~~~~~~~~~~~l~YLigeL~rrlg~~~eA~~~fs~vi~~~~~s  198 (214)
T PF09986_consen  119 GLCLRLAWLYRDLGDEENEKRFLRKALEFYEEAYENEDFPIEGMDEATLLYLIGELNRRLGNYDEAKRWFSRVIGSKKAS  198 (214)
T ss_pred             HHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCCC
Confidence            356667777887888555555555544       32  222    24667889999999999999999999998865544


Q ss_pred             C
Q 040394          668 S  668 (691)
Q Consensus       668 ~  668 (691)
                      .
T Consensus       199 ~  199 (214)
T PF09986_consen  199 K  199 (214)
T ss_pred             C
Confidence            3

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized 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=86.46  E-value=1  Score=38.28  Aligned_cols=83  Identities=14%  Similarity=0.096  Sum_probs=41.0

Q ss_pred             HHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCH
Q 040394          218 IAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNI  297 (691)
Q Consensus       218 i~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~  297 (691)
                      |..+.+.+.+.....+++.+...+...+....+.++..|++.++.+....+++.       .+..-...++..|.+.|.+
T Consensus        14 i~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~-------~~~yd~~~~~~~c~~~~l~   86 (143)
T PF00637_consen   14 ISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKT-------SNNYDLDKALRLCEKHGLY   86 (143)
T ss_dssp             HHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTS-------SSSS-CTHHHHHHHTTTSH
T ss_pred             HHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHccc-------ccccCHHHHHHHHHhcchH
Confidence            444445555555666666665544444555556666666666555555555441       1112223344445555555


Q ss_pred             HHHHHHHHhc
Q 040394          298 RDARSVFDEL  307 (691)
Q Consensus       298 ~~A~~~~~~~  307 (691)
                      ++|.-++.++
T Consensus        87 ~~a~~Ly~~~   96 (143)
T PF00637_consen   87 EEAVYLYSKL   96 (143)
T ss_dssp             HHHHHHHHCC
T ss_pred             HHHHHHHHHc
Confidence            5555555444

These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents the 7-fold alpha-alpha-superhelical ARM-type repeat found at the C-terminal of clathrin heavy chains and in VPS (vacuolar protein sorting-associated) proteins. In clathrin heavy chains, the C-terminal 7-fold ARM-type repeats interact to form the central hub of the triskelion. VPS proteins are required for vacuolar assembly and vacuolar traffick, and contain one clathrin-type repeat []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport; PDB: 3LVH_A 3LVG_C 1B89_A 3QIL_L.

>PF14853 Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repeat; PDB: 1IYG_A 1PC2_A 1NZN_A 3UUX_C 1Y8M_A 2PQR_A 2PQN_A 3O48_A

Probab=86.42  E-value=2.1  Score=28.67  Aligned_cols=36  Identities=17%  Similarity=0.195  Sum_probs=28.2

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHH
Q 040394          605 AFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLV  640 (691)
Q Consensus       605 ~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l  640 (691)
                      .+.-++.+.|++++|....+.+++.+|+|.......
T Consensus         6 ~lAig~ykl~~Y~~A~~~~~~lL~~eP~N~Qa~~L~   41 (53)
T PF14853_consen    6 YLAIGHYKLGEYEKARRYCDALLEIEPDNRQAQSLK   41 (53)
T ss_dssp             HHHHHHHHTT-HHHHHHHHHHHHHHTTS-HHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHhhCCCcHHHHHHH
Confidence            355678899999999999999999999987665543

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=86.28  E-value=53  Score=35.50  Aligned_cols=123  Identities=11%  Similarity=-0.004  Sum_probs=62.5

Q ss_pred             HHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCC---hhhHHHHHHHHHHHCCCCchHHHHHHHHHH
Q 040394          215 TSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRA---LHQGKWLHGYILKIGIEINSHLVTALLDMY  291 (691)
Q Consensus       215 ~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~---~~~a~~~~~~~~~~g~~~~~~~~~~li~~~  291 (691)
                      ..+|+-+...+.+..|.++-+.+...-..- ...|.....-+.+..+   -+.+..+-+++... . .+...|..+..-.
T Consensus       441 ~~vi~Rl~~r~~Y~vaIQva~~l~~p~~~~-~~Vl~~Wa~~kI~~~d~~d~~vld~I~~kls~~-~-~~~iSy~~iA~~A  517 (829)
T KOG2280|consen  441 EVVIDRLVDRHLYSVAIQVAKLLNLPESQG-DRVLLEWARRKIKQSDKMDEEVLDKIDEKLSAK-L-TPGISYAAIARRA  517 (829)
T ss_pred             hhhhHHHHhcchhHHHHHHHHHhCCccccc-cHHHHHHHHHHHhccCccchHHHHHHHHHhccc-C-CCceeHHHHHHHH
Confidence            345666677777777777776664321111 3444444444444322   22222222222221 2 2344566666666


Q ss_pred             HhcCCHHHHHHHHHhcCCC--------ChhHHHHHHHHHHhcCCchhHHHHHHHhhH
Q 040394          292 VKCGNIRDARSVFDELCSI--------DLVSWTAMIVGYTQSGYPDKALKLFTDKKW  340 (691)
Q Consensus       292 ~~~g~~~~A~~~~~~~~~~--------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  340 (691)
                      ..+|+.+-|..+++.=+..        +..-+..-+.-....|+.+-...++-.|..
T Consensus       518 y~~GR~~LA~kLle~E~~~~~qV~lLL~m~~~~~AL~kaies~d~~Li~~Vllhlk~  574 (829)
T KOG2280|consen  518 YQEGRFELARKLLELEPRSGEQVPLLLKMKDSSLALKKAIESGDTDLIIQVLLHLKN  574 (829)
T ss_pred             HhcCcHHHHHHHHhcCCCccchhHHHhccchHHHHHHHHHhcCCchhHHHHHHHHHH
Confidence            6778888887777643211        112233444455556666666665555544

>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=86.18  E-value=7.2  Score=34.44  Aligned_cols=60  Identities=13%  Similarity=0.090  Sum_probs=27.9

Q ss_pred             HHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCH--HHHHHHHHHhcccCCHHHHHHHHHHc
Q 040394          499 TWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNE--VIFTTILSACSHTGMVGEGWKCFYSM  558 (691)
Q Consensus       499 ~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~--~~~~~ll~~~~~~g~~~~A~~~~~~m  558 (691)
                      .+..+..-|++.|+.+.|++.|.++.+.-..|..  ..+-.+|+.....+++..+.....+.
T Consensus        38 ~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka   99 (177)
T PF10602_consen   38 ALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKA   99 (177)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            3444445555555555555555555544333332  23334444444455555554444443

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.

>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=86.00  E-value=24  Score=31.23  Aligned_cols=89  Identities=8%  Similarity=-0.074  Sum_probs=52.8

Q ss_pred             HHhcccCCHHHHHHHHHHchhhcCCCCChhHHH-----HHHHHHHhcCChHHHHHHHHhCCCC-CCHHHHHHHHHHHHhc
Q 040394          540 SACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYV-----CMVDLLARAGRLEEALEFMENMPIE-PDVSLFGAFLHGCGLY  613 (691)
Q Consensus       540 ~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~-----~li~~~~~~g~~~~A~~~~~~~~~~-p~~~~~~~l~~~~~~~  613 (691)
                      ..+...+++++|...++...   +. |....+.     .|.......|.+++|+..++....+ -.......-...+...
T Consensus        97 k~~ve~~~~d~A~aqL~~~l---~~-t~De~lk~l~~lRLArvq~q~~k~D~AL~~L~t~~~~~w~~~~~elrGDill~k  172 (207)
T COG2976          97 KAEVEANNLDKAEAQLKQAL---AQ-TKDENLKALAALRLARVQLQQKKADAALKTLDTIKEESWAAIVAELRGDILLAK  172 (207)
T ss_pred             HHHHhhccHHHHHHHHHHHH---cc-chhHHHHHHHHHHHHHHHHHhhhHHHHHHHHhccccccHHHHHHHHhhhHHHHc
Confidence            35566777777777776542   11 2222222     3445667778888888877766311 1122233344567777


Q ss_pred             CCHHHHHHHHHHHHhcCCC
Q 040394          614 SRFDLGEVMIKKMLELHPD  632 (691)
Q Consensus       614 g~~~~A~~~~~~~~~~~p~  632 (691)
                      |+-++|+.-|+++++..++
T Consensus       173 g~k~~Ar~ay~kAl~~~~s  191 (207)
T COG2976         173 GDKQEARAAYEKALESDAS  191 (207)
T ss_pred             CchHHHHHHHHHHHHccCC
Confidence            8888888888887776644

>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models

Probab=85.97  E-value=1  Score=24.81  Aligned_cols=23  Identities=4%  Similarity=-0.000  Sum_probs=16.2

Q ss_pred             hHHHHHHHHHhCCCcHHHHHHHH
Q 040394          636 YYVLVSNLYASDGRWIRVNQVRE  658 (691)
Q Consensus       636 ~~~~l~~~~~~~g~~~~A~~~~~  658 (691)
                      ....++.++...|++++|.++++
T Consensus         3 a~~~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    3 ARLALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHh
Confidence            45567777777777777777664

The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding

>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=85.56  E-value=1.7  Score=25.64  Aligned_cols=28  Identities=14%  Similarity=0.137  Sum_probs=25.4

Q ss_pred             hhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          635 CYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       635 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      .+|..++.+|...|++++|.+.+++..+
T Consensus         2 ~~~~~lg~~y~~~~~~~~A~~~~~~a~~   29 (34)
T PF13181_consen    2 EAYYNLGKIYEQLGDYEEALEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHHTTSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            4678899999999999999999998876

...

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=85.54  E-value=2.8  Score=39.96  Aligned_cols=86  Identities=19%  Similarity=0.094  Sum_probs=59.8

Q ss_pred             HHHHhcCCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcC
Q 040394          504 IGGYGMQGDGGGSLALFSDMLNEEVQP-NEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAG  582 (691)
Q Consensus       504 i~~~~~~~~~~~A~~~~~~m~~~g~~p-~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g  582 (691)
                      ..-|.++|.+++|+.+|.+-+.  +.| |.+++..-..+|.+...+..|..-....+     ..|    ...+.+|.|.+
T Consensus       104 GN~yFKQgKy~EAIDCYs~~ia--~~P~NpV~~~NRA~AYlk~K~FA~AE~DC~~Ai-----aLd----~~Y~KAYSRR~  172 (536)
T KOG4648|consen  104 GNTYFKQGKYEEAIDCYSTAIA--VYPHNPVYHINRALAYLKQKSFAQAEEDCEAAI-----ALD----KLYVKAYSRRM  172 (536)
T ss_pred             hhhhhhccchhHHHHHhhhhhc--cCCCCccchhhHHHHHHHHHHHHHHHHhHHHHH-----Hhh----HHHHHHHHHHH
Confidence            4579999999999999998887  567 88999888889999988887776655432     112    23455666554


Q ss_pred             -------ChHHHHHHHHhC-CCCCCH
Q 040394          583 -------RLEEALEFMENM-PIEPDV  600 (691)
Q Consensus       583 -------~~~~A~~~~~~~-~~~p~~  600 (691)
                             +..+|.+-++.. ...|+.
T Consensus       173 ~AR~~Lg~~~EAKkD~E~vL~LEP~~  198 (536)
T KOG4648|consen  173 QARESLGNNMEAKKDCETVLALEPKN  198 (536)
T ss_pred             HHHHHHhhHHHHHHhHHHHHhhCccc
Confidence                   455555444444 566663

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=85.30  E-value=30  Score=31.66  Aligned_cols=197  Identities=18%  Similarity=0.178  Sum_probs=141.8

Q ss_pred             HHHHHHHHHHHhccCcHHHHHHHHHHHHHc-CCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--CCH-hHHHHHHH
Q 040394          430 AVTLVSVISACASLGAVQVGSSLHAYSTKQ-GLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--KNT-VTWSAMIG  505 (691)
Q Consensus       430 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~-~~~~~li~  505 (691)
                      ...+......+...++...+...+...... .. +.....+......+...+++..+...+.....  ++. ........
T Consensus        59 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  137 (291)
T COG0457          59 AGLLLLLALALLKLGRLEEALELLEKALELELL-PNLAEALLNLGLLLEALGKYEEALELLEKALALDPDPDLAEALLAL  137 (291)
T ss_pred             hHHHHHHHHHHHHcccHHHHHHHHHHHHhhhhc-cchHHHHHHHHHHHHHHhhHHHHHHHHHHHHcCCCCcchHHHHHHH
Confidence            456666667777778888877777776652 22 56666777777788888888888888887775  222 22333333


Q ss_pred             -HHhcCCChHHHHHHHHHHHHCCCCC----CHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC--hhHHHHHHHHH
Q 040394          506 -GYGMQGDGGGSLALFSDMLNEEVQP----NEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS--MKHYVCMVDLL  578 (691)
Q Consensus       506 -~~~~~~~~~~A~~~~~~m~~~g~~p----~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~--~~~~~~li~~~  578 (691)
                       .+...|+++.|...+.+...  ..|    ....+......+...++.+.+...+.....   ..++  ...+..+...+
T Consensus       138 ~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~~~~~~~~~~  212 (291)
T COG0457         138 GALYELGDYEEALELYEKALE--LDPELNELAEALLALGALLEALGRYEEALELLEKALK---LNPDDDAEALLNLGLLY  212 (291)
T ss_pred             HHHHHcCCHHHHHHHHHHHHh--cCCCccchHHHHHHhhhHHHHhcCHHHHHHHHHHHHh---hCcccchHHHHHhhHHH
Confidence             78889999999999999865  343    233344444456678899999999987743   3333  56777888888


Q ss_pred             HhcCChHHHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040394          579 ARAGRLEEALEFMENM-PIEPD-VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPD  632 (691)
Q Consensus       579 ~~~g~~~~A~~~~~~~-~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~  632 (691)
                      ...++++.|...+... ...|+ ...+..+...+...++.+.+...+.+.....|.
T Consensus       213 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  268 (291)
T COG0457         213 LKLGKYEEALEYYEKALELDPDNAEALYNLALLLLELGRYEEALEALEKALELDPD  268 (291)
T ss_pred             HHcccHHHHHHHHHHHHhhCcccHHHHhhHHHHHHHcCCHHHHHHHHHHHHHhCcc
Confidence            8999999999998887 44554 445555555555777899999999999998887

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=85.29  E-value=24  Score=30.60  Aligned_cols=46  Identities=9%  Similarity=0.050  Sum_probs=23.4

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHH
Q 040394          470 TALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGG  515 (691)
Q Consensus       470 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~  515 (691)
                      ..+++.+...|++-+|.++.+....-+......++.+..+.+|...
T Consensus        93 ~~iievLL~~g~vl~ALr~ar~~~~~~~~~~~~fLeAA~~~~D~~l  138 (167)
T PF07035_consen   93 EEIIEVLLSKGQVLEALRYARQYHKVDSVPARKFLEAAANSNDDQL  138 (167)
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHcCCcccCCHHHHHHHHHHcCCHHH
Confidence            3455566666666666666665443333333334444444444433

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=85.25  E-value=61  Score=35.26  Aligned_cols=101  Identities=9%  Similarity=0.040  Sum_probs=52.4

Q ss_pred             HHcccCChhHHHHHHHHHHHhCCC--ChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHH
Q 040394          155 ACCELRDIDEGMKVHCEIVKVGGP--DSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLV  232 (691)
Q Consensus       155 ~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~  232 (691)
                      .+.+.+.+++|...-+.....-+.  -...+..++..+.-.|++++|-...-.|...+...|--.+..+...++......
T Consensus       365 Wll~~k~yeeAl~~~k~~~~~~~~~~i~kv~~~yI~HLl~~~~y~~Aas~~p~m~gn~~~eWe~~V~~f~e~~~l~~Ia~  444 (846)
T KOG2066|consen  365 WLLEKKKYEEALDAAKASIGNEERFVIKKVGKTYIDHLLFEGKYDEAASLCPKMLGNNAAEWELWVFKFAELDQLTDIAP  444 (846)
T ss_pred             HHHHhhHHHHHHHHHHhccCCccccchHHHHHHHHHHHHhcchHHHHHhhhHHHhcchHHHHHHHHHHhccccccchhhc
Confidence            334444555555444332222111  234556666667777777777777777766666666666666666555443222


Q ss_pred             HHHHHHhCCCCCChhhHHHHHHHHHc
Q 040394          233 LFNRMREGFVEGNQITLGSLVTACAK  258 (691)
Q Consensus       233 ~~~~m~~~~~~p~~~t~~~li~~~~~  258 (691)
                      +   +.......+...|..++..+..
T Consensus       445 ~---lPt~~~rL~p~vYemvLve~L~  467 (846)
T KOG2066|consen  445 Y---LPTGPPRLKPLVYEMVLVEFLA  467 (846)
T ss_pred             c---CCCCCcccCchHHHHHHHHHHH
Confidence            2   2222222344455555555544

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=85.11  E-value=15  Score=28.31  Aligned_cols=86  Identities=15%  Similarity=0.176  Sum_probs=57.3

Q ss_pred             hhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHC
Q 040394          262 LHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWA  341 (691)
Q Consensus       262 ~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  341 (691)
                      -++|.-|-+.+...+.. ...+--.-+..+...|++++|..+.+.++-||...|-+|-.  .+.|..+++..-+.+|...
T Consensus        21 HqEA~tIAdwL~~~~~~-~E~v~lIRlsSLmNrG~Yq~Al~l~~~~~~pdlepw~ALce--~rlGl~s~l~~rl~rla~s   97 (115)
T TIGR02508        21 HQEANTIADWLHLKGES-EEAVQLIRLSSLMNRGDYQSALQLGNKLCYPDLEPWLALCE--WRLGLGSALESRLNRLAAS   97 (115)
T ss_pred             HHHHHHHHHHHhcCCch-HHHHHHHHHHHHHccchHHHHHHhcCCCCCchHHHHHHHHH--HhhccHHHHHHHHHHHHhC
Confidence            45555555555444322 22333333456788999999999999999999999987765  4667777777777777766


Q ss_pred             CCCCcHHHHH
Q 040394          342 DFFPNHVTIA  351 (691)
Q Consensus       342 g~~p~~~t~~  351 (691)
                      | .|....|.
T Consensus        98 g-~p~lq~Fa  106 (115)
T TIGR02508        98 G-DPRLQTFV  106 (115)
T ss_pred             C-CHHHHHHH
Confidence            5 45555553

YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.

>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=85.01  E-value=27  Score=30.93  Aligned_cols=88  Identities=10%  Similarity=0.040  Sum_probs=51.5

Q ss_pred             HHHcccCChhHHHHHHHHHHHhCCC---ChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhh--HHHHHHHHHhCCChh
Q 040394          154 KACCELRDIDEGMKVHCEIVKVGGP---DSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVS--WTSMIAGYVQNDCAQ  228 (691)
Q Consensus       154 ~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~--~~~li~~~~~~g~~~  228 (691)
                      +.+...|++++|+..++.......+   ...+--.|.......|.+|+|+++++...+++-..  ...-.+.+...|+-+
T Consensus        97 k~~ve~~~~d~A~aqL~~~l~~t~De~lk~l~~lRLArvq~q~~k~D~AL~~L~t~~~~~w~~~~~elrGDill~kg~k~  176 (207)
T COG2976          97 KAEVEANNLDKAEAQLKQALAQTKDENLKALAALRLARVQLQQKKADAALKTLDTIKEESWAAIVAELRGDILLAKGDKQ  176 (207)
T ss_pred             HHHHhhccHHHHHHHHHHHHccchhHHHHHHHHHHHHHHHHHhhhHHHHHHHHhccccccHHHHHHHHhhhHHHHcCchH
Confidence            4455667777777776665543322   22333445566666777777777777665553322  333345666667777


Q ss_pred             HHHHHHHHHHhCC
Q 040394          229 EGLVLFNRMREGF  241 (691)
Q Consensus       229 ~A~~~~~~m~~~~  241 (691)
                      +|..-|++..+.+
T Consensus       177 ~Ar~ay~kAl~~~  189 (207)
T COG2976         177 EARAAYEKALESD  189 (207)
T ss_pred             HHHHHHHHHHHcc
Confidence            7777777666654

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=84.61  E-value=1.1  Score=26.12  Aligned_cols=28  Identities=11%  Similarity=0.074  Sum_probs=24.9

Q ss_pred             hHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          636 YYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       636 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      .+..++.++.+.|++++|.+.++++++.
T Consensus         2 a~~~~a~~~~~~g~~~~A~~~~~~~~~~   29 (33)
T PF13174_consen    2 ALYRLARCYYKLGDYDEAIEYFQRLIKR   29 (33)
T ss_dssp             HHHHHHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            4677899999999999999999999875

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized 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=84.50  E-value=0.84  Score=38.78  Aligned_cols=84  Identities=14%  Similarity=0.168  Sum_probs=59.9

Q ss_pred             HHHHHHcccCChhHHHHHHHHHHHhCCC-ChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhH
Q 040394          151 KVLKACCELRDIDEGMKVHCEIVKVGGP-DSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQE  229 (691)
Q Consensus       151 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  229 (691)
                      .++..+.+.+.+......++.+...+.. +....+.++..|++.++.+...++++....   .-...++..+.+.|.+++
T Consensus        12 ~vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~~~---yd~~~~~~~c~~~~l~~~   88 (143)
T PF00637_consen   12 EVISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKTSNN---YDLDKALRLCEKHGLYEE   88 (143)
T ss_dssp             CCHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTSSSS---S-CTHHHHHHHTTTSHHH
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcccccc---cCHHHHHHHHHhcchHHH
Confidence            4567777788888888888888877755 788888888888888887888887774322   333455666666677777


Q ss_pred             HHHHHHHH
Q 040394          230 GLVLFNRM  237 (691)
Q Consensus       230 A~~~~~~m  237 (691)
                      |.-++.++
T Consensus        89 a~~Ly~~~   96 (143)
T PF00637_consen   89 AVYLYSKL   96 (143)
T ss_dssp             HHHHHHCC
T ss_pred             HHHHHHHc
Confidence            66666665

These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents the 7-fold alpha-alpha-superhelical ARM-type repeat found at the C-terminal of clathrin heavy chains and in VPS (vacuolar protein sorting-associated) proteins. In clathrin heavy chains, the C-terminal 7-fold ARM-type repeats interact to form the central hub of the triskelion. VPS proteins are required for vacuolar assembly and vacuolar traffick, and contain one clathrin-type repeat []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport; PDB: 3LVH_A 3LVG_C 1B89_A 3QIL_L.

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=84.13  E-value=5.9  Score=30.21  Aligned_cols=59  Identities=12%  Similarity=0.121  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHH
Q 040394          129 DIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLV  187 (691)
Q Consensus       129 ~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~  187 (691)
                      ++.+-++.+....+.|++......+++|.+.+|+..|..+++-++.....+...|..++
T Consensus        25 e~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~~~~~~y~~~l   83 (103)
T cd00923          25 ELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCGAHKEIYPYIL   83 (103)
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccCchhhHHHHH
Confidence            44555666666778899999999999999999999999999887744322333555444

Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=84.03  E-value=1.9  Score=26.90  Aligned_cols=28  Identities=18%  Similarity=0.223  Sum_probs=24.3

Q ss_pred             hhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          635 CYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       635 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      .++..++.+|...|++++|..++++..+
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            4678899999999999999999999876

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=83.92  E-value=9.9  Score=36.10  Aligned_cols=104  Identities=17%  Similarity=0.117  Sum_probs=74.0

Q ss_pred             HCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCC-CCh-----hHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHH
Q 040394          275 IGIEINSHLVTALLDMYVKCGNIRDARSVFDELCS-IDL-----VSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHV  348 (691)
Q Consensus       275 ~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~-~~~-----~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  348 (691)
                      .|......+...++.......+++.+...+-++.. ++.     .+-.+.++. +-.-++++++-++..=++-|+-||..
T Consensus        58 ~g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~~irl-llky~pq~~i~~l~npIqYGiF~dqf  136 (418)
T KOG4570|consen   58 RGLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHTWIRL-LLKYDPQKAIYTLVNPIQYGIFPDQF  136 (418)
T ss_pred             cCCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHHHHHHH-HHccChHHHHHHHhCcchhccccchh
Confidence            45555666667777777777788888888877622 211     111122333 33446778999998888999999999


Q ss_pred             HHHHHHHHHhcCCChhhHHHHHHHHHHhCCC
Q 040394          349 TIASVLSASAQLGNLNMGRMVHSLGIRLGLE  379 (691)
Q Consensus       349 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  379 (691)
                      +++.++..+.+.+++.+|..+.-.+.....-
T Consensus       137 ~~c~l~D~flk~~n~~~aa~vvt~~~~qe~~  167 (418)
T KOG4570|consen  137 TFCLLMDSFLKKENYKDAASVVTEVMMQEAF  167 (418)
T ss_pred             hHHHHHHHHHhcccHHHHHHHHHHHHHHHHh
Confidence            9999999999999999988887666655443

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=83.22  E-value=2.9  Score=37.30  Aligned_cols=65  Identities=11%  Similarity=0.130  Sum_probs=49.7

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040394          570 HYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKA  634 (691)
Q Consensus       570 ~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~  634 (691)
                      +.+.-+..+.+.+++++|+...+.- +.+| |...-..+++.++-.|++++|..-++-.-++.|+..
T Consensus         3 Tl~~t~seLL~~~sL~dai~~a~~qVkakPtda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p~~t   69 (273)
T COG4455           3 TLRDTISELLDDNSLQDAIGLARDQVKAKPTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSPQDT   69 (273)
T ss_pred             chHHHHHHHHHhccHHHHHHHHHHHHhcCCccccchhHHHHHHhhcchHHHHHHHHHHHhhcCcccc
Confidence            3445567788888999998877665 5555 444566678888899999999999998888888864

>KOG1586 consensus Protein required for fusion of vesicles in vesicular transport, alpha-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=83.14  E-value=20  Score=32.58  Aligned_cols=16  Identities=6%  Similarity=-0.012  Sum_probs=9.2

Q ss_pred             cccCCHHHHHHHHHHc
Q 040394          543 SHTGMVGEGWKCFYSM  558 (691)
Q Consensus       543 ~~~g~~~~A~~~~~~m  558 (691)
                      .-.+.+++|.++|.+.
T Consensus        25 gg~~k~eeAadl~~~A   40 (288)
T KOG1586|consen   25 GGSNKYEEAAELYERA   40 (288)
T ss_pred             CCCcchHHHHHHHHHH
Confidence            3444666666666644

>KOG1586 consensus Protein required for fusion of vesicles in vesicular transport, alpha-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=83.03  E-value=36  Score=31.11  Aligned_cols=89  Identities=8%  Similarity=0.068  Sum_probs=49.1

Q ss_pred             HHHHHHhc-CChHHHHHHHHhC-----CCCCCHHH---HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchh-------H
Q 040394          574 MVDLLARA-GRLEEALEFMENM-----PIEPDVSL---FGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACY-------Y  637 (691)
Q Consensus       574 li~~~~~~-g~~~~A~~~~~~~-----~~~p~~~~---~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~-------~  637 (691)
                      +...|... .++++|+..++..     +-+.+...   +.-....-...+++.+|+.+|++.....-+++..       +
T Consensus       119 iaEiyEsdl~d~ekaI~~YE~Aae~yk~ees~ssANKC~lKvA~yaa~leqY~~Ai~iyeqva~~s~~n~LLKys~Kdyf  198 (288)
T KOG1586|consen  119 IAEIYESDLQDFEKAIAHYEQAAEYYKGEESVSSANKCLLKVAQYAAQLEQYSKAIDIYEQVARSSLDNNLLKYSAKDYF  198 (288)
T ss_pred             HHHHHhhhHHHHHHHHHHHHHHHHHHcchhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccchHHHhHHHHHH
Confidence            44444433 5667777777766     21222222   2223333456789999999999988755554332       2


Q ss_pred             HHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          638 VLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       638 ~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      ..-+.++...++.-.+.+.+++-.+
T Consensus       199 lkAgLChl~~~D~v~a~~ALeky~~  223 (288)
T KOG1586|consen  199 LKAGLCHLCKADEVNAQRALEKYQE  223 (288)
T ss_pred             HHHHHHhHhcccHHHHHHHHHHHHh
Confidence            3333344444666566666655444

>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=83.01  E-value=13  Score=32.40  Aligned_cols=44  Identities=14%  Similarity=0.308  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCc
Q 040394          616 FDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLS  666 (691)
Q Consensus       616 ~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~  666 (691)
                      +++|...|+++.+.+|++..+...|-..       .+|=++..++.+.+..
T Consensus        96 F~kA~~~FqkAv~~~P~ne~Y~ksLe~~-------~kap~lh~e~~~~~~~  139 (186)
T PF06552_consen   96 FEKATEYFQKAVDEDPNNELYRKSLEMA-------AKAPELHMEIHKQGLG  139 (186)
T ss_dssp             HHHHHHHHHHHHHH-TT-HHHHHHHHHH-------HTHHHHHHHHHHSSS-
T ss_pred             HHHHHHHHHHHHhcCCCcHHHHHHHHHH-------HhhHHHHHHHHHHHhh
Confidence            6777888888888999987777766332       3477777777666543

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.

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=82.78  E-value=2.4  Score=27.02  Aligned_cols=28  Identities=14%  Similarity=0.152  Sum_probs=22.6

Q ss_pred             HHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          638 VLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       638 ~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      ..|+.+|...|+.+.|+++++++.+.|-
T Consensus         3 LdLA~ayie~Gd~e~Ar~lL~evl~~~~   30 (44)
T TIGR03504         3 LDLARAYIEMGDLEGARELLEEVIEEGD   30 (44)
T ss_pred             hHHHHHHHHcCChHHHHHHHHHHHHcCC
Confidence            4578888999999999999988886553

This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.

>KOG4642 consensus Chaperone-dependent E3 ubiquitin protein ligase (contains TPR repeats) [Posttranslational modification, protein turnover, chaperones]

Probab=82.75  E-value=5.2  Score=36.30  Aligned_cols=50  Identities=10%  Similarity=0.055  Sum_probs=25.2

Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHH
Q 040394          611 GLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELM  660 (691)
Q Consensus       611 ~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  660 (691)
                      .+..+++.+..--.+++++.|+.....+.++..+.....+++|+..+.+.
T Consensus        55 lk~~~~~~v~~dcrralql~~N~vk~h~flg~~~l~s~~~~eaI~~Lqra  104 (284)
T KOG4642|consen   55 LKLKHWEPVEEDCRRALQLDPNLVKAHYFLGQWLLQSKGYDEAIKVLQRA  104 (284)
T ss_pred             HHhhhhhhhhhhHHHHHhcChHHHHHHHHHHHHHHhhccccHHHHHHHHH
Confidence            34444555555555555555554445555555555555555555555444

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=82.64  E-value=6.5  Score=29.97  Aligned_cols=62  Identities=10%  Similarity=0.166  Sum_probs=44.7

Q ss_pred             hHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHH
Q 040394          513 GGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVD  576 (691)
Q Consensus       513 ~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~  576 (691)
                      .=++.+-+..+....+.|++....+.+++|-+..++..|.++++.+..+  +..+...|..++.
T Consensus        23 ~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K--~~~~~~~y~~~lq   84 (103)
T cd00923          23 GWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDK--CGAHKEIYPYILQ   84 (103)
T ss_pred             HHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH--ccCchhhHHHHHH
Confidence            3345666677777778899999999999999999999999999877434  2224445665543

Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=82.55  E-value=21  Score=31.64  Aligned_cols=93  Identities=13%  Similarity=0.134  Sum_probs=57.4

Q ss_pred             HHHHhcCCChHHHHHHHHHHHHCCCCCCH-----HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHH
Q 040394          504 IGGYGMQGDGGGSLALFSDMLNEEVQPNE-----VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDL  577 (691)
Q Consensus       504 i~~~~~~~~~~~A~~~~~~m~~~g~~p~~-----~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~  577 (691)
                      ..-+...|++++|..-|.+.+.. ++|..     ..|..-..++.+.+.++.|+.-..+.   ..+.|+ ......-..+
T Consensus       102 GN~~F~ngdyeeA~skY~~Ale~-cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKa---iel~pty~kAl~RRAea  177 (271)
T KOG4234|consen  102 GNELFKNGDYEEANSKYQEALES-CPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKA---IELNPTYEKALERRAEA  177 (271)
T ss_pred             HHHhhhcccHHHHHHHHHHHHHh-CccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhh---HhcCchhHHHHHHHHHH
Confidence            34567788888888888888874 23322     22333334667777887777766643   245554 2233333456


Q ss_pred             HHhcCChHHHHHHHHhC-CCCCCH
Q 040394          578 LARAGRLEEALEFMENM-PIEPDV  600 (691)
Q Consensus       578 ~~~~g~~~~A~~~~~~~-~~~p~~  600 (691)
                      |.+...+++|++-|+++ ...|..
T Consensus       178 yek~ek~eealeDyKki~E~dPs~  201 (271)
T KOG4234|consen  178 YEKMEKYEEALEDYKKILESDPSR  201 (271)
T ss_pred             HHhhhhHHHHHHHHHHHHHhCcch
Confidence            77777888888877777 445544

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=82.44  E-value=8.6  Score=34.19  Aligned_cols=74  Identities=15%  Similarity=0.115  Sum_probs=48.9

Q ss_pred             hcCChHHHHHHHHhCCCCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC----CchhHHHHHHHHHhCCCcHHH
Q 040394          580 RAGRLEEALEFMENMPIEP--DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPD----KACYYVLVSNLYASDGRWIRV  653 (691)
Q Consensus       580 ~~g~~~~A~~~~~~~~~~p--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~----~~~~~~~l~~~~~~~g~~~~A  653 (691)
                      +.|+ ++|.+.|-.+...|  +....-..+..|....|.+++++++.+++++.+.    |+..+..|+.++.+.|+++.|
T Consensus       119 r~~d-~~A~~~fL~~E~~~~l~t~elq~aLAtyY~krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e~A  197 (203)
T PF11207_consen  119 RFGD-QEALRRFLQLEGTPELETAELQYALATYYTKRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYEQA  197 (203)
T ss_pred             ccCc-HHHHHHHHHHcCCCCCCCHHHHHHHHHHHHccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchhhh
Confidence            3344 56666666663222  2233333444555677889999999998884322    378888899999999998887


Q ss_pred             H
Q 040394          654 N  654 (691)
Q Consensus       654 ~  654 (691)
                      -
T Consensus       198 Y  198 (203)
T PF11207_consen  198 Y  198 (203)
T ss_pred             h
Confidence            4

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=82.27  E-value=4.6  Score=36.06  Aligned_cols=72  Identities=8%  Similarity=0.056  Sum_probs=47.7

Q ss_pred             HHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhcc---CC---CChhhHHHHHHH
Q 040394          149 FSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDET---LD---KNVVSWTSMIAG  220 (691)
Q Consensus       149 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~---~~---~~~~~~~~li~~  220 (691)
                      .+..++.+.+.+.+.+++...++-++..|.|......++..||-.|+|++|..-++-.   ..   +....|..+|.+
T Consensus         4 l~~t~seLL~~~sL~dai~~a~~qVkakPtda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p~~t~~a~lyr~lir~   81 (273)
T COG4455           4 LRDTISELLDDNSLQDAIGLARDQVKAKPTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSPQDTVGASLYRHLIRC   81 (273)
T ss_pred             hHHHHHHHHHhccHHHHHHHHHHHHhcCCccccchhHHHHHHhhcchHHHHHHHHHHHhhcCcccchHHHHHHHHHHH
Confidence            3444556667777777777777777776667777777888888888888876655543   22   233456666654

>smart00028 TPR Tetratricopeptide repeats

Probab=82.10  E-value=2.8  Score=23.66  Aligned_cols=28  Identities=21%  Similarity=0.160  Sum_probs=13.8

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCC
Q 040394          604 GAFLHGCGLYSRFDLGEVMIKKMLELHP  631 (691)
Q Consensus       604 ~~l~~~~~~~g~~~~A~~~~~~~~~~~p  631 (691)
                      ..+...+...|+++.|...+++.++..|
T Consensus         5 ~~~a~~~~~~~~~~~a~~~~~~~~~~~~   32 (34)
T smart00028        5 YNLGNAYLKLGDYDEALEYYEKALELDP   32 (34)
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHccCC
Confidence            3344444455555555555555554444

Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=81.95  E-value=5.7  Score=37.20  Aligned_cols=61  Identities=15%  Similarity=0.013  Sum_probs=53.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          602 LFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       602 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      +++.....|..+|.+.+|.++.++++.++|-+...+..|...+...|+--.|...++++.+
T Consensus       281 llgkva~~yle~g~~neAi~l~qr~ltldpL~e~~nk~lm~~la~~gD~is~~khyerya~  341 (361)
T COG3947         281 LLGKVARAYLEAGKPNEAIQLHQRALTLDPLSEQDNKGLMASLATLGDEISAIKHYERYAE  341 (361)
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHhhcChhhhHHHHHHHHHHHHhccchhhhhHHHHHHH
Confidence            3445556788999999999999999999999999999999999999998888888877753

>PRK11619 lytic murein transglycosylase; Provisional

Probab=81.60  E-value=89  Score=34.36  Aligned_cols=243  Identities=5%  Similarity=-0.113  Sum_probs=120.1

Q ss_pred             cCChhhHHHHHHHHHHHC-CCCch--HHHHHHHHHHHhcCCHHHHHHHHHhcCC--CChhHHHHHHHHHHhcCCchhHHH
Q 040394          259 LRALHQGKWLHGYILKIG-IEINS--HLVTALLDMYVKCGNIRDARSVFDELCS--IDLVSWTAMIVGYTQSGYPDKALK  333 (691)
Q Consensus       259 ~~~~~~a~~~~~~~~~~g-~~~~~--~~~~~li~~~~~~g~~~~A~~~~~~~~~--~~~~~~~~li~~~~~~g~~~~a~~  333 (691)
                      ..+.+.|..++....... +.+..  .+...+.......+..++|...++....  .+.....--+..-.+.++++.+..
T Consensus       254 r~d~~~A~~~~~~~~~~~~~~~~~~~~~~~~lA~~~a~~~~~~~a~~w~~~~~~~~~~~~~~e~r~r~Al~~~dw~~~~~  333 (644)
T PRK11619        254 RQDAENARLMIPSLVRAQKLNEDQRQELRDIVAWRLMGNDVTDEQAKWRDDVIMRSQSTSLLERRVRMALGTGDRRGLNT  333 (644)
T ss_pred             HhCHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHhcccccCCcHHHHHHHHHHHHccCHHHHHH
Confidence            345577777777764433 22221  2344444444444335667777776532  244444444555557888888888


Q ss_pred             HHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCch
Q 040394          334 LFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVI  413 (691)
Q Consensus       334 ~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  413 (691)
                      .+..|.... .-...-.--+..++...|+.++|...++.+...    ...|..+...  +.|..-.       +...   
T Consensus       334 ~i~~L~~~~-~~~~rw~YW~aRa~~~~g~~~~A~~~~~~~a~~----~~fYG~LAa~--~Lg~~~~-------~~~~---  396 (644)
T PRK11619        334 WLARLPMEA-KEKDEWRYWQADLLLEQGRKAEAEEILRQLMQQ----RGFYPMVAAQ--RLGEEYP-------LKID---  396 (644)
T ss_pred             HHHhcCHhh-ccCHhhHHHHHHHHHHcCCHHHHHHHHHHHhcC----CCcHHHHHHH--HcCCCCC-------CCCC---
Confidence            888875432 223333444555655667777777777665331    1122222111  1111000       0000   


Q ss_pred             hHHHHHHhhhCCCCCCH-----HHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHH
Q 040394          414 AWNSIISGLDDNVSPDA-----VTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMV  488 (691)
Q Consensus       414 ~~~~li~~~~~~~~p~~-----~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  488 (691)
                                 ..++..     ..-..-+..+...|....|...+..+....    +......+.....+.|..+.+...
T Consensus       397 -----------~~~~~~~~~~~~~~~~ra~~L~~~g~~~~a~~ew~~~~~~~----~~~~~~~la~~A~~~g~~~~ai~~  461 (644)
T PRK11619        397 -----------KAPKPDSALTQGPEMARVRELMYWNMDNTARSEWANLVASR----SKTEQAQLARYAFNQQWWDLSVQA  461 (644)
T ss_pred             -----------CCCchhhhhccChHHHHHHHHHHCCCHHHHHHHHHHHHhcC----CHHHHHHHHHHHHHCCCHHHHHHH
Confidence                       000000     011223344556788888888887777642    233445555556667777777665


Q ss_pred             HHhcccC------CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHH
Q 040394          489 FDAMREK------NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEV  533 (691)
Q Consensus       489 ~~~~~~~------~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~  533 (691)
                      ......-      -+..|...+..+.+.-.++.++-.---.++.++.|+..
T Consensus       462 ~~~~~~~~~~~~rfp~~~~~~~~~~a~~~~v~~~lv~ai~rqES~f~p~a~  512 (644)
T PRK11619        462 TIAGKLWDHLEERFPLAWNDEFRRYTSGKGIPQSYAMAIARQESAWNPKAR  512 (644)
T ss_pred             HhhchhHHHHHHhCCcchHHHHHHHHHHcCCCHHHHHHHHHHhcCCCCCCc
Confidence            5433221      11234455555555555555443333334555666543

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=81.15  E-value=17  Score=33.68  Aligned_cols=120  Identities=13%  Similarity=0.137  Sum_probs=78.8

Q ss_pred             cCCHHHHHHHHHHchhhcCCCCC--hhHHHHHHHHHHhcCChHHHHHHHHhC--------CCCCCHHHHHHHHHHHHhcC
Q 040394          545 TGMVGEGWKCFYSMCRDFKFVPS--MKHYVCMVDLLARAGRLEEALEFMENM--------PIEPDVSLFGAFLHGCGLYS  614 (691)
Q Consensus       545 ~g~~~~A~~~~~~m~~~~~~~p~--~~~~~~li~~~~~~g~~~~A~~~~~~~--------~~~p~~~~~~~l~~~~~~~g  614 (691)
                      ...+++|+.-|++.++--|-+-+  ......+|....+.|++++..+.+.++        .-.-+..+.++++.....+.
T Consensus        40 e~~p~~Al~sF~kVlelEgEKgeWGFKALKQmiKI~f~l~~~~eMm~~Y~qlLTYIkSAVTrNySEKsIN~IlDyiStS~  119 (440)
T KOG1464|consen   40 EDEPKEALSSFQKVLELEGEKGEWGFKALKQMIKINFRLGNYKEMMERYKQLLTYIKSAVTRNYSEKSINSILDYISTSK  119 (440)
T ss_pred             ccCHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHhhhh
Confidence            34667777777655422221111  234445677778888888887777776        12234567788888777777


Q ss_pred             CHHHHHHHHHHHHh--cCCCCc----hhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          615 RFDLGEVMIKKMLE--LHPDKA----CYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       615 ~~~~A~~~~~~~~~--~~p~~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      +.+.-.++++.-++  .+..+.    .+...|+.+|...|.+.+-.++++++.+..
T Consensus       120 ~m~LLQ~FYeTTL~ALkdAKNeRLWFKTNtKLgkl~fd~~e~~kl~KIlkqLh~SC  175 (440)
T KOG1464|consen  120 NMDLLQEFYETTLDALKDAKNERLWFKTNTKLGKLYFDRGEYTKLQKILKQLHQSC  175 (440)
T ss_pred             hhHHHHHHHHHHHHHHHhhhcceeeeeccchHhhhheeHHHHHHHHHHHHHHHHHh
Confidence            77777777776554  122222    334578999999999999999999987643

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=81.10  E-value=11  Score=29.07  Aligned_cols=60  Identities=10%  Similarity=0.166  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHH
Q 040394          515 GSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVD  576 (691)
Q Consensus       515 ~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~  576 (691)
                      +..+-+..+....+.|++....+.+.+|-+..++..|.++++.+..+.+  +....|..++.
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~--~~~~~Y~~~lq   87 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCG--NKKEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTT--T-TTHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHcc--ChHHHHHHHHH
Confidence            4555566666777889999999999999999999999999998855533  33436766654

9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....

>PF14561 TPR_20: Tetratricopeptide repeat; PDB: 3QOU_A 2R5S_A 3QDN_B

Probab=80.41  E-value=6.2  Score=30.11  Aligned_cols=49  Identities=6%  Similarity=-0.036  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC--chhHHHHHHHHHhCCC
Q 040394          601 SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK--ACYYVLVSNLYASDGR  649 (691)
Q Consensus       601 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~--~~~~~~l~~~~~~~g~  649 (691)
                      ..-..+...+...|++++|.+.+-++++.+|+.  ...-..+..++...|.
T Consensus        23 ~ar~~lA~~~~~~g~~e~Al~~Ll~~v~~dr~~~~~~ar~~ll~~f~~lg~   73 (90)
T PF14561_consen   23 DARYALADALLAAGDYEEALDQLLELVRRDRDYEDDAARKRLLDIFELLGP   73 (90)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHCC-TTCCCCHHHHHHHHHHHHH-T
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCccccccHHHHHHHHHHHHcCC
Confidence            444445555555555555555555555544332  3444444455554444

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=80.14  E-value=20  Score=27.67  Aligned_cols=79  Identities=11%  Similarity=-0.001  Sum_probs=51.5

Q ss_pred             ChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhC
Q 040394          161 DIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREG  240 (691)
Q Consensus       161 ~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  240 (691)
                      ..++|..+-+.+...+-....+--.-++.+...|++++|..+.+.+..||...|-+|-.  .+.|..+++..-+.+|..+
T Consensus        20 cHqEA~tIAdwL~~~~~~~E~v~lIRlsSLmNrG~Yq~Al~l~~~~~~pdlepw~ALce--~rlGl~s~l~~rl~rla~s   97 (115)
T TIGR02508        20 CHQEANTIADWLHLKGESEEAVQLIRLSSLMNRGDYQSALQLGNKLCYPDLEPWLALCE--WRLGLGSALESRLNRLAAS   97 (115)
T ss_pred             HHHHHHHHHHHHhcCCchHHHHHHHHHHHHHccchHHHHHHhcCCCCCchHHHHHHHHH--HhhccHHHHHHHHHHHHhC
Confidence            34455555554444332233333344556778899999999999998899988887765  3566667666667677655


Q ss_pred             C
Q 040394          241 F  241 (691)
Q Consensus       241 ~  241 (691)
                      |
T Consensus        98 g   98 (115)
T TIGR02508        98 G   98 (115)
T ss_pred             C
Confidence            4

YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.

---

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	691
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-09
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	2e-08
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	4e-07
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	2e-05
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	6e-04

>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 = 61.8 bits (149), Expect = 6e-10
 Identities = 95/659 (14%), Positives = 188/659 (28%), Gaps = 178/659 (27%)

Query: 33  TQHELDQTFASFHSLPSIPCLNLLGLCKSTGS--LKAFHALLIVDGLTNDKCNTKLVSMY 90
           ++ E+D    S  ++     L L     S     ++ F    + + L  +         Y
Sbjct: 47  SKEEIDHIIMSKDAVSGT--LRLFWTLLSKQEEMVQKF----VEEVLRIN---------Y 91

Query: 91  GSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFS 150
             F                  Y  Q        + LY D   F K    RL+ +      
Sbjct: 92  K-FLMSPIKTEQRQPSMMTRMYIEQR-------DRLYNDNQVFAKYNVSRLQPYL----- 138

Query: 151 KVLKACCELRDID----EGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDET 206
           K+ +A  ELR       +G+          G     +   V     C       ++  + 
Sbjct: 139 KLRQALLELRPAKNVLIDGV---------LGSGKTWVALDV-----CLSYKVQCKMDFK- 183

Query: 207 LDKNVVSWTSMIAGYVQ--NDCAQEGLVLFNRMREGFVEGNQITLG---SLVTACAKLRA 261
                + W ++            +    L  ++   +   +  +      + +  A+LR 
Sbjct: 184 -----IFWLNL--KNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRR 236

Query: 262 LHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSV--FDELCSIDLV-----S 314
           L + K    Y        N  LV   L       N+++A++   F+  C I L+      
Sbjct: 237 LLKSK---PY-------ENCLLV---LL------NVQNAKAWNAFNLSCKI-LLTTRFKQ 276

Query: 315 WTAMIVGYTQSGYP-DKALKLFTDKKWADFFPNHVTI-ASVLSASAQLGN---LNM-GRM 368
            T  +   T +    D      T  +       ++      L       N   L++    
Sbjct: 277 VTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAES 336

Query: 369 VHSLGIRL-GLEDYTV--INALVDMYAKCHVIADARYIFETTS--EKDV--------IAW 415
           +          +      +  +++        A+ R +F+  S              + W
Sbjct: 337 IRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIW 396

Query: 416 NSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYS-TKQGLLSSNVYVGTALLN 474
             +I      V                       + LH YS  ++    S + + +  L 
Sbjct: 397 FDVIKSDVMVVV----------------------NKLHKYSLVEKQPKESTISIPSIYLE 434

Query: 475 FYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQG--DGGGSLALFSDMLNEEVQPNE 532
              K  +         A+          ++  Y +    D    +  + D          
Sbjct: 435 LKVKLENEY-------ALHRS-------IVDHYNIPKTFDSDDLIPPYLDQY-------- 472

Query: 533 VIFTTI---LSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKH----YVCMVDLLARAGRL 584
             ++ I   L    H     E    F  +  DF+F+   ++H    +     +L    +L
Sbjct: 473 -FYSHIGHHLKNIEHP----ERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQL 527

Query: 585 EEALEFM-ENMPI-EPDVSLFGAFLHGCG---LYSRF-DLGEVMIKKMLELHPDKACYY 637
           +    ++ +N P  E  V+    FL       + S++ DL  + I  M     D+A + 
Sbjct: 528 KFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDL--LRIALM---AEDEAIFE 581

>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 = 57.9 bits (139), Expect = 8e-09
 Identities = 82/567 (14%), Positives = 144/567 (25%), Gaps = 211/567 (37%)

Query: 127 YKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGL 186
           YKDI+  +      +   D      + K+     +ID        I+      S  L  L
Sbjct: 18  YKDILSVF--EDAFVDNFDCKDVQDMPKSILSKEEIDH-------IIMSKDAVSGTLR-L 67

Query: 187 VDMYAKCRDIGSS--RQVFDETLDKNVVSWTSMIAGYVQNDCAQEGL--VLFNRMREGFV 242
                          ++  +E L  N   +   +   ++ +  Q  +   ++   R+   
Sbjct: 68  FWTL---LSKQEEMVQKFVEEVLRINY-KF---LMSPIKTEQRQPSMMTRMYIEQRDRLY 120

Query: 243 EGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARS 302
             NQ+     V+       L Q                     ALL        +R A++
Sbjct: 121 NDNQVFAKYNVSRLQPYLKLRQ---------------------ALL-------ELRPAKN 152

Query: 303 VFDELCSIDLVSWTAMIVGYTQSGYPDK---ALKLFTDKKWADFFPNHV---TIASVLSA 356
           V               I G   SG   K   AL +    K        +    + +  S 
Sbjct: 153 VL--------------IDGVLGSG---KTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSP 195

Query: 357 SAQLGNLN----------MGRMVHSLGIRLGLEDYTVINALVD-----MYAKCHVIADAR 401
              L  L             R  HS  I+L +    +   L        Y  C ++    
Sbjct: 196 ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHS--IQAELRRLLKSKPYENCLLVLL-- 251

Query: 402 YIFETTSEKDVIAWNS-IISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQG 460
                    +V   N+   +  + +              C                  + 
Sbjct: 252 ---------NV--QNAKAWNAFNLS--------------C------------------KI 268

Query: 461 LLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALF 520
           LL++                  Q    V D +    T   S       +  D     +L 
Sbjct: 269 LLTTR---------------FKQ----VTDFLSAATTTHISLDHHSMTLTPDE--VKSLL 307

Query: 521 SDMLNEEVQ--PNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSM----KHYVCM 574
              L+   Q  P EV+ T          ++ E         RD     +     KH  C 
Sbjct: 308 LKYLDCRPQDLPREVLTTNPR----RLSIIAE-------SIRDG---LATWDNWKHVNC- 352

Query: 575 VDLLARAGRLEEALE----------------FMENMPIEPDVSLFGAFLHGCGLYSRFDL 618
            D L     +E +L                 F  +  I   + L         ++     
Sbjct: 353 -DKLTTI--IESSLNVLEPAEYRKMFDRLSVFPPSAHIPTIL-L-------SLIWFDVIK 401

Query: 619 GEVMI-------KKMLELHPDKACYYV 638
            +VM+         ++E  P ++   +
Sbjct: 402 SDVMVVVNKLHKYSLVEKQPKESTISI 428

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 56.7 bits (135), Expect = 2e-08
 Identities = 25/165 (15%), Positives = 61/165 (36%), Gaps = 11/165 (6%)

Query: 425 NVSPDAVTLVSVISACASLG----AVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCG 480
            +S     L++    C        A  +    H    K+ LL+ ++Y   A++  +A+ G
Sbjct: 122 QLSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMY--NAVMLGWARQG 179

Query: 481 DAQSARMVFDAMREK----NTVTWSAMIGGYGMQGDGGGSLA-LFSDMLNEEVQPNEVIF 535
             +    V   +++     + ++++A +   G Q    G++      M  E ++   +  
Sbjct: 180 AFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFT 239

Query: 536 TTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLAR 580
             +LS      ++    K   +     +  P +     + D+ A+
Sbjct: 240 AVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAK 284

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 52.5 bits (124), Expect = 4e-07
 Identities = 17/137 (12%), Positives = 44/137 (32%), Gaps = 7/137 (5%)

Query: 233 LFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYV 292
           L +  R+      +  L  L+       +L   +   G   +  +      + A     +
Sbjct: 79  LEDCTRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCCL 138

Query: 293 KCGNIRDARSVFDEL-------CSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFP 345
               +  A  +             + L  + A+++G+ + G   + + +    K A   P
Sbjct: 139 LTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTP 198

Query: 346 NHVTIASVLSASAQLGN 362
           + ++ A+ L    +   
Sbjct: 199 DLLSYAAALQCMGRQDQ 215

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7 Length = 308

 Score = 45.8 bits (108), Expect = 2e-05
 Identities = 18/131 (13%), Positives = 45/131 (34%), Gaps = 8/131 (6%)

Query: 286 ALLDMYVKCGNIRDARSVFDELCSID----LVSWTAMIVGYTQSGYPDKALKLFTDKKWA 341
           A  D            S+++ L +I+     + +   +    ++        +F  KK  
Sbjct: 104 AYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIF--KKAR 161

Query: 342 DFFPN--HVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIAD 399
           +      HV + + L       + ++   +  LG++   +    + A +D  +  +   +
Sbjct: 162 EDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNN 221

Query: 400 ARYIFETTSEK 410
            R +FE     
Sbjct: 222 TRVLFERVLTS 232

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus} Length = 291

 Score = 41.3 bits (96), Expect = 6e-04
 Identities = 18/180 (10%), Positives = 46/180 (25%), Gaps = 12/180 (6%)

Query: 476 YAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIF 535
           Y                                        +A     ++  V      F
Sbjct: 44  YLAQRKYGVVLDEIKPSSAPELQAVRMFAEYLASHSRRDAIVAELDREMSRSVDVTNTTF 103

Query: 536 TTILSAC-SHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM 594
             + ++   +        +  +          S++     V +L +  RL+ A + ++ M
Sbjct: 104 LLMAASIYFYDQNPDAALRTLHQGD-------SLECMAMTVQILLKLDRLDLARKELKKM 156

Query: 595 -PIEPDVSLFGAFLHGCGLYS---RFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRW 650
              + D +L         L +   +      + ++M +            +  + + GRW
Sbjct: 157 QDQDEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRW 216

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	691
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.96
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.96
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.96
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.95
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.92
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.92
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.91
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.9
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.9
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.89
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.85
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.84
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.83
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.82
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.82
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.78
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.78
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.78
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.77
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.77
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.76
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.76
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.75
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.75
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.74
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.73
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.73
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.72
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.7
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.7
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.7
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.69
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.67
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.64
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.61
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.6
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.55
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.54
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.53
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.53
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.53
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.52
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.51
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.51
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.51
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.5
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.49
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.49
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.49
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.49
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.48
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.47
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.46
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.45
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.43
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.43
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.42
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.41
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.41
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.41
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.39
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.39
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.37
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.32
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.31
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.28
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.28
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.27
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.27
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.26
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.24
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.23
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.22
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.22
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.2
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.2
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.18
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.18
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.17
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.16
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.1
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.07
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	99.0
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.97
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.97
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.97
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.96
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.96
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.96
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.94
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.94
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.91
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.9
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.88
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.86
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.86
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.86
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.86
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	98.84
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.83
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.81
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.8
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.79
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.79
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.75
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.75
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.72
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.72
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.72
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.71
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.7
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.69
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.69
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.68
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	98.67
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.62
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.62
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.62
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.59
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.59
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.58
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.57
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.56
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.56
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.55
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.55
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.53
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.53
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.52
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.52
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.52
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.49
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.48
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.47
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.45
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.45
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.44
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.41
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.41
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.4
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.4
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.39
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.39
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.37
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.35
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.34
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.34
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.33
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.32
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.32
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.32
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.32
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.3
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.29
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.29
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.27
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.26
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.25
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.24
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.24
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.22
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.22
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.2
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.19
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.18
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.15
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.15
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.11
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.11
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.1
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.08
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.08
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.06
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.06
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.03
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.03
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.02
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.01
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	97.99
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.98
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.98
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.98
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.97
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.96
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.96
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.87
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.87
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.87
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	97.85
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.85
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.82
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.82
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	97.79
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.74
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.73
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.72
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.65
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.63
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.61
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.57
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	97.51
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.45
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.35
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.26
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.22
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.15
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	97.15
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	97.13
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.11
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	97.1
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	97.09
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.07
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.06
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.05
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	96.91
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.84
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.64
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	96.56
1pc2_A	152	Mitochondria fission protein; unknown function; NM	96.54
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.53
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	96.51
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	96.49
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	96.16
1pc2_A	152	Mitochondria fission protein; unknown function; NM	95.93
1qsa_A	618	Protein (soluble lytic transglycosylase SLT70); al	95.92
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	95.86
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	95.85
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	95.83
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	95.52
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	95.38
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	94.75
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	94.74
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	94.37
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	94.1
2wpv_A	312	GET4, UPF0363 protein YOR164C; golgi-ER traffickin	92.89
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	92.85
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	92.44
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	92.41
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	92.4
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	91.44
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	90.91
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	90.87
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	90.58
2wpv_A	312	GET4, UPF0363 protein YOR164C; golgi-ER traffickin	90.21
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	90.02
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	89.4
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	89.37
2p58_C	116	Putative type III secretion protein YSCG; type III	89.17
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	88.33
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	88.27
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	87.96
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	87.76
1qsa_A	618	Protein (soluble lytic transglycosylase SLT70); al	87.14
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	87.06
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	85.03
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	84.04
3esl_A	202	Checkpoint serine/threonine-protein kinase BUB1; m	83.83
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	83.63
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	83.33
2p58_C	116	Putative type III secretion protein YSCG; type III	83.06
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	82.69
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	82.29
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	81.65
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	81.29
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	81.26
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	80.34

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=2.5e-41  Score=368.42  Aligned_cols=501  Identities=9%  Similarity=-0.071  Sum_probs=343.8

Q ss_pred             HHhcCCChHHHHHHhccCCCCCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHH
Q 040394           89 MYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKV  168 (691)
Q Consensus        89 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~  168 (691)
                      .+.+.|....+...|..++.++...|+.++..+.+.|++++|+.+|++|...  .|+..++..++.+|.+.|++++|..+
T Consensus        62 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~l~~~~~~~g~~~~A~~~  139 (597)
T 2xpi_A           62 NTSTDGSFLKERNAQNTDSLSREDYLRLWRHDALMQQQYKCAAFVGEKVLDI--TGNPNDAFWLAQVYCCTGDYARAKCL  139 (597)
T ss_dssp             --------------------CHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--HCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cccccCccCCCCCccccchHHHHHHHHHHHHHHHHccCchHHHHHHHHHHhh--CCCchHHHHHHHHHHHcCcHHHHHHH
Confidence            3556778888888999888889999999999999999999999999999864  67888999999999999999999999


Q ss_pred             HHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCC-------------------ChhhHHHHHHHHHhCCChhH
Q 040394          169 HCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDK-------------------NVVSWTSMIAGYVQNDCAQE  229 (691)
Q Consensus       169 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-------------------~~~~~~~li~~~~~~g~~~~  229 (691)
                      |+.+... +++..+++.++.+|.+.|++++|.++|+++...                   +..+|+.++.+|.+.|++++
T Consensus       140 ~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  218 (597)
T 2xpi_A          140 LTKEDLY-NRSSACRYLAAFCLVKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDR  218 (597)
T ss_dssp             HHHTCGG-GTCHHHHHHHHHHHHHTTCHHHHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHhcc-ccchhHHHHHHHHHHHHhhHHHHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHH
Confidence            9987643 448899999999999999999999999965433                   36788888888888888888


Q ss_pred             HHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhH--HHH-HHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHh
Q 040394          230 GLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQG--KWL-HGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDE  306 (691)
Q Consensus       230 A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a--~~~-~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~  306 (691)
                      |+++|++|.+.+.. +...+..+...+...+..+.+  ..+ +..+...+..+...+|+.++..|.+.|++++|.++|++
T Consensus       219 A~~~~~~~~~~~p~-~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~  297 (597)
T 2xpi_A          219 AKECYKEALMVDAK-CYEAFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSS  297 (597)
T ss_dssp             HHHHHHHHHHHCTT-CHHHHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCch-hhHHHHHHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHH
Confidence            88888888775421 333444444433332222211  111 34444444444555666667777777777777777777


Q ss_pred             cCC--CChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHH
Q 040394          307 LCS--IDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVI  384 (691)
Q Consensus       307 ~~~--~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  384 (691)
                      +..  ++..+|+.++..|.+.|++++|.++|+++...+. .+..++..++.++...|++++|..+++.+.+..+.+    
T Consensus       298 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~----  372 (597)
T 2xpi_A          298 INGLEKSSDLLLCKADTLFVRSRFIDVLAITTKILEIDP-YNLDVYPLHLASLHESGEKNKLYLISNDLVDRHPEK----  372 (597)
T ss_dssp             STTGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTS----
T ss_pred             hhcCCchHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcCc-ccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhCccc----
Confidence            755  5667777777777777777777777777765432 244445555555555555555555555444443334    


Q ss_pred             HHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC
Q 040394          385 NALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSS  464 (691)
Q Consensus       385 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~  464 (691)
                                                                   ..++..+...|.+.|++++|..+|+++.+..  +.
T Consensus       373 ---------------------------------------------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~  405 (597)
T 2xpi_A          373 ---------------------------------------------AVTWLAVGIYYLCVNKISEARRYFSKSSTMD--PQ  405 (597)
T ss_dssp             ---------------------------------------------HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TT
T ss_pred             ---------------------------------------------HHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CC
Confidence                                                         4455555555555555555555555555544  45


Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 040394          465 NVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSA  541 (691)
Q Consensus       465 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~  541 (691)
                      +..+++.++.+|.+.|++++|.++|+++.+   .+..+|+.++.+|.+.|++++|.++|+++.+.. +.+..+|+.+...
T Consensus       406 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~  484 (597)
T 2xpi_A          406 FGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQGTHLPYLFLGMQHMQLGNILLANEYLQSSYALF-QYDPLLLNELGVV  484 (597)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHH
Confidence            566666666666666666666666666543   255667777777777777777777777776642 3456777777777


Q ss_pred             hcccCCHHHHHHHHHHchhhc---CCCCC--hhHHHHHHHHHHhcCChHHHHHHHHhC-CC-CCCHHHHHHHHHHHHhcC
Q 040394          542 CSHTGMVGEGWKCFYSMCRDF---KFVPS--MKHYVCMVDLLARAGRLEEALEFMENM-PI-EPDVSLFGAFLHGCGLYS  614 (691)
Q Consensus       542 ~~~~g~~~~A~~~~~~m~~~~---~~~p~--~~~~~~li~~~~~~g~~~~A~~~~~~~-~~-~p~~~~~~~l~~~~~~~g  614 (691)
                      +.+.|++++|.++|+++.+..   +..|+  ..+|..++.+|.+.|++++|.+.++++ .. +.+..+|..+..+|.+.|
T Consensus       485 ~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g  564 (597)
T 2xpi_A          485 AFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLSTNDANVHTAIALVYLHKK  564 (597)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHTT
T ss_pred             HHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhC
Confidence            777777777777777774332   55676  678888888888888998888888887 33 347789999999999999


Q ss_pred             CHHHHHHHHHHHHhcCCCCchhHHHHHHHHHh
Q 040394          615 RFDLGEVMIKKMLELHPDKACYYVLVSNLYAS  646 (691)
Q Consensus       615 ~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~  646 (691)
                      ++++|...++++++++|+++..+..++.+|..
T Consensus       565 ~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~  596 (597)
T 2xpi_A          565 IPGLAITHLHESLAISPNEIMASDLLKRALEE  596 (597)
T ss_dssp             CHHHHHHHHHHHHHHCTTCHHHHHHHHHTTC-
T ss_pred             CHHHHHHHHHHHHhcCCCChHHHHHHHHHHhc
Confidence            99999999999999999999999999887653

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=1.8e-38  Score=345.76  Aligned_cols=446  Identities=10%  Similarity=-0.035  Sum_probs=329.1

Q ss_pred             CChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHH
Q 040394          194 RDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYIL  273 (691)
Q Consensus       194 g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~  273 (691)
                      |....+...+..++.+++..|+.++..+.+.|++++|..+|++|..  ..|+..++..+..+|.+.|++++|..+|+.+.
T Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~--~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  144 (597)
T 2xpi_A           67 GSFLKERNAQNTDSLSREDYLRLWRHDALMQQQYKCAAFVGEKVLD--ITGNPNDAFWLAQVYCCTGDYARAKCLLTKED  144 (597)
T ss_dssp             ---------------CHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HHCCHHHHHHHHHHHHHTTCHHHHHHHHHHTC
T ss_pred             CccCCCCCccccchHHHHHHHHHHHHHHHHccCchHHHHHHHHHHh--hCCCchHHHHHHHHHHHcCcHHHHHHHHHHHh
Confidence            3333444444444444444455555555555555555555555442  23444444445555555555555555544443


Q ss_pred             HHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCC-------------------ChhHHHHHHHHHHhcCCchhHHHH
Q 040394          274 KIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSI-------------------DLVSWTAMIVGYTQSGYPDKALKL  334 (691)
Q Consensus       274 ~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~-------------------~~~~~~~li~~~~~~g~~~~a~~~  334 (691)
                      ..  +++..+++.++.+|.+.|++++|.++|+++...                   +..+|+.++.+|.+.|++++|.++
T Consensus       145 ~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  222 (597)
T 2xpi_A          145 LY--NRSSACRYLAAFCLVKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKEC  222 (597)
T ss_dssp             GG--GTCHHHHHHHHHHHHHTTCHHHHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cc--ccchhHHHHHHHHHHHHhhHHHHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHHH
Confidence            21  334445555555555555555555555433221                   234455555555555555555555


Q ss_pred             HHHhhHC-------------------------------------CCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhC
Q 040394          335 FTDKKWA-------------------------------------DFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLG  377 (691)
Q Consensus       335 ~~~m~~~-------------------------------------g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~  377 (691)
                      |++|...                                     +..+...+|..++..|.+.|++++|..+++.+.+. 
T Consensus       223 ~~~~~~~~p~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~-  301 (597)
T 2xpi_A          223 YKEALMVDAKCYEAFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGL-  301 (597)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTSTTG-
T ss_pred             HHHHHHhCchhhHHHHHHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhhcC-
Confidence            5555443                                     22333344555566778889999999999998877 


Q ss_pred             CCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHH
Q 040394          378 LEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYST  457 (691)
Q Consensus       378 ~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  457 (691)
                      +.+..+++.++..|.+.|++++|..+|+++.+.               .+.+..++..++.++.+.|+.++|..+++.+.
T Consensus       302 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---------------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  366 (597)
T 2xpi_A          302 EKSSDLLLCKADTLFVRSRFIDVLAITTKILEI---------------DPYNLDVYPLHLASLHESGEKNKLYLISNDLV  366 (597)
T ss_dssp             GGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------------CTTCCTTHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHhcCHHHHHHHHHHHHHc---------------CcccHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            358889999999999999999999999998754               23466789999999999999999999999999


Q ss_pred             HcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHH
Q 040394          458 KQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVI  534 (691)
Q Consensus       458 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~  534 (691)
                      +..  +.+..+++.++.+|.+.|++++|.++|+++.+   .+..+|+.++.+|.+.|++++|+++|+++.+.+ +.+..+
T Consensus       367 ~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~  443 (597)
T 2xpi_A          367 DRH--PEKAVTWLAVGIYYLCVNKISEARRYFSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLP  443 (597)
T ss_dssp             HHC--TTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHH
T ss_pred             hhC--cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHH
Confidence            876  78899999999999999999999999998864   468899999999999999999999999999864 457789


Q ss_pred             HHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-------CCCCC--HHHHHH
Q 040394          535 FTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-------PIEPD--VSLFGA  605 (691)
Q Consensus       535 ~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-------~~~p~--~~~~~~  605 (691)
                      ++.+..+|.+.|++++|.++|+++.+.  .+.+..+|+.++..|.+.|++++|+++|+++       +..|+  ..+|..
T Consensus       444 ~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~  521 (597)
T 2xpi_A          444 YLFLGMQHMQLGNILLANEYLQSSYAL--FQYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWAN  521 (597)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHH
Confidence            999999999999999999999999654  2335889999999999999999999999998       44777  679999


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          606 FLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       606 l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      ++.+|.+.|++++|...++++.+..|+++.++..++.+|.+.|++++|.+.++++.+..
T Consensus       522 l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~  580 (597)
T 2xpi_A          522 LGHAYRKLKMYDAAIDALNQGLLLSTNDANVHTAIALVYLHKKIPGLAITHLHESLAIS  580 (597)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHhcC
Confidence            99999999999999999999999999999999999999999999999999999998854

>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=99.96  E-value=4.2e-26  Score=233.65  Aligned_cols=375  Identities=12%  Similarity=0.078  Sum_probs=258.8

Q ss_pred             HHHHhCCChhHHHHHHHHHHhCCCCCC-hhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCH
Q 040394          219 AGYVQNDCAQEGLVLFNRMREGFVEGN-QITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNI  297 (691)
Q Consensus       219 ~~~~~~g~~~~A~~~~~~m~~~~~~p~-~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~  297 (691)
                      ..+.+.|++++|.+.++++.+..  |+ ...+..+...+...|++++|...++...+.. +.+..+|..+...+      
T Consensus         7 ~~~~~~g~~~~A~~~~~~~~~~~--p~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~-p~~~~~~~~lg~~~------   77 (388)
T 1w3b_A            7 HREYQAGDFEAAERHCMQLWRQE--PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVY------   77 (388)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH------
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHH------
Confidence            44555666666666666655432  22 2333333344444555555555555444432 22344444444444      


Q ss_pred             HHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCc-HHHHHHHHHHHhcCCChhhHHHHHHHHHHh
Q 040394          298 RDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPN-HVTIASVLSASAQLGNLNMGRMVHSLGIRL  376 (691)
Q Consensus       298 ~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~  376 (691)
                                               .+.|++++|.+.|+++...  .|+ ..++..+..++...|++++|...+..+.+.
T Consensus        78 -------------------------~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  130 (388)
T 1w3b_A           78 -------------------------KERGQLQEAIEHYRHALRL--KPDFIDGYINLAAALVAAGDMEGAVQAYVSALQY  130 (388)
T ss_dssp             -------------------------HHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHH
T ss_pred             -------------------------HHCCCHHHHHHHHHHHHHc--CcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence                                     4444555555444444432  222 233444444555555555555555555555


Q ss_pred             CCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHH
Q 040394          377 GLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYS  456 (691)
Q Consensus       377 ~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~  456 (691)
                      .+.....+..+...+...|++++|...|+++...               .+.+..++..+...+...|+++.|...++++
T Consensus       131 ~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~---------------~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a  195 (388)
T 1w3b_A          131 NPDLYCVRSDLGNLLKALGRLEEAKACYLKAIET---------------QPNFAVAWSNLGCVFNAQGEIWLAIHHFEKA  195 (388)
T ss_dssp             CTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHH---------------CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHh---------------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            5555555566666666667777777766665532               1234566777777777777788888888877


Q ss_pred             HHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHH
Q 040394          457 TKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--K-NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEV  533 (691)
Q Consensus       457 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~  533 (691)
                      .+.+  |.+...+..+...+...|++++|...+++..+  | +..+|..+...+...|++++|+..++++.+.+ +.+..
T Consensus       196 l~~~--p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~  272 (388)
T 1w3b_A          196 VTLD--PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPD  272 (388)
T ss_dssp             HHHC--TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHH
T ss_pred             HhcC--CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHH
Confidence            7776  67778888888888888888888888887653  3 56788888889999999999999999988853 33467


Q ss_pred             HHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHH
Q 040394          534 IFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCG  611 (691)
Q Consensus       534 ~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~  611 (691)
                      ++..+..++.+.|++++|.+.++++.+.  .+.+..++..+...+.+.|++++|.+.++++ ...| +..++..+...+.
T Consensus       273 ~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~  350 (388)
T 1w3b_A          273 AYCNLANALKEKGSVAEAEDCYNTALRL--CPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQ  350 (388)
T ss_dssp             HHHHHHHHHHHHSCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhh--CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHH
Confidence            7888888999999999999999988544  2345788899999999999999999999988 4444 5678999999999


Q ss_pred             hcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCC
Q 040394          612 LYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGR  649 (691)
Q Consensus       612 ~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  649 (691)
                      +.|++++|...++++++..|+++..+..++.++...|+
T Consensus       351 ~~g~~~~A~~~~~~a~~~~p~~~~a~~~lg~~~~~~~~  388 (388)
T 1w3b_A          351 QQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             TTTCCHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTCC
T ss_pred             HcCCHHHHHHHHHHHHhhCCCCHHHHHhHHHHHHHccC
Confidence            99999999999999999999999999999998887764

>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=99.96  E-value=2.4e-25  Score=228.05  Aligned_cols=352  Identities=11%  Similarity=0.026  Sum_probs=309.6

Q ss_pred             HHHHHhcCCHHHHHHHHHhc---CCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChh
Q 040394          288 LDMYVKCGNIRDARSVFDEL---CSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLN  364 (691)
Q Consensus       288 i~~~~~~g~~~~A~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~  364 (691)
                      ...+.+.|++++|.+.++.+   .+.+...+..+...+...|++++|..+++..... .+.+..+|..+...+...|+++
T Consensus         6 a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~-~p~~~~~~~~lg~~~~~~g~~~   84 (388)
T 1w3b_A            6 AHREYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQ-NPLLAEAYSNLGNVYKERGQLQ   84 (388)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc-CCCchHHHHHHHHHHHHCCCHH
Confidence            44566778888888888776   3334556777778888899999999999887765 3457788999999999999999


Q ss_pred             hHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCC-HHHHHHHHHHHhcc
Q 040394          365 MGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPD-AVTLVSVISACASL  443 (691)
Q Consensus       365 ~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~-~~~~~~ll~~~~~~  443 (691)
                      +|...++.+.+..+.+...+..+..++.+.|++++|...|+++.+.                .|+ ...+..+...+...
T Consensus        85 ~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~----------------~p~~~~~~~~l~~~~~~~  148 (388)
T 1w3b_A           85 EAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQY----------------NPDLYCVRSDLGNLLKAL  148 (388)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHH----------------CTTCTHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----------------CCCcHHHHHHHHHHHHHc
Confidence            9999999999999888889999999999999999999999988643                344 45677788888999


Q ss_pred             CcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-CHhHHHHHHHHHhcCCChHHHHHHH
Q 040394          444 GAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--K-NTVTWSAMIGGYGMQGDGGGSLALF  520 (691)
Q Consensus       444 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~A~~~~  520 (691)
                      |++++|...++.+.+..  |.+...+..+...+.+.|++++|...|+++.+  | +...|..+...+...|++++|+..+
T Consensus       149 g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~  226 (388)
T 1w3b_A          149 GRLEEAKACYLKAIETQ--PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAY  226 (388)
T ss_dssp             SCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHH
T ss_pred             cCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            99999999999999987  78889999999999999999999999999874  3 5678999999999999999999999


Q ss_pred             HHHHHCCCCC-CHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC--CC
Q 040394          521 SDMLNEEVQP-NEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM--PI  596 (691)
Q Consensus       521 ~~m~~~g~~p-~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~--~~  596 (691)
                      ++..+.  .| +..++..+..++...|++++|.+.++++.+   ..|+ ..++..+...+.+.|++++|++.++++  ..
T Consensus       227 ~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  301 (388)
T 1w3b_A          227 LRALSL--SPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIE---LQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC  301 (388)
T ss_dssp             HHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---TCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC
T ss_pred             HHHHhh--CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh---hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            999885  45 467888899999999999999999998854   4565 678999999999999999999999998  34


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          597 EPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       597 ~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      +.+..++..+...+...|++++|...++++++..|++...+..++.+|.+.|++++|.+.++++.+.
T Consensus       302 p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~  368 (388)
T 1w3b_A          302 PTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI  368 (388)
T ss_dssp             TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            5577899999999999999999999999999999999999999999999999999999999999874

>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=99.96  E-value=1.4e-27  Score=248.17  Aligned_cols=209  Identities=13%  Similarity=0.067  Sum_probs=164.2

Q ss_pred             HHHHHHHHHHcCCCCCc-chHHHHHHHHcccCChhHHHHHHHHHHHhCCC-ChhHHHHHHHHhHhcCChHHHHHHHhccC
Q 040394          130 IVEFYKCMRKRLKEHDN-FVFSKVLKACCELRDIDEGMKVHCEIVKVGGP-DSFVLTGLVDMYAKCRDIGSSRQVFDETL  207 (691)
Q Consensus       130 a~~~~~~m~~~~~~~~~-~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  207 (691)
                      +..+.+++.+++..+.+ ..++.+|.+|++.|++++|.++|++|.+.|.. |..+|++||.+|++.+...++        
T Consensus         9 ~e~L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~--------   80 (501)
T 4g26_A            9 SENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATES--------   80 (501)
T ss_dssp             ---------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSS--------
T ss_pred             HHHHHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhh--------
Confidence            34455556666555444 34667777777777777777777777777743 666666666666555443221        


Q ss_pred             CCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHH
Q 040394          208 DKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTAL  287 (691)
Q Consensus       208 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l  287 (691)
                                    .+.+..++|.++|++|.+.|+.||..||+++|.+|++.|++++|.++|++|.+.|+.||..+|+.+
T Consensus        81 --------------~~~~~l~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~l  146 (501)
T 4g26_A           81 --------------SPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPA  146 (501)
T ss_dssp             --------------SCCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             --------------hhcchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHH
Confidence                          123456889999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCHHHHHHHHHhc----CCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcC
Q 040394          288 LDMYVKCGNIRDARSVFDEL----CSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQL  360 (691)
Q Consensus       288 i~~~~~~g~~~~A~~~~~~~----~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~  360 (691)
                      |.+|++.|++++|.++|++|    ..||..+|++||.+|++.|+.++|.++|++|.+.|..|+..||+.++..++..
T Consensus       147 I~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          147 LFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcC
Confidence            99999999999999999999    67899999999999999999999999999999999999999999999988764

>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=99.95  E-value=4.1e-27  Score=244.53  Aligned_cols=183  Identities=14%  Similarity=0.186  Sum_probs=168.8

Q ss_pred             HHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccC---------cHHHHHHHH
Q 040394          383 VINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLG---------AVQVGSSLH  453 (691)
Q Consensus       383 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~---------~~~~a~~~~  453 (691)
                      +++.+|++|++.|++++|.++|++|.+.              |+.||..||+.||.+|++.+         .++.|.++|
T Consensus        28 ~l~~~id~c~k~G~~~~A~~lf~~M~~~--------------Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf   93 (501)
T 4g26_A           28 LLKQKLDMCSKKGDVLEALRLYDEARRN--------------GVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIF   93 (501)
T ss_dssp             HHHHHHHHTTTSCCHHHHHHHHHHHHHH--------------TCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHc--------------CCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHH
Confidence            4566777888888888888888888776              89999999999999998655         478999999


Q ss_pred             HHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc----CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCC
Q 040394          454 AYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE----KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQ  529 (691)
Q Consensus       454 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~  529 (691)
                      ++|.+.|+ .|+..+|+++|.+|++.|++++|.++|++|.+    ||..+|+++|.+|++.|++++|.++|++|.+.|+.
T Consensus        94 ~~M~~~G~-~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~  172 (501)
T 4g26_A           94 KQMIVDKV-VPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVV  172 (501)
T ss_dssp             HHHHHTTC-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHhCC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCC
Confidence            99999998 99999999999999999999999999999984    79999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhc
Q 040394          530 PNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARA  581 (691)
Q Consensus       530 p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~  581 (691)
                      ||..||+.+|.+|++.|++++|.+++++| ++.++.|+..||+.++..|+..
T Consensus       173 Pd~~ty~~Li~~~~~~g~~d~A~~ll~~M-r~~g~~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          173 PEEPELAALLKVSMDTKNADKVYKTLQRL-RDLVRQVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHTSSBCHHHHHHHHHHHHSH
T ss_pred             CCHHHHHHHHHHHhhCCCHHHHHHHHHHH-HHhCCCcCHHHHHHHHHHHhcC
Confidence            99999999999999999999999999999 6779999999999999988753

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.92  E-value=1.4e-22  Score=216.04  Aligned_cols=426  Identities=10%  Similarity=-0.045  Sum_probs=293.1

Q ss_pred             hHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHH
Q 040394          213 SWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYV  292 (691)
Q Consensus       213 ~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~  292 (691)
                      .|......+.+.|++++|+..|+++...+  |+..++..+..++...|++++|...++.+.+.+ +.+..++..+..++.
T Consensus         8 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~   84 (514)
T 2gw1_A            8 ALKDKGNQFFRNKKYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRASANE   84 (514)
T ss_dssp             HHHHHHHHHHHTSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHHHHH
Confidence            34455555666666666666666665543  556666666666666666666666666666554 224456666666666


Q ss_pred             hcCCHHHHHHHHHhc---CCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCC-------------------CCCcHHHH
Q 040394          293 KCGNIRDARSVFDEL---CSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWAD-------------------FFPNHVTI  350 (691)
Q Consensus       293 ~~g~~~~A~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-------------------~~p~~~t~  350 (691)
                      +.|++++|...|+++   .+.+......++..+........+.+.+..+...+                   ..|+....
T Consensus        85 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (514)
T 2gw1_A           85 GLGKFADAMFDLSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSM  164 (514)
T ss_dssp             HTTCHHHHHHHHHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCHHHH
T ss_pred             HHhhHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHH
Confidence            666666666666665   22233333333333333222222222222222111                   12232222


Q ss_pred             HHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHh---cCChHHHHHHHHhCCC-----C--CchhHHHHHH
Q 040394          351 ASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAK---CHVIADARYIFETTSE-----K--DVIAWNSIIS  420 (691)
Q Consensus       351 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~---~g~~~~a~~~~~~~~~-----~--~~~~~~~li~  420 (691)
                      ...+..+.........         ..+.+...+......+..   .|++++|...|+++..     .  +...-.    
T Consensus       165 ~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~----  231 (514)
T 2gw1_A          165 ASFFGIFKPELTFANY---------DESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEK----  231 (514)
T ss_dssp             HHHHTTSCCCCCCSSC---------CSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHH----
T ss_pred             HHHHhhcCHHHHHHHh---------cCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccc----
Confidence            2222111111110000         001134444445554444   8999999999988754     1  000000    


Q ss_pred             hhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCH
Q 040394          421 GLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNT  497 (691)
Q Consensus       421 ~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~  497 (691)
                          ..+.+..++..+...+...|+++.|...++.+.+..  +. ...+..+...|...|++++|...++.+.+   .+.
T Consensus       232 ----~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--~~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~  304 (514)
T 2gw1_A          232 ----LKEKLAISLEHTGIFKFLKNDPLGAHEDIKKAIELF--PR-VNSYIYMALIMADRNDSTEYYNYFDKALKLDSNNS  304 (514)
T ss_dssp             ----HHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHC--CC-HHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCTTCT
T ss_pred             ----cChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--cc-HHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCcCCH
Confidence                002235677888889999999999999999999987  44 88899999999999999999999998875   367


Q ss_pred             hHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCC-ChhHHHHHHH
Q 040394          498 VTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVP-SMKHYVCMVD  576 (691)
Q Consensus       498 ~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~  576 (691)
                      ..|..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|...++.+.+.   .| +...+..+..
T Consensus       305 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~~~~la~  380 (514)
T 2gw1_A          305 SVYYHRGQMNFILQNYDQAGKDFDKAKELD-PENIFPYIQLACLAYRENKFDDCETLFSEAKRK---FPEAPEVPNFFAE  380 (514)
T ss_dssp             HHHHHHHHHHHHTTCTTHHHHHHHHHHHTC-SSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHH---STTCSHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH---cccCHHHHHHHHH
Confidence            789999999999999999999999999863 335678888888999999999999999988654   34 4678889999


Q ss_pred             HHHhcCChHHHHHHHHhC----CCCCC----HHHHHHHHHHHHh---cCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHH
Q 040394          577 LLARAGRLEEALEFMENM----PIEPD----VSLFGAFLHGCGL---YSRFDLGEVMIKKMLELHPDKACYYVLVSNLYA  645 (691)
Q Consensus       577 ~~~~~g~~~~A~~~~~~~----~~~p~----~~~~~~l~~~~~~---~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~  645 (691)
                      .+.+.|++++|.+.++++    +..++    ...+..+...+..   .|++++|...++++++..|+++.++..++.+|.
T Consensus       381 ~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~  460 (514)
T 2gw1_A          381 ILTDKNDFDKALKQYDLAIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLDPRSEQAKIGLAQMKL  460 (514)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHH
Confidence            999999999999999988    22222    3488899999999   999999999999999999999999999999999


Q ss_pred             hCCCcHHHHHHHHHHHhCCC
Q 040394          646 SDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       646 ~~g~~~~A~~~~~~~~~~g~  665 (691)
                      +.|++++|.+.+++..+...
T Consensus       461 ~~g~~~~A~~~~~~a~~~~~  480 (514)
T 2gw1_A          461 QQEDIDEAITLFEESADLAR  480 (514)
T ss_dssp             HTTCHHHHHHHHHHHHHHCS
T ss_pred             HhcCHHHHHHHHHHHHHhcc
Confidence            99999999999999988543

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.92  E-value=5.6e-22  Score=211.32  Aligned_cols=425  Identities=9%  Similarity=-0.022  Sum_probs=249.6

Q ss_pred             hHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHh
Q 040394          113 SFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAK  192 (691)
Q Consensus       113 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~  192 (691)
                      .|......+.+.|++++|+..|+++.+..  |+..++..+..++.+.|++++|...++.+.+..|.+..++..++.+|.+
T Consensus         8 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~   85 (514)
T 2gw1_A            8 ALKDKGNQFFRNKKYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELKPDYSKVLLRRASANEG   85 (514)
T ss_dssp             HHHHHHHHHHHTSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccChHHHHHHHHHHHHHHH
Confidence            45556666777777777777777777764  5677777777777777777777777777777776677777777777777


Q ss_pred             cCChHHHHHHHhccCC---CChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHH
Q 040394          193 CRDIGSSRQVFDETLD---KNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLH  269 (691)
Q Consensus       193 ~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~  269 (691)
                      .|++++|...|+++..   ++......++..+........+.+.+..+...+..|+...+..-...............+.
T Consensus        86 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (514)
T 2gw1_A           86 LGKFADAMFDLSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSMA  165 (514)
T ss_dssp             TTCHHHHHHHHHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCHHHHH
T ss_pred             HhhHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHHH
Confidence            7777777777766522   2333334444444333333333333322222222222111111111111111111111111


Q ss_pred             HHHHHHCC---------CCchHHHHHHHHHHHh---cCCHHHHHHHHHhcCC-----------------CChhHHHHHHH
Q 040394          270 GYILKIGI---------EINSHLVTALLDMYVK---CGNIRDARSVFDELCS-----------------IDLVSWTAMIV  320 (691)
Q Consensus       270 ~~~~~~g~---------~~~~~~~~~li~~~~~---~g~~~~A~~~~~~~~~-----------------~~~~~~~~li~  320 (691)
                      ..+.....         +.+...+......+..   .|++++|...|+++..                 .+..+|..+..
T Consensus       166 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (514)
T 2gw1_A          166 SFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGI  245 (514)
T ss_dssp             HHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHH
Confidence            11111000         1113333333333333   5667777666665522                 12345666677


Q ss_pred             HHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHH
Q 040394          321 GYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADA  400 (691)
Q Consensus       321 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a  400 (691)
                      .+...|++++|...++++....  |+...+..+...+...|++++|...++.+.+..+.+..++..+...|...|++++|
T Consensus       246 ~~~~~~~~~~A~~~~~~~l~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A  323 (514)
T 2gw1_A          246 FKFLKNDPLGAHEDIKKAIELF--PRVNSYIYMALIMADRNDSTEYYNYFDKALKLDSNNSSVYYHRGQMNFILQNYDQA  323 (514)
T ss_dssp             HHHHSSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCTTCTHHHHHHHHHHHHTTCTTHH
T ss_pred             HHHHCCCHHHHHHHHHHHHhhC--ccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCcCCHHHHHHHHHHHHHhCCHHHH
Confidence            7777777777777777776653  33666666777777777777777777777777666666777777777777777777


Q ss_pred             HHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcC
Q 040394          401 RYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCG  480 (691)
Q Consensus       401 ~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  480 (691)
                      ...+++....               .+.+..++..+...+...|+++.|...++.+.+..  +.+...+..+...|.+.|
T Consensus       324 ~~~~~~~~~~---------------~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~~~~~~~  386 (514)
T 2gw1_A          324 GKDFDKAKEL---------------DPENIFPYIQLACLAYRENKFDDCETLFSEAKRKF--PEAPEVPNFFAEILTDKN  386 (514)
T ss_dssp             HHHHHHHHHT---------------CSSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHS--TTCSHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHh---------------ChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHc--ccCHHHHHHHHHHHHHCC
Confidence            7777776543               12345566667777777777777777777777665  556667777777777777


Q ss_pred             CHHHHHHHHHhccc--C-C------HhHHHHHHHHHhc---CCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCH
Q 040394          481 DAQSARMVFDAMRE--K-N------TVTWSAMIGGYGM---QGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMV  548 (691)
Q Consensus       481 ~~~~A~~~~~~~~~--~-~------~~~~~~li~~~~~---~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~  548 (691)
                      ++++|...++++.+  | +      ...|..+...+..   .|++++|...++++.+.. +.+..++..+..++...|++
T Consensus       387 ~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~  465 (514)
T 2gw1_A          387 DFDKALKQYDLAIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLD-PRSEQAKIGLAQMKLQQEDI  465 (514)
T ss_dssp             CHHHHHHHHHHHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             CHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhcCH
Confidence            77777777776653  1 1      2266667777777   777777777777776642 23445566666677777777


Q ss_pred             HHHHHHHHHch
Q 040394          549 GEGWKCFYSMC  559 (691)
Q Consensus       549 ~~A~~~~~~m~  559 (691)
                      ++|.+.+++..
T Consensus       466 ~~A~~~~~~a~  476 (514)
T 2gw1_A          466 DEAITLFEESA  476 (514)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            77777777654

>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=99.91  E-value=1.6e-21  Score=203.97  Aligned_cols=329  Identities=12%  Similarity=0.047  Sum_probs=245.5

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhH
Q 040394          313 VSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYA  392 (691)
Q Consensus       313 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~  392 (691)
                      ..|..+...+.+.|++++|+.+|+++... .+.+..++..+..++...|++++|...++.+.+.++.+..++..+..+|.
T Consensus        27 ~~~~~~~~~~~~~g~~~~A~~~~~~~l~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~  105 (450)
T 2y4t_A           27 EKHLELGKKLLAAGQLADALSQFHAAVDG-DPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLKMDFTAARLQRGHLLL  105 (450)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHh-CCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHH
Confidence            34444555555555555555555555443 12234455555555555555555555555555555555556666666677


Q ss_pred             hcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCH----HHHH------------HHHHHHhccCcHHHHHHHHHHH
Q 040394          393 KCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDA----VTLV------------SVISACASLGAVQVGSSLHAYS  456 (691)
Q Consensus       393 ~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~----~~~~------------~ll~~~~~~~~~~~a~~~~~~~  456 (691)
                      +.|++++|...|+++...                .|+.    .++.            .+...+...|+++.|...++.+
T Consensus       106 ~~g~~~~A~~~~~~~~~~----------------~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~  169 (450)
T 2y4t_A          106 KQGKLDEAEDDFKKVLKS----------------NPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKI  169 (450)
T ss_dssp             HTTCHHHHHHHHHHHHTS----------------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHhc----------------CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            777777777777666543                2222    2222            3345588899999999999999


Q ss_pred             HHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCH-
Q 040394          457 TKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNE-  532 (691)
Q Consensus       457 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~-  532 (691)
                      .+..  |.+...+..+...|.+.|++++|...|+++.+   .+..+|..+...|...|++++|+..++++.+.  .|+. 
T Consensus       170 ~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~p~~~  245 (450)
T 2y4t_A          170 LEVC--VWDAELRELRAECFIKEGEPRKAISDLKAASKLKNDNTEAFYKISTLYYQLGDHELSLSEVRECLKL--DQDHK  245 (450)
T ss_dssp             HHHC--TTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCH
T ss_pred             HHhC--CCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCChH
Confidence            9987  78899999999999999999999999999874   47889999999999999999999999999974  4544 


Q ss_pred             HHHHHH------------HHHhcccCCHHHHHHHHHHchhhcCCCCC-----hhHHHHHHHHHHhcCChHHHHHHHHhC-
Q 040394          533 VIFTTI------------LSACSHTGMVGEGWKCFYSMCRDFKFVPS-----MKHYVCMVDLLARAGRLEEALEFMENM-  594 (691)
Q Consensus       533 ~~~~~l------------l~~~~~~g~~~~A~~~~~~m~~~~~~~p~-----~~~~~~li~~~~~~g~~~~A~~~~~~~-  594 (691)
                      ..+..+            ...+...|++++|...|+++...   .|+     ...+..+..++.+.|++++|++.++++ 
T Consensus       246 ~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~---~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~  322 (450)
T 2y4t_A          246 RCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT---EPSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVL  322 (450)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---CCSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc---CCcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            344333            67889999999999999998654   454     347888999999999999999999997 


Q ss_pred             CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHH------------HHHhCC-----CcHHHHHH
Q 040394          595 PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSN------------LYASDG-----RWIRVNQV  656 (691)
Q Consensus       595 ~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~------------~~~~~g-----~~~~A~~~  656 (691)
                      ...| +..+|..+..+|...|++++|...+++++++.|+++..+..++.            .|...|     +.+++.+.
T Consensus       323 ~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~~~~y~~lg~~~~~~~~~~~~~  402 (450)
T 2y4t_A          323 QMEPDNVNALKDRAEAYLIEEMYDEAIQDYETAQEHNENDQQIREGLEKAQRLLKQSQKRDYYKILGVKRNAKKQEIIKA  402 (450)
T ss_dssp             HHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHHHHHHHSCCSGGGSCSSTTCCTTHHHHH
T ss_pred             HhCcccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcchHHHHHHHHHHHHHhhcccchhHHHHhCCCccCCHHHHHHH
Confidence            4344 67899999999999999999999999999999999999999984            455556     56677887


Q ss_pred             HHH-HHhCCC
Q 040394          657 REL-MKQRGL  665 (691)
Q Consensus       657 ~~~-~~~~g~  665 (691)
                      +++ .++...
T Consensus       403 y~~~~l~~~p  412 (450)
T 2y4t_A          403 YRKLALQWHP  412 (450)
T ss_dssp             HHHHHHHSCG
T ss_pred             HHHHHHHhCC
Confidence            776 444433

>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=99.90  E-value=1.4e-21  Score=209.45  Aligned_cols=424  Identities=12%  Similarity=0.038  Sum_probs=291.1

Q ss_pred             hhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHH
Q 040394          212 VSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMY  291 (691)
Q Consensus       212 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~  291 (691)
                      ..|..+...+.+.|++++|++.|+++.+... .+..++..+..++...|++++|...++.+.+.+ +.+..++..+..++
T Consensus        26 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~  103 (537)
T 3fp2_A           26 VQLKNRGNHFFTAKNFNEAIKYYQYAIELDP-NEPVFYSNISACYISTGDLEKVIEFTTKALEIK-PDHSKALLRRASAN  103 (537)
T ss_dssp             HHHHHHHHHHHHTTCCC-CHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHhhCC-CCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CchHHHHHHHHHHH
Confidence            3455566666666666666666666665432 245566666666666666666666666666654 23456666677777


Q ss_pred             HhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHC------CCCCcHHHHHHHHHHHhcCCChhh
Q 040394          292 VKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWA------DFFPNHVTIASVLSASAQLGNLNM  365 (691)
Q Consensus       292 ~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~------g~~p~~~t~~~ll~~~~~~~~~~~  365 (691)
                      ...|++++|...|+.+ ..+....+..+..+...+...+|...++++...      ...|+.......+    ...+.+.
T Consensus       104 ~~~g~~~~A~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~----~~~~~~~  178 (537)
T 3fp2_A          104 ESLGNFTDAMFDLSVL-SLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFF----GIFDSHL  178 (537)
T ss_dssp             HHHTCHHHHHHHHHHH-C-----------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHH----HTSCHHH
T ss_pred             HHcCCHHHHHHHHHHH-hcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHH----HhcChHH
Confidence            7777777777777543 111112222233444445556677777666442      2234443333322    2222222


Q ss_pred             HHHHHHHHHHhCCCchhHHHHHHHHhHh--------cCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCC--------
Q 040394          366 GRMVHSLGIRLGLEDYTVINALVDMYAK--------CHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPD--------  429 (691)
Q Consensus       366 a~~~~~~~~~~~~~~~~~~~~l~~~~~~--------~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~--------  429 (691)
                      +...+................+...+..        .|++++|..+++++.+.+                |+        
T Consensus       179 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~----------------p~~~~~~~~~  242 (537)
T 3fp2_A          179 EVSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSAN----------------TVDDPLRENA  242 (537)
T ss_dssp             HHHTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC------------------CCCHHHHHHH
T ss_pred             HHHHHhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHC----------------CCcchhhHHH
Confidence            2221111111111111123333333322        257889999999887642                33        


Q ss_pred             HHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHH
Q 040394          430 AVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGG  506 (691)
Q Consensus       430 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~  506 (691)
                      ..++..+...+...|+++.|...++...+..  |. ...+..+...|...|++++|...++++.+   .+..+|..+...
T Consensus       243 ~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~--~~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~  319 (537)
T 3fp2_A          243 ALALCYTGIFHFLKNNLLDAQVLLQESINLH--PT-PNSYIFLALTLADKENSQEFFKFFQKAVDLNPEYPPTYYHRGQM  319 (537)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CC-HHHHHHHHHHTCCSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHhcC--CC-chHHHHHHHHHHHhcCHHHHHHHHHHHhccCCCCHHHHHHHHHH
Confidence            2356667778889999999999999999986  34 88888999999999999999999998874   367889999999


Q ss_pred             HhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChH
Q 040394          507 YGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLE  585 (691)
Q Consensus       507 ~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~  585 (691)
                      +...|++++|...++++.+.. +.+...+..+..++...|++++|.+.++++.+.   .|+ ...+..+...+...|+++
T Consensus       320 ~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~~~~l~~~~~~~g~~~  395 (537)
T 3fp2_A          320 YFILQDYKNAKEDFQKAQSLN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLK---FPTLPEVPTFFAEILTDRGDFD  395 (537)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCTHHHHHHHHHHHHTTCHH
T ss_pred             HHhcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCChHHHHHHHHHHHHhCCHH
Confidence            999999999999999999853 334577888888999999999999999988654   344 678889999999999999


Q ss_pred             HHHHHHHhC----C----CCCCHHHHHHHHHHHHhc----------CCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhC
Q 040394          586 EALEFMENM----P----IEPDVSLFGAFLHGCGLY----------SRFDLGEVMIKKMLELHPDKACYYVLVSNLYASD  647 (691)
Q Consensus       586 ~A~~~~~~~----~----~~p~~~~~~~l~~~~~~~----------g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~  647 (691)
                      +|.+.++++    +    .......+......+...          |++++|...++++++..|+++.++..++.+|.+.
T Consensus       396 ~A~~~~~~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~~~  475 (537)
T 3fp2_A          396 TAIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELDPRSEQAKIGLAQLKLQM  475 (537)
T ss_dssp             HHHHHHHHHHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHh
Confidence            999999987    1    111223345556677777          9999999999999999999999999999999999


Q ss_pred             CCcHHHHHHHHHHHhCCC
Q 040394          648 GRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       648 g~~~~A~~~~~~~~~~g~  665 (691)
                      |++++|.+.+++..+...
T Consensus       476 g~~~~A~~~~~~al~~~~  493 (537)
T 3fp2_A          476 EKIDEAIELFEDSAILAR  493 (537)
T ss_dssp             TCHHHHHHHHHHHHHHC-
T ss_pred             ccHHHHHHHHHHHHHhCC
Confidence            999999999999987543

>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=99.90  E-value=3.8e-21  Score=206.10  Aligned_cols=445  Identities=9%  Similarity=0.006  Sum_probs=289.9

Q ss_pred             chHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhH
Q 040394          112 YSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYA  191 (691)
Q Consensus       112 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~  191 (691)
                      ..|..+...+.+.|++++|+..|+++.+.. +.+..++..+..++.+.|++++|...++.+.+..+.+..++..+..++.
T Consensus        26 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~  104 (537)
T 3fp2_A           26 VQLKNRGNHFFTAKNFNEAIKYYQYAIELD-PNEPVFYSNISACYISTGDLEKVIEFTTKALEIKPDHSKALLRRASANE  104 (537)
T ss_dssp             HHHHHHHHHHHHTTCCC-CHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCchHHHHHHHHHHHH
Confidence            456777778888888888888888888763 4466778888888888888888888888888887778888888888888


Q ss_pred             hcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHH
Q 040394          192 KCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGY  271 (691)
Q Consensus       192 ~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~  271 (691)
                      ..|++++|...|+.+ ..+....+..+..+...+...+|...++++....  |+.                         
T Consensus       105 ~~g~~~~A~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~--~~~-------------------------  156 (537)
T 3fp2_A          105 SLGNFTDAMFDLSVL-SLNGDFDGASIEPMLERNLNKQAMKVLNENLSKD--EGR-------------------------  156 (537)
T ss_dssp             HHTCHHHHHHHHHHH-C-----------CHHHHHHHHHHHHHHHHHCC--------------------------------
T ss_pred             HcCCHHHHHHHHHHH-hcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhC--ccc-------------------------
Confidence            888888888888643 2222222233444445555566777777764421  100                         


Q ss_pred             HHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChh---HHHHHHHHHHh--------cCCchhHHHHHHHhhH
Q 040394          272 ILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLV---SWTAMIVGYTQ--------SGYPDKALKLFTDKKW  340 (691)
Q Consensus       272 ~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~---~~~~li~~~~~--------~g~~~~a~~~~~~m~~  340 (691)
                        .....|+..    .+..+....+.+.+...+......+..   ....+...+..        .|++++|..+++++..
T Consensus       157 --~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~  230 (537)
T 3fp2_A          157 --GSQVLPSNT----SLASFFGIFDSHLEVSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLS  230 (537)
T ss_dssp             ----CCCCCHH----HHHHHHHTSCHHHHHHTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             --cccccchHh----HHHHHHHhcChHHHHHHHhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence              001122222    223344455556555555555333322   22222222221        2366777777777665


Q ss_pred             CCCCCcH-HHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHH
Q 040394          341 ADFFPNH-VTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSII  419 (691)
Q Consensus       341 ~g~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li  419 (691)
                      .  .|+. ..+..+.                           .++..+...+...|++++|...|++...          
T Consensus       231 ~--~p~~~~~~~~~~---------------------------~~~~~~g~~~~~~~~~~~A~~~~~~~~~----------  271 (537)
T 3fp2_A          231 A--NTVDDPLRENAA---------------------------LALCYTGIFHFLKNNLLDAQVLLQESIN----------  271 (537)
T ss_dssp             ----CCCHHHHHHHH---------------------------HHHHHHHHHHHHTTCHHHHHHHHHHHHH----------
T ss_pred             H--CCCcchhhHHHH---------------------------HHHHHHHHHHHhcccHHHHHHHHHHHHh----------
Confidence            4  2321 1111111                           1234455566666777777777766653          


Q ss_pred             HhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CC
Q 040394          420 SGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KN  496 (691)
Q Consensus       420 ~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~  496 (691)
                            ..|+..++..+...+...|+++.|...++.+.+..  |.+..++..+...|...|++++|...+++..+   .+
T Consensus       272 ------~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~  343 (537)
T 3fp2_A          272 ------LHPTPNSYIFLALTLADKENSQEFFKFFQKAVDLN--PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLNPEN  343 (537)
T ss_dssp             ------HCCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTC
T ss_pred             ------cCCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC--CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCC
Confidence                  24556667777777777788888888888777776  66777788888888888888888888887763   25


Q ss_pred             HhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC----hhHHH
Q 040394          497 TVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS----MKHYV  572 (691)
Q Consensus       497 ~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~----~~~~~  572 (691)
                      ...|..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|.+.++++.+...-.++    ...+.
T Consensus       344 ~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~  422 (537)
T 3fp2_A          344 VYPYIQLACLLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGPLI  422 (537)
T ss_dssp             SHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCSSTTHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhHHHHHHHH
Confidence            6678888888888888888888888888753 334567777778888888999988888877543211111    22344


Q ss_pred             HHHHHHHhc----------CChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHH
Q 040394          573 CMVDLLARA----------GRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVL  639 (691)
Q Consensus       573 ~li~~~~~~----------g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~  639 (691)
                      .+...+.+.          |++++|.+.+++. . .+.+...+..+...+...|++++|...+++++++.|++......
T Consensus       423 ~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  501 (537)
T 3fp2_A          423 GKATILARQSSQDPTQLDEEKFNAAIKLLTKACELDPRSEQAKIGLAQLKLQMEKIDEAIELFEDSAILARTMDEKLQA  501 (537)
T ss_dssp             HHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CHHHHHH
T ss_pred             HHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCcHHHHHH
Confidence            455677777          9999999999988 3 33456788999999999999999999999999999997665543

>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=99.89  E-value=2.2e-20  Score=195.27  Aligned_cols=362  Identities=10%  Similarity=-0.031  Sum_probs=262.6

Q ss_pred             ChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhc---CCCChhHHHHHHHH
Q 040394          245 NQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDEL---CSIDLVSWTAMIVG  321 (691)
Q Consensus       245 ~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~---~~~~~~~~~~li~~  321 (691)
                      +...+..+...+.+.|++++|..+|+.+.+.. +.+..++..+..++...|++++|...|+++   .+.+..+|..+...
T Consensus        25 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~  103 (450)
T 2y4t_A           25 DVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLKMDFTAARLQRGHL  103 (450)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHH
Confidence            44556666666667777777777777666553 234566666666666777777777766665   22345566666666


Q ss_pred             HHhcCCchhHHHHHHHhhHCCCCCcH----HHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCCh
Q 040394          322 YTQSGYPDKALKLFTDKKWADFFPNH----VTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVI  397 (691)
Q Consensus       322 ~~~~g~~~~a~~~~~~m~~~g~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  397 (691)
                      |.+.|++++|.+.|+++...  .|+.    ..+..+...+..                      ..+..+...+...|++
T Consensus       104 ~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~----------------------~~~~~~a~~~~~~~~~  159 (450)
T 2y4t_A          104 LLKQGKLDEAEDDFKKVLKS--NPSENEEKEAQSQLIKSDEM----------------------QRLRSQALNAFGSGDY  159 (450)
T ss_dssp             HHHTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHH----------------------HHHHHHHHHHHHHTCH
T ss_pred             HHHcCCHHHHHHHHHHHHhc--CCCChhhHHHHHHHHHHHHH----------------------HHHHHHHHHHHHcCCH
Confidence            66666777776666666654  3332    333333322111                      1123345568889999


Q ss_pred             HHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHH
Q 040394          398 ADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYA  477 (691)
Q Consensus       398 ~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~  477 (691)
                      ++|...|+++.+.               .+.+..++..+..++...|++++|...++.+.+..  |.+..++..+...|.
T Consensus       160 ~~A~~~~~~~~~~---------------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~  222 (450)
T 2y4t_A          160 TAAIAFLDKILEV---------------CVWDAELRELRAECFIKEGEPRKAISDLKAASKLK--NDNTEAFYKISTLYY  222 (450)
T ss_dssp             HHHHHHHHHHHHH---------------CTTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHH--CSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh---------------CCCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHH
Confidence            9999999988653               24567889999999999999999999999999887  788999999999999


Q ss_pred             hcCCHHHHHHHHHhccc--C-CHhHHHHH------------HHHHhcCCChHHHHHHHHHHHHCCCCCC-----HHHHHH
Q 040394          478 KCGDAQSARMVFDAMRE--K-NTVTWSAM------------IGGYGMQGDGGGSLALFSDMLNEEVQPN-----EVIFTT  537 (691)
Q Consensus       478 ~~g~~~~A~~~~~~~~~--~-~~~~~~~l------------i~~~~~~~~~~~A~~~~~~m~~~g~~p~-----~~~~~~  537 (691)
                      ..|++++|...|+++.+  | +...+..+            ...+...|++++|...|+++.+.  .|+     ...+..
T Consensus       223 ~~g~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~  300 (450)
T 2y4t_A          223 QLGDHELSLSEVRECLKLDQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT--EPSIAEYTVRSKER  300 (450)
T ss_dssp             HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CCSSHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcchHHHHHHHHH
Confidence            99999999999998874  3 44455544            88899999999999999999984  555     346788


Q ss_pred             HHHHhcccCCHHHHHHHHHHchhhcCCCC-ChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCC-HHHHHHHHHH-----
Q 040394          538 ILSACSHTGMVGEGWKCFYSMCRDFKFVP-SMKHYVCMVDLLARAGRLEEALEFMENM-PIEPD-VSLFGAFLHG-----  609 (691)
Q Consensus       538 ll~~~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~-~~~~~~l~~~-----  609 (691)
                      +..++.+.|++++|...++++...   .| +...+..+..+|...|++++|.+.++++ ...|+ ...+..+..+     
T Consensus       301 l~~~~~~~g~~~~A~~~~~~a~~~---~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~  377 (450)
T 2y4t_A          301 ICHCFSKDEKPVEAIRVCSEVLQM---EPDNVNALKDRAEAYLIEEMYDEAIQDYETAQEHNENDQQIREGLEKAQRLLK  377 (450)
T ss_dssp             HHHHHHTTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHh---CcccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcchHHHHHHHHHHHHHhh
Confidence            888999999999999999988543   45 4789999999999999999999999998 66665 4566555532     


Q ss_pred             -------HHhcC-----CHHHHHHHHHH-HHhcCCCCch----------hHHHHHHHHHhCCCcHHH
Q 040394          610 -------CGLYS-----RFDLGEVMIKK-MLELHPDKAC----------YYVLVSNLYASDGRWIRV  653 (691)
Q Consensus       610 -------~~~~g-----~~~~A~~~~~~-~~~~~p~~~~----------~~~~l~~~~~~~g~~~~A  653 (691)
                             |...|     +.+++.+.+++ +++.+|++..          .+..+..+|...|+.+++
T Consensus       378 ~~~~~~~y~~lg~~~~~~~~~~~~~y~~~~l~~~pd~~~~~~~~~~a~~~~~~i~~ay~~L~d~~~r  444 (450)
T 2y4t_A          378 QSQKRDYYKILGVKRNAKKQEIIKAYRKLALQWHPDNFQNEEEKKKAEKKFIDIAAAKEVLSDPEMR  444 (450)
T ss_dssp             HHHSCCSGGGSCSSTTCCTTHHHHHHHHHHHHSCGGGCCSHHHHHHHHHHHHHHHHHHHHSSGGGGC
T ss_pred             cccchhHHHHhCCCccCCHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHHHHHhCCHHHH
Confidence                   33334     66788888887 6778887532          344555566666655544

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.85  E-value=1.8e-18  Score=174.56  Aligned_cols=309  Identities=12%  Similarity=0.047  Sum_probs=213.4

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhH
Q 040394          313 VSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYA  392 (691)
Q Consensus       313 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~  392 (691)
                      ..+..+...+...|++++|+..|+++.... +.+..++..+...+...|++++|...++.+.+..+.+...+..+...+.
T Consensus         4 ~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~   82 (359)
T 3ieg_A            4 EKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALKMDFTAARLQRGHLLL   82 (359)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCcchHHHHHHHHHH
Confidence            345555566666666666666666665542 2234555566666666666666666666666666666667777777777


Q ss_pred             hcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCC----CHHHHHHH------------HHHHhccCcHHHHHHHHHHH
Q 040394          393 KCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSP----DAVTLVSV------------ISACASLGAVQVGSSLHAYS  456 (691)
Q Consensus       393 ~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p----~~~~~~~l------------l~~~~~~~~~~~a~~~~~~~  456 (691)
                      ..|++++|...|++..+.                .|    +...+..+            ...+...|+++.|...++.+
T Consensus        83 ~~~~~~~A~~~~~~~~~~----------------~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~  146 (359)
T 3ieg_A           83 KQGKLDEAEDDFKKVLKS----------------NPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKI  146 (359)
T ss_dssp             HHTCHHHHHHHHHHHHTS----------------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HcCChHHHHHHHHHHHhc----------------CCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            778888887777776543                23    22222222            56778889999999999998


Q ss_pred             HHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCH-
Q 040394          457 TKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNE-  532 (691)
Q Consensus       457 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~-  532 (691)
                      .+..  |.+...+..+...+...|++++|...+++..+   .+...|..+...+...|++++|...+++..+.  .|+. 
T Consensus       147 ~~~~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~--~~~~~  222 (359)
T 3ieg_A          147 LEVC--VWDAELRELRAECFIKEGEPRKAISDLKAASKLKSDNTEAFYKISTLYYQLGDHELSLSEVRECLKL--DQDHK  222 (359)
T ss_dssp             HHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCH
T ss_pred             HHhC--CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--Cccch
Confidence            8887  67788888888999999999999999988764   36778888888888899999999999888874  3433 


Q ss_pred             HHHHH------------HHHHhcccCCHHHHHHHHHHchhhcCCCCCh-----hHHHHHHHHHHhcCChHHHHHHHHhC-
Q 040394          533 VIFTT------------ILSACSHTGMVGEGWKCFYSMCRDFKFVPSM-----KHYVCMVDLLARAGRLEEALEFMENM-  594 (691)
Q Consensus       533 ~~~~~------------ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~-----~~~~~li~~~~~~g~~~~A~~~~~~~-  594 (691)
                      ..+..            +...+...|++++|...+++..+.   .|+.     ..+..+...+...|++++|++.+++. 
T Consensus       223 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~  299 (359)
T 3ieg_A          223 RCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT---EPSVAEYTVRSKERICHCFSKDEKPVEAIRICSEVL  299 (359)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CCSSHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc---CCCchHHHHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            32221            244566777888888777776543   2331     23445666777777777777777776 


Q ss_pred             CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHH
Q 040394          595 PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYA  645 (691)
Q Consensus       595 ~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~  645 (691)
                      ...| +..++..+...+...|++++|...++++++..|+++..+..+..+..
T Consensus       300 ~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~  351 (359)
T 3ieg_A          300 QMEPDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEHNENDQQIREGLEKAQR  351 (359)
T ss_dssp             HHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHH
T ss_pred             HhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCChHHHHHHHHHHH
Confidence            3233 55677777777777777777777777777777777777666665543

>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=99.84  E-value=2.9e-15  Score=164.59  Aligned_cols=509  Identities=12%  Similarity=0.092  Sum_probs=350.4

Q ss_pred             HHHHHHHHHHhCCCCchhhhHHHHHHhcCCChHHHHHHhccCCCCCcchHH-HHHHHHHhCCChhHHHHHHHH------H
Q 040394           65 LKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQ-VMIRWYFLNDLYKDIVEFYKC------M  137 (691)
Q Consensus        65 a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~-~ll~~~~~~~~~~~a~~~~~~------m  137 (691)
                      .....+..+..|.....++|.|+.+|...++-.+.  ++.+=     .-|. .++.-||...++.-|.-.|++      +
T Consensus       858 l~p~LE~~~~~g~~~~~~hnalakiyid~n~npe~--fL~~n-----~~yd~~~vgkyce~rDp~la~iay~~g~~d~el  930 (1630)
T 1xi4_A          858 LLPWLEARIHEGCEEPATHNALAKIYIDSNNNPER--FLREN-----PYYDSRVVGKYCEKRDPHLACVAYERGQCDLEL  930 (1630)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHHhccCCCHHH--Hhhcc-----CcccHHHHHHHHHhcCcchHHHHhcccCCcHHH
Confidence            33345555555554444899999999977664432  22211     1122 233445555554444444432      0


Q ss_pred             HHcCCCCCcchHHHHHHHHcccCChh-----------HHHHHHHHHHHhCCC---ChhHHHHHHHHhHhcCChHHHHHHH
Q 040394          138 RKRLKEHDNFVFSKVLKACCELRDID-----------EGMKVHCEIVKVGGP---DSFVLTGLVDMYAKCRDIGSSRQVF  203 (691)
Q Consensus       138 ~~~~~~~~~~~~~~ll~~~~~~~~~~-----------~a~~~~~~~~~~~~~---~~~~~~~l~~~~~~~g~~~~A~~~~  203 (691)
                      +.  +.-....|....+-+.+..+.+           .=..+.++......|   ++.--...+..|...|.+.+|++++
T Consensus       931 i~--vt~~n~l~k~~arylv~r~d~~lW~~vl~~~n~~RR~Lidqv~a~aL~e~~~PeeVs~~vKaf~~aglp~EaieLL 1008 (1630)
T 1xi4_A          931 IN--VCNENSLFKSLSRYLVRRKDPELWGSVLLESNPYRRPLIDQVVQTALSETQDPEEVSVTVKAFMTADLPNELIELL 1008 (1630)
T ss_pred             HH--HHhcchhHHHHHHHHHHhcCHHHHHHHhcCCcHHHHHHHHHHHHhhcccccCHHHhHHHHHHHHhCCCHHHHHHHH
Confidence            00  1111122333333333332222           223444444444433   6667778888899999999999999


Q ss_pred             hccCC-C-----ChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCC
Q 040394          204 DETLD-K-----NVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGI  277 (691)
Q Consensus       204 ~~~~~-~-----~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~  277 (691)
                      +++.- |     +...-+.++.+..+. +..+..+...+....    +   ..-+...+...|.+++|..+|+...    
T Consensus      1009 EKivl~~s~fs~n~~LqnlLi~tAIka-D~~Rv~eyI~kLd~~----d---~~eIA~Iai~lglyEEAf~IYkKa~---- 1076 (1630)
T 1xi4_A         1009 EKIVLDNSVFSEHRNLQNLLILTAIKA-DRTRVMEYINRLDNY----D---APDIANIAISNELFEEAFAIFRKFD---- 1076 (1630)
T ss_pred             HHHHcCCCcccccHHHHHHHHHHHHHh-ChhhHHHHHHHhhhc----c---HHHHHHHHHhCCCHHHHHHHHHHcC----
Confidence            98742 2     234566677777766 556777776665421    1   2336677888999999999998852    


Q ss_pred             CCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHH
Q 040394          278 EINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSAS  357 (691)
Q Consensus       278 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~  357 (691)
                       -.....+.++.   ..|++++|.++.+++.  +..+|..+..++...|++++|++.|.+.      -|...|..++.++
T Consensus      1077 -~~~~A~~VLie---~i~nldrAiE~Aervn--~p~vWsqLAKAql~~G~~kEAIdsYiKA------dD~say~eVa~~~ 1144 (1630)
T 1xi4_A         1077 -VNTSAVQVLIE---HIGNLDRAYEFAERCN--EPAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAA 1144 (1630)
T ss_pred             -CHHHHHHHHHH---HHhhHHHHHHHHHhcC--CHHHHHHHHHHHHhCCCHHHHHHHHHhc------CChHHHHHHHHHH
Confidence             12222333433   7788999999999773  4678889999999999999999999663      4778888899999


Q ss_pred             hcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHH
Q 040394          358 AQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVI  437 (691)
Q Consensus       358 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll  437 (691)
                      .+.|+++++.+++....+... ++.+.+.++.+|++.+++++.....+                     .|+...+..+.
T Consensus      1145 ~~lGkyEEAIeyL~mArk~~~-e~~Idt~LafaYAKl~rleele~fI~---------------------~~n~ad~~~iG 1202 (1630)
T 1xi4_A         1145 NTSGNWEELVKYLQMARKKAR-ESYVETELIFALAKTNRLAELEEFIN---------------------GPNNAHIQQVG 1202 (1630)
T ss_pred             HHcCCHHHHHHHHHHHHhhcc-cccccHHHHHHHHhhcCHHHHHHHHh---------------------CCCHHHHHHHH
Confidence            999999999999998877663 33334469999999999886444431                     24556777888


Q ss_pred             HHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHH
Q 040394          438 SACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSL  517 (691)
Q Consensus       438 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~  517 (691)
                      ..|...|++++|..+|...          ..|..+...|.+.|++++|.+.+++.  .+..+|..+..+|...|++..|.
T Consensus      1203 d~le~eg~YeeA~~~Y~kA----------~ny~rLA~tLvkLge~q~AIEaarKA--~n~~aWkev~~acve~~Ef~LA~ 1270 (1630)
T 1xi4_A         1203 DRCYDEKMYDAAKLLYNNV----------SNFGRLASTLVHLGEYQAAVDGARKA--NSTRTWKEVCFACVDGKEFRLAQ 1270 (1630)
T ss_pred             HHHHhcCCHHHHHHHHHhh----------hHHHHHHHHHHHhCCHHHHHHHHHHh--CCHHHHHHHHHHHhhhhHHHHHH
Confidence            9999999999999999874          47888999999999999999999987  46789999999999999999888


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhc--CChHHHHHHHHhC
Q 040394          518 ALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARA--GRLEEALEFMENM  594 (691)
Q Consensus       518 ~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~--g~~~~A~~~~~~~  594 (691)
                      .....     +..+...+..++..|.+.|.+++|+.+++..   .++.|. ..+|.-|..+|.+-  ++..+++++|..-
T Consensus      1271 ~cgl~-----Iiv~~deLeeli~yYe~~G~feEAI~LlE~a---L~LeraH~gmftELaiLyaKy~peklmEhlk~f~~r 1342 (1630)
T 1xi4_A         1271 MCGLH-----IVVHADELEELINYYQDRGYFEELITMLEAA---LGLERAHMGMFTELAILYSKFKPQKMREHLELFWSR 1342 (1630)
T ss_pred             HHHHh-----hhcCHHHHHHHHHHHHHcCCHHHHHHHHHHH---hccChhHhHHHHHHHHHHHhCCHHHHHHHHHHHHHh
Confidence            87653     3446667778889999999999999999744   366655 56777777777654  4566666665554


Q ss_pred             -CCCC------CHHHHHHHHHHHHhcCCHHHHHHHHHHHHh------------cCCCCchhHHHHHHHHHhCC
Q 040394          595 -PIEP------DVSLFGAFLHGCGLYSRFDLGEVMIKKMLE------------LHPDKACYYVLVSNLYASDG  648 (691)
Q Consensus       595 -~~~p------~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~------------~~p~~~~~~~~l~~~~~~~g  648 (691)
                       .++|      +...|..++-.|.+.|+++.|...+-+-..            ..+.++..|+..+..|...+
T Consensus      1343 ini~k~~r~~e~~~lW~elv~LY~~~~e~dnA~~tm~~h~~~a~~~~~Fk~~i~kv~n~elyykai~Fyl~~~ 1415 (1630)
T 1xi4_A         1343 VNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYLEFK 1415 (1630)
T ss_pred             cccchHhHHHHHHHHHHHHHHHHHhcccHHHHHHHHHhccHhhhhhHHHHHHhcccccHHHHHHHHHHHHhhC
Confidence             5444      556899999999999999999843333221            25667888887778777666

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.83  E-value=4.6e-18  Score=171.59  Aligned_cols=298  Identities=11%  Similarity=-0.000  Sum_probs=254.6

Q ss_pred             cHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCC
Q 040394          346 NHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDN  425 (691)
Q Consensus       346 ~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~  425 (691)
                      |...+..+...+...|++++|...++.+.+..+.+...+..+...+...|++++|...++++.+.               
T Consensus         2 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~---------------   66 (359)
T 3ieg_A            2 DVEKHLELGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIAL---------------   66 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---------------
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh---------------
Confidence            45567778888999999999999999999999999999999999999999999999999988653               


Q ss_pred             CCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCC---CchhHHHHH------------HHHHHhcCCHHHHHHHHH
Q 040394          426 VSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLS---SNVYVGTAL------------LNFYAKCGDAQSARMVFD  490 (691)
Q Consensus       426 ~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~~l------------~~~~~~~g~~~~A~~~~~  490 (691)
                      .+.+...+..+...+...|++++|...++.+.+..  |   .+...+..+            ...+...|++++|...++
T Consensus        67 ~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~  144 (359)
T 3ieg_A           67 KMDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSN--PSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLD  144 (359)
T ss_dssp             CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             CCCcchHHHHHHHHHHHcCChHHHHHHHHHHHhcC--CcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHH
Confidence            12356788899999999999999999999999876  5   566666555            578899999999999999


Q ss_pred             hccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC
Q 040394          491 AMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS  567 (691)
Q Consensus       491 ~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~  567 (691)
                      ++.+   .+...+..+...+...|++++|...++++.+.. +.+..++..+...+...|++++|.+.++...+.   .|+
T Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~---~~~  220 (359)
T 3ieg_A          145 KILEVCVWDAELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLKL---DQD  220 (359)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---CTT
T ss_pred             HHHHhCCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh---Ccc
Confidence            8874   367889999999999999999999999999863 456778888889999999999999999988544   444


Q ss_pred             -hhHHH------------HHHHHHHhcCChHHHHHHHHhC-CCCCCH-----HHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040394          568 -MKHYV------------CMVDLLARAGRLEEALEFMENM-PIEPDV-----SLFGAFLHGCGLYSRFDLGEVMIKKMLE  628 (691)
Q Consensus       568 -~~~~~------------~li~~~~~~g~~~~A~~~~~~~-~~~p~~-----~~~~~l~~~~~~~g~~~~A~~~~~~~~~  628 (691)
                       ...+.            .+...+.+.|++++|.+.++++ ...|+.     ..+..+...+...|++++|...++++.+
T Consensus       221 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  300 (359)
T 3ieg_A          221 HKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTEPSVAEYTVRSKERICHCFSKDEKPVEAIRICSEVLQ  300 (359)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence             33222            2366789999999999999998 333442     2355677889999999999999999999


Q ss_pred             cCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          629 LHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       629 ~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      ..|+++.++..++.+|...|++++|.+.+++..+..
T Consensus       301 ~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~  336 (359)
T 3ieg_A          301 MEPDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEHN  336 (359)
T ss_dssp             HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             hCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            999999999999999999999999999999999864

>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=99.82  E-value=1.1e-14  Score=160.05  Aligned_cols=313  Identities=10%  Similarity=0.091  Sum_probs=199.2

Q ss_pred             HHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCCh
Q 040394          117 MIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDI  196 (691)
Q Consensus       117 ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  196 (691)
                      +...+...|.+++|..+|++..     -.....+.++.   ..+++++|.++.++.     .++.+|..+..++.+.|++
T Consensus      1055 IA~Iai~lglyEEAf~IYkKa~-----~~~~A~~VLie---~i~nldrAiE~Aerv-----n~p~vWsqLAKAql~~G~~ 1121 (1630)
T 1xi4_A         1055 IANIAISNELFEEAFAIFRKFD-----VNTSAVQVLIE---HIGNLDRAYEFAERC-----NEPAVWSQLAKAQLQKGMV 1121 (1630)
T ss_pred             HHHHHHhCCCHHHHHHHHHHcC-----CHHHHHHHHHH---HHhhHHHHHHHHHhc-----CCHHHHHHHHHHHHhCCCH
Confidence            4455566666777777666641     11111222222   445666666665533     3567777788888888888


Q ss_pred             HHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHC
Q 040394          197 GSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIG  276 (691)
Q Consensus       197 ~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g  276 (691)
                      ++|...|.+.  .|...|..++..+.+.|++++|.+.|...++..  +++...+.+..+|++.+++++...+.    +  
T Consensus      1122 kEAIdsYiKA--dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~rleele~fI----~-- 1191 (1630)
T 1xi4_A         1122 KEAIDSYIKA--DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNRLAELEEFI----N-- 1191 (1630)
T ss_pred             HHHHHHHHhc--CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHHHHH----h--
Confidence            8888777653  566677777778888888888888777766543  33223334777777777776544332    1  


Q ss_pred             CCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHH
Q 040394          277 IEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSA  356 (691)
Q Consensus       277 ~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~  356 (691)
                       .++...+..+...|...|++++|..+|...     ..|..+...|++.|++++|.+.+++.      -+..+|..+-.+
T Consensus      1192 -~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA-----~ny~rLA~tLvkLge~q~AIEaarKA------~n~~aWkev~~a 1259 (1630)
T 1xi4_A         1192 -GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV-----SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFA 1259 (1630)
T ss_pred             -CCCHHHHHHHHHHHHhcCCHHHHHHHHHhh-----hHHHHHHHHHHHhCCHHHHHHHHHHh------CCHHHHHHHHHH
Confidence             345555666777777888888888888774     47777888888888888888887764      355777777777


Q ss_pred             HhcCCChhhHHHHHHHHHHhCCC-chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHH
Q 040394          357 SAQLGNLNMGRMVHSLGIRLGLE-DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVS  435 (691)
Q Consensus       357 ~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~  435 (691)
                      |...|++..|......     +. ++..+..++..|.+.|.+++|..+++.....+               +-....|+.
T Consensus      1260 cve~~Ef~LA~~cgl~-----Iiv~~deLeeli~yYe~~G~feEAI~LlE~aL~Le---------------raH~gmftE 1319 (1630)
T 1xi4_A         1260 CVDGKEFRLAQMCGLH-----IVVHADELEELINYYQDRGYFEELITMLEAALGLE---------------RAHMGMFTE 1319 (1630)
T ss_pred             HhhhhHHHHHHHHHHh-----hhcCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccC---------------hhHhHHHHH
Confidence            7777777777665432     22 55566778888888888888888887765432               123334555


Q ss_pred             HHHHHhc--cCcHHHHHHHHHHHHHcCCCC------CchhHHHHHHHHHHhcCCHHHHHH
Q 040394          436 VISACAS--LGAVQVGSSLHAYSTKQGLLS------SNVYVGTALLNFYAKCGDAQSARM  487 (691)
Q Consensus       436 ll~~~~~--~~~~~~a~~~~~~~~~~~~~~------~~~~~~~~l~~~~~~~g~~~~A~~  487 (691)
                      +...+++  -+++.++.+.|..-  .++ |      .+...|..++..|.+.|+++.|..
T Consensus      1320 LaiLyaKy~peklmEhlk~f~~r--ini-~k~~r~~e~~~lW~elv~LY~~~~e~dnA~~ 1376 (1630)
T 1xi4_A         1320 LAILYSKFKPQKMREHLELFWSR--VNI-PKVLRAAEQAHLWAELVFLYDKYEEYDNAII 1376 (1630)
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHh--ccc-chHhHHHHHHHHHHHHHHHHHhcccHHHHHH
Confidence            5555544  33444444444422  221 2      245667778888888888888773

>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=99.82  E-value=5.6e-18  Score=168.86  Aligned_cols=281  Identities=11%  Similarity=0.057  Sum_probs=173.4

Q ss_pred             HHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHH
Q 040394          353 VLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVT  432 (691)
Q Consensus       353 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~  432 (691)
                      +...+...|++++|..+++.+.+..+.+...+..++..+...|++++|...++++.+.               .+.+...
T Consensus        28 ~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~---------------~~~~~~~   92 (330)
T 3hym_B           28 LAERHYYNCDFKMCYKLTSVVMEKDPFHASCLPVHIGTLVELNKANELFYLSHKLVDL---------------YPSNPVS   92 (330)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHH---------------CTTSTHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHcCCCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHh---------------CcCCHHH
Confidence            3333333444444444444444444444444444444444555555555555444322               1123344


Q ss_pred             HHHHHHHHhccC-cHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-CHhHHHHHHHHHh
Q 040394          433 LVSVISACASLG-AVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--K-NTVTWSAMIGGYG  508 (691)
Q Consensus       433 ~~~ll~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~li~~~~  508 (691)
                      +..+...+...| +++.|...++...+..  |.+...+..+...+...|++++|...+++..+  | +...+..+...|.
T Consensus        93 ~~~l~~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~  170 (330)
T 3hym_B           93 WFAVGCYYLMVGHKNEHARRYLSKATTLE--KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKGCHLPMLYIGLEYG  170 (330)
T ss_dssp             HHHHHHHHHHSCSCHHHHHHHHHHHHTTC--TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhccccHHHHHHHHHHHH
Confidence            444455555555 5555555555555544  44555566666666666666666666665543  2 3445555666666


Q ss_pred             cCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcC-------CCCChhHHHHHHHHHHhc
Q 040394          509 MQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFK-------FVPSMKHYVCMVDLLARA  581 (691)
Q Consensus       509 ~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~-------~~p~~~~~~~li~~~~~~  581 (691)
                      ..|++++|...+++..+.. +.+...+..+...+...|++++|...+++......       .......+..+...+.+.
T Consensus       171 ~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~  249 (330)
T 3hym_B          171 LTNNSKLAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKL  249 (330)
T ss_dssp             HTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHT
T ss_pred             HHhhHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHh
Confidence            6777777777777666642 33455666666677777777777777776644321       122356788888888899


Q ss_pred             CChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHH-HhCCCcH
Q 040394          582 GRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLY-ASDGRWI  651 (691)
Q Consensus       582 g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~-~~~g~~~  651 (691)
                      |++++|++.+++. . .+.+...+..+...+...|++++|...++++++..|+++..+..++.++ ...|+.+
T Consensus       250 g~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~g~~~  322 (330)
T 3hym_B          250 KKYAEALDYHRQALVLIPQNASTYSAIGYIHSLMGNFENAVDYFHTALGLRRDDTFSVTMLGHCIEMYIGDSE  322 (330)
T ss_dssp             TCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTTCSCCHHHHHHHHHHHHTTTTC--
T ss_pred             cCHHHHHHHHHHHHhhCccchHHHHHHHHHHHHhccHHHHHHHHHHHHccCCCchHHHHHHHHHHHHHhCchh
Confidence            9999999888887 2 2335678888999999999999999999999999999999999999888 4555543

>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=99.78  E-value=5.8e-17  Score=159.94  Aligned_cols=286  Identities=13%  Similarity=0.105  Sum_probs=104.1

Q ss_pred             cCCChHHHHHHhccCCCCCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHH
Q 040394           92 SFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCE  171 (691)
Q Consensus        92 ~~g~~~~A~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~  171 (691)
                      +.|++++|.+.+++++.|+  +|..|..++.+.|++++|++.|.+      .+|..+|..++.++...|++++|+..++.
T Consensus        15 ~~~~ld~A~~fae~~~~~~--vWs~La~A~l~~g~~~eAIdsfik------a~D~~~y~~V~~~ae~~g~~EeAi~yl~~   86 (449)
T 1b89_A           15 HIGNLDRAYEFAERCNEPA--VWSQLAKAQLQKGMVKEAIDSYIK------ADDPSSYMEVVQAANTSGNWEELVKYLQM   86 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HccCHHHHHHHHHhCCChH--HHHHHHHHHHHcCCHHHHHHHHHc------CCCHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            5566777777777775543  677777777777777777777743      24666777777777777777777775555


Q ss_pred             HHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHH
Q 040394          172 IVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGS  251 (691)
Q Consensus       172 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~  251 (691)
                      ..+. .+++.+.+.|+.+|.+.|+++++.++++.   |+..+|+.+...|...|++++|...|..+         ..|..
T Consensus        87 ark~-~~~~~i~~~Li~~Y~Klg~l~e~e~f~~~---pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a---------~n~~~  153 (449)
T 1b89_A           87 ARKK-ARESYVETELIFALAKTNRLAELEEFING---PNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGR  153 (449)
T ss_dssp             -----------------------CHHHHTTTTTC---C----------------CTTTHHHHHHHT---------TCHHH
T ss_pred             HHHh-CccchhHHHHHHHHHHhCCHHHHHHHHcC---CcHHHHHHHHHHHHHcCCHHHHHHHHHHh---------hhHHH
Confidence            5443 33566677777777777777777666643   55667777777777777777777777765         35667


Q ss_pred             HHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhH
Q 040394          252 LVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKA  331 (691)
Q Consensus       252 li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a  331 (691)
                      +..++.+.|++++|.+.+..+      .++.+|..++.+|+..|+++.|......+. .++.-...++..|.+.|++++|
T Consensus       154 LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~-~~ad~l~~lv~~Yek~G~~eEa  226 (449)
T 1b89_A          154 LASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHIV-VHADELEELINYYQDRGYFEEL  226 (449)
T ss_dssp             HHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTTT-TCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHHHH-hCHhhHHHHHHHHHHCCCHHHH
Confidence            777777777777777777666      256677777777777777777766555543 3333344566667777777777


Q ss_pred             HHHHHHhhHCCCCCcHHHHHHHHHHHhc--CCChhhHHHHHHHHHHhCC-----CchhHHHHHHHHhHhcCChHHHHHHH
Q 040394          332 LKLFTDKKWADFFPNHVTIASVLSASAQ--LGNLNMGRMVHSLGIRLGL-----EDYTVINALVDMYAKCHVIADARYIF  404 (691)
Q Consensus       332 ~~~~~~m~~~g~~p~~~t~~~ll~~~~~--~~~~~~a~~~~~~~~~~~~-----~~~~~~~~l~~~~~~~g~~~~a~~~~  404 (691)
                      ..+++...... +.....|+.+--.+++  .+++.+..+.|.......+     .....|..++..|.+.++++.|....
T Consensus       227 i~lLe~aL~le-~ah~~~ftel~il~~ky~p~k~~ehl~~~~~~ini~k~~~~~~~~~~w~e~~~ly~~~~e~d~A~~tm  305 (449)
T 1b89_A          227 ITMLEAALGLE-RAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITM  305 (449)
T ss_dssp             HHHHHHHTTST-TCCHHHHHHHHHHHHTTCHHHHHHHHHHHSTTSCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHhCCc-HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHHHhhchHHHHHHHH
Confidence            77776655432 2233444444333332  3334444443332222221     13556677777777788888776644


Q ss_pred             Hh
Q 040394          405 ET  406 (691)
Q Consensus       405 ~~  406 (691)
                      -.
T Consensus       306 ~~  307 (449)
T 1b89_A          306 MN  307 (449)
T ss_dssp             HH
T ss_pred             Hh
Confidence            43

>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=99.78  E-value=4.3e-16  Score=155.08  Aligned_cols=265  Identities=11%  Similarity=0.014  Sum_probs=169.0

Q ss_pred             CCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHH
Q 040394          109 PDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVD  188 (691)
Q Consensus       109 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  188 (691)
                      .+...+..+...+...|++++|+++|+++.+.. +.+...+..++..+...|++++|...++.+.+..+.+..++..+..
T Consensus        20 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~   98 (330)
T 3hym_B           20 ENLDVVVSLAERHYYNCDFKMCYKLTSVVMEKD-PFHASCLPVHIGTLVELNKANELFYLSHKLVDLYPSNPVSWFAVGC   98 (330)
T ss_dssp             CCCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHH
Confidence            455566666777777777777777777776653 3344555566666667777777777777777766666666666666


Q ss_pred             HhHhcC-ChHHHHHHHhccCC---CChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhh
Q 040394          189 MYAKCR-DIGSSRQVFDETLD---KNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQ  264 (691)
Q Consensus       189 ~~~~~g-~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~  264 (691)
                      .+...| ++++|...|++..+   .+...|..+...+...|++++|.+.|++..+....                     
T Consensus        99 ~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~---------------------  157 (330)
T 3hym_B           99 YYLMVGHKNEHARRYLSKATTLEKTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKG---------------------  157 (330)
T ss_dssp             HHHHSCSCHHHHHHHHHHHHTTCTTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTT---------------------
T ss_pred             HHHHhhhhHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhccc---------------------
Confidence            666666 66666666665432   23455666666666666666666666666543211                     


Q ss_pred             HHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhc---CCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHC
Q 040394          265 GKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDEL---CSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWA  341 (691)
Q Consensus       265 a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  341 (691)
                                     +...+..+...+...|++++|.+.|++.   .+.+..++..+...+...|++++|...+++....
T Consensus       158 ---------------~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~  222 (330)
T 3hym_B          158 ---------------CHLPMLYIGLEYGLTNNSKLAERFFSQALSIAPEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEK  222 (330)
T ss_dssp             ---------------CSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ---------------cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcccHHHHHHHHHHHHHH
Confidence                           2233344455555555555555555554   1223445556666666666666666666665443


Q ss_pred             C--------CCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCC
Q 040394          342 D--------FFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEK  410 (691)
Q Consensus       342 g--------~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  410 (691)
                      .        ...+..++..+...+...|++++|...++.+.+..+.+..++..+...|.+.|++++|...|++..+.
T Consensus       223 ~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  299 (330)
T 3hym_B          223 IKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLIPQNASTYSAIGYIHSLMGNFENAVDYFHTALGL  299 (330)
T ss_dssp             HTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTT
T ss_pred             hhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhCccchHHHHHHHHHHHHhccHHHHHHHHHHHHcc
Confidence            1        12234566667777777777777777777777777777777888888888888888888888888754

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.78  E-value=4.2e-15  Score=158.31  Aligned_cols=417  Identities=9%  Similarity=0.003  Sum_probs=226.1

Q ss_pred             CcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCC--CChhhHHHHHHHH-
Q 040394          145 DNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLD--KNVVSWTSMIAGY-  221 (691)
Q Consensus       145 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~~~~li~~~-  221 (691)
                      +...|..++.. .+.|++++|..+|+.+++..|.+...|..++..+.+.|++++|.++|++...  |++..|...+... 
T Consensus        12 ~~~~w~~l~~~-~~~~~~~~a~~~~e~al~~~P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~p~~~lw~~~~~~~~   90 (530)
T 2ooe_A           12 DLDAWSILIRE-AQNQPIDKARKTYERLVAQFPSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKVLHIDLWKCYLSYVR   90 (530)
T ss_dssp             CHHHHHHHHHH-HHSSCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTCCCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHH-HHhCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCChHHHHHHHHHHH
Confidence            55566666663 5667777777777777776666777777777777777777777777777644  5555565555422 


Q ss_pred             HhCCChhHHHH----HHHHHHh-CCCCC-ChhhHHHHHHHHHc---------cCChhhHHHHHHHHHHHCCCCchHHHHH
Q 040394          222 VQNDCAQEGLV----LFNRMRE-GFVEG-NQITLGSLVTACAK---------LRALHQGKWLHGYILKIGIEINSHLVTA  286 (691)
Q Consensus       222 ~~~g~~~~A~~----~~~~m~~-~~~~p-~~~t~~~li~~~~~---------~~~~~~a~~~~~~~~~~g~~~~~~~~~~  286 (691)
                      ...|+.++|.+    +|++... .|..| +...|...+.....         .|+++.|..+|+..++....+....|..
T Consensus        91 ~~~~~~~~a~~~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~P~~~~~~~~~~  170 (530)
T 2ooe_A           91 ETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINIEQLWRD  170 (530)
T ss_dssp             HHTTTSTTHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTSCCTTHHHHHHH
T ss_pred             HHccchhhHHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhchhhhHHHHHHH
Confidence            34566665554    5554433 23333 23344444443332         4555566666655554110001122222


Q ss_pred             HHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHh------hHCC---CCCc--------HHH
Q 040394          287 LLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDK------KWAD---FFPN--------HVT  349 (691)
Q Consensus       287 li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m------~~~g---~~p~--------~~t  349 (691)
                      ........|. ..+..++.                 .+.++++.|..++.++      .+..   +.|+        ...
T Consensus       171 ~~~~e~~~~~-~~~~~~l~-----------------~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~  232 (530)
T 2ooe_A          171 YNKYEEGINI-HLAKKMIE-----------------DRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDM  232 (530)
T ss_dssp             HHHHHHHHCH-HHHHHHHH-----------------TTHHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC--CCHHHHHHH
T ss_pred             HHHHHHhhch-hHHHHHHH-----------------HhhHHHHHHHHHHHHHHHHHHHhccccccCCCCCChhHHHHHHH
Confidence            2111100000 00111110                 1234456666655542      1111   2343        234


Q ss_pred             HHHHHHHHhcC----CCh----hhHHHHHHHHHHhCCCchhHHHHHHHHhHh-------cCChH-------HHHHHHHhC
Q 040394          350 IASVLSASAQL----GNL----NMGRMVHSLGIRLGLEDYTVINALVDMYAK-------CHVIA-------DARYIFETT  407 (691)
Q Consensus       350 ~~~ll~~~~~~----~~~----~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~-------~g~~~-------~a~~~~~~~  407 (691)
                      |...+......    ++.    ..+..+++.+....+.++.+|..++..+.+       .|+++       +|..+|++.
T Consensus       233 w~~~~~~e~~~~~~~~~~~~~~~~a~~~y~~al~~~p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~A  312 (530)
T 2ooe_A          233 WKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERA  312 (530)
T ss_dssp             HHHHHHHHHHCSSCCSCSHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCccCCcchhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHH
Confidence            44444332221    222    366778999999888888899888888876       78877       788888887


Q ss_pred             CCCCchhHHHHHHhhhCCCCC-CHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCch-hHHHHHHHHHHhcCCHHHH
Q 040394          408 SEKDVIAWNSIISGLDDNVSP-DAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNV-YVGTALLNFYAKCGDAQSA  485 (691)
Q Consensus       408 ~~~~~~~~~~li~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~g~~~~A  485 (691)
                      .+.               +.| +...|..+...+.+.|+++.|..+|+.+.+..  |.+. ..|..++..+.+.|++++|
T Consensus       313 l~~---------------~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~~~~~~~A  375 (530)
T 2ooe_A          313 IST---------------LLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIE--DIDPTLVYIQYMKFARRAEGIKSG  375 (530)
T ss_dssp             TTT---------------TCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSS--SSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHH---------------hCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCcc--ccCchHHHHHHHHHHHHhcCHHHH
Confidence            642               223 35566666666666677777777777766643  2232 3455555555555555555


Q ss_pred             HHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHH-HhcccCCHHHHHHHHHHchhhcCC
Q 040394          486 RMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILS-ACSHTGMVGEGWKCFYSMCRDFKF  564 (691)
Q Consensus       486 ~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~-~~~~~g~~~~A~~~~~~m~~~~~~  564 (691)
                      ..+|++                               ..+.. +.+...|..... .+...|+.++|..+|+...+.   
T Consensus       376 ~~~~~~-------------------------------Al~~~-~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~---  420 (530)
T 2ooe_A          376 RMIFKK-------------------------------AREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKK---  420 (530)
T ss_dssp             HHHHHH-------------------------------HHTCT-TCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHH---
T ss_pred             HHHHHH-------------------------------HHhcc-CCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHH---
Confidence            555554                               44321 111112211111 122356666666666655433   


Q ss_pred             CCC-hhHHHHHHHHHHhcCChHHHHHHHHhC----CCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040394          565 VPS-MKHYVCMVDLLARAGRLEEALEFMENM----PIEPD--VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPD  632 (691)
Q Consensus       565 ~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~----~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~  632 (691)
                      .|+ ...|..++..+.+.|+.++|..+|++.    +..|+  ...|...+......|+.+.+..+.+++.+..|+
T Consensus       421 ~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~~~~lw~~~~~~e~~~G~~~~~~~~~~r~~~~~p~  495 (530)
T 2ooe_A          421 YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAFRE  495 (530)
T ss_dssp             HTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGGCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHTHH
T ss_pred             CCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCch
Confidence            233 455666666666666666666666665    11222  236666666666777777777777777776664

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.77  E-value=5.3e-15  Score=155.85  Aligned_cols=364  Identities=11%  Similarity=-0.011  Sum_probs=229.9

Q ss_pred             cCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHh----cCCHHHHHHHHHhcCC-CChhHHHHHHHHHHh----cCCch
Q 040394          259 LRALHQGKWLHGYILKIGIEINSHLVTALLDMYVK----CGNIRDARSVFDELCS-IDLVSWTAMIVGYTQ----SGYPD  329 (691)
Q Consensus       259 ~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~----~g~~~~A~~~~~~~~~-~~~~~~~~li~~~~~----~g~~~  329 (691)
                      .++.++|...|+...+.|   +...+..|...|..    .++.++|.+.|++... .+...+..|...|..    .++++
T Consensus        56 ~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~  132 (490)
T 2xm6_A           56 TKDLTQAMDWFRRAAEQG---YTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKGLPQAQQNLGVMYHEGNGVKVDKA  132 (490)
T ss_dssp             CCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHH
T ss_pred             CcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHH
Confidence            444445555554444432   33344444444444    4555555555554422 233444444444544    45555


Q ss_pred             hHHHHHHHhhHCCCCCcHHHHHHHHHHHhc----CCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHh----cCChHHHH
Q 040394          330 KALKLFTDKKWADFFPNHVTIASVLSASAQ----LGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAK----CHVIADAR  401 (691)
Q Consensus       330 ~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~  401 (691)
                      +|++.|++..+.|   +...+..+...+..    .++.++|...++...+.+  +...+..+...|..    .++.++|.
T Consensus       133 ~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~--~~~a~~~Lg~~y~~g~g~~~~~~~A~  207 (490)
T 2xm6_A          133 ESVKWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQG--NVWSCNQLGYMYSRGLGVERNDAISA  207 (490)
T ss_dssp             HHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT--CHHHHHHHHHHHHHTSSSCCCHHHHH
T ss_pred             HHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC--CHHHHHHHHHHHhcCCCCCcCHHHHH
Confidence            5555555555443   23334444444443    455666666665555543  34455556666665    67777777


Q ss_pred             HHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhc----cCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHH
Q 040394          402 YIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACAS----LGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYA  477 (691)
Q Consensus       402 ~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~  477 (691)
                      ..|++..+.                 .+...+..+...+..    .++.++|...++...+.+    ++..+..+...|.
T Consensus       208 ~~~~~a~~~-----------------~~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~----~~~a~~~lg~~y~  266 (490)
T 2xm6_A          208 QWYRKSATS-----------------GDELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQG----NSIAQFRLGYILE  266 (490)
T ss_dssp             HHHHHHHHT-----------------TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTT----CHHHHHHHHHHHH
T ss_pred             HHHHHHHHC-----------------CCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC----CHHHHHHHHHHHH
Confidence            777765433                 234455555555554    677888888888777655    2445556666676


Q ss_pred             h----cCCHHHHHHHHHhcccC-CHhHHHHHHHHHhcC-----CChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccC-
Q 040394          478 K----CGDAQSARMVFDAMREK-NTVTWSAMIGGYGMQ-----GDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTG-  546 (691)
Q Consensus       478 ~----~g~~~~A~~~~~~~~~~-~~~~~~~li~~~~~~-----~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g-  546 (691)
                      .    .++.++|...|++..+. +...+..+...|...     +++++|+..+++..+.|   +...+..+-..+...| 
T Consensus       267 ~g~~~~~d~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~~g~  343 (490)
T 2xm6_A          267 QGLAGAKEPLKALEWYRKSAEQGNSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQG---DATAQANLGAIYFRLGS  343 (490)
T ss_dssp             HTTTSSCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHSCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhCCC
Confidence            6    78888888888887654 566777777777776     88999999999988865   3445555555555545 


Q ss_pred             --CHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHh----cCChHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCH
Q 040394          547 --MVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLAR----AGRLEEALEFMENMPIEPDVSLFGAFLHGCGL----YSRF  616 (691)
Q Consensus       547 --~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~----~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~  616 (691)
                        ++++|.+.|++..+.    .+...+..|...|..    .+++++|+++|++.-...+...+..|...|..    .+|.
T Consensus       344 ~~~~~~A~~~~~~a~~~----~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~~~~~a~~~Lg~~y~~g~g~~~d~  419 (490)
T 2xm6_A          344 EEEHKKAVEWFRKAAAK----GEKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQGLSAAQVQLGEIYYYGLGVERDY  419 (490)
T ss_dssp             HHHHHHHHHHHHHHHHT----TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCH
T ss_pred             cccHHHHHHHHHHHHHC----CCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCCCCCH
Confidence              788999999887433    356778888888888    78999999999987323467788888888887    7999


Q ss_pred             HHHHHHHHHHHhcCCC---CchhHHHHHHHHHhCCCcHHHHHHHHHH
Q 040394          617 DLGEVMIKKMLELHPD---KACYYVLVSNLYASDGRWIRVNQVRELM  660 (691)
Q Consensus       617 ~~A~~~~~~~~~~~p~---~~~~~~~l~~~~~~~g~~~~A~~~~~~~  660 (691)
                      ++|...++++.+..|+   ++.....++.++..  +.+.+.+..+++
T Consensus       420 ~~A~~~~~~A~~~~~~~~~~~~a~~~l~~~~~~--~~~~a~~~a~~~  464 (490)
T 2xm6_A          420 VQAWAWFDTASTNDMNLFGTENRNITEKKLTAK--QLQQAELLSQQY  464 (490)
T ss_dssp             HHHHHHHHHHHHHHCCHHHHHHHHHHHTTSCHH--HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCcCCHHHHHHHHhcCHh--HHHHHHHHHHHH
Confidence            9999999999998854   66677777666554  334444333333

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.77  E-value=6.9e-15  Score=156.64  Aligned_cols=415  Identities=10%  Similarity=0.060  Sum_probs=270.8

Q ss_pred             ChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHH
Q 040394          210 NVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLD  289 (691)
Q Consensus       210 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~  289 (691)
                      +...|..++. +.+.|++++|..+|+++.+.. +-+...|...+..+.+.|+.++|..+|+..++..  |+...|..++.
T Consensus        12 ~~~~w~~l~~-~~~~~~~~~a~~~~e~al~~~-P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~--p~~~lw~~~~~   87 (530)
T 2ooe_A           12 DLDAWSILIR-EAQNQPIDKARKTYERLVAQF-PSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKV--LHIDLWKCYLS   87 (530)
T ss_dssp             CHHHHHHHHH-HHHSSCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTC--CCHHHHHHHHH
T ss_pred             CHHHHHHHHH-HHHhCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC--CChHHHHHHHH
Confidence            5667777777 467788888888888887642 2345566777777777777777777777776653  46656666554


Q ss_pred             HH-HhcCCHHHHHH----HHHhc------CCCChhHHHHHHHHHHh---------cCCchhHHHHHHHhhHCCCCCcHHH
Q 040394          290 MY-VKCGNIRDARS----VFDEL------CSIDLVSWTAMIVGYTQ---------SGYPDKALKLFTDKKWADFFPNHVT  349 (691)
Q Consensus       290 ~~-~~~g~~~~A~~----~~~~~------~~~~~~~~~~li~~~~~---------~g~~~~a~~~~~~m~~~g~~p~~~t  349 (691)
                      .. ...|+.+.|.+    +|+..      ...+...|...+....+         .|++++|..+|++.......+....
T Consensus        88 ~~~~~~~~~~~a~~~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~P~~~~~~~  167 (530)
T 2ooe_A           88 YVRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINIEQL  167 (530)
T ss_dssp             HHHHHTTTSTTHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTSCCTTHHHH
T ss_pred             HHHHHccchhhHHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhchhhhHHHH
Confidence            32 33455555544    44443      11244556666554443         4666677777776665211111222


Q ss_pred             HHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhC---CC
Q 040394          350 IASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDD---NV  426 (691)
Q Consensus       350 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~---~~  426 (691)
                      |..........|. ..+.                  .++.  .+.+++..|..+++...        ....++..   .+
T Consensus       168 ~~~~~~~e~~~~~-~~~~------------------~~l~--~~~~~~~~A~~~~~~~~--------~~~~~l~~~~~~~  218 (530)
T 2ooe_A          168 WRDYNKYEEGINI-HLAK------------------KMIE--DRSRDYMNARRVAKEYE--------TVMKGLDRNAPSV  218 (530)
T ss_dssp             HHHHHHHHHHHCH-HHHH------------------HHHH--TTHHHHHHHHHHHHHHH--------HHHHHCCSSSCCC
T ss_pred             HHHHHHHHHhhch-hHHH------------------HHHH--HhhHHHHHHHHHHHHHH--------HHHHHhccccccC
Confidence            2222111000000 0000                  0010  12344555655554310        00011111   13


Q ss_pred             CCC--------HHHHHHHHHHHhcc----CcH----HHHHHHHHHHHHcCCCCCchhHHHHHHHHHHh-------cCCHH
Q 040394          427 SPD--------AVTLVSVISACASL----GAV----QVGSSLHAYSTKQGLLSSNVYVGTALLNFYAK-------CGDAQ  483 (691)
Q Consensus       427 ~p~--------~~~~~~ll~~~~~~----~~~----~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------~g~~~  483 (691)
                      +|+        ...|...+......    ++.    +.+..+|++.....  |.++..|..++..+.+       .|+++
T Consensus       219 ~p~~~~~~~~~~~~w~~~~~~e~~~~~~~~~~~~~~~~a~~~y~~al~~~--p~~~~~w~~~~~~~~~~~~~~~~~g~~~  296 (530)
T 2ooe_A          219 PPQNTPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVL--GHHPDIWYEAAQYLEQSSKLLAEKGDMN  296 (530)
T ss_dssp             CCC--CCHHHHHHHHHHHHHHHHHCSSCCSCSHHHHHHHHHHHHHHHHHH--TTCHHHHHHHHHHHHHHHHHHHTTTCCH
T ss_pred             CCCCChhHHHHHHHHHHHHHHHHcCCccCCcchhHHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhchhhhhccchh
Confidence            443        23444444332221    222    46778899988876  7888999888888876       68877


Q ss_pred             -------HHHHHHHhccc---C-CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCH--HHHHHHHHHhcccCCHHH
Q 040394          484 -------SARMVFDAMRE---K-NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNE--VIFTTILSACSHTGMVGE  550 (691)
Q Consensus       484 -------~A~~~~~~~~~---~-~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~--~~~~~ll~~~~~~g~~~~  550 (691)
                             +|..+|++..+   | +...|..++..+.+.|++++|..+|+++.+.  .|+.  ..|..+...+.+.|++++
T Consensus       297 ~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~  374 (530)
T 2ooe_A          297 NAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKS  374 (530)
T ss_dssp             HHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCc--cccCchHHHHHHHHHHHHhcCHHH
Confidence                   89999998874   3 5788999999999999999999999999984  5653  478888888888999999


Q ss_pred             HHHHHHHchhhcCCCCC-hhHHHHHHHH-HHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040394          551 GWKCFYSMCRDFKFVPS-MKHYVCMVDL-LARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKM  626 (691)
Q Consensus       551 A~~~~~~m~~~~~~~p~-~~~~~~li~~-~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~  626 (691)
                      |.++|++..+   ..|+ ...|...+.. +...|+.++|.++|++. ...| +...|..++..+.+.|+.++|..+|+++
T Consensus       375 A~~~~~~Al~---~~~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~a  451 (530)
T 2ooe_A          375 GRMIFKKARE---DARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERV  451 (530)
T ss_dssp             HHHHHHHHHT---CTTCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHh---ccCCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHCCCCHHHHHHHHHHHHhCCCHhhHHHHHHHH
Confidence            9999998753   3443 3333332222 33689999999999987 3334 5788999999999999999999999999


Q ss_pred             HhcCCCCch----hHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          627 LELHPDKAC----YYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       627 ~~~~p~~~~----~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      +...|.++.    .|...+......|+.+.+..+.+++.+.-
T Consensus       452 l~~~~~~~~~~~~lw~~~~~~e~~~G~~~~~~~~~~r~~~~~  493 (530)
T 2ooe_A          452 LTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAF  493 (530)
T ss_dssp             HHSCCSCGGGCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHT
T ss_pred             HhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            998776554    77777888889999999999999988753

>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=99.76  E-value=2.4e-16  Score=155.56  Aligned_cols=374  Identities=11%  Similarity=0.070  Sum_probs=135.2

Q ss_pred             hcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHH
Q 040394          192 KCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGY  271 (691)
Q Consensus       192 ~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~  271 (691)
                      +.|++++|.+.++++..|  .+|..|+.++.+.|++++|++.|.+.      +|..+|..++.++...|++++|..+++.
T Consensus        15 ~~~~ld~A~~fae~~~~~--~vWs~La~A~l~~g~~~eAIdsfika------~D~~~y~~V~~~ae~~g~~EeAi~yl~~   86 (449)
T 1b89_A           15 HIGNLDRAYEFAERCNEP--AVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVKYLQM   86 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HccCHHHHHHHHHhCCCh--HHHHHHHHHHHHcCCHHHHHHHHHcC------CCHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            344555555555555333  25555555555555555555555432      3445555555555555556555555544


Q ss_pred             HHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHH
Q 040394          272 ILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIA  351 (691)
Q Consensus       272 ~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~  351 (691)
                      ..+.  .+++.+.+.++.+|.+.|+++++.++++.   |+..+|+.+...|...|++++|..+|..+         ..|.
T Consensus        87 ark~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~~---pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a---------~n~~  152 (449)
T 1b89_A           87 ARKK--ARESYVETELIFALAKTNRLAELEEFING---PNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFG  152 (449)
T ss_dssp             ------------------------CHHHHTTTTTC---C----------------CTTTHHHHHHHT---------TCHH
T ss_pred             HHHh--CccchhHHHHHHHHHHhCCHHHHHHHHcC---CcHHHHHHHHHHHHHcCCHHHHHHHHHHh---------hhHH
Confidence            4442  23345555556666666666555555532   44455666666666666666666666544         2455


Q ss_pred             HHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHH
Q 040394          352 SVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAV  431 (691)
Q Consensus       352 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~  431 (691)
                      .+..++.+.|++++|.+.+..+     .++.+|..++.+|...|+++.|......+.                 +.|+. 
T Consensus       153 ~LA~~L~~Lg~yq~AVea~~KA-----~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~-----------------~~ad~-  209 (449)
T 1b89_A          153 RLASTLVHLGEYQAAVDGARKA-----NSTRTWKEVCFACVDGKEFRLAQMCGLHIV-----------------VHADE-  209 (449)
T ss_dssp             HHHHHHHTTTCHHHHHHHHHHH-----TCHHHHHHHHHHHHHTTCHHHHHHTTTTTT-----------------TCHHH-
T ss_pred             HHHHHHHHhccHHHHHHHHHHc-----CCchhHHHHHHHHHHcCcHHHHHHHHHHHH-----------------hCHhh-
Confidence            5555566666666655555554     245555556666666666666644333322                 12222 


Q ss_pred             HHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhc--CCHHHHHHHHHhccc--------CCHhHHH
Q 040394          432 TLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKC--GDAQSARMVFDAMRE--------KNTVTWS  501 (691)
Q Consensus       432 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--g~~~~A~~~~~~~~~--------~~~~~~~  501 (691)
                       ...++..|.+.|.+++|..+++......  +.....|+-+.-+|++-  ++..+.++.|..-..        .+...|.
T Consensus       210 -l~~lv~~Yek~G~~eEai~lLe~aL~le--~ah~~~ftel~il~~ky~p~k~~ehl~~~~~~ini~k~~~~~~~~~~w~  286 (449)
T 1b89_A          210 -LEELINYYQDRGYFEELITMLEAALGLE--RAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWA  286 (449)
T ss_dssp             -HHHHHHHHHHTTCHHHHHHHHHHHTTST--TCCHHHHHHHHHHHHTTCHHHHHHHHHHHSTTSCHHHHHHHHHTTTCHH
T ss_pred             -HHHHHHHHHHCCCHHHHHHHHHHHhCCc--HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence             3345556666666666666666665444  44555555555555543  344444444442221        2456788


Q ss_pred             HHHHHHhcCCChHHHHHHHHHHHHC-CCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHh
Q 040394          502 AMIGGYGMQGDGGGSLALFSDMLNE-EVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLAR  580 (691)
Q Consensus       502 ~li~~~~~~~~~~~A~~~~~~m~~~-g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~  580 (691)
                      .++-.|.+.++++.|..+   |.+. ...-+...|..++.--....-+-+|..++-   .   -.|  ...+-|+.++..
T Consensus       287 e~~~ly~~~~e~d~A~~t---m~~h~~~a~~~~~f~~~~~kv~n~elyYkai~fyl---~---~~p--~~l~~ll~~l~~  355 (449)
T 1b89_A          287 ELVFLYDKYEEYDNAIIT---MMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYL---E---FKP--LLLNDLLMVLSP  355 (449)
T ss_dssp             HHHHHHHHTTCHHHHHHH---HHHSTTTTCCHHHHHHHHHHCSSTHHHHHHHHHHH---H---HCG--GGHHHHHHHHGG
T ss_pred             HHHHHHHhhchHHHHHHH---HHhCChhhhhhHHHHHHHhchhHHHHHHHHHHHHH---h---cCH--HHHHHHHHHHHh
Confidence            888888888888877763   3432 111223333333322222222223333322   1   122  235555555555


Q ss_pred             cCChHHHHHHHHhCCC-------------CCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 040394          581 AGRLEEALEFMENMPI-------------EPDVSLFGAFLHGCGLYSRFDLGEVMIK  624 (691)
Q Consensus       581 ~g~~~~A~~~~~~~~~-------------~p~~~~~~~l~~~~~~~g~~~~A~~~~~  624 (691)
                      .=+...+..+|++.+.             ..+...-.++-..|....|++.-+...+
T Consensus       356 ~ld~~r~v~~~~~~~~l~l~~~yl~~v~~~n~~~vnealn~l~ieeed~~~lr~si~  412 (449)
T 1b89_A          356 RLDHTRAVNYFSKVKQLPLVKPYLRSVQNHNNKSVNESLNNLFITEEDYQALRTSID  412 (449)
T ss_dssp             GCCHHHHHHHHHHTTCTTTTHHHHHHHHTTCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             ccCcHHHHHHHHHcCCcHHHHHHHHHHHHhhHHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence            5566666666666532             2233344455555666677666544444

>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=99.76  E-value=1e-16  Score=162.43  Aligned_cols=296  Identities=8%  Similarity=-0.045  Sum_probs=159.7

Q ss_pred             HhcCCChHHHHH-HhccCCC-----C--CcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCC
Q 040394           90 YGSFGHVKYARS-VFDSMPN-----P--DFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRD  161 (691)
Q Consensus        90 ~~~~g~~~~A~~-~~~~~~~-----~--~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~  161 (691)
                      +...|++++|.. .|++...     |  +...+..+...+.+.|++++|+..|+++.+.. +.+..++..+..++...|+
T Consensus        35 ~~~~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~  113 (368)
T 1fch_A           35 HPWLSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQ  113 (368)
T ss_dssp             -----------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTC
T ss_pred             hHHHHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcC
Confidence            334455666665 5554321     1  23445555666666666666666666665542 3344455555555666666


Q ss_pred             hhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCC--C-ChhhHHHHHHHHHhCCChhHHHHHHHHHH
Q 040394          162 IDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLD--K-NVVSWTSMIAGYVQNDCAQEGLVLFNRMR  238 (691)
Q Consensus       162 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~  238 (691)
                      +++|...++.+.+..+.+..++..+...|...|++++|...|+++..  | +...+..+...       ..         
T Consensus       114 ~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~-------~~---------  177 (368)
T 1fch_A          114 ELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEG-------AG---------  177 (368)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC-----------------------
T ss_pred             HHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHH-------hh---------
Confidence            66666666666655555555555555555555555555555554422  1 11111110000       00         


Q ss_pred             hCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCC-chHHHHHHHHHHHhcCCHHHHHHHHHhc---CCCChhH
Q 040394          239 EGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEI-NSHLVTALLDMYVKCGNIRDARSVFDEL---CSIDLVS  314 (691)
Q Consensus       239 ~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~-~~~~~~~li~~~~~~g~~~~A~~~~~~~---~~~~~~~  314 (691)
                        ...+. ..+. .+..+...|++++|...++.+.+..... +..++..+...+.+.|++++|...|+++   .+.+..+
T Consensus       178 --~~~~~-~~~~-~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~  253 (368)
T 1fch_A          178 --GAGLG-PSKR-ILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLL  253 (368)
T ss_dssp             -----------C-TTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH
T ss_pred             --hhccc-HHHH-HHHHHhhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHH
Confidence              00000 0000 1222235566666666666666553221 3556666666666777777777666665   2234556


Q ss_pred             HHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCc-----------hhH
Q 040394          315 WTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLED-----------YTV  383 (691)
Q Consensus       315 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~-----------~~~  383 (691)
                      |..+...+...|++++|.+.++++.... +.+...+..+...+...|++++|...++.+.+..+.+           ..+
T Consensus       254 ~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~  332 (368)
T 1fch_A          254 WNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENI  332 (368)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHH
Confidence            6667777777777777777777766542 2345566666667777777777777777766655443           677


Q ss_pred             HHHHHHHhHhcCChHHHHHHHHhC
Q 040394          384 INALVDMYAKCHVIADARYIFETT  407 (691)
Q Consensus       384 ~~~l~~~~~~~g~~~~a~~~~~~~  407 (691)
                      +..+..+|...|+.++|..++++.
T Consensus       333 ~~~l~~~~~~~g~~~~A~~~~~~~  356 (368)
T 1fch_A          333 WSTLRLALSMLGQSDAYGAADARD  356 (368)
T ss_dssp             HHHHHHHHHHHTCGGGHHHHHTTC
T ss_pred             HHHHHHHHHHhCChHhHHHhHHHH
Confidence            888888888889988888887743

>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=99.75  E-value=3.5e-17  Score=165.85  Aligned_cols=226  Identities=9%  Similarity=-0.036  Sum_probs=163.0

Q ss_pred             HHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC---CHhHHHH----
Q 040394          430 AVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK---NTVTWSA----  502 (691)
Q Consensus       430 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~----  502 (691)
                      ..++..+..++...|+++.|...++.+.+..  |.+...+..+...|...|++++|...++++.+.   +...+..    
T Consensus        98 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~  175 (368)
T 1fch_A           98 MEAWQYLGTTQAENEQELLAISALRRCLELK--PDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEG  175 (368)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC-----
T ss_pred             HHHHHHHHHHHHHCcCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHH
Confidence            3444444455555555555555555555544  445555555555555555555555555554421   1111110    


Q ss_pred             -----------HHHHHhcCCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hh
Q 040394          503 -----------MIGGYGMQGDGGGSLALFSDMLNEEVQP-NEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MK  569 (691)
Q Consensus       503 -----------li~~~~~~~~~~~A~~~~~~m~~~g~~p-~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~  569 (691)
                                 .+..+...|++++|+..++++.+..... +..++..+...+...|++++|...++++...   .|+ ..
T Consensus       176 ~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~---~~~~~~  252 (368)
T 1fch_A          176 AGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSV---RPNDYL  252 (368)
T ss_dssp             ----------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHH
T ss_pred             hhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CcCCHH
Confidence                       1223337889999999999998853211 4778888888999999999999999987543   454 67


Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhC-CCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC-----------chh
Q 040394          570 HYVCMVDLLARAGRLEEALEFMENM-PIE-PDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK-----------ACY  636 (691)
Q Consensus       570 ~~~~li~~~~~~g~~~~A~~~~~~~-~~~-p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~-----------~~~  636 (691)
                      .+..+...+.+.|++++|++.++++ ... .+...+..+...+.+.|++++|...++++++..|++           ..+
T Consensus       253 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~  332 (368)
T 1fch_A          253 LWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENI  332 (368)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHH
Confidence            8899999999999999999999997 333 456789999999999999999999999999988887           789


Q ss_pred             HHHHHHHHHhCCCcHHHHHHHHHH
Q 040394          637 YVLVSNLYASDGRWIRVNQVRELM  660 (691)
Q Consensus       637 ~~~l~~~~~~~g~~~~A~~~~~~~  660 (691)
                      +..++.+|...|++++|..++++.
T Consensus       333 ~~~l~~~~~~~g~~~~A~~~~~~~  356 (368)
T 1fch_A          333 WSTLRLALSMLGQSDAYGAADARD  356 (368)
T ss_dssp             HHHHHHHHHHHTCGGGHHHHHTTC
T ss_pred             HHHHHHHHHHhCChHhHHHhHHHH
Confidence            999999999999999999887643

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.75  E-value=2.4e-14  Score=150.76  Aligned_cols=362  Identities=9%  Similarity=0.006  Sum_probs=293.2

Q ss_pred             HHHHHHHHHHCCCCchHHHHHHHHHHHh----cCCHHHHHHHHHhcC-CCChhHHHHHHHHHHh----cCCchhHHHHHH
Q 040394          266 KWLHGYILKIGIEINSHLVTALLDMYVK----CGNIRDARSVFDELC-SIDLVSWTAMIVGYTQ----SGYPDKALKLFT  336 (691)
Q Consensus       266 ~~~~~~~~~~g~~~~~~~~~~li~~~~~----~g~~~~A~~~~~~~~-~~~~~~~~~li~~~~~----~g~~~~a~~~~~  336 (691)
                      ...+....+.|   +...+..+...|..    .+++++|...|++.. ..+...+..|...|..    .+++++|.++|+
T Consensus        27 ~~~~~~~a~~g---~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~  103 (490)
T 2xm6_A           27 LEQLKQKAESG---EAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQGYTPAEYVLGLRYMNGEGVPQDYAQAVIWYK  103 (490)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHH
T ss_pred             HHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence            34444444433   66777778888887    899999999999873 3567788888899998    899999999999


Q ss_pred             HhhHCCCCCcHHHHHHHHHHHhc----CCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHh----cCChHHHHHHHHhCC
Q 040394          337 DKKWADFFPNHVTIASVLSASAQ----LGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAK----CHVIADARYIFETTS  408 (691)
Q Consensus       337 ~m~~~g~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~  408 (691)
                      +..+.|   +...+..+-..+..    .+++++|...++...+.+  ++..+..+...|..    .++.++|...|++..
T Consensus       104 ~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~--~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~  178 (490)
T 2xm6_A          104 KAALKG---LPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG--RDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAA  178 (490)
T ss_dssp             HHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT--CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHH
T ss_pred             HHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC--CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHH
Confidence            998875   55566667777776    789999999999998876  56667778888887    889999999999876


Q ss_pred             CCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhc----cCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHh----cC
Q 040394          409 EKDVIAWNSIISGLDDNVSPDAVTLVSVISACAS----LGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAK----CG  480 (691)
Q Consensus       409 ~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g  480 (691)
                      +.                 .+...+..+...+..    .++.++|...+++..+.+    ++..+..+...|..    .+
T Consensus       179 ~~-----------------~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~----~~~a~~~lg~~y~~g~g~~~  237 (490)
T 2xm6_A          179 EQ-----------------GNVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSG----DELGQLHLADMYYFGIGVTQ  237 (490)
T ss_dssp             HT-----------------TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT----CHHHHHHHHHHHHHTSSSCC
T ss_pred             HC-----------------CCHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC----CHHHHHHHHHHHHcCCCCCC
Confidence            54                 356677777777777    899999999999998866    35667778888876    88


Q ss_pred             CHHHHHHHHHhccc-CCHhHHHHHHHHHhc----CCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhccc-----CCHHH
Q 040394          481 DAQSARMVFDAMRE-KNTVTWSAMIGGYGM----QGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHT-----GMVGE  550 (691)
Q Consensus       481 ~~~~A~~~~~~~~~-~~~~~~~~li~~~~~----~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~-----g~~~~  550 (691)
                      ++++|..+|++..+ .+...+..+...|..    .++.++|+..|++..+.|   +...+..+-..+...     +++++
T Consensus       238 ~~~~A~~~~~~a~~~~~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~~~  314 (490)
T 2xm6_A          238 DYTQSRVLFSQSAEQGNSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNREQ  314 (490)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCHHH
Confidence            99999999998775 466777788888877    899999999999998765   445556666666665     89999


Q ss_pred             HHHHHHHchhhcCCCCChhHHHHHHHHHHhcC---ChHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHH
Q 040394          551 GWKCFYSMCRDFKFVPSMKHYVCMVDLLARAG---RLEEALEFMENMPIEPDVSLFGAFLHGCGL----YSRFDLGEVMI  623 (691)
Q Consensus       551 A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g---~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~A~~~~  623 (691)
                      |...+++..+.    -+...+..+...|.+.|   +.++|++++++.-...+...+..|...|..    .+++++|...+
T Consensus       315 A~~~~~~a~~~----~~~~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~  390 (490)
T 2xm6_A          315 AISWYTKSAEQ----GDATAQANLGAIYFRLGSEEEHKKAVEWFRKAAAKGEKAAQFNLGNALLQGKGVKKDEQQAAIWM  390 (490)
T ss_dssp             HHHHHHHHHHT----TCHHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHH
T ss_pred             HHHHHHHHHhc----CCHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Confidence            99999988433    24567777888888766   789999999998323577888899999988    89999999999


Q ss_pred             HHHHhcCCCCchhHHHHHHHHHh----CCCcHHHHHHHHHHHhCCC
Q 040394          624 KKMLELHPDKACYYVLVSNLYAS----DGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       624 ~~~~~~~p~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~g~  665 (691)
                      +++.+..  ++..+..|+.+|..    .+++++|.+.+++..+.|.
T Consensus       391 ~~A~~~~--~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~  434 (490)
T 2xm6_A          391 RKAAEQG--LSAAQVQLGEIYYYGLGVERDYVQAWAWFDTASTNDM  434 (490)
T ss_dssp             HHHHHTT--CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHHHC
T ss_pred             HHHHhCC--CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCC
Confidence            9998864  57889999999998    8999999999999998774

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.74  E-value=8.6e-16  Score=148.91  Aligned_cols=245  Identities=8%  Similarity=-0.009  Sum_probs=193.8

Q ss_pred             HHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC
Q 040394          385 NALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSS  464 (691)
Q Consensus       385 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~  464 (691)
                      ..+.++|...|+++.|...++..                  -+|+..++..+...+...++.+.|.+.++.+...+..|.
T Consensus        38 ~~l~r~yi~~g~~~~al~~~~~~------------------~~~~~~a~~~la~~~~~~~~~~~A~~~l~~ll~~~~~P~   99 (291)
T 3mkr_A           38 VFLYRAYLAQRKYGVVLDEIKPS------------------SAPELQAVRMFAEYLASHSRRDAIVAELDREMSRSVDVT   99 (291)
T ss_dssp             HHHHHHHHHTTCHHHHHHHSCTT------------------SCHHHHHHHHHHHHHHCSTTHHHHHHHHHHHHHSCCCCS
T ss_pred             HHHHHHHHHCCCHHHHHHHhccc------------------CChhHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcccCCC
Confidence            45667788888888888766542                  246777888888899999999999999999988763266


Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHH---HHHHH
Q 040394          465 NVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFT---TILSA  541 (691)
Q Consensus       465 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~---~ll~~  541 (691)
                      +...+..+...+...|++++|++.+++  ..+...+..++..+.+.|++++|.+.++++.+.  .|+....+   ..+..
T Consensus       100 ~~~~~~~la~~~~~~g~~~~Al~~l~~--~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~l~~a~~~l  175 (291)
T 3mkr_A          100 NTTFLLMAASIYFYDQNPDAALRTLHQ--GDSLECMAMTVQILLKLDRLDLARKELKKMQDQ--DEDATLTQLATAWVSL  175 (291)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHTT--CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhh--CcCcHHHHHHHHHHHH
Confidence            777888888999999999999999998  457889999999999999999999999999986  46543221   23344


Q ss_pred             hcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHH-
Q 040394          542 CSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDL-  618 (691)
Q Consensus       542 ~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~-  618 (691)
                      +...|++++|..+|+++...  .+.+...++.+..++.+.|++++|.+.+++. ...| +..++..++..+...|+.++ 
T Consensus       176 ~~~~~~~~eA~~~~~~~l~~--~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~p~~~~~l~~l~~~~~~~g~~~ea  253 (291)
T 3mkr_A          176 AAGGEKLQDAYYIFQEMADK--CSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKDSGHPETLINLVVLSQHLGKPPEV  253 (291)
T ss_dssp             HHCTTHHHHHHHHHHHHHHH--SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHH
T ss_pred             HhCchHHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCCHHH
Confidence            44568999999999999665  3445788999999999999999999999997 4344 56788889988989998875 


Q ss_pred             HHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHH
Q 040394          619 GEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVR  657 (691)
Q Consensus       619 A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~  657 (691)
                      +..+++++++.+|+++.+..    ...+.+.++++..-|
T Consensus       254 a~~~~~~~~~~~P~~~~~~d----~~~~~~~fd~~~~~~  288 (291)
T 3mkr_A          254 TNRYLSQLKDAHRSHPFIKE----YRAKENDFDRLVLQY  288 (291)
T ss_dssp             HHHHHHHHHHHCTTCHHHHH----HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCChHHHH----HHHHHHHHHHHHHHc
Confidence            67899999999999876654    345566666665444

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.73  E-value=9.8e-16  Score=160.98  Aligned_cols=378  Identities=12%  Similarity=-0.045  Sum_probs=214.3

Q ss_pred             ChhhHHHHHHHHHccCChhhHHHHHHHHHHH-----C--CCC-chHHHHHHHHHHHhcCCHHHHHHHHHhc-------CC
Q 040394          245 NQITLGSLVTACAKLRALHQGKWLHGYILKI-----G--IEI-NSHLVTALLDMYVKCGNIRDARSVFDEL-------CS  309 (691)
Q Consensus       245 ~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~-----g--~~~-~~~~~~~li~~~~~~g~~~~A~~~~~~~-------~~  309 (691)
                      ....|+.+-..+...|+.++|.+.|++..+.     +  ..| ...+|+.+..+|...|++++|...+++.       ..
T Consensus        50 ~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~  129 (472)
T 4g1t_A           50 KATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSS  129 (472)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhccc
Confidence            3556777777788888888888888776542     1  122 2456777777788888888877777654       11


Q ss_pred             ----CChhHHHHHHHHHHh--cCCchhHHHHHHHhhHCCCCCcH-HHHHHHHHH---HhcCCChhhHHHHHHHHHHhCCC
Q 040394          310 ----IDLVSWTAMIVGYTQ--SGYPDKALKLFTDKKWADFFPNH-VTIASVLSA---SAQLGNLNMGRMVHSLGIRLGLE  379 (691)
Q Consensus       310 ----~~~~~~~~li~~~~~--~g~~~~a~~~~~~m~~~g~~p~~-~t~~~ll~~---~~~~~~~~~a~~~~~~~~~~~~~  379 (691)
                          ....++..+..++..  .+++++|++.|++....  .|+. ..+..+..+   +...++.++|...++...+..+.
T Consensus       130 ~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~--~p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~p~  207 (472)
T 4g1t_A          130 PYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEK--KPKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLNPD  207 (472)
T ss_dssp             SSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHCSS
T ss_pred             ccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcCCc
Confidence                122345444444443  34567777777776654  3432 223222222   34456666777777777776666


Q ss_pred             chhHHHHHHHHhHhc----CChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHH
Q 040394          380 DYTVINALVDMYAKC----HVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAY  455 (691)
Q Consensus       380 ~~~~~~~l~~~~~~~----g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~  455 (691)
                      +..++..+...+...    |+.++|...+++....               .+.+..++..+...+...|+.+.|...+++
T Consensus       208 ~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~---------------~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~  272 (472)
T 4g1t_A          208 NQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEK---------------APGVTDVLRSAAKFYRRKDEPDKAIELLKK  272 (472)
T ss_dssp             CHHHHHHHHHHHHHCC------CHHHHHHHHHHHH---------------CSSCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHh---------------CccHHHHHHHHHHHHHHcCchHHHHHHHHH
Confidence            666665555555443    3445566666655432               233445556666666666666666666666


Q ss_pred             HHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHH
Q 040394          456 STKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIF  535 (691)
Q Consensus       456 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~  535 (691)
                      ..+..  |.+..++..+...|...+....+.      ...      .........+..+.|...+++..+.. +.+..++
T Consensus       273 al~~~--p~~~~~~~~lg~~y~~~~~~~~~~------~~~------~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~  337 (472)
T 4g1t_A          273 ALEYI--PNNAYLHCQIGCCYRAKVFQVMNL------REN------GMYGKRKLLELIGHAVAHLKKADEAN-DNLFRVC  337 (472)
T ss_dssp             HHHHS--TTCHHHHHHHHHHHHHHHHHHHHC------------------CHHHHHHHHHHHHHHHHHHHHHC-TTTCCCH
T ss_pred             HHHhC--CChHHHHHHHHHHHHHHHHHhhhH------HHH------HHHHHHHHHhhHHHHHHHHHHHhhcC-Cchhhhh
Confidence            66655  455555555554443221110000      000      00000011123566777777777642 2334556


Q ss_pred             HHHHHHhcccCCHHHHHHHHHHchhhcCCCCChh----HHHHHHHH-HHhcCChHHHHHHHHhC-CCCCCHHHHHHHHHH
Q 040394          536 TTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMK----HYVCMVDL-LARAGRLEEALEFMENM-PIEPDVSLFGAFLHG  609 (691)
Q Consensus       536 ~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~----~~~~li~~-~~~~g~~~~A~~~~~~~-~~~p~~~~~~~l~~~  609 (691)
                      ..+...+...|++++|.+.|++...   ..|+..    .+..+... +...|+.++|++.+++. .+.|+......    
T Consensus       338 ~~lg~~~~~~~~~~~A~~~~~kaL~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i~~~~~~~~~----  410 (472)
T 4g1t_A          338 SILASLHALADQYEEAEYYFQKEFS---KELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKINQKSREKEK----  410 (472)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH---SCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHSCCCCHHHHH----
T ss_pred             hhHHHHHHHhccHHHHHHHHHHHHh---cCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCcccHHHHH----
Confidence            6777788888899999988887643   233322    22333332 34678899999888886 56666543322    


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCc
Q 040394          610 CGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLS  666 (691)
Q Consensus       610 ~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~  666 (691)
                           ....+..++++.++.+|+++.++..++.+|...|++++|++.+++.++.|..
T Consensus       411 -----~~~~l~~~~~~~l~~~p~~~~~~~~LG~~~~~~g~~~~A~~~y~kALe~~~~  462 (472)
T 4g1t_A          411 -----MKDKLQKIAKMRLSKNGADSEALHVLAFLQELNEKMQQADEDSERGLESGSL  462 (472)
T ss_dssp             -----HHHHHHHHHHHHHHHCC-CTTHHHHHHHHHHHHHHCC---------------
T ss_pred             -----HHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC
Confidence                 2345667788888999999999999999999999999999999999987653

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.73  E-value=8e-17  Score=163.02  Aligned_cols=259  Identities=12%  Similarity=-0.030  Sum_probs=196.2

Q ss_pred             hhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcC
Q 040394          381 YTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQG  460 (691)
Q Consensus       381 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  460 (691)
                      ...+..+...+.+.|++++|...|+++.+.               .+.+..++..+...+...|+++.|...++++.+..
T Consensus        65 ~~~~~~~~~~~~~~g~~~~A~~~~~~al~~---------------~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~  129 (365)
T 4eqf_A           65 WPGAFEEGLKRLKEGDLPVTILFMEAAILQ---------------DPGDAEAWQFLGITQAENENEQAAIVALQRCLELQ  129 (365)
T ss_dssp             CTTHHHHHHHHHHHTCHHHHHHHHHHHHHH---------------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             hhHHHHHHHHHHHCCCHHHHHHHHHHHHHh---------------CcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence            334566666777777777777777766543               23355667777777777777777777777777776


Q ss_pred             CCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCC-------------HhHHHHHHHHHhcCCChHHHHHHHHHHHHCC
Q 040394          461 LLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKN-------------TVTWSAMIGGYGMQGDGGGSLALFSDMLNEE  527 (691)
Q Consensus       461 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-------------~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g  527 (691)
                        |.+...+..+...|...|++++|...|+++.+.+             ...+..+...+...|++++|+..++++.+..
T Consensus       130 --p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  207 (365)
T 4eqf_A          130 --PNNLKALMALAVSYTNTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQN  207 (365)
T ss_dssp             --TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCHHHHCC-------------------CCHHHHHHHHHHHHHHHHS
T ss_pred             --CCCHHHHHHHHHHHHccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhC
Confidence              6677788888888888888888888888776421             2233445788899999999999999999863


Q ss_pred             CC-CCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHH
Q 040394          528 VQ-PNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLF  603 (691)
Q Consensus       528 ~~-p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~  603 (691)
                      .. ++..++..+...+...|++++|.+.+++..+.   .|+ ..++..+..+|.+.|++++|++.++++ ...| +..++
T Consensus       208 p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~  284 (365)
T 4eqf_A          208 GDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTV---RPEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQPGFIRSR  284 (365)
T ss_dssp             CSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             cCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHH
Confidence            21 15788888889999999999999999988544   444 778999999999999999999999998 4344 47789


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCCC------------CchhHHHHHHHHHhCCCcHHHHHHHHH
Q 040394          604 GAFLHGCGLYSRFDLGEVMIKKMLELHPD------------KACYYVLVSNLYASDGRWIRVNQVREL  659 (691)
Q Consensus       604 ~~l~~~~~~~g~~~~A~~~~~~~~~~~p~------------~~~~~~~l~~~~~~~g~~~~A~~~~~~  659 (691)
                      ..+...|...|++++|...++++++..|+            +...+..++.++...|+.+.+.+..++
T Consensus       285 ~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  352 (365)
T 4eqf_A          285 YNLGISCINLGAYREAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANLG  352 (365)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHTT
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHh
Confidence            99999999999999999999999998776            367889999999999999988877644

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.72  E-value=3.2e-16  Score=158.57  Aligned_cols=232  Identities=10%  Similarity=-0.010  Sum_probs=197.7

Q ss_pred             CHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHH
Q 040394          429 DAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIG  505 (691)
Q Consensus       429 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~  505 (691)
                      +...+..+...+.+.|+++.|...++.+.+..  |.+...+..+...|.+.|++++|...|+++.+   .+..+|..+..
T Consensus        64 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~  141 (365)
T 4eqf_A           64 DWPGAFEEGLKRLKEGDLPVTILFMEAAILQD--PGDAEAWQFLGITQAENENEQAAIVALQRCLELQPNNLKALMALAV  141 (365)
T ss_dssp             TCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHH
Confidence            45568888899999999999999999999988  78899999999999999999999999998874   36789999999


Q ss_pred             HHhcCCChHHHHHHHHHHHHCCCCCCH-----------HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHH
Q 040394          506 GYGMQGDGGGSLALFSDMLNEEVQPNE-----------VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCM  574 (691)
Q Consensus       506 ~~~~~~~~~~A~~~~~~m~~~g~~p~~-----------~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~l  574 (691)
                      .|...|++++|+..++++.+.  .|+.           ..+..+...+...|++++|.+.++++.+...-.++...+..+
T Consensus       142 ~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l  219 (365)
T 4eqf_A          142 SYTNTSHQQDACEALKNWIKQ--NPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGL  219 (365)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--CHHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHH
T ss_pred             HHHccccHHHHHHHHHHHHHh--CccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHH
Confidence            999999999999999999884  3442           223344678889999999999999986653332357889999


Q ss_pred             HHHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHH
Q 040394          575 VDLLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIR  652 (691)
Q Consensus       575 i~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  652 (691)
                      ...|.+.|++++|++.++++ . .+.+..+|..+..++...|++++|+..++++++..|+++.++..++.+|...|++++
T Consensus       220 ~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~  299 (365)
T 4eqf_A          220 GVLFHLSGEFNRAIDAFNAALTVRPEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQPGFIRSRYNLGISCINLGAYRE  299 (365)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHCCCHHH
Confidence            99999999999999999998 3 344678999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCC
Q 040394          653 VNQVRELMKQRG  664 (691)
Q Consensus       653 A~~~~~~~~~~g  664 (691)
                      |.+.++++++..
T Consensus       300 A~~~~~~al~~~  311 (365)
T 4eqf_A          300 AVSNFLTALSLQ  311 (365)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC
Confidence            999999998743

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.70  E-value=2e-15  Score=146.33  Aligned_cols=247  Identities=12%  Similarity=0.028  Sum_probs=204.5

Q ss_pred             HHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCH--HHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCc
Q 040394          388 VDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDA--VTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSN  465 (691)
Q Consensus       388 ~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~--~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~  465 (691)
                      ++-....|+++.|+..++.....                .|+.  .....+.+++...|+++.|...++.   ..  +|+
T Consensus         6 ~~~~~~~g~y~~ai~~~~~~~~~----------------~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~---~~--~~~   64 (291)
T 3mkr_A            6 VKNAFYIGSYQQCINEAQRVKPS----------------SPERDVERDVFLYRAYLAQRKYGVVLDEIKP---SS--APE   64 (291)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSCCC----------------SHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT---TS--CHH
T ss_pred             HHHHHHHHHHHHHHHHHHhcccC----------------CchhhHHHHHHHHHHHHHCCCHHHHHHHhcc---cC--Chh
Confidence            34456789999999999887654                3443  3456678899999999999986654   22  678


Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhccc----C-CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 040394          466 VYVGTALLNFYAKCGDAQSARMVFDAMRE----K-NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILS  540 (691)
Q Consensus       466 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----~-~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~  540 (691)
                      ...+..+...+...++.++|.+.++++..    | +...+..+...+...|++++|++.+++      +.+...+..+..
T Consensus        65 ~~a~~~la~~~~~~~~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~  138 (291)
T 3mkr_A           65 LQAVRMFAEYLASHSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQ  138 (291)
T ss_dssp             HHHHHHHHHHHHCSTTHHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCcHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHH
Confidence            88889999999999999999999998752    4 566778888999999999999999987      567788888999


Q ss_pred             HhcccCCHHHHHHHHHHchhhcCCCCChhHH---HHHHHHHHhcCChHHHHHHHHhC--CCCCCHHHHHHHHHHHHhcCC
Q 040394          541 ACSHTGMVGEGWKCFYSMCRDFKFVPSMKHY---VCMVDLLARAGRLEEALEFMENM--PIEPDVSLFGAFLHGCGLYSR  615 (691)
Q Consensus       541 ~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~---~~li~~~~~~g~~~~A~~~~~~~--~~~p~~~~~~~l~~~~~~~g~  615 (691)
                      .+.+.|++++|.+.++++.+.   .|+....   ..++..+...|++++|.++|+++  ..+.+...++.+..++.+.|+
T Consensus       139 ~~~~~g~~~~A~~~l~~~~~~---~p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p~~~~~~~~la~~~~~~g~  215 (291)
T 3mkr_A          139 ILLKLDRLDLARKELKKMQDQ---DEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGR  215 (291)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHCCCHHHHHHHHHHHHhh---CcCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCC
Confidence            999999999999999998544   4663221   23445555669999999999998  345678899999999999999


Q ss_pred             HHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHH-HHHHHHHHHhCC
Q 040394          616 FDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIR-VNQVRELMKQRG  664 (691)
Q Consensus       616 ~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~-A~~~~~~~~~~g  664 (691)
                      +++|+..++++++.+|+++.++..++.++...|++++ +.++++++++..
T Consensus       216 ~~eA~~~l~~al~~~p~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~~  265 (291)
T 3mkr_A          216 WEAAEGVLQEALDKDSGHPETLINLVVLSQHLGKPPEVTNRYLSQLKDAH  265 (291)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhC
Confidence            9999999999999999999999999999999999986 578888888754

>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=99.70  E-value=5.3e-16  Score=154.20  Aligned_cols=261  Identities=12%  Similarity=-0.012  Sum_probs=217.9

Q ss_pred             chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHc
Q 040394          380 DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQ  459 (691)
Q Consensus       380 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  459 (691)
                      +...+..+...+...|++++|..+|+++.+.               .+.+..++..+...+...|+++.|...++.+.+.
T Consensus        20 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~---------------~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~   84 (327)
T 3cv0_A           20 YHENPMEEGLSMLKLANLAEAALAFEAVCQA---------------APEREEAWRSLGLTQAENEKDGLAIIALNHARML   84 (327)
T ss_dssp             GSSCHHHHHHHHHHTTCHHHHHHHHHHHHHH---------------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhccHHHHHHHHHHHHHh---------------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            3445567778888999999999999987653               2346678888899999999999999999999998


Q ss_pred             CCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC---CHhHHHHH--------------HH-HHhcCCChHHHHHHHH
Q 040394          460 GLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK---NTVTWSAM--------------IG-GYGMQGDGGGSLALFS  521 (691)
Q Consensus       460 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~l--------------i~-~~~~~~~~~~A~~~~~  521 (691)
                      .  |.+...+..+...|...|++++|...++++.+.   +...+..+              .. .+...|++++|...++
T Consensus        85 ~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~  162 (327)
T 3cv0_A           85 D--PKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLH  162 (327)
T ss_dssp             C--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTTTC--------------------CCTTSHHHHHHHHHHHH
T ss_pred             C--cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHH
Confidence            7  778899999999999999999999999988752   22233333              22 3778899999999999


Q ss_pred             HHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CC-CC
Q 040394          522 DMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PI-EP  598 (691)
Q Consensus       522 ~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~-~p  598 (691)
                      ++.+.. +.+...+..+...+...|++++|.+.++++.+.   .|+ ...+..+...+...|++++|.+.++++ .. +.
T Consensus       163 ~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~  238 (327)
T 3cv0_A          163 AALEMN-PNDAQLHASLGVLYNLSNNYDSAAANLRRAVEL---RPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPG  238 (327)
T ss_dssp             HHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHhhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHh---CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC
Confidence            999863 446788888889999999999999999988544   444 778899999999999999999999997 33 34


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC------------CchhHHHHHHHHHhCCCcHHHHHHHHHHH
Q 040394          599 DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPD------------KACYYVLVSNLYASDGRWIRVNQVRELMK  661 (691)
Q Consensus       599 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~------------~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  661 (691)
                      +..++..+...+...|++++|...++++.+..|+            ++..+..++.++...|++++|.+++++.+
T Consensus       239 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l  313 (327)
T 3cv0_A          239 YVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNV  313 (327)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCCS
T ss_pred             CHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            5778999999999999999999999999999999            78899999999999999999999886543

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.70  E-value=1.4e-17  Score=177.21  Aligned_cols=148  Identities=6%  Similarity=0.066  Sum_probs=121.4

Q ss_pred             ChhHHHHHHHHhHhcCChHHHHHHHhcc-------CCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHH
Q 040394          179 DSFVLTGLVDMYAKCRDIGSSRQVFDET-------LDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGS  251 (691)
Q Consensus       179 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~-------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~  251 (691)
                      -..+|++||++||+.|++++|.++|++|       ..||+++||+||.+||+.|++++|.++|++|.+.|+.||..||++
T Consensus       126 ~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYnt  205 (1134)
T 3spa_A          126 QQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAA  205 (1134)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHH
Confidence            4458999999999999999999999665       468999999999999999999999999999999999999999999


Q ss_pred             HHHHHHccCCh-hhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCC-----CChhHHHHHHHHHHhc
Q 040394          252 LVTACAKLRAL-HQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCS-----IDLVSWTAMIVGYTQS  325 (691)
Q Consensus       252 li~~~~~~~~~-~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~-----~~~~~~~~li~~~~~~  325 (691)
                      +|.++|+.|+. ++|.++|++|.+.|+.||..+|+.++....+.+-++...++...+..     +.+.+.+.|...|.+.
T Consensus       206 LI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~vL~~Vrkv~P~f~p~~~~~~~~~t~~LL~dl~s~d  285 (1134)
T 3spa_A          206 ALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKD  285 (1134)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHHHHHHGGGCCCCCCCCCCCCCCCCCTTTHHHHCCC
T ss_pred             HHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHHHHHHHHhCcccCCCCCCcccccchHHHHHHHccC
Confidence            99999999985 78999999999999999999999999887776555554444433311     1123444455555554


Q ss_pred             C
Q 040394          326 G  326 (691)
Q Consensus       326 g  326 (691)
                      +
T Consensus       286 ~  286 (1134)
T 3spa_A          286 G  286 (1134)
T ss_dssp             S
T ss_pred             C
Confidence            4

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.69  E-value=9.3e-15  Score=153.52  Aligned_cols=387  Identities=9%  Similarity=-0.026  Sum_probs=240.6

Q ss_pred             ChhhHHHHHHHHHhCCChhHHHHHHHHHHhC-----C--CCC-ChhhHHHHHHHHHccCChhhHHHHHHHHHHHC---C-
Q 040394          210 NVVSWTSMIAGYVQNDCAQEGLVLFNRMREG-----F--VEG-NQITLGSLVTACAKLRALHQGKWLHGYILKIG---I-  277 (691)
Q Consensus       210 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-----~--~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g---~-  277 (691)
                      ....||.|...+...|++++|++.|++..+-     +  ..| ...+|+.+..++...|++++|...++...+..   . 
T Consensus        50 ~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~  129 (472)
T 4g1t_A           50 KATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSS  129 (472)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhccc
Confidence            4567999999999999999999999987541     1  122 35689999999999999999999999886631   1 


Q ss_pred             --CC-chHHHHHHHHHHHhc--CCHHHHHHHHHhc---CCCChhHHHHHHHH---HHhcCCchhHHHHHHHhhHCCCCCc
Q 040394          278 --EI-NSHLVTALLDMYVKC--GNIRDARSVFDEL---CSIDLVSWTAMIVG---YTQSGYPDKALKLFTDKKWADFFPN  346 (691)
Q Consensus       278 --~~-~~~~~~~li~~~~~~--g~~~~A~~~~~~~---~~~~~~~~~~li~~---~~~~g~~~~a~~~~~~m~~~g~~p~  346 (691)
                        .+ ...++..+..++.+.  +++++|.+.|++.   .+.+...+..+...   +...++.++|++.+++..+.. +.+
T Consensus       130 ~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~-p~~  208 (472)
T 4g1t_A          130 PYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKKPKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLN-PDN  208 (472)
T ss_dssp             SSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHC-SSC
T ss_pred             ccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcC-Ccc
Confidence              11 245666665556554  4699999999987   23345555555544   445688899999999887753 223


Q ss_pred             HHHHHHHHHHHh----cCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhh
Q 040394          347 HVTIASVLSASA----QLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGL  422 (691)
Q Consensus       347 ~~t~~~ll~~~~----~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~  422 (691)
                      ...+..+...+.    ..++.++|...++......+....++..+...|...|++++|...+++..+.            
T Consensus       209 ~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~------------  276 (472)
T 4g1t_A          209 QYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKAPGVTDVLRSAAKFYRRKDEPDKAIELLKKALEY------------  276 (472)
T ss_dssp             HHHHHHHHHHHHHCC------CHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH------------
T ss_pred             hHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHh------------
Confidence            444544443433    4577899999999999999999999999999999999999999999987653            


Q ss_pred             hCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhH
Q 040394          423 DDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVT  499 (691)
Q Consensus       423 ~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~  499 (691)
                         .+-+..++..+..++...+....         ...  ..      .........+..+.|...++...+   .+..+
T Consensus       277 ---~p~~~~~~~~lg~~y~~~~~~~~---------~~~--~~------~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~  336 (472)
T 4g1t_A          277 ---IPNNAYLHCQIGCCYRAKVFQVM---------NLR--EN------GMYGKRKLLELIGHAVAHLKKADEANDNLFRV  336 (472)
T ss_dssp             ---STTCHHHHHHHHHHHHHHHHHHH---------HC--------------CHHHHHHHHHHHHHHHHHHHHHCTTTCCC
T ss_pred             ---CCChHHHHHHHHHHHHHHHHHhh---------hHH--HH------HHHHHHHHHhhHHHHHHHHHHHhhcCCchhhh
Confidence               22344556666555432211110         000  00      001111122345677777776653   35567


Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHH--HHHHHHH-HhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHH
Q 040394          500 WSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEV--IFTTILS-ACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVD  576 (691)
Q Consensus       500 ~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~--~~~~ll~-~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~  576 (691)
                      +..+...|...|++++|+..|++..+....|...  .+..+.. .....|++++|+..|++..   .+.|+.......+ 
T Consensus       337 ~~~lg~~~~~~~~~~~A~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal---~i~~~~~~~~~~~-  412 (472)
T 4g1t_A          337 CSILASLHALADQYEEAEYYFQKEFSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGV---KINQKSREKEKMK-  412 (472)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHH---HSCCCCHHHHHHH-
T ss_pred             hhhHHHHHHHhccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH---hcCcccHHHHHHH-
Confidence            8888899999999999999999988854333221  2222222 3356789999999998664   3566643322222 


Q ss_pred             HHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHH
Q 040394          577 LLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVS  641 (691)
Q Consensus       577 ~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~  641 (691)
                              ..+.+++++. . .+.+..+|..+...+...|++++|++.|+++++..|.+|.....+|
T Consensus       413 --------~~l~~~~~~~l~~~p~~~~~~~~LG~~~~~~g~~~~A~~~y~kALe~~~~~p~a~~~~G  471 (472)
T 4g1t_A          413 --------DKLQKIAKMRLSKNGADSEALHVLAFLQELNEKMQQADEDSERGLESGSLIPSASSWNG  471 (472)
T ss_dssp             --------HHHHHHHHHHHHHCC-CTTHHHHHHHHHHHHHHCC------------------------
T ss_pred             --------HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCcHhhcCC
Confidence                    2233344433 2 3445678999999999999999999999999999998887766554

>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=99.67  E-value=1.7e-14  Score=143.26  Aligned_cols=275  Identities=8%  Similarity=-0.036  Sum_probs=174.8

Q ss_pred             CcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHH
Q 040394          110 DFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDM  189 (691)
Q Consensus       110 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  189 (691)
                      +...|..+...+...|++++|+.+|+++.+.. +.+...+..+...+...|++++|...++.+.+..+.+..++..+...
T Consensus        20 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~   98 (327)
T 3cv0_A           20 YHENPMEEGLSMLKLANLAEAALAFEAVCQAA-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVS   98 (327)
T ss_dssp             GSSCHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcCCHHHHHHHHHH
Confidence            34456667777777777777777777777653 33555666666777777777777777777777665566666666666


Q ss_pred             hHhcCChHHHHHHHhccCC--C-ChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHH--HHHccCChhh
Q 040394          190 YAKCRDIGSSRQVFDETLD--K-NVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVT--ACAKLRALHQ  264 (691)
Q Consensus       190 ~~~~g~~~~A~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~--~~~~~~~~~~  264 (691)
                      +...|++++|.+.+++..+  | +...+..++..                      .|+......+..  .+...|++++
T Consensus        99 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~----------------------~~~~~~~~~~~~~~~~~~~~~~~~  156 (327)
T 3cv0_A           99 HTNEHNANAALASLRAWLLSQPQYEQLGSVNLQA----------------------DVDIDDLNVQSEDFFFAAPNEYRE  156 (327)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTSTTTTTC------------------------------------------CCTTSHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCccHHHHHHHhHH----------------------HHHHHHHHHHHHhHHHHHcccHHH
Confidence            6666666666666665422  1 22222222000                      000011111102  2455566666


Q ss_pred             HHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhc---CCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHC
Q 040394          265 GKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDEL---CSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWA  341 (691)
Q Consensus       265 a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  341 (691)
                      |...++.+.+... .+..++..+...+.+.|++++|.+.++++   .+.+..+|..+...+...|++++|.+.+++....
T Consensus       157 A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~  235 (327)
T 3cv0_A          157 CRTLLHAALEMNP-NDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDI  235 (327)
T ss_dssp             HHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhCC-CCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            6666666666542 25566666777777777777777777665   2334566777777777777777777777776664


Q ss_pred             CCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCC------------chhHHHHHHHHhHhcCChHHHHHHHHhCCC
Q 040394          342 DFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLE------------DYTVINALVDMYAKCHVIADARYIFETTSE  409 (691)
Q Consensus       342 g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~------------~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  409 (691)
                      . +.+..++..+...+...|++++|...++.+.+..+.            ...++..+..++.+.|+.++|..++++..+
T Consensus       236 ~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~  314 (327)
T 3cv0_A          236 N-PGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNVE  314 (327)
T ss_dssp             C-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCCSH
T ss_pred             C-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            2 234566667777777778888887777777776666            677888899999999999999999887653

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.64  E-value=1.8e-16  Score=168.77  Aligned_cols=161  Identities=11%  Similarity=0.073  Sum_probs=122.5

Q ss_pred             CCchhHHHHHHHHHHhcCCHHHHHHHHHhcc-------cCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHH
Q 040394          463 SSNVYVGTALLNFYAKCGDAQSARMVFDAMR-------EKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIF  535 (691)
Q Consensus       463 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-------~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~  535 (691)
                      .....+|+++|++|++.|++++|.++|++|.       .||++|||+||.+||+.|++++|.++|++|.+.|+.||..||
T Consensus       124 ~~~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTY  203 (1134)
T 3spa_A          124 SGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSY  203 (1134)
T ss_dssp             CHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHH
T ss_pred             HhHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHH
Confidence            3445678888888888888888888887764       479999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcccCC-HHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC--CCCCC------HHHHHHH
Q 040394          536 TTILSACSHTGM-VGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM--PIEPD------VSLFGAF  606 (691)
Q Consensus       536 ~~ll~~~~~~g~-~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~--~~~p~------~~~~~~l  606 (691)
                      +++|.++++.|+ .++|.++|++| ...|+.||..+|++++....+.    .+++.++++  ++.|+      ..+...|
T Consensus       204 ntLI~glcK~G~~~e~A~~Ll~EM-~~kG~~PD~vtY~~ll~~~eR~----~vL~~Vrkv~P~f~p~~~~~~~~~t~~LL  278 (1134)
T 3spa_A          204 AAALQCMGRQDQDAGTIERCLEQM-SQEGLKLQALFTAVLLSEEDRA----TVLKAVHKVKPTFSLPPQLPPPVNTSKLL  278 (1134)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHHHH-HHHTCCSHHHHHHSCCCHHHHH----HHHHHHGGGCCCCCCCCCCCCCCCCCTTT
T ss_pred             HHHHHHHHhCCCcHHHHHHHHHHH-HHcCCCCChhhcccccChhhHH----HHHHHHHHhCcccCCCCCCcccccchHHH
Confidence            999999999887 47888999999 5559999999999888766665    444444444  22322      3344555


Q ss_pred             HHHHHhcC---------CHHHHHHHHHHHHh
Q 040394          607 LHGCGLYS---------RFDLGEVMIKKMLE  628 (691)
Q Consensus       607 ~~~~~~~g---------~~~~A~~~~~~~~~  628 (691)
                      ...|.+.+         ..++-..++++-++
T Consensus       279 ~dl~s~d~~~s~pk~~~~~~~L~~~~~~Ql~  309 (1134)
T 3spa_A          279 RDVYAKDGRVSYPKLHLPLKTLQCLFEKQLH  309 (1134)
T ss_dssp             HHHHCCCSCCCCCCCSSCHHHHHHHHHHHHH
T ss_pred             HHHHccCCCCcCccccCCHHHHHHHHHHHHH
Confidence            56665544         24566666666553

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.61  E-value=2.9e-14  Score=131.85  Aligned_cols=195  Identities=12%  Similarity=0.007  Sum_probs=143.2

Q ss_pred             CCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 040394          463 SSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTIL  539 (691)
Q Consensus       463 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll  539 (691)
                      |+++..+..+...+.+.|++++|...|++..+   .+...|..+...+.+.|++++|+..+++..+.. +.+...+..+.
T Consensus         2 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg   80 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYALGRYDAALTLFERALKENPQDPEALYWLARTQLKLGLVNPALENGKTLVART-PRYLGGYMVLS   80 (217)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHH
Confidence            55666667777777777777777777776654   255677777777777777778887777777742 22445666666


Q ss_pred             HHhccc-----------CCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCHHHHHHH
Q 040394          540 SACSHT-----------GMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEPDVSLFGAF  606 (691)
Q Consensus       540 ~~~~~~-----------g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~~~~~~l  606 (691)
                      .++...           |++++|...+++..+   +.|+ ...+..+..+|...|++++|++.+++. ....+...+..+
T Consensus        81 ~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~---~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~l  157 (217)
T 2pl2_A           81 EAYVALYRQAEDRERGKGYLEQALSVLKDAER---VNPRYAPLHLQRGLVYALLGERDKAEASLKQALALEDTPEIRSAL  157 (217)
T ss_dssp             HHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHH
T ss_pred             HHHHHhhhhhhhhcccccCHHHHHHHHHHHHH---hCcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccchHHHHHH
Confidence            677777           999999999997753   4665 678888999999999999999999997 212778899999


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHH
Q 040394          607 LHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMK  661 (691)
Q Consensus       607 ~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  661 (691)
                      ..++...|++++|+..++++++..|+++..+..++.++...|++++|++.+++..
T Consensus       158 a~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~~  212 (217)
T 2pl2_A          158 AELYLSMGRLDEALAQYAKALEQAPKDLDLRVRYASALLLKGKAEEAARAAALEH  212 (217)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTC---------------
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999999999999999999997754

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.60  E-value=9.8e-14  Score=132.44  Aligned_cols=220  Identities=9%  Similarity=-0.006  Sum_probs=192.3

Q ss_pred             HHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-C-------HhH
Q 040394          430 AVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--K-N-------TVT  499 (691)
Q Consensus       430 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~-------~~~  499 (691)
                      ...+..+...+...|+++.|...++...+..   .+...+..+...|...|++++|...+++..+  | +       ...
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~---~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~   81 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAWELH---KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKS   81 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS---CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhh---ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHH
Confidence            3567788889999999999999999999876   5678889999999999999999999998774  2 2       578


Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHH
Q 040394          500 WSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLL  578 (691)
Q Consensus       500 ~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~  578 (691)
                      |..+...+...|++++|+..+++..+.  .|+..       .+...|++++|...++.+..   ..|+ ...+..+...+
T Consensus        82 ~~~l~~~~~~~~~~~~A~~~~~~a~~~--~~~~~-------~~~~~~~~~~a~~~~~~~~~---~~~~~~~~~~~~~~~~  149 (258)
T 3uq3_A           82 FARIGNAYHKLGDLKKTIEYYQKSLTE--HRTAD-------ILTKLRNAEKELKKAEAEAY---VNPEKAEEARLEGKEY  149 (258)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCHH-------HHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHhc--CchhH-------HHHHHhHHHHHHHHHHHHHH---cCcchHHHHHHHHHHH
Confidence            899999999999999999999999984  56643       34566889999999998743   4555 67888899999


Q ss_pred             HhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHH
Q 040394          579 ARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQV  656 (691)
Q Consensus       579 ~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~  656 (691)
                      ...|++++|++.+++. . .+.+..++..+...+...|++++|...++++++..|+++..+..++.++...|++++|.+.
T Consensus       150 ~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  229 (258)
T 3uq3_A          150 FTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQIAVKEYASALET  229 (258)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence            9999999999999998 3 3446788999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhCC
Q 040394          657 RELMKQRG  664 (691)
Q Consensus       657 ~~~~~~~g  664 (691)
                      +++..+..
T Consensus       230 ~~~a~~~~  237 (258)
T 3uq3_A          230 LDAARTKD  237 (258)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHhC
Confidence            99988754

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.55  E-value=9.9e-13  Score=136.15  Aligned_cols=372  Identities=9%  Similarity=-0.036  Sum_probs=227.8

Q ss_pred             HHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCH---HHHHHHHHhcCCCChhHHHHHHHHHHhcC----
Q 040394          254 TACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNI---RDARSVFDELCSIDLVSWTAMIVGYTQSG----  326 (691)
Q Consensus       254 ~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~---~~A~~~~~~~~~~~~~~~~~li~~~~~~g----  326 (691)
                      ..+.+.|++++|..+|+...+.|.   ...+..|...|...|+.   ++|.+.|++..+.+...+..|...+...+    
T Consensus        11 ~~~~~~g~~~~A~~~~~~aa~~g~---~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~~~~A~~~Lg~~~~~~~~~~~   87 (452)
T 3e4b_A           11 NEALKRGDTVTAQQNYQQLAELGY---SEAQVGLADIQVGTRDPAQIKQAEATYRAAADTSPRAQARLGRLLAAKPGATE   87 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTC---CTGGGTCC----------------------------CHHHHHHHHHTC--CCH
T ss_pred             HHHHhCCCHHHHHHHHHHHHHCCC---HHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCCCC
Confidence            334455556666666666555542   22233344444555555   67777777665445555666655444444    


Q ss_pred             -CchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhH---HHHHHHHHHhCCCchhHHHHHHHHhHhcCC----hH
Q 040394          327 -YPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMG---RMVHSLGIRLGLEDYTVINALVDMYAKCHV----IA  398 (691)
Q Consensus       327 -~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a---~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~----~~  398 (691)
                       ++++|+..|++..+.|...   .+..+...|...+..+.+   ...+......|  ++.....+...|...+.    .+
T Consensus        88 ~~~~~A~~~~~~Aa~~g~~~---A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g--~~~a~~~Lg~~y~~~~~~~~~~~  162 (452)
T 3e4b_A           88 AEHHEAESLLKKAFANGEGN---TLIPLAMLYLQYPHSFPNVNAQQQISQWQAAG--YPEAGLAQVLLYRTQGTYDQHLD  162 (452)
T ss_dssp             HHHHHHHHHHHHHHHTTCSS---CHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHT--CTTHHHHHHHHHHHHTCGGGGHH
T ss_pred             cCHHHHHHHHHHHHHCCCHH---HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCC--CHHHHHHHHHHHHcCCCcccCHH
Confidence             5667777777777665433   333444444444443333   33333333333  34555667777777764    44


Q ss_pred             HHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccC---cHHHHHHHHHHHHHcCCCCCchhHHHHHHHH
Q 040394          399 DARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLG---AVQVGSSLHAYSTKQGLLSSNVYVGTALLNF  475 (691)
Q Consensus       399 ~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~  475 (691)
                      .+..+++.....                .|+  .+..+...+...|   +.++|...|+...+.|  ++....+..+...
T Consensus       163 ~a~~~~~~a~~~----------------~~~--a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g--~~~a~~~~~Lg~~  222 (452)
T 3e4b_A          163 DVERICKAALNT----------------TDI--CYVELATVYQKKQQPEQQAELLKQMEAGVSRG--TVTAQRVDSVARV  222 (452)
T ss_dssp             HHHHHHHHHTTT----------------CTT--HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT--CSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcC----------------CHH--HHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC--CHHHHHHHHHHHH
Confidence            455555555432                233  7777778888888   9999999999999998  6777766677777


Q ss_pred             HHhc----CCHHHHHHHHHhcccCCHhHHHHHHHH-H--hcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccC--
Q 040394          476 YAKC----GDAQSARMVFDAMREKNTVTWSAMIGG-Y--GMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTG--  546 (691)
Q Consensus       476 ~~~~----g~~~~A~~~~~~~~~~~~~~~~~li~~-~--~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g--  546 (691)
                      |...    +++++|..+|+.....+...+..|... +  ...+++++|+..|++..+.|   +...+..+-..|. .|  
T Consensus       223 y~~g~~~~~d~~~A~~~~~~aa~g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g  298 (452)
T 3e4b_A          223 LGDATLGTPDEKTAQALLEKIAPGYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKW  298 (452)
T ss_dssp             HTCGGGSSCCHHHHHHHHHHHGGGSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSS
T ss_pred             HhCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCC
Confidence            7665    799999999999883367778888777 4  56899999999999999877   5555555555555 44  


Q ss_pred             ---CHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHh----cCChHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCC
Q 040394          547 ---MVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLAR----AGRLEEALEFMENMPIEPDVSLFGAFLHGCGL----YSR  615 (691)
Q Consensus       547 ---~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~----~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~----~g~  615 (691)
                         ++++|.+.|++..     .-+...+..|...|..    ..++++|.++|++.-..-+......|...|..    ..|
T Consensus       299 ~~~d~~~A~~~~~~Aa-----~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~~G~g~~~d  373 (452)
T 3e4b_A          299 VPADAKAAEAHFEKAV-----GREVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNGQNSADFAIAQLFSQGKGTKPD  373 (452)
T ss_dssp             SCCCHHHHHHHHHTTT-----TTCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTTCTTHHHHHHHHHHSCTTBCCC
T ss_pred             CCCCHHHHHHHHHHHh-----CCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhChHHHHHHHHHHHHhCCCCCCC
Confidence               9999999999662     3446777778877776    34999999999998323345556667777764    469


Q ss_pred             HHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          616 FDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       616 ~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      .++|..+++++.+..+................++..+|.+..++..+
T Consensus       374 ~~~A~~~~~~A~~~g~~~a~~~l~~l~~~~~~~~~~~a~~~~~~~~~  420 (452)
T 3e4b_A          374 PLNAYVFSQLAKAQDTPEANDLATQLEAPLTPAQRAEGQRLVQQELA  420 (452)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHH
Confidence            99999999999887665433332222222334577778888777655

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.54  E-value=2.4e-13  Score=131.16  Aligned_cols=247  Identities=9%  Similarity=-0.092  Sum_probs=196.2

Q ss_pred             HhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHH
Q 040394          390 MYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVG  469 (691)
Q Consensus       390 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  469 (691)
                      .+...|++++|...|+++.+....           .-+.+..++..+...+...|++++|...++.+.+..  |.+...+
T Consensus        14 ~~~~~~~~~~A~~~~~~~~~~~~~-----------~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~   80 (275)
T 1xnf_A           14 PLQPTLQQEVILARMEQILASRAL-----------TDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR--PDMPEVF   80 (275)
T ss_dssp             CCCCCHHHHHHHHHHHHHHTSSCC-----------CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCCHHHH
T ss_pred             ccCccchHHHHHHHHHHHHhcccc-----------cCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC--CCcHHHH
Confidence            344567888999999887654100           011245678888999999999999999999999987  7889999


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccC
Q 040394          470 TALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTG  546 (691)
Q Consensus       470 ~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g  546 (691)
                      ..+...|...|++++|...|++..+   .+...|..+...|...|++++|...++++.+.  .|+.......+..+...|
T Consensus        81 ~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~  158 (275)
T 1xnf_A           81 NYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--DPNDPFRSLWLYLAEQKL  158 (275)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHhcCccccHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHhc
Confidence            9999999999999999999998875   36789999999999999999999999999984  566655555566667789


Q ss_pred             CHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCC-----HHHHHHHHHHHHhcCCHHHHH
Q 040394          547 MVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PIEPD-----VSLFGAFLHGCGLYSRFDLGE  620 (691)
Q Consensus       547 ~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~-----~~~~~~l~~~~~~~g~~~~A~  620 (691)
                      ++++|...++.....  .+++...+ .++..+...++.++|++.+++. ...|+     ...+..+...+...|++++|.
T Consensus       159 ~~~~A~~~~~~~~~~--~~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~  235 (275)
T 1xnf_A          159 DEKQAKEVLKQHFEK--SDKEQWGW-NIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSAT  235 (275)
T ss_dssp             CHHHHHHHHHHHHHH--SCCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             CHHHHHHHHHHHHhc--CCcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHH
Confidence            999999999877554  23334444 4777788888999999999887 33332     468888999999999999999


Q ss_pred             HHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHH
Q 040394          621 VMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVR  657 (691)
Q Consensus       621 ~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~  657 (691)
                      ..++++++..|++...+   +.++...|++++|++.+
T Consensus       236 ~~~~~al~~~p~~~~~~---~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          236 ALFKLAVANNVHNFVEH---RYALLELSLLGQDQDDL  269 (275)
T ss_dssp             HHHHHHHTTCCTTCHHH---HHHHHHHHHHHHC----
T ss_pred             HHHHHHHhCCchhHHHH---HHHHHHHHHHHhhHHHH
Confidence            99999999999875544   56678889999988776

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.53  E-value=2.4e-13  Score=129.65  Aligned_cols=234  Identities=12%  Similarity=-0.027  Sum_probs=193.8

Q ss_pred             hhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcC
Q 040394          381 YTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQG  460 (691)
Q Consensus       381 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  460 (691)
                      ...+..+...+...|++++|...|++..+.              .  .+..++..+..++...|+++.|...++...+..
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~--------------~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~   68 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAWEL--------------H--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQG   68 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------------S--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHh--------------h--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhC
Confidence            345677888888999999999999887654              3  677889999999999999999999999988765


Q ss_pred             CCCCc-------hhHHHHHHHHHHhcCCHHHHHHHHHhccc--CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCC
Q 040394          461 LLSSN-------VYVGTALLNFYAKCGDAQSARMVFDAMRE--KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPN  531 (691)
Q Consensus       461 ~~~~~-------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~  531 (691)
                        +.+       ...+..+...|...|++++|...|++..+  ++.       ..+...|++++|...++++...  .|+
T Consensus        69 --~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~-------~~~~~~~~~~~a~~~~~~~~~~--~~~  137 (258)
T 3uq3_A           69 --REMRADYKVISKSFARIGNAYHKLGDLKKTIEYYQKSLTEHRTA-------DILTKLRNAEKELKKAEAEAYV--NPE  137 (258)
T ss_dssp             --HHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCH-------HHHHHHHHHHHHHHHHHHHHHC--CHH
T ss_pred             --cccccchHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCchh-------HHHHHHhHHHHHHHHHHHHHHc--Ccc
Confidence              222       68889999999999999999999998875  442       3466678899999999999985  444


Q ss_pred             -HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CC-CCCHHHHHHHHH
Q 040394          532 -EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PI-EPDVSLFGAFLH  608 (691)
Q Consensus       532 -~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~-~p~~~~~~~l~~  608 (691)
                       ...+..+...+...|++++|...+++.....  +.+...+..+...+.+.|++++|++.+++. .. +.+...|..+..
T Consensus       138 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~  215 (258)
T 3uq3_A          138 KAEEARLEGKEYFTKSDWPNAVKAYTEMIKRA--PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKAT  215 (258)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC--cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCHHHHHHHHHHHH
Confidence             4567777889999999999999999886542  234778999999999999999999999998 33 345778999999


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcC------CCCchhHHHHHHH
Q 040394          609 GCGLYSRFDLGEVMIKKMLELH------PDKACYYVLVSNL  643 (691)
Q Consensus       609 ~~~~~g~~~~A~~~~~~~~~~~------p~~~~~~~~l~~~  643 (691)
                      .+...|++++|...++++++..      |++...+..+..+
T Consensus       216 ~~~~~g~~~~A~~~~~~a~~~~~~~~~~p~~~~~~~~l~~~  256 (258)
T 3uq3_A          216 AQIAVKEYASALETLDAARTKDAEVNNGSSAREIDQLYYKA  256 (258)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHHHTTTTHHHHHHHHHHT
T ss_pred             HHHHHhhHHHHHHHHHHHHHhChhhcCCCchHHHHHHHHHh
Confidence            9999999999999999999988      8877777666543

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.53  E-value=4.4e-12  Score=131.27  Aligned_cols=245  Identities=11%  Similarity=0.044  Sum_probs=126.7

Q ss_pred             HHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCCh---HHHHHHHhccCCCChhhHHHHHHHHHhCC---
Q 040394          152 VLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDI---GSSRQVFDETLDKNVVSWTSMIAGYVQND---  225 (691)
Q Consensus       152 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~---~~A~~~~~~~~~~~~~~~~~li~~~~~~g---  225 (691)
                      +...+.+.|++++|.++|+...+.|  ++.++..|...|...|+.   ++|...|++..+.+...+..|...+...+   
T Consensus         9 la~~~~~~g~~~~A~~~~~~aa~~g--~~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~~~~A~~~Lg~~~~~~~~~~   86 (452)
T 3e4b_A            9 LANEALKRGDTVTAQQNYQQLAELG--YSEAQVGLADIQVGTRDPAQIKQAEATYRAAADTSPRAQARLGRLLAAKPGAT   86 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHT--CCTGGGTCC----------------------------CHHHHHHHHHTC--CC
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCC--CHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCCC
Confidence            3444556677777777777776665  344455566666666666   77777777766656666777766555554   


Q ss_pred             --ChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCCh---hhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCC----
Q 040394          226 --CAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRAL---HQGKWLHGYILKIGIEINSHLVTALLDMYVKCGN----  296 (691)
Q Consensus       226 --~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~---~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~----  296 (691)
                        ++++|++.|++..+.|...   .+..+...|...+..   ..+.+.+....+.|   +......|...|...+.    
T Consensus        87 ~~~~~~A~~~~~~Aa~~g~~~---A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g---~~~a~~~Lg~~y~~~~~~~~~  160 (452)
T 3e4b_A           87 EAEHHEAESLLKKAFANGEGN---TLIPLAMLYLQYPHSFPNVNAQQQISQWQAAG---YPEAGLAQVLLYRTQGTYDQH  160 (452)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSS---CHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHT---CTTHHHHHHHHHHHHTCGGGG
T ss_pred             CcCHHHHHHHHHHHHHCCCHH---HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcccC
Confidence              6678888888887765432   455555555544443   33444444444444   34455666666766663    


Q ss_pred             HHHHHHHHHhcCCCChhHHHHHHHHHHhcC---CchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcC----CChhhHHHH
Q 040394          297 IRDARSVFDELCSIDLVSWTAMIVGYTQSG---YPDKALKLFTDKKWADFFPNHVTIASVLSASAQL----GNLNMGRMV  369 (691)
Q Consensus       297 ~~~A~~~~~~~~~~~~~~~~~li~~~~~~g---~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~----~~~~~a~~~  369 (691)
                      .+.+..+++.....+..++..|...|...|   +.++|++.|+...+.|.. +...+..+...|...    ++.++|...
T Consensus       161 ~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~-~a~~~~~Lg~~y~~g~~~~~d~~~A~~~  239 (452)
T 3e4b_A          161 LDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGTV-TAQRVDSVARVLGDATLGTPDEKTAQAL  239 (452)
T ss_dssp             HHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCS-CHHHHHHHHHHHTCGGGSSCCHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCCH-HHHHHHHHHHHHhCCCCCCCCHHHHHHH
Confidence            444555566656666667777777787788   777888888877776533 333333333344332    456666666


Q ss_pred             HHHHHHhCCCchhHHHHHHHH-h--HhcCChHHHHHHHHhCC
Q 040394          370 HSLGIRLGLEDYTVINALVDM-Y--AKCHVIADARYIFETTS  408 (691)
Q Consensus       370 ~~~~~~~~~~~~~~~~~l~~~-~--~~~g~~~~a~~~~~~~~  408 (691)
                      ++...   +.++..+..+... |  ...++.++|...|++..
T Consensus       240 ~~~aa---~g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa  278 (452)
T 3e4b_A          240 LEKIA---PGYPASWVSLAQLLYDFPELGDVEQMMKYLDNGR  278 (452)
T ss_dssp             HHHHG---GGSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHH
T ss_pred             HHHHc---CCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Confidence            66555   2234444444443 2  33455555555555443

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.53  E-value=1.6e-12  Score=125.08  Aligned_cols=256  Identities=9%  Similarity=-0.067  Sum_probs=151.4

Q ss_pred             HHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCH
Q 040394          351 ASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDA  430 (691)
Q Consensus       351 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~  430 (691)
                      ......+...|++++|...++.+.+..+.+..++..+...|...|++++|...+++..+...            ......
T Consensus         7 ~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~------------~~~~~~   74 (272)
T 3u4t_A            7 FRYADFLFKNNNYAEAIEVFNKLEAKKYNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVN------------ATKAKS   74 (272)
T ss_dssp             HHHHHHHHTTTCHHHHHHHHHHHHHTTCCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSC------------TTTCCH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccC------------chhHHH
Confidence            34445566666777777777776666666666667777777777888888777777654200            011123


Q ss_pred             HHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-CHhHHHHHHHHH
Q 040394          431 VTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--K-NTVTWSAMIGGY  507 (691)
Q Consensus       431 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~li~~~  507 (691)
                      .++..+...+...|+++.|...++...+..  |.+...+..+...|...|++++|...|++..+  | +...|..+...+
T Consensus        75 ~~~~~lg~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~  152 (272)
T 3u4t_A           75 ADFEYYGKILMKKGQDSLAIQQYQAAVDRD--TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPTTTDPKVFYELGQAY  152 (272)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHhcC--cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Confidence            346667777777777777777777777766  56666777777777777777777777776654  2 344555555222


Q ss_pred             hcCCChHHHHHHHHHHHHCCCCCC-HHHHHHHHHHhcccCC---HHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCC
Q 040394          508 GMQGDGGGSLALFSDMLNEEVQPN-EVIFTTILSACSHTGM---VGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGR  583 (691)
Q Consensus       508 ~~~~~~~~A~~~~~~m~~~g~~p~-~~~~~~ll~~~~~~g~---~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~  583 (691)
                      ...+++++|.+.++++.+.  .|+ ...+..+..++...|+   +++|...+++..+...-.|+.. -            
T Consensus       153 ~~~~~~~~A~~~~~~a~~~--~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~-~------------  217 (272)
T 3u4t_A          153 YYNKEYVKADSSFVKVLEL--KPNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKY-K------------  217 (272)
T ss_dssp             HHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGG-H------------
T ss_pred             HHHHHHHHHHHHHHHHHHh--CccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccc-h------------
Confidence            2333666666666665553  232 3333333333333333   3334443333321111111100 0            


Q ss_pred             hHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCC
Q 040394          584 LEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDG  648 (691)
Q Consensus       584 ~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g  648 (691)
                                   ..-..+|..+...+...|++++|...++++++++|+++.....+..+....+
T Consensus       218 -------------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~l~~~~~~~~  269 (272)
T 3u4t_A          218 -------------DELIEANEYIAYYYTINRDKVKADAAWKNILALDPTNKKAIDGLKMKLEHHH  269 (272)
T ss_dssp             -------------HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHC-------
T ss_pred             -------------HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCccHHHHHHHhhhhhcccc
Confidence                         0012467778888999999999999999999999999988888877655543

>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=99.52  E-value=1.4e-12  Score=123.86  Aligned_cols=194  Identities=9%  Similarity=-0.019  Sum_probs=102.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcc
Q 040394          468 VGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSH  544 (691)
Q Consensus       468 ~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~  544 (691)
                      .+..+...+...|++++|...|+++.+   .+...|..+...+...|++++|.+.++++.+.. +.+...+..+...+..
T Consensus        39 ~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~  117 (252)
T 2ho1_A           39 AYIQLGLGYLQRGNTEQAKVPLRKALEIDPSSADAHAALAVVFQTEMEPKLADEEYRKALASD-SRNARVLNNYGGFLYE  117 (252)
T ss_dssp             HHHHHHHHHHHTTCTGGGHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHhcCCChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHH
Confidence            334444444444555555444444432   133444445555555555555555555555432 2234444455555555


Q ss_pred             cCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHH
Q 040394          545 TGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEV  621 (691)
Q Consensus       545 ~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~  621 (691)
                      .|++++|.++++++.. .+..|+ ...+..+...+...|++++|.+.+++. . .+.+...+..+...+...|++++|..
T Consensus       118 ~g~~~~A~~~~~~~~~-~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  196 (252)
T 2ho1_A          118 QKRYEEAYQRLLEASQ-DTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNRNQPSVALEMADLLYKEREYVPARQ  196 (252)
T ss_dssp             TTCHHHHHHHHHHHTT-CTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HhHHHHHHHHHHHHHh-CccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCCHHHHHH
Confidence            5555555555555432 123332 344555555555666666666655554 2 12234555556666666666666666


Q ss_pred             HHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          622 MIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       622 ~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      .++++.+..|++...+..++.++...|++++|.++++++.+.
T Consensus       197 ~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~  238 (252)
T 2ho1_A          197 YYDLFAQGGGQNARSLLLGIRLAKVFEDRDTAASYGLQLKRL  238 (252)
T ss_dssp             HHHHHHTTSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCcCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            666666666666666666666666666666666666666553

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.51  E-value=2.3e-12  Score=119.96  Aligned_cols=195  Identities=13%  Similarity=0.031  Sum_probs=104.8

Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHh
Q 040394          466 VYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSAC  542 (691)
Q Consensus       466 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~  542 (691)
                      ...+..+...+...|++++|...++++.+   .+...|..+...+...|++++|...++++.+.. +.+..++..+...+
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~   86 (225)
T 2vq2_A            8 SNIKTQLAMEYMRGQDYRQATASIEDALKSDPKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGWFL   86 (225)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHHHH
Confidence            33444444444555555555555544432   133445555555555555555555555555432 22344455555555


Q ss_pred             ccc-CCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCC-CCHHHHHHHHHHHHhcCCHHH
Q 040394          543 SHT-GMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIE-PDVSLFGAFLHGCGLYSRFDL  618 (691)
Q Consensus       543 ~~~-g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~-p~~~~~~~l~~~~~~~g~~~~  618 (691)
                      ... |++++|...++++.+ .+..|+ ...+..+...+...|++++|++.++++ ... .+...+..+...+...|++++
T Consensus        87 ~~~~~~~~~A~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~  165 (225)
T 2vq2_A           87 CGRLNRPAESMAYFDKALA-DPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQFPPAFKELARTKMLAGQLGD  165 (225)
T ss_dssp             HTTTCCHHHHHHHHHHHHT-STTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHH
T ss_pred             HHhcCcHHHHHHHHHHHHc-CcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHH
Confidence            555 566666655555533 222232 344555555566666666666665555 222 234555666666666666666


Q ss_pred             HHHHHHHHHhcCC-CCchhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          619 GEVMIKKMLELHP-DKACYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       619 A~~~~~~~~~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      |...++++.+..| +++..+..++.++...|+.++|..+++.+.+
T Consensus       166 A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  210 (225)
T 2vq2_A          166 ADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQA  210 (225)
T ss_dssp             HHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence            6666666666666 6566666666666666666666666666554

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.51  E-value=5e-13  Score=126.20  Aligned_cols=211  Identities=11%  Similarity=0.052  Sum_probs=122.5

Q ss_pred             CCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHH
Q 040394          428 PDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMI  504 (691)
Q Consensus       428 p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li  504 (691)
                      ....++..+...+...|+++.|...++.+.+..  +.+...+..+...|...|++++|...+++..+   .+...+..+.
T Consensus        21 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la   98 (243)
T 2q7f_A           21 MASMTGGQQMGRGSEFGDYEKAAEAFTKAIEEN--KEDAIPYINFANLLSSVNELERALAFYDKALELDSSAATAYYGAG   98 (243)
T ss_dssp             ---------------------CCTTHHHHHTTC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcchHHHHHHH
Confidence            344556666667777778888888777777765  56677777777777777777777777776653   2556666777


Q ss_pred             HHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCCh
Q 040394          505 GGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRL  584 (691)
Q Consensus       505 ~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~  584 (691)
                      ..+...|++++|...++++.+.. +.+...+..+...+...|++++|...++++.+.  .+.+...+..+...+.+.|++
T Consensus        99 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~  175 (243)
T 2q7f_A           99 NVYVVKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVEL--NENDTEARFQFGMCLANEGML  175 (243)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHcCCH
Confidence            77777777777777777776642 334555666666666777777777777666433  122355566666666666666


Q ss_pred             HHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHH
Q 040394          585 EEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNL  643 (691)
Q Consensus       585 ~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~  643 (691)
                      ++|++.++++ . .+.+..++..+...+...|++++|...++++++..|+++..+..++.+
T Consensus       176 ~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~l  236 (243)
T 2q7f_A          176 DEALSQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKAIDIQPDHMLALHAKKLL  236 (243)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHCTTCHHHHHHHTC-
T ss_pred             HHHHHHHHHHHHhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHccCcchHHHHHHHHHH
Confidence            6666666665 2 223455666666666666666666666666666666666655555443

>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=99.51  E-value=3.8e-12  Score=120.89  Aligned_cols=205  Identities=10%  Similarity=0.015  Sum_probs=177.4

Q ss_pred             HHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHH
Q 040394          430 AVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGG  506 (691)
Q Consensus       430 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~  506 (691)
                      ...+..+...+...|++++|...++.+.+..  +.+...+..+...|...|++++|...++++.+   .+...|..+...
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~  114 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID--PSSADAHAALAVVFQTEMEPKLADEEYRKALASDSRNARVLNNYGGF  114 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC--CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHH
Confidence            4567888888999999999999999999887  77889999999999999999999999998764   367789999999


Q ss_pred             HhcCCChHHHHHHHHHHHHCCCCCC-HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCC-ChhHHHHHHHHHHhcCCh
Q 040394          507 YGMQGDGGGSLALFSDMLNEEVQPN-EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVP-SMKHYVCMVDLLARAGRL  584 (691)
Q Consensus       507 ~~~~~~~~~A~~~~~~m~~~g~~p~-~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~  584 (691)
                      |...|++++|.++++++.+.+..|+ ...+..+...+...|++++|.+.+++..+.   .| +...+..+...+...|++
T Consensus       115 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~~~~la~~~~~~g~~  191 (252)
T 2ho1_A          115 LYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRL---NRNQPSVALEMADLLYKEREY  191 (252)
T ss_dssp             HHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CSCCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc---CcccHHHHHHHHHHHHHcCCH
Confidence            9999999999999999988444564 467777888999999999999999988544   34 477888999999999999


Q ss_pred             HHHHHHHHhC-CC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHH
Q 040394          585 EEALEFMENM-PI-EPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVL  639 (691)
Q Consensus       585 ~~A~~~~~~~-~~-~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~  639 (691)
                      ++|.+.++++ .. +.+...+..+...+...|++++|...++++.+..|+++.....
T Consensus       192 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~  248 (252)
T 2ho1_A          192 VPARQYYDLFAQGGGQNARSLLLGIRLAKVFEDRDTAASYGLQLKRLYPGSLEYQEF  248 (252)
T ss_dssp             HHHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSHHHHHH
T ss_pred             HHHHHHHHHHHHhCcCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCHHHHHH
Confidence            9999999998 43 3456788888889999999999999999999999998766543

>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=99.50  E-value=3.8e-10  Score=120.67  Aligned_cols=206  Identities=8%  Similarity=-0.018  Sum_probs=159.2

Q ss_pred             CCCCHHHHHHHHHHHhccCcHHHHH-HHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc----------
Q 040394          426 VSPDAVTLVSVISACASLGAVQVGS-SLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE----------  494 (691)
Q Consensus       426 ~~p~~~~~~~ll~~~~~~~~~~~a~-~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----------  494 (691)
                      ++-+...|.....-+...|+.+.|. .+++......  |.+...+...+....+.|+++.|..+|+.+.+          
T Consensus       339 ~p~~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~~--P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~  416 (679)
T 4e6h_A          339 VCFAPEIWFNMANYQGEKNTDSTVITKYLKLGQQCI--PNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALM  416 (679)
T ss_dssp             TTTCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhh
Confidence            3446677888888788889988996 9999998765  77787888889999999999999999998764          


Q ss_pred             ---CC------------HhHHHHHHHHHhcCCChHHHHHHHHHHHHC-CCCCCHHHHHHHHHHhcc-cCCHHHHHHHHHH
Q 040394          495 ---KN------------TVTWSAMIGGYGMQGDGGGSLALFSDMLNE-EVQPNEVIFTTILSACSH-TGMVGEGWKCFYS  557 (691)
Q Consensus       495 ---~~------------~~~~~~li~~~~~~~~~~~A~~~~~~m~~~-g~~p~~~~~~~ll~~~~~-~g~~~~A~~~~~~  557 (691)
                         |+            ...|...+....+.|+.+.|..+|.+..+. + .+....|......-.+ .++.+.|.++|+.
T Consensus       417 ~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~-~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~  495 (679)
T 4e6h_A          417 EDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRLKK-LVTPDIYLENAYIEYHISKDTKTACKVLEL  495 (679)
T ss_dssp             HHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTGG-GSCTHHHHHHHHHHHTTTSCCHHHHHHHHH
T ss_pred             hccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence               21            236888888888889999999999999886 2 1223334332222223 3569999999998


Q ss_pred             chhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC----CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040394          558 MCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PIEP----DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPD  632 (691)
Q Consensus       558 m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p----~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~  632 (691)
                      .++.+  .-+...+...++.....|+.+.|..+|++. ...|    ....|...+.--.+.|+.+.+..+.+++.+..|+
T Consensus       496 ~Lk~~--p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~~P~  573 (679)
T 4e6h_A          496 GLKYF--ATDGEYINKYLDFLIYVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEKFPE  573 (679)
T ss_dssp             HHHHH--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHSTT
T ss_pred             HHHHC--CCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC
Confidence            87763  234556678888888999999999999997 3333    2357888888888999999999999999999999


Q ss_pred             Cchh
Q 040394          633 KACY  636 (691)
Q Consensus       633 ~~~~  636 (691)
                      ++.+
T Consensus       574 ~~~~  577 (679)
T 4e6h_A          574 VNKL  577 (679)
T ss_dssp             CCHH
T ss_pred             CcHH
Confidence            6543

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.49  E-value=2.5e-12  Score=123.83  Aligned_cols=227  Identities=7%  Similarity=-0.024  Sum_probs=188.1

Q ss_pred             HHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--CC----HhHHHHHHH
Q 040394          432 TLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--KN----TVTWSAMIG  505 (691)
Q Consensus       432 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~----~~~~~~li~  505 (691)
                      .+......+...|+++.|...++...+..  |.+...+..+...|...|++++|...+++..+  ++    ...|..+..
T Consensus         5 ~~~~~a~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~   82 (272)
T 3u4t_A            5 VEFRYADFLFKNNNYAEAIEVFNKLEAKK--YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGK   82 (272)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHHHHTT--CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHH
Confidence            45556678889999999999999999887  67777888899999999999999999998875  22    234889999


Q ss_pred             HHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCCh
Q 040394          506 GYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRL  584 (691)
Q Consensus       506 ~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~  584 (691)
                      .+...|++++|+..+++..+.. +.+...+..+...+...|++++|.+.+++..   ...|+ ...+..+...+...+++
T Consensus        83 ~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al---~~~~~~~~~~~~l~~~~~~~~~~  158 (272)
T 3u4t_A           83 ILMKKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQI---RPTTTDPKVFYELGQAYYYNKEY  158 (272)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGC---CSSCCCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHh---hcCCCcHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999853 3355788888889999999999999999764   44665 66777777344555699


Q ss_pred             HHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCC---HHHHHHHHHHHHhcC---CCC-----chhHHHHHHHHHhCCCcH
Q 040394          585 EEALEFMENM-PIEP-DVSLFGAFLHGCGLYSR---FDLGEVMIKKMLELH---PDK-----ACYYVLVSNLYASDGRWI  651 (691)
Q Consensus       585 ~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~---~~~A~~~~~~~~~~~---p~~-----~~~~~~l~~~~~~~g~~~  651 (691)
                      ++|++.++++ ...| +...+..+...+...|+   +++|...++++.+..   |+.     ...+..++.+|...|+++
T Consensus       159 ~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  238 (272)
T 3u4t_A          159 VKADSSFVKVLELKPNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYYYTINRDKV  238 (272)
T ss_dssp             HHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHhCccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHcCCHH
Confidence            9999999998 4444 46778888888888888   888999999999864   542     257888999999999999


Q ss_pred             HHHHHHHHHHhCC
Q 040394          652 RVNQVRELMKQRG  664 (691)
Q Consensus       652 ~A~~~~~~~~~~g  664 (691)
                      +|.+.+++..+..
T Consensus       239 ~A~~~~~~al~~~  251 (272)
T 3u4t_A          239 KADAAWKNILALD  251 (272)
T ss_dssp             HHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhcC
Confidence            9999999998854

>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=99.49  E-value=1.6e-11  Score=118.18  Aligned_cols=224  Identities=10%  Similarity=-0.054  Sum_probs=193.5

Q ss_pred             CHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHh----cCCHHHHHHHHHhcccC-CHhHHHHH
Q 040394          429 DAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAK----CGDAQSARMVFDAMREK-NTVTWSAM  503 (691)
Q Consensus       429 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~-~~~~~~~l  503 (691)
                      +..++..+...+...|++++|...|++..+.+    +...+..+...|..    .+++++|...|++..+. +...+..+
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~~----~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~l   80 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK----ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYSNGCHLL   80 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT----CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHCC----CHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            55677788888999999999999999999843    45677788899999    99999999999988754 77888999


Q ss_pred             HHHHhc----CCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcc----cCCHHHHHHHHHHchhhcCCCCChhHHHHHH
Q 040394          504 IGGYGM----QGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSH----TGMVGEGWKCFYSMCRDFKFVPSMKHYVCMV  575 (691)
Q Consensus       504 i~~~~~----~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~----~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li  575 (691)
                      ...|..    .+++++|+..|++..+.+   +...+..+-..+..    .+++++|.+.+++..+. +   +...+..+.
T Consensus        81 g~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~-~---~~~a~~~lg  153 (273)
T 1ouv_A           81 GNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDL-N---DGDGCTILG  153 (273)
T ss_dssp             HHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHT-T---CHHHHHHHH
T ss_pred             HHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhc-C---cHHHHHHHH
Confidence            999999    999999999999999875   67778888888888    99999999999988543 3   566777888


Q ss_pred             HHHHh----cCChHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHh-
Q 040394          576 DLLAR----AGRLEEALEFMENMPIEPDVSLFGAFLHGCGL----YSRFDLGEVMIKKMLELHPDKACYYVLVSNLYAS-  646 (691)
Q Consensus       576 ~~~~~----~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~-  646 (691)
                      ..|..    .+++++|++.+++.-...+...+..+...+..    .+++++|...++++.+..|  +..+..++.+|.. 
T Consensus       154 ~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~--~~a~~~l~~~~~~g  231 (273)
T 1ouv_A          154 SLYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKNFKEALARYSKACELEN--GGGCFNLGAMQYNG  231 (273)
T ss_dssp             HHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTC--HHHHHHHHHHHHTT
T ss_pred             HHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCCC--HHHHHHHHHHHHcC
Confidence            88888    89999999999988222456788889999999    9999999999999999866  6788899999999 


Q ss_pred             ---CCCcHHHHHHHHHHHhCCC
Q 040394          647 ---DGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       647 ---~g~~~~A~~~~~~~~~~g~  665 (691)
                         .|++++|.+.+++..+.|.
T Consensus       232 ~~~~~~~~~A~~~~~~a~~~~~  253 (273)
T 1ouv_A          232 EGVTRNEKQAIENFKKGCKLGA  253 (273)
T ss_dssp             SSSSCCSTTHHHHHHHHHHHTC
T ss_pred             CCcccCHHHHHHHHHHHHHcCC
Confidence               9999999999999998775

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.49  E-value=8.6e-12  Score=115.99  Aligned_cols=207  Identities=9%  Similarity=-0.037  Sum_probs=178.2

Q ss_pred             CHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHH
Q 040394          429 DAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIG  505 (691)
Q Consensus       429 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~  505 (691)
                      +...+..+...+...|+++.|...++.+.+..  +.+...+..+...|...|++++|...+++..+   .+...+..+..
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~   84 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDALKSD--PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIKPDSAEINNNYGW   84 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC--ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHH
Confidence            45677888889999999999999999999987  67888999999999999999999999998864   36778999999


Q ss_pred             HHhcC-CChHHHHHHHHHHHHCCCCCC-HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcC
Q 040394          506 GYGMQ-GDGGGSLALFSDMLNEEVQPN-EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAG  582 (691)
Q Consensus       506 ~~~~~-~~~~~A~~~~~~m~~~g~~p~-~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g  582 (691)
                      .+... |++++|...++++.+.+..|+ ...+..+..++...|++++|...++++.+.   .|+ ...+..+...+.+.|
T Consensus        85 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~~~~la~~~~~~~  161 (225)
T 2vq2_A           85 FLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAA---QPQFPPAFKELARTKMLAG  161 (225)
T ss_dssp             HHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHHHT
T ss_pred             HHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCCchHHHHHHHHHHHcC
Confidence            99999 999999999999998434454 467778888999999999999999988544   444 778889999999999


Q ss_pred             ChHHHHHHHHhC-CC-C-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHH
Q 040394          583 RLEEALEFMENM-PI-E-PDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLV  640 (691)
Q Consensus       583 ~~~~A~~~~~~~-~~-~-p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l  640 (691)
                      ++++|.+.++++ .. + .+...+..+...+...|+.+.|..+++.+.+..|+++.....+
T Consensus       162 ~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l  222 (225)
T 2vq2_A          162 QLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQANFPYSEELQTVL  222 (225)
T ss_dssp             CHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhCCCCHHHHHHh
Confidence            999999999998 32 3 4666777788888899999999999999999999988776554

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.49  E-value=1.6e-12  Score=120.03  Aligned_cols=193  Identities=8%  Similarity=-0.065  Sum_probs=103.8

Q ss_pred             CcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHH
Q 040394          110 DFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDM  189 (691)
Q Consensus       110 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  189 (691)
                      +...+..+...+.+.|++++|+..|++..+.. +.+...+..+...+.+.|++++|...+++.++..|.+...+..+..+
T Consensus         4 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~   82 (217)
T 2pl2_A            4 AEQNPLRLGVQLYALGRYDAALTLFERALKEN-PQDPEALYWLARTQLKLGLVNPALENGKTLVARTPRYLGGYMVLSEA   82 (217)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHH
Confidence            44456666666666666777776666666542 33445566666666666777777777777666666666666666666


Q ss_pred             hHhc-----------CChHHHHHHHhccCC--C-ChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHH
Q 040394          190 YAKC-----------RDIGSSRQVFDETLD--K-NVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTA  255 (691)
Q Consensus       190 ~~~~-----------g~~~~A~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~  255 (691)
                      +.+.           |++++|...|++..+  | +...|..+...+...|++++|++.|++..+..  .+...+..+..+
T Consensus        83 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~la~~  160 (217)
T 2pl2_A           83 YVALYRQAEDRERGKGYLEQALSVLKDAERVNPRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSALAEL  160 (217)
T ss_dssp             HHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHH
T ss_pred             HHHhhhhhhhhcccccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHHHHH
Confidence            6666           555555555554422  2 34455555555555555555555555555544  344555555555


Q ss_pred             HHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHh
Q 040394          256 CAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDE  306 (691)
Q Consensus       256 ~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~  306 (691)
                      +...|++++|...++...+.. +.+...+..+...+.+.|++++|.+.|++
T Consensus       161 ~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~  210 (217)
T 2pl2_A          161 YLSMGRLDEALAQYAKALEQA-PKDLDLRVRYASALLLKGKAEEAARAAAL  210 (217)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTC-------------
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            555555555555555555442 12344455555555555555555555544

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.48  E-value=1.3e-12  Score=123.24  Aligned_cols=199  Identities=13%  Similarity=0.076  Sum_probs=156.2

Q ss_pred             CCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 040394          463 SSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTIL  539 (691)
Q Consensus       463 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll  539 (691)
                      ......+..+...+...|++++|...|+++.+   .+...+..+...+...|++++|+..++++.+.. +.+...+..+.
T Consensus        20 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la   98 (243)
T 2q7f_A           20 HMASMTGGQQMGRGSEFGDYEKAAEAFTKAIEENKEDAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGAG   98 (243)
T ss_dssp             ----------------------CCTTHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHH
Confidence            34566777788889999999999999998875   367789999999999999999999999999863 44677888888


Q ss_pred             HHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHH
Q 040394          540 SACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFD  617 (691)
Q Consensus       540 ~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~  617 (691)
                      ..+...|++++|.+.++++.+.  .+.+...+..+...+.+.|++++|.+.++++ . .+.+...+..+...+...|+++
T Consensus        99 ~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  176 (243)
T 2q7f_A           99 NVYVVKEMYKEAKDMFEKALRA--GMENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNENDTEARFQFGMCLANEGMLD  176 (243)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH--TCCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCH
T ss_pred             HHHHHhccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHcCCHH
Confidence            8999999999999999988554  2334778888999999999999999999998 3 3446778899999999999999


Q ss_pred             HHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          618 LGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       618 ~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      +|...++++.+..|+++.++..++.+|...|++++|.+.++++.+..
T Consensus       177 ~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  223 (243)
T 2q7f_A          177 EALSQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKAIDIQ  223 (243)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHccC
Confidence            99999999999999999999999999999999999999999998754

>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=99.47  E-value=1.9e-12  Score=129.69  Aligned_cols=246  Identities=11%  Similarity=0.046  Sum_probs=199.8

Q ss_pred             chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCc-HHHHHHHHHHHHH
Q 040394          380 DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGA-VQVGSSLHAYSTK  458 (691)
Q Consensus       380 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~-~~~a~~~~~~~~~  458 (691)
                      ...++..+..++.+.|++++|+..++++...+               +-+..+|..+..++...|+ +++|...++++.+
T Consensus        96 ~~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~---------------P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~  160 (382)
T 2h6f_A           96 FRDVYDYFRAVLQRDERSERAFKLTRDAIELN---------------AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIE  160 (382)
T ss_dssp             HHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC---------------TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHCCChHHHHHHHHHHHHhC---------------ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHH
Confidence            44556777788888899999999888876532               2346778888889999996 9999999999999


Q ss_pred             cCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHH
Q 040394          459 QGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIF  535 (691)
Q Consensus       459 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~  535 (691)
                      ..  |.+...|..+..++...|++++|+..|+++.+   .+...|..+..++...|++++|+..++++++.. +-+...|
T Consensus       161 l~--P~~~~a~~~~g~~~~~~g~~~eAl~~~~kal~ldP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~-P~~~~a~  237 (382)
T 2h6f_A          161 EQ--PKNYQVWHHRRVLVEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED-VRNNSVW  237 (382)
T ss_dssp             HC--TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHH
T ss_pred             HC--CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCCHHHH
Confidence            88  78899999999999999999999999998874   377899999999999999999999999999853 3356778


Q ss_pred             HHHHHHhcc-cCCHHHH-----HHHHHHchhhcCCCCC-hhHHHHHHHHHHhcC--ChHHHHHHHHhCCCCC-CHHHHHH
Q 040394          536 TTILSACSH-TGMVGEG-----WKCFYSMCRDFKFVPS-MKHYVCMVDLLARAG--RLEEALEFMENMPIEP-DVSLFGA  605 (691)
Q Consensus       536 ~~ll~~~~~-~g~~~~A-----~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g--~~~~A~~~~~~~~~~p-~~~~~~~  605 (691)
                      +.+..++.. .|..++|     ++.+++.++   +.|+ ...|..+..++...|  ++++|++.+.++...| +...+..
T Consensus       238 ~~lg~~l~~l~~~~~eA~~~~el~~~~~Al~---l~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~~~~p~~~~al~~  314 (382)
T 2h6f_A          238 NQRYFVISNTTGYNDRAVLEREVQYTLEMIK---LVPHNESAWNYLKGILQDRGLSKYPNLLNQLLDLQPSHSSPYLIAF  314 (382)
T ss_dssp             HHHHHHHHHTTCSCSHHHHHHHHHHHHHHHH---HSTTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHHTTTCCCHHHHHH
T ss_pred             HHHHHHHHHhcCcchHHHHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHccCccchHHHHHHHHHhccCCCCHHHHHH
Confidence            877778877 5665777     477776643   5676 678888888888888  6899999988874444 4568888


Q ss_pred             HHHHHHhcC--------C-HHHHHHHHHHH-HhcCCCCchhHHHHHHHHHh
Q 040394          606 FLHGCGLYS--------R-FDLGEVMIKKM-LELHPDKACYYVLVSNLYAS  646 (691)
Q Consensus       606 l~~~~~~~g--------~-~~~A~~~~~~~-~~~~p~~~~~~~~l~~~~~~  646 (691)
                      ++..|.+.|        + .++|..+++++ .+.+|....+|..++..+..
T Consensus       315 La~~~~~~~~~~~~~~~~~~~~A~~~~~~l~~~~DP~r~~~w~~~~~~l~~  365 (382)
T 2h6f_A          315 LVDIYEDMLENQCDNKEDILNKALELCEILAKEKDTIRKEYWRYIGRSLQS  365 (382)
T ss_dssp             HHHHHHHHHHTTCSSHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcccccchHHHHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHH
Confidence            888888764        2 58999999999 89999999999888776654

>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=99.46  E-value=2.1e-12  Score=129.30  Aligned_cols=227  Identities=10%  Similarity=0.024  Sum_probs=195.1

Q ss_pred             HHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCC-HHHHHHHHHhccc---CCHhHHHHHHH
Q 040394          430 AVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGD-AQSARMVFDAMRE---KNTVTWSAMIG  505 (691)
Q Consensus       430 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~-~~~A~~~~~~~~~---~~~~~~~~li~  505 (691)
                      ...|..+...+...|+.++|...++.+.+..  |.+...|+.+...+...|+ +++|+..|++..+   .+...|+.+..
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~--P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P~~~~a~~~~g~  174 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAFKLTRDAIELN--AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRV  174 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhC--ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            3567777888889999999999999999998  7899999999999999997 9999999999875   37789999999


Q ss_pred             HHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHh-cCC
Q 040394          506 GYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLAR-AGR  583 (691)
Q Consensus       506 ~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~-~g~  583 (691)
                      ++...|++++|+..|+++++.. +-+...|..+..++...|++++|+..++++++   +.|+ ...|+.+..++.+ .|.
T Consensus       175 ~~~~~g~~~eAl~~~~kal~ld-P~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~---l~P~~~~a~~~lg~~l~~l~~~  250 (382)
T 2h6f_A          175 LVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLK---EDVRNNSVWNQRYFVISNTTGY  250 (382)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCS
T ss_pred             HHHHccCHHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcCChHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHhcCc
Confidence            9999999999999999999853 33567888888899999999999999998864   4565 7889999999999 666


Q ss_pred             hHHH-----HHHHHhC-CCCC-CHHHHHHHHHHHHhcC--CHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCC------
Q 040394          584 LEEA-----LEFMENM-PIEP-DVSLFGAFLHGCGLYS--RFDLGEVMIKKMLELHPDKACYYVLVSNLYASDG------  648 (691)
Q Consensus       584 ~~~A-----~~~~~~~-~~~p-~~~~~~~l~~~~~~~g--~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g------  648 (691)
                      .++|     ++.+++. ...| +...|..+...+...|  ++++|...++++ +..|+++..+..++.+|.+.|      
T Consensus       251 ~~eA~~~~el~~~~~Al~l~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~~p~~~~al~~La~~~~~~~~~~~~~  329 (382)
T 2h6f_A          251 NDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQDRGLSKYPNLLNQLLDL-QPSHSSPYLIAFLVDIYEDMLENQCDN  329 (382)
T ss_dssp             CSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TTTCCCHHHHHHHHHHHHHHHHTTCSS
T ss_pred             chHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHccCccchHHHHHHHHHh-ccCCCCHHHHHHHHHHHHHHhcccccc
Confidence            5777     4777776 4445 5678999998898888  699999999998 999999999999999999874      


Q ss_pred             ---CcHHHHHHHHHH-HhC
Q 040394          649 ---RWIRVNQVRELM-KQR  663 (691)
Q Consensus       649 ---~~~~A~~~~~~~-~~~  663 (691)
                         .+++|+++++++ .+.
T Consensus       330 ~~~~~~~A~~~~~~l~~~~  348 (382)
T 2h6f_A          330 KEDILNKALELCEILAKEK  348 (382)
T ss_dssp             HHHHHHHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHHHHHHHh
Confidence               358999999998 554

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.45  E-value=4.6e-13  Score=129.19  Aligned_cols=239  Identities=8%  Similarity=-0.089  Sum_probs=116.6

Q ss_pred             CCChhHHHHHHHHHHHcCCC---CCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHH
Q 040394          124 NDLYKDIVEFYKCMRKRLKE---HDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSR  200 (691)
Q Consensus       124 ~~~~~~a~~~~~~m~~~~~~---~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  200 (691)
                      .|++++|+..|+++.+....   .+..++..+...+...|++++|...++.+.+..+.+..++..+...|...|++++|.
T Consensus        18 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~   97 (275)
T 1xnf_A           18 TLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAY   97 (275)
T ss_dssp             CHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             cchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCHHHHH
Confidence            34455555555555443211   122344444555555555555555555555555445555555555555555555555


Q ss_pred             HHHhccCC---CChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCC
Q 040394          201 QVFDETLD---KNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGI  277 (691)
Q Consensus       201 ~~~~~~~~---~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~  277 (691)
                      ..|++..+   .+..+|..+...+...|++++|.+.|+++.+.  .|+.......+..+...|+.++|...+....... 
T Consensus        98 ~~~~~al~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-  174 (275)
T 1xnf_A           98 EAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--DPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKS-  174 (275)
T ss_dssp             HHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHS-
T ss_pred             HHHHHHHhcCccccHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-
Confidence            55554422   23445555555555555555555555555542  2333333333333444555666666665555442 


Q ss_pred             CCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCC-------hhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHH
Q 040394          278 EINSHLVTALLDMYVKCGNIRDARSVFDELCSID-------LVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTI  350 (691)
Q Consensus       278 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~-------~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~  350 (691)
                      +++...+. ++..+...++.++|...++.....+       ..+|..+...+.+.|++++|...|++....  .|+.  +
T Consensus       175 ~~~~~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~--~  249 (275)
T 1xnf_A          175 DKEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVAN--NVHN--F  249 (275)
T ss_dssp             CCCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CCTT--C
T ss_pred             CcchHHHH-HHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--Cchh--H
Confidence            22222222 4444555555566666665553321       245555666666666666666666666554  2322  1


Q ss_pred             HHHHHHHhcCCChhhHHHHH
Q 040394          351 ASVLSASAQLGNLNMGRMVH  370 (691)
Q Consensus       351 ~~ll~~~~~~~~~~~a~~~~  370 (691)
                      .....++...|++++|...+
T Consensus       250 ~~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          250 VEHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             HHHHHHHHHHHHHHHC----
T ss_pred             HHHHHHHHHHHHHHhhHHHH
Confidence            11123444445555554443

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.43  E-value=1e-11  Score=127.29  Aligned_cols=293  Identities=12%  Similarity=0.021  Sum_probs=185.6

Q ss_pred             HHHHHhcCCChhhHHHHHHHHHHhCCCc----hhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCC
Q 040394          353 VLSASAQLGNLNMGRMVHSLGIRLGLED----YTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSP  428 (691)
Q Consensus       353 ll~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p  428 (691)
                      ....+...|++++|...++.+.+..+.+    ..++..+...|...|++++|...+++......          ..+-.|
T Consensus        15 ~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~----------~~~~~~   84 (406)
T 3sf4_A           15 EGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLAR----------TIGDQL   84 (406)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH----------HTTCHH
T ss_pred             HHHHHHHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHH----------hccccH
Confidence            3334444444444444444444444332    23455666667777777777776665432100          001111


Q ss_pred             -CHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCC----CCCchhHHHHHHHHHHhcCC--------------------HH
Q 040394          429 -DAVTLVSVISACASLGAVQVGSSLHAYSTKQGL----LSSNVYVGTALLNFYAKCGD--------------------AQ  483 (691)
Q Consensus       429 -~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~----~~~~~~~~~~l~~~~~~~g~--------------------~~  483 (691)
                       ...++..+...+...|+++.|...++...+...    .+....++..+...|...|+                    ++
T Consensus        85 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~  164 (406)
T 3sf4_A           85 GEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQ  164 (406)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHH
Confidence             244677777888889999999999888765421    01124467778888888888                    88


Q ss_pred             HHHHHHHhccc-----C----CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCC-CCC----HHHHHHHHHHhcccCCHH
Q 040394          484 SARMVFDAMRE-----K----NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEV-QPN----EVIFTTILSACSHTGMVG  549 (691)
Q Consensus       484 ~A~~~~~~~~~-----~----~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~-~p~----~~~~~~ll~~~~~~g~~~  549 (691)
                      +|...+++..+     .    ...++..+...|...|++++|...+++..+... .++    ..++..+...+...|+++
T Consensus       165 ~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  244 (406)
T 3sf4_A          165 AAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFE  244 (406)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChH
Confidence            88888876542     1    234677778888888888888888888775310 122    135666777788888888


Q ss_pred             HHHHHHHHchhhcCCCCC----hhHHHHHHHHHHhcCChHHHHHHHHhC----CCCCC----HHHHHHHHHHHHhcCCHH
Q 040394          550 EGWKCFYSMCRDFKFVPS----MKHYVCMVDLLARAGRLEEALEFMENM----PIEPD----VSLFGAFLHGCGLYSRFD  617 (691)
Q Consensus       550 ~A~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~g~~~~A~~~~~~~----~~~p~----~~~~~~l~~~~~~~g~~~  617 (691)
                      +|...+++......-.++    ..++..+...|...|++++|.+.+++.    ...++    ..++..+...+...|+++
T Consensus       245 ~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  324 (406)
T 3sf4_A          245 TASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHD  324 (406)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHH
Confidence            888888876433211111    456677788888888888888887776    11122    346777777788888888


Q ss_pred             HHHHHHHHHHhcCCCCc------hhHHHHHHHHHhCCCcHHHHH
Q 040394          618 LGEVMIKKMLELHPDKA------CYYVLVSNLYASDGRWIRVNQ  655 (691)
Q Consensus       618 ~A~~~~~~~~~~~p~~~------~~~~~l~~~~~~~g~~~~A~~  655 (691)
                      +|...+++++++.+...      .++..++.++...|+...+..
T Consensus       325 ~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~  368 (406)
T 3sf4_A          325 QAMHFAEKHLEISREVGDKSGELTARLNLSDLQMVLGLSYSTNN  368 (406)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTSCC--
T ss_pred             HHHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHhhHhHHHHH
Confidence            88888888888887762      345566666666666654433

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.43  E-value=1.6e-12  Score=133.58  Aligned_cols=265  Identities=10%  Similarity=-0.008  Sum_probs=204.0

Q ss_pred             HHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCC-H----HHHHHHHHHHhccCcHHHHHHHHHHHH
Q 040394          383 VINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPD-A----VTLVSVISACASLGAVQVGSSLHAYST  457 (691)
Q Consensus       383 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~-~----~~~~~ll~~~~~~~~~~~a~~~~~~~~  457 (691)
                      .+..+...+...|++++|...|++..+.                .|+ .    ..+..+...+...|+++.|...+++..
T Consensus        50 ~l~~~g~~~~~~g~~~~A~~~~~~al~~----------------~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al  113 (411)
T 4a1s_A           50 ELALEGERLCNAGDCRAGVAFFQAAIQA----------------GTEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDL  113 (411)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH----------------CCSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCcHHHHHHHHHHHHHh----------------cccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3445667788889999999888887643                233 2    467788888999999999999999877


Q ss_pred             Hc----CCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC---------CHhHHHHHHHHHhcCCC------------
Q 040394          458 KQ----GLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK---------NTVTWSAMIGGYGMQGD------------  512 (691)
Q Consensus       458 ~~----~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---------~~~~~~~li~~~~~~~~------------  512 (691)
                      +.    +..+.....+..+...|...|++++|...+++..+-         ...++..+...|...|+            
T Consensus       114 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~  193 (411)
T 4a1s_A          114 TLAKSMNDRLGEAKSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGD  193 (411)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCH
T ss_pred             HHHHHccCchHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhh
Confidence            54    111345677888899999999999999999887631         24478888899999999            


Q ss_pred             -----hHHHHHHHHHHHHC----CCCCC-HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC----hhHHHHHHHHH
Q 040394          513 -----GGGSLALFSDMLNE----EVQPN-EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS----MKHYVCMVDLL  578 (691)
Q Consensus       513 -----~~~A~~~~~~m~~~----g~~p~-~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~----~~~~~~li~~~  578 (691)
                           +++|+..+++..+.    +-.|. ..++..+...+...|++++|.+.+++..+...-.++    ...+..+...|
T Consensus       194 ~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~  273 (411)
T 4a1s_A          194 DVKEALTRAVEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSH  273 (411)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHH
Confidence                 99999998887652    11122 246777777899999999999999887543221122    23788899999


Q ss_pred             HhcCChHHHHHHHHhC-C---CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC------chhHHHHHHHH
Q 040394          579 ARAGRLEEALEFMENM-P---IEPD----VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK------ACYYVLVSNLY  644 (691)
Q Consensus       579 ~~~g~~~~A~~~~~~~-~---~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~------~~~~~~l~~~~  644 (691)
                      ...|++++|.+.+++. .   ...+    ..++..+...+...|++++|...++++++..++.      ...+..++.+|
T Consensus       274 ~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~  353 (411)
T 4a1s_A          274 IFLGQFEDAAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAH  353 (411)
T ss_dssp             HTTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH
T ss_pred             HHCcCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHH
Confidence            9999999999999887 1   1111    4578888899999999999999999999864432      34788999999


Q ss_pred             HhCCCcHHHHHHHHHHHhC
Q 040394          645 ASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       645 ~~~g~~~~A~~~~~~~~~~  663 (691)
                      ...|++++|.+.+++..+.
T Consensus       354 ~~~g~~~~A~~~~~~al~~  372 (411)
T 4a1s_A          354 SAIGGHERALKYAEQHLQL  372 (411)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHH
Confidence            9999999999999998764

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.42  E-value=1.4e-11  Score=110.63  Aligned_cols=165  Identities=9%  Similarity=0.069  Sum_probs=122.1

Q ss_pred             CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHH
Q 040394          496 NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCM  574 (691)
Q Consensus       496 ~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~l  574 (691)
                      +...|..+...|.+.|++++|++.|++..+.. +-+...+..+..++...|++++|...++.....   .|+ ...+..+
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~   79 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVL---DTTSAEAYYIL   79 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc---CchhHHHHHHH
Confidence            34556666666666777777777777766642 224455666666777777777777777765332   333 5556666


Q ss_pred             HHHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHH
Q 040394          575 VDLLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIR  652 (691)
Q Consensus       575 i~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  652 (691)
                      ...+...++++.|.+.+.+. . .+.+...+..+...+.+.|++++|+..++++++.+|+++.++..++.+|.+.|++++
T Consensus        80 ~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~lg~~~~~~g~~~~  159 (184)
T 3vtx_A           80 GSANFMIDEKQAAIDALQRAIALNTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPGFIRAYQSIGLAYEGKGLRDE  159 (184)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcchhhhHHHHHHHHHHHCCCHHH
Confidence            77777788888888877776 2 233566788888889999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCC
Q 040394          653 VNQVRELMKQRG  664 (691)
Q Consensus       653 A~~~~~~~~~~g  664 (691)
                      |++.+++.++..
T Consensus       160 A~~~~~~al~~~  171 (184)
T 3vtx_A          160 AVKYFKKALEKE  171 (184)
T ss_dssp             HHHHHHHHHHTT
T ss_pred             HHHHHHHHHhCC
Confidence            999999988753

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.41  E-value=4.4e-12  Score=126.10  Aligned_cols=265  Identities=12%  Similarity=0.032  Sum_probs=203.6

Q ss_pred             HHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCC-----HHHHHHHHHHHhccCcHHHHHHHHHHHHH
Q 040394          384 INALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPD-----AVTLVSVISACASLGAVQVGSSLHAYSTK  458 (691)
Q Consensus       384 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~-----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  458 (691)
                      +......+...|++++|...|++..+.                .|+     ...+..+...+...|+++.|...++...+
T Consensus         8 l~~~g~~~~~~g~~~~A~~~~~~al~~----------------~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~   71 (338)
T 3ro2_A            8 LALEGERLCKSGDCRAGVSFFEAAVQV----------------GTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLT   71 (338)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH----------------CCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHhh----------------CcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            345567788899999999999887643                222     35677888899999999999999988654


Q ss_pred             c----CCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc-----CC----HhHHHHHHHHHhcCCC-------------
Q 040394          459 Q----GLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE-----KN----TVTWSAMIGGYGMQGD-------------  512 (691)
Q Consensus       459 ~----~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~----~~~~~~li~~~~~~~~-------------  512 (691)
                      .    +..+.....+..+...|...|++++|...+++..+     ++    ..++..+...+...|+             
T Consensus        72 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~  151 (338)
T 3ro2_A           72 LARTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEF  151 (338)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----C
T ss_pred             HhhcccccHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhh
Confidence            3    21133466788889999999999999999988763     22    3378888899999999             


Q ss_pred             -------hHHHHHHHHHHHHC----CCCCC-HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC----hhHHHHHHH
Q 040394          513 -------GGGSLALFSDMLNE----EVQPN-EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS----MKHYVCMVD  576 (691)
Q Consensus       513 -------~~~A~~~~~~m~~~----g~~p~-~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~----~~~~~~li~  576 (691)
                             +++|...+++..+.    +-.|. ...+..+...+...|++++|.+.+++..+...-.++    ...+..+..
T Consensus       152 ~~~a~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~  231 (338)
T 3ro2_A          152 PEDVRNALQAAVDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGN  231 (338)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHH
Confidence                   99999998887642    11121 246677777889999999999999887543221222    337888899


Q ss_pred             HHHhcCChHHHHHHHHhC----CCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC------chhHHHHHH
Q 040394          577 LLARAGRLEEALEFMENM----PIEPD----VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK------ACYYVLVSN  642 (691)
Q Consensus       577 ~~~~~g~~~~A~~~~~~~----~~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~------~~~~~~l~~  642 (691)
                      .+...|++++|.+.+++.    +..++    ..++..+...+...|++++|...++++++..|..      ..++..++.
T Consensus       232 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~  311 (338)
T 3ro2_A          232 AYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGN  311 (338)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHH
Confidence            999999999999998887    11122    4577888889999999999999999999865432      347888999


Q ss_pred             HHHhCCCcHHHHHHHHHHHhCC
Q 040394          643 LYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       643 ~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      +|...|++++|.+.+++..+..
T Consensus       312 ~~~~~g~~~~A~~~~~~a~~~~  333 (338)
T 3ro2_A          312 AYTALGNHDQAMHFAEKHLEIS  333 (338)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHC-
T ss_pred             HHHHcCChHHHHHHHHHHHHHH
Confidence            9999999999999999998743

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.41  E-value=2.8e-12  Score=133.69  Aligned_cols=207  Identities=9%  Similarity=-0.025  Sum_probs=180.9

Q ss_pred             cHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCH-HHHHHHHHhccc--C-CHhHHHHHHHHHhcCCChHHHHHHH
Q 040394          445 AVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDA-QSARMVFDAMRE--K-NTVTWSAMIGGYGMQGDGGGSLALF  520 (691)
Q Consensus       445 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~-~~A~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~A~~~~  520 (691)
                      .++.+...++......  +.+...+..+...|...|++ ++|+..|++..+  | +...|..+...|...|++++|...|
T Consensus        83 ~~~~al~~l~~~~~~~--~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~  160 (474)
T 4abn_A           83 EMEKTLQQMEEVLGSA--QVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEPELVEAWNQLGEVYWKKGDVTSAHTCF  160 (474)
T ss_dssp             HHHHHHHHHHHHHTTC--CCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccC--chhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            3566677777666554  67888999999999999999 999999998864  3 5789999999999999999999999


Q ss_pred             HHHHHCCCCCCHHHHHHHHHHhccc---------CCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhc--------C
Q 040394          521 SDMLNEEVQPNEVIFTTILSACSHT---------GMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARA--------G  582 (691)
Q Consensus       521 ~~m~~~g~~p~~~~~~~ll~~~~~~---------g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~--------g  582 (691)
                      ++..+.  .|+...+..+..++...         |++++|.+.+++..+   +.|+ ...|..+..+|...        |
T Consensus       161 ~~al~~--~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~lg~~~~~~~~~~~~~~g  235 (474)
T 4abn_A          161 SGALTH--CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQ---MDVLDGRSWYILGNAYLSLYFNTGQNPK  235 (474)
T ss_dssp             HHHHTT--CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHHHHTTCCHH
T ss_pred             HHHHhh--CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHHHHhhccccc
Confidence            999985  68878888888899999         999999999998754   3565 77889999999998        9


Q ss_pred             ChHHHHHHHHhC-CCCC----CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHH
Q 040394          583 RLEEALEFMENM-PIEP----DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVR  657 (691)
Q Consensus       583 ~~~~A~~~~~~~-~~~p----~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~  657 (691)
                      ++++|++.|++. ...|    +...|..+..++...|++++|...++++++++|+++..+..++.++...|++++|.+.+
T Consensus       236 ~~~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~a~~~l~~~~~~lg~~~eAi~~~  315 (474)
T 4abn_A          236 ISQQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALDPAWPEPQQREQQLLEFLSRLTSLLESK  315 (474)
T ss_dssp             HHHHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999998 4455    77899999999999999999999999999999999999999999999999999998754


Q ss_pred             H
Q 040394          658 E  658 (691)
Q Consensus       658 ~  658 (691)
                      .
T Consensus       316 ~  316 (474)
T 4abn_A          316 G  316 (474)
T ss_dssp             T
T ss_pred             c
Confidence            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=99.41  E-value=3.2e-09  Score=113.50  Aligned_cols=436  Identities=9%  Similarity=0.051  Sum_probs=242.8

Q ss_pred             CCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCC---hhHHHHHHHHHHHhCC--CChhHH
Q 040394          109 PDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRD---IDEGMKVHCEIVKVGG--PDSFVL  183 (691)
Q Consensus       109 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~---~~~a~~~~~~~~~~~~--~~~~~~  183 (691)
                      .|..+|..++..+.+.+.++.+..+|+++... ++.....|..-+..-.+.++   .+.+..+|++.+...+  ++...|
T Consensus        64 ~d~~~W~~yi~~~~~~~~~~~aR~vyEraL~~-fP~~~~lW~~Yi~~E~~~~~~~~~~~v~~lfeRal~~~~~~~sv~LW  142 (679)
T 4e6h_A           64 TDIFLYVKLLKHHVSLKQWKQVYETFDKLHDR-FPLMANIWCMRLSLEFDKMEELDAAVIEPVLARCLSKELGNNDLSLW  142 (679)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTC--CCCHHHHHHHHHHHTCSSSCCCCHHHH
T ss_pred             CCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHHhcCCCCCHHHH
Confidence            35556666666666666666677777766665 34455556666665556666   6666677766666553  455566


Q ss_pred             HHHHHHhHhcCCh--------HHHHHHHhcc-----C-CC-ChhhHHHHHHHHH---------hCCChhHHHHHHHHHHh
Q 040394          184 TGLVDMYAKCRDI--------GSSRQVFDET-----L-DK-NVVSWTSMIAGYV---------QNDCAQEGLVLFNRMRE  239 (691)
Q Consensus       184 ~~l~~~~~~~g~~--------~~A~~~~~~~-----~-~~-~~~~~~~li~~~~---------~~g~~~~A~~~~~~m~~  239 (691)
                      ...+....+.++.        +...++|+..     . ++ +...|...+.-..         .+++++.+..+|++...
T Consensus       143 ~~Yl~f~~~~~~~~~~~~~~r~~vr~~FErAl~~vG~~d~~s~~iW~~Yi~f~~~~~~~~~~eeq~~~~~~R~iy~raL~  222 (679)
T 4e6h_A          143 LSYITYVRKKNDIITGGEEARNIVIQAFQVVVDKCAIFEPKSIQFWNEYLHFLEHWKPVNKFEEQQRVQYIRKLYKTLLC  222 (679)
T ss_dssp             HHHHHHHHHHSCSTTTHHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHTCCCCSHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhcccccccchhHHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHhccccCcHHHHhHHHHHHHHHHHHHh
Confidence            6666555554433        2223444432     1 22 2335555554332         12334555666666553


Q ss_pred             CCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhc-------C----
Q 040394          240 GFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDEL-------C----  308 (691)
Q Consensus       240 ~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~-------~----  308 (691)
                      .....-..+|......-... +...+.+++.+.                     ..+++.|...+.++       .    
T Consensus       223 iP~~~~~~~w~~Y~~fe~~~-~~~~a~~~~~e~---------------------~~~y~~Ar~~~~e~~~~~~~l~r~~p  280 (679)
T 4e6h_A          223 QPMDCLESMWQRYTQWEQDV-NQLTARRHIGEL---------------------SAQYMNARSLYQDWLNITKGLKRNLP  280 (679)
T ss_dssp             SCCSSHHHHHHHHHHHHHHH-CTTTHHHHHHHH---------------------HHHHHHHHHHHHHHHHHTTTCCCCCC
T ss_pred             CccHHHHHHHHHHHHHHHhc-CcchHHHHHHHh---------------------hHHHHHHHHHHHHHHHHHHhHhhccc
Confidence            11110111221111110000 111111111110                     11223333333321       0    


Q ss_pred             C----------C--C------hhHHHHHHHHHHhcCC-------chhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCCh
Q 040394          309 S----------I--D------LVSWTAMIVGYTQSGY-------PDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNL  363 (691)
Q Consensus       309 ~----------~--~------~~~~~~li~~~~~~g~-------~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~  363 (691)
                      .          |  +      ...|...+.---..+.       .+.+..+|++.... +.-+...|.....-+...|+.
T Consensus       281 ~~~~~~~~~~~p~~~~~~~~ql~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~-~p~~~~lW~~ya~~~~~~~~~  359 (679)
T 4e6h_A          281 ITLNQATESNLPKPNEYDVQQLLIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQH-VCFAPEIWFNMANYQGEKNTD  359 (679)
T ss_dssp             SSSTTCCTTTSCCTTCCCHHHHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHH-TTTCHHHHHHHHHHHHHHSCC
T ss_pred             cccccchhccCCCCchhHHHHHHHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHH-cCCCHHHHHHHHHHHHhcCcH
Confidence            0          0  0      1245555543322221       23355677777665 344677787888888888999


Q ss_pred             hhHH-HHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCC------------H
Q 040394          364 NMGR-MVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPD------------A  430 (691)
Q Consensus       364 ~~a~-~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~------------~  430 (691)
                      ++|. .+++.+....|.+...+-..+....+.|++++|..+|+++...-...+..    +..+. |+            .
T Consensus       360 ~~a~r~il~rAi~~~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~----~~~~~-p~~~~~~~~~~~~~~  434 (679)
T 4e6h_A          360 STVITKYLKLGQQCIPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAA----LMEDD-PTNESAINQLKSKLT  434 (679)
T ss_dssp             TTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHH----HHHHS-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhh----hhhcc-CcchhhhhhhccchH
Confidence            9996 99999999888788888889999999999999999999876420000000    00001 31            2


Q ss_pred             HHHHHHHHHHhccCcHHHHHHHHHHHHHc-CCCCCchhHHHHHHHHHHhc-CCHHHHHHHHHhccc---CCHhHHHHHHH
Q 040394          431 VTLVSVISACASLGAVQVGSSLHAYSTKQ-GLLSSNVYVGTALLNFYAKC-GDAQSARMVFDAMRE---KNTVTWSAMIG  505 (691)
Q Consensus       431 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~~~~---~~~~~~~~li~  505 (691)
                      .+|...+....+.|+.+.|..+|....+. +  +.....|...+..-.+. ++.+.|.++|+...+   .+...|...+.
T Consensus       435 ~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~--~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~~  512 (679)
T 4e6h_A          435 YVYCVYMNTMKRIQGLAASRKIFGKCRRLKK--LVTPDIYLENAYIEYHISKDTKTACKVLELGLKYFATDGEYINKYLD  512 (679)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHHHHHTGG--GSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhcC--CCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCchHHHHHHHH
Confidence            35677777777788888888888888776 3  23334444333333344 347888888887764   35556667777


Q ss_pred             HHhcCCChHHHHHHHHHHHHCCCCC--CHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHH
Q 040394          506 GYGMQGDGGGSLALFSDMLNEEVQP--NEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLL  578 (691)
Q Consensus       506 ~~~~~~~~~~A~~~~~~m~~~g~~p--~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~  578 (691)
                      .....|+.+.|..+|++.......+  ....|...+..-...|+.+.+..+.+++.+.   .|+......+++-|
T Consensus       513 fe~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~---~P~~~~~~~f~~ry  584 (679)
T 4e6h_A          513 FLIYVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEK---FPEVNKLEEFTNKY  584 (679)
T ss_dssp             HHHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHH---STTCCHHHHHHHHT
T ss_pred             HHHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCCcHHHHHHHHh
Confidence            7777788888888888877653222  2245666666666778888888888777544   34433333344433

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.39  E-value=5.2e-12  Score=129.47  Aligned_cols=258  Identities=10%  Similarity=-0.009  Sum_probs=170.3

Q ss_pred             HHHHHHHHhcCCChhhHHHHHHHHHHh----CCC--chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhh
Q 040394          350 IASVLSASAQLGNLNMGRMVHSLGIRL----GLE--DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLD  423 (691)
Q Consensus       350 ~~~ll~~~~~~~~~~~a~~~~~~~~~~----~~~--~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~  423 (691)
                      +..+...+...|++++|...++.+...    +..  ...++..+...|...|++++|...+++.......        . 
T Consensus        50 ~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~--------~-  120 (406)
T 3sf4_A           50 YSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRE--------L-  120 (406)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH--------H-
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHh--------c-
Confidence            333334444444444444444433222    111  3445666777777778888887777765432000        0 


Q ss_pred             CCCCCCHHHHHHHHHHHhccCc--------------------HHHHHHHHHHHHHc----CCCCCchhHHHHHHHHHHhc
Q 040394          424 DNVSPDAVTLVSVISACASLGA--------------------VQVGSSLHAYSTKQ----GLLSSNVYVGTALLNFYAKC  479 (691)
Q Consensus       424 ~~~~p~~~~~~~ll~~~~~~~~--------------------~~~a~~~~~~~~~~----~~~~~~~~~~~~l~~~~~~~  479 (691)
                      ........++..+...+...|+                    ++.|...++...+.    +..+.....+..+...|...
T Consensus       121 ~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~  200 (406)
T 3sf4_A          121 NDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLL  200 (406)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             ccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHc
Confidence            0001113477788888999999                    99999999887653    21023345778889999999


Q ss_pred             CCHHHHHHHHHhccc-----CC----HhHHHHHHHHHhcCCChHHHHHHHHHHHHCCC-CCC----HHHHHHHHHHhccc
Q 040394          480 GDAQSARMVFDAMRE-----KN----TVTWSAMIGGYGMQGDGGGSLALFSDMLNEEV-QPN----EVIFTTILSACSHT  545 (691)
Q Consensus       480 g~~~~A~~~~~~~~~-----~~----~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~-~p~----~~~~~~ll~~~~~~  545 (691)
                      |++++|...+++..+     ++    ..+|..+...|...|++++|...+++..+... .++    ..++..+...+...
T Consensus       201 g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~  280 (406)
T 3sf4_A          201 GNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLL  280 (406)
T ss_dssp             TBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             cCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHh
Confidence            999999999998764     22    23788899999999999999999999876311 111    45677788899999


Q ss_pred             CCHHHHHHHHHHchhhcCCCCC----hhHHHHHHHHHHhcCChHHHHHHHHhC-------CCCC-CHHHHHHHHHHHHhc
Q 040394          546 GMVGEGWKCFYSMCRDFKFVPS----MKHYVCMVDLLARAGRLEEALEFMENM-------PIEP-DVSLFGAFLHGCGLY  613 (691)
Q Consensus       546 g~~~~A~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~g~~~~A~~~~~~~-------~~~p-~~~~~~~l~~~~~~~  613 (691)
                      |++++|.+.+++......-.++    ..++..+...|...|++++|.+.+++.       +..+ ...++..+...+...
T Consensus       281 g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~  360 (406)
T 3sf4_A          281 QDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEISREVGDKSGELTARLNLSDLQMVL  360 (406)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHh
Confidence            9999999999987543222222    557888899999999999999998886       1111 123455555555555


Q ss_pred             CCH
Q 040394          614 SRF  616 (691)
Q Consensus       614 g~~  616 (691)
                      |+.
T Consensus       361 g~~  363 (406)
T 3sf4_A          361 GLS  363 (406)
T ss_dssp             HTT
T ss_pred             hHh
Confidence            544

>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=99.39  E-value=1.7e-10  Score=110.94  Aligned_cols=224  Identities=11%  Similarity=0.076  Sum_probs=119.0

Q ss_pred             CcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcc----cCChhHHHHHHHHHHHhCCCChhHHHH
Q 040394          110 DFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCE----LRDIDEGMKVHCEIVKVGGPDSFVLTG  185 (691)
Q Consensus       110 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~  185 (691)
                      +..++..+...+...|++++|+..|++..+.   -+...+..+...+..    .+++++|...|++..+.+  +..++..
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~---~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~--~~~a~~~   79 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDL---KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN--YSNGCHL   79 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT--CHHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC--CHHHHHH
Confidence            3445566666666666777776666666652   233455555555555    666666666666666554  4455555


Q ss_pred             HHHHhHh----cCChHHHHHHHhccCC-CChhhHHHHHHHHHh----CCChhHHHHHHHHHHhCCCCCChhhHHHHHHHH
Q 040394          186 LVDMYAK----CRDIGSSRQVFDETLD-KNVVSWTSMIAGYVQ----NDCAQEGLVLFNRMREGFVEGNQITLGSLVTAC  256 (691)
Q Consensus       186 l~~~~~~----~g~~~~A~~~~~~~~~-~~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~  256 (691)
                      +...|..    .+++++|...|++..+ .+..++..+...|..    .+++++|++.|++..+                 
T Consensus        80 lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~-----------------  142 (273)
T 1ouv_A           80 LGNLYYSGQGVSQNTNKALQYYSKACDLKYAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACD-----------------  142 (273)
T ss_dssp             HHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHH-----------------
T ss_pred             HHHHHhCCCCcccCHHHHHHHHHHHHHcCCccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHh-----------------
Confidence            5555555    5555555555554322 233444444444544    4555555555555444                 


Q ss_pred             HccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHh----cCCHHHHHHHHHhcCC-CChhHHHHHHHHHHh----cCC
Q 040394          257 AKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVK----CGNIRDARSVFDELCS-IDLVSWTAMIVGYTQ----SGY  327 (691)
Q Consensus       257 ~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~----~g~~~~A~~~~~~~~~-~~~~~~~~li~~~~~----~g~  327 (691)
                                        .+   +...+..+...|..    .+++++|...|++..+ .+..++..+...|..    .++
T Consensus       143 ------------------~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~  201 (273)
T 1ouv_A          143 ------------------LN---DGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKN  201 (273)
T ss_dssp             ------------------TT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCCC
T ss_pred             ------------------cC---cHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCcc
Confidence                              33   23334444444444    4555555555554421 233445555555555    566


Q ss_pred             chhHHHHHHHhhHCCCCCcHHHHHHHHHHHhc----CCChhhHHHHHHHHHHhCCC
Q 040394          328 PDKALKLFTDKKWADFFPNHVTIASVLSASAQ----LGNLNMGRMVHSLGIRLGLE  379 (691)
Q Consensus       328 ~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~  379 (691)
                      +++|++.|++..+.+.   ...+..+...+..    .++.++|...++...+.++.
T Consensus       202 ~~~A~~~~~~a~~~~~---~~a~~~l~~~~~~g~~~~~~~~~A~~~~~~a~~~~~~  254 (273)
T 1ouv_A          202 FKEALARYSKACELEN---GGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLGAK  254 (273)
T ss_dssp             HHHHHHHHHHHHHTTC---HHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHTCH
T ss_pred             HHHHHHHHHHHHhCCC---HHHHHHHHHHHHcCCCcccCHHHHHHHHHHHHHcCCH
Confidence            6666666665555432   3444444555555    56666666666666555543

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.37  E-value=1.1e-11  Score=127.42  Aligned_cols=268  Identities=10%  Similarity=0.024  Sum_probs=185.1

Q ss_pred             HHhcCCChhhHHHHHHHHHHhCCCch----hHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHH
Q 040394          356 ASAQLGNLNMGRMVHSLGIRLGLEDY----TVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAV  431 (691)
Q Consensus       356 ~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~  431 (691)
                      .+...|++++|...++.+.+..+.+.    .++..+...|...|++++|...+++.....        ... ...+....
T Consensus        57 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--------~~~-~~~~~~~~  127 (411)
T 4a1s_A           57 RLCNAGDCRAGVAFFQAAIQAGTEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLA--------KSM-NDRLGEAK  127 (411)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH--------HHT-TCHHHHHH
T ss_pred             HHHHhCcHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH--------HHc-cCchHHHH
Confidence            33344444444444444444433321    344556666666677766666666543210        000 00122345


Q ss_pred             HHHHHHHHHhccCcHHHHHHHHHHHHHcC----CCCCchhHHHHHHHHHHhcCC-----------------HHHHHHHHH
Q 040394          432 TLVSVISACASLGAVQVGSSLHAYSTKQG----LLSSNVYVGTALLNFYAKCGD-----------------AQSARMVFD  490 (691)
Q Consensus       432 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~----~~~~~~~~~~~l~~~~~~~g~-----------------~~~A~~~~~  490 (691)
                      ++..+...+...|+++.|...+++..+..    ..+.....+..+...|...|+                 +++|...++
T Consensus       128 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~  207 (411)
T 4a1s_A          128 SSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQ  207 (411)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHH
Confidence            67788888999999999999998876541    103445678888999999999                 999999888


Q ss_pred             hccc-----C----CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCC-CCC----HHHHHHHHHHhcccCCHHHHHHHHH
Q 040394          491 AMRE-----K----NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEV-QPN----EVIFTTILSACSHTGMVGEGWKCFY  556 (691)
Q Consensus       491 ~~~~-----~----~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~-~p~----~~~~~~ll~~~~~~g~~~~A~~~~~  556 (691)
                      +..+     .    ....+..+...|...|++++|+..+++..+... .++    ...+..+...+...|++++|.+.++
T Consensus       208 ~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  287 (411)
T 4a1s_A          208 ENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYK  287 (411)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHH
Confidence            7653     1    234788889999999999999999999876311 112    1367778889999999999999998


Q ss_pred             HchhhcCCCCC----hhHHHHHHHHHHhcCChHHHHHHHHhC-C---CCCC----HHHHHHHHHHHHhcCCHHHHHHHHH
Q 040394          557 SMCRDFKFVPS----MKHYVCMVDLLARAGRLEEALEFMENM-P---IEPD----VSLFGAFLHGCGLYSRFDLGEVMIK  624 (691)
Q Consensus       557 ~m~~~~~~~p~----~~~~~~li~~~~~~g~~~~A~~~~~~~-~---~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~  624 (691)
                      +......-..+    ..++..+...|...|++++|.+.+++. .   ..++    ..++..+...+...|++++|...++
T Consensus       288 ~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  367 (411)
T 4a1s_A          288 RTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKYAE  367 (411)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHHH
Confidence            77543221111    467788899999999999999999887 1   1112    3477888899999999999999999


Q ss_pred             HHHhcCCC
Q 040394          625 KMLELHPD  632 (691)
Q Consensus       625 ~~~~~~p~  632 (691)
                      +++++.+.
T Consensus       368 ~al~~~~~  375 (411)
T 4a1s_A          368 QHLQLAXX  375 (411)
T ss_dssp             HHHHHCCH
T ss_pred             HHHHHHhh
Confidence            99998766

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.32  E-value=2.9e-11  Score=120.08  Aligned_cols=266  Identities=11%  Similarity=0.041  Sum_probs=180.2

Q ss_pred             HhcCCChhhHHHHHHHHHHhCCCc----hhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCC-CCHH
Q 040394          357 SAQLGNLNMGRMVHSLGIRLGLED----YTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVS-PDAV  431 (691)
Q Consensus       357 ~~~~~~~~~a~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~-p~~~  431 (691)
                      +...|++++|...++.+.+..+.+    ..++..+...|...|++++|...+++......        ..  +.. ....
T Consensus        15 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~--------~~--~~~~~~~~   84 (338)
T 3ro2_A           15 LCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLAR--------TI--GDQLGEAK   84 (338)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH--------HH--TCHHHHHH
T ss_pred             HHHhccHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhh--------cc--cccHHHHH
Confidence            334444444444444444443332    23455666666677777777666665432100        00  111 1245


Q ss_pred             HHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC----chhHHHHHHHHHHhcCC--------------------HHHHHH
Q 040394          432 TLVSVISACASLGAVQVGSSLHAYSTKQGLLSS----NVYVGTALLNFYAKCGD--------------------AQSARM  487 (691)
Q Consensus       432 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~~l~~~~~~~g~--------------------~~~A~~  487 (691)
                      ++..+...+...|+++.|...+++..+.....+    ...++..+...|...|+                    +++|..
T Consensus        85 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~  164 (338)
T 3ro2_A           85 ASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVD  164 (338)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHH
Confidence            677788888999999999999988765421011    23477788889999999                    999998


Q ss_pred             HHHhccc-----CC----HhHHHHHHHHHhcCCChHHHHHHHHHHHHCCC-CCC----HHHHHHHHHHhcccCCHHHHHH
Q 040394          488 VFDAMRE-----KN----TVTWSAMIGGYGMQGDGGGSLALFSDMLNEEV-QPN----EVIFTTILSACSHTGMVGEGWK  553 (691)
Q Consensus       488 ~~~~~~~-----~~----~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~-~p~----~~~~~~ll~~~~~~g~~~~A~~  553 (691)
                      .+++..+     ++    ...+..+...+...|++++|...+++..+... .++    ..++..+...+...|++++|..
T Consensus       165 ~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  244 (338)
T 3ro2_A          165 LYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASE  244 (338)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            8887653     12    34678888999999999999999998875310 111    2367777788899999999999


Q ss_pred             HHHHchhhcCCCCC----hhHHHHHHHHHHhcCChHHHHHHHHhC-C---CCCC----HHHHHHHHHHHHhcCCHHHHHH
Q 040394          554 CFYSMCRDFKFVPS----MKHYVCMVDLLARAGRLEEALEFMENM-P---IEPD----VSLFGAFLHGCGLYSRFDLGEV  621 (691)
Q Consensus       554 ~~~~m~~~~~~~p~----~~~~~~li~~~~~~g~~~~A~~~~~~~-~---~~p~----~~~~~~l~~~~~~~g~~~~A~~  621 (691)
                      .+++......-.++    ..++..+...+...|++++|.+.+++. .   ..++    ..++..+...+...|++++|..
T Consensus       245 ~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  324 (338)
T 3ro2_A          245 YYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMH  324 (338)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHH
Confidence            99877443221222    457778889999999999999999887 1   1112    3477888899999999999999


Q ss_pred             HHHHHHhcCCC
Q 040394          622 MIKKMLELHPD  632 (691)
Q Consensus       622 ~~~~~~~~~p~  632 (691)
                      .+++++++.+.
T Consensus       325 ~~~~a~~~~~~  335 (338)
T 3ro2_A          325 FAEKHLEISRE  335 (338)
T ss_dssp             HHHHHHHC---
T ss_pred             HHHHHHHHHHh
Confidence            99999987765

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.31  E-value=6.3e-12  Score=123.53  Aligned_cols=233  Identities=14%  Similarity=0.111  Sum_probs=171.1

Q ss_pred             CHHHHHHHHHHHhccCcHHHHHHHHHHHHHc-------CCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc-------
Q 040394          429 DAVTLVSVISACASLGAVQVGSSLHAYSTKQ-------GLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE-------  494 (691)
Q Consensus       429 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-------~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-------  494 (691)
                      +..++..+...+...|+++.|..+++.+.+.       .. +.....+..+...|...|++++|...+++..+       
T Consensus        26 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~  104 (311)
T 3nf1_A           26 RLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDH-PDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLG  104 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSS-HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCC-HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhC
Confidence            4567888889999999999999999998874       32 55677888899999999999999999988753       


Q ss_pred             C----CHhHHHHHHHHHhcCCChHHHHHHHHHHHHC------CCCCC-HHHHHHHHHHhcccCCHHHHHHHHHHchhhc-
Q 040394          495 K----NTVTWSAMIGGYGMQGDGGGSLALFSDMLNE------EVQPN-EVIFTTILSACSHTGMVGEGWKCFYSMCRDF-  562 (691)
Q Consensus       495 ~----~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~------g~~p~-~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~-  562 (691)
                      +    ....+..+...|...|++++|...+++..+.      +-.|+ ...+..+...+...|++++|.+++++..... 
T Consensus       105 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~  184 (311)
T 3nf1_A          105 KDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQ  184 (311)
T ss_dssp             TTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHH
T ss_pred             CCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence            1    2457888899999999999999999998874      22233 3567777789999999999999999875431 


Q ss_pred             ----CCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-C---------CCCCH-------HHHHHHHHHHHhcCCHHHHH
Q 040394          563 ----KFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-P---------IEPDV-------SLFGAFLHGCGLYSRFDLGE  620 (691)
Q Consensus       563 ----~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~---------~~p~~-------~~~~~l~~~~~~~g~~~~A~  620 (691)
                          +..|. ..++..+...|...|++++|.+.++++ .         ..+..       ..+..+...+...+.+.++.
T Consensus       185 ~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~  264 (311)
T 3nf1_A          185 TKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYG  264 (311)
T ss_dssp             HTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-------CCSCCCC
T ss_pred             HHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHHHHHHHH
Confidence                11333 567888999999999999999998887 1         11111       12222333344566777778


Q ss_pred             HHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          621 VMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       621 ~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      ..+++.....|....++..++.+|.+.|++++|.+.+++.++
T Consensus       265 ~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          265 GWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             ---------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            888888888899899999999999999999999999998876

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.28  E-value=1.9e-10  Score=116.68  Aligned_cols=237  Identities=8%  Similarity=-0.070  Sum_probs=121.2

Q ss_pred             HHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCC-CHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCC--
Q 040394          386 ALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSP-DAVTLVSVISACASLGAVQVGSSLHAYSTKQGLL--  462 (691)
Q Consensus       386 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~--  462 (691)
                      .....+...|++++|...|++....-..          .+-.+ ...++..+...+...|+.+.|...+++..+....  
T Consensus       108 ~~g~~~~~~g~~~~A~~~~~~al~~~~~----------~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~  177 (383)
T 3ulq_A          108 FRGMYELDQREYLSAIKFFKKAESKLIF----------VKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHE  177 (383)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTGGG----------CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCS
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHHHhh----------CCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCc
Confidence            3556677788888888888776432000          00011 2345667777777788888888777776653210  


Q ss_pred             ---CCchhHHHHHHHHHHhcCCHHHHHHHHHhccc-----CC----HhHHHHHHHHHhcCCChHHHHHHHHHHHHC----
Q 040394          463 ---SSNVYVGTALLNFYAKCGDAQSARMVFDAMRE-----KN----TVTWSAMIGGYGMQGDGGGSLALFSDMLNE----  526 (691)
Q Consensus       463 ---~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~----~~~~~~li~~~~~~~~~~~A~~~~~~m~~~----  526 (691)
                         +....+++.+...|...|++++|...+++..+     ++    ..++..+...|...|++++|+..+++..+.    
T Consensus       178 ~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~  257 (383)
T 3ulq_A          178 AYNIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEES  257 (383)
T ss_dssp             TTHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             cchHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence               11234556666666777777777766665542     11    124555566666666666666666555541    


Q ss_pred             CCCC-CHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHH
Q 040394          527 EVQP-NEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGA  605 (691)
Q Consensus       527 g~~p-~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~  605 (691)
                      +..| ...++..+..++...|++++|.+.+++......-..+                             +.....+..
T Consensus       258 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~-----------------------------~~~~~~~~~  308 (383)
T 3ulq_A          258 NILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGD-----------------------------VIYLSEFEF  308 (383)
T ss_dssp             TCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTC-----------------------------HHHHHHHHH
T ss_pred             ccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCC-----------------------------HHHHHHHHH
Confidence            1112 2233444444555555555555555443221100001                             001112333


Q ss_pred             HHHHHHhcCC---HHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          606 FLHGCGLYSR---FDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       606 l~~~~~~~g~---~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      +...+...|+   +++|..++++. ...|....++..++.+|...|++++|.+.+++..+
T Consensus       309 l~~~~~~~~~~~~~~~al~~~~~~-~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          309 LKSLYLSGPDEEAIQGFFDFLESK-MLYADLEDFAIDVAKYYHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             HHHHHTSSCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCcHHHHHHHHHHHHHC-cCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4444445555   44444444443 22223334555566666666666666666665544

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.28  E-value=5.8e-10  Score=109.17  Aligned_cols=212  Identities=9%  Similarity=0.019  Sum_probs=162.2

Q ss_pred             HHHHHHHHHHHHcCCCCCchhHHHHHHHHHHh-------cCCH-------HHHHHHHHhccc---C-CHhHHHHHHHHHh
Q 040394          447 QVGSSLHAYSTKQGLLSSNVYVGTALLNFYAK-------CGDA-------QSARMVFDAMRE---K-NTVTWSAMIGGYG  508 (691)
Q Consensus       447 ~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------~g~~-------~~A~~~~~~~~~---~-~~~~~~~li~~~~  508 (691)
                      +.|..+|++..+..  |.++..|..++..+..       .|++       ++|..+|++..+   | +...|..++..+.
T Consensus        33 ~~a~~~~~~al~~~--p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~  110 (308)
T 2ond_A           33 KRVMFAYEQCLLVL--GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEE  110 (308)
T ss_dssp             HHHHHHHHHHHHHH--TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHH
Confidence            67778888888876  7788888888777753       4775       889999988764   3 5568888888999


Q ss_pred             cCCChHHHHHHHHHHHHCCCCCCH-H-HHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHH-hcCCh
Q 040394          509 MQGDGGGSLALFSDMLNEEVQPNE-V-IFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLA-RAGRL  584 (691)
Q Consensus       509 ~~~~~~~A~~~~~~m~~~g~~p~~-~-~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~-~~g~~  584 (691)
                      +.|++++|..+|++..+  +.|+. . .|..+...+.+.|++++|..+|++..+   ..|+ ...|........ ..|++
T Consensus       111 ~~~~~~~A~~~~~~al~--~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~---~~p~~~~~~~~~a~~~~~~~~~~  185 (308)
T 2ond_A          111 SRMKYEKVHSIYNRLLA--IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARE---DARTRHHVYVTAALMEYYCSKDK  185 (308)
T ss_dssp             HTTCHHHHHHHHHHHHT--SSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHT---STTCCTHHHHHHHHHHHHTSCCH
T ss_pred             hcCCHHHHHHHHHHHHh--ccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHcCCH
Confidence            99999999999999987  45543 3 688888888888999999999997743   3343 444443333322 36899


Q ss_pred             HHHHHHHHhC-CC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc---CCC-CchhHHHHHHHHHhCCCcHHHHHHHH
Q 040394          585 EEALEFMENM-PI-EPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLEL---HPD-KACYYVLVSNLYASDGRWIRVNQVRE  658 (691)
Q Consensus       585 ~~A~~~~~~~-~~-~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~  658 (691)
                      ++|.++|++. .. +.+...|..++..+.+.|++++|..+|+++++.   .|+ +...|..++..+.+.|+.++|..+++
T Consensus       186 ~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~  265 (308)
T 2ond_A          186 SVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEK  265 (308)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            9999999887 22 335678888888888899999999999999985   453 56678888888888999999999998


Q ss_pred             HHHhCCC
Q 040394          659 LMKQRGL  665 (691)
Q Consensus       659 ~~~~~g~  665 (691)
                      ++.+...
T Consensus       266 ~a~~~~p  272 (308)
T 2ond_A          266 RRFTAFR  272 (308)
T ss_dssp             HHHHHTT
T ss_pred             HHHHHcc
Confidence            8887544

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.27  E-value=6.5e-11  Score=120.20  Aligned_cols=187  Identities=10%  Similarity=-0.037  Sum_probs=119.0

Q ss_pred             HHHHhcCCHHHHHHHHHhccc-----C----CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCC--C---CC-CHHHHHHH
Q 040394          474 NFYAKCGDAQSARMVFDAMRE-----K----NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEE--V---QP-NEVIFTTI  538 (691)
Q Consensus       474 ~~~~~~g~~~~A~~~~~~~~~-----~----~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g--~---~p-~~~~~~~l  538 (691)
                      ..+...|++++|...|++..+     +    ...+|..+...|...|++++|+..+++..+.-  .   .| ...+++.+
T Consensus       111 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~l  190 (383)
T 3ulq_A          111 MYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLF  190 (383)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHH
Confidence            344455555555555554432     1    12345555566666666666666666555420  0   11 12355556


Q ss_pred             HHHhcccCCHHHHHHHHHHchhhcCCCCC----hhHHHHHHHHHHhcCChHHHHHHHHhC-------CCCCC-HHHHHHH
Q 040394          539 LSACSHTGMVGEGWKCFYSMCRDFKFVPS----MKHYVCMVDLLARAGRLEEALEFMENM-------PIEPD-VSLFGAF  606 (691)
Q Consensus       539 l~~~~~~g~~~~A~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~g~~~~A~~~~~~~-------~~~p~-~~~~~~l  606 (691)
                      ..+|...|++++|.+.+++......-.++    ..++..+...|...|++++|++.+++.       +..|+ ..++..+
T Consensus       191 g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l  270 (383)
T 3ulq_A          191 ATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLI  270 (383)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHH
Confidence            66777777777777777665432111121    246777888888888888888887776       22133 4578888


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhc-----CCCCchhHHHHHHHHHhCCC---cHHHHHHHHHH
Q 040394          607 LHGCGLYSRFDLGEVMIKKMLEL-----HPDKACYYVLVSNLYASDGR---WIRVNQVRELM  660 (691)
Q Consensus       607 ~~~~~~~g~~~~A~~~~~~~~~~-----~p~~~~~~~~l~~~~~~~g~---~~~A~~~~~~~  660 (691)
                      ...+...|++++|...++++++.     +|.....+..++.+|...|+   +++|..++++.
T Consensus       271 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~  332 (383)
T 3ulq_A          271 TQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESK  332 (383)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHC
Confidence            99999999999999999999985     34333446779999999999   77777776654

>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=99.27  E-value=7.6e-11  Score=127.67  Aligned_cols=161  Identities=14%  Similarity=0.166  Sum_probs=127.5

Q ss_pred             HhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCC-HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHH
Q 040394          497 TVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPN-EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCM  574 (691)
Q Consensus       497 ~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~-~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~l  574 (691)
                      ...|+.|...|.+.|++++|++.|++.++.  .|+ ...+..+..++.+.|++++|++.|++.++   +.|+ ...|..+
T Consensus         9 a~al~nLG~~~~~~G~~~eAi~~~~kAl~l--~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~---l~P~~~~a~~nL   83 (723)
T 4gyw_A            9 ADSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIR---ISPTFADAYSNM   83 (723)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHH
Confidence            345666666677777777777777776663  443 45666677777777777777777776543   4565 6678888


Q ss_pred             HHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHH
Q 040394          575 VDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIR  652 (691)
Q Consensus       575 i~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  652 (691)
                      ..+|.+.|++++|++.|++. ...| +...|..+..++...|++++|+..++++++++|+++..+..++.+|...|++++
T Consensus        84 g~~l~~~g~~~~A~~~~~kAl~l~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~~~g~~~~  163 (723)
T 4gyw_A           84 GNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTD  163 (723)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCCTT
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHHHhcccHHH
Confidence            88888888888888888887 4445 456889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHh
Q 040394          653 VNQVRELMKQ  662 (691)
Q Consensus       653 A~~~~~~~~~  662 (691)
                      |.+.++++++
T Consensus       164 A~~~~~kal~  173 (723)
T 4gyw_A          164 YDERMKKLVS  173 (723)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999888765

>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=99.26  E-value=1.8e-10  Score=103.21  Aligned_cols=130  Identities=14%  Similarity=0.043  Sum_probs=85.4

Q ss_pred             HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC--CCCCCHHHHHHHHHHH
Q 040394          533 VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM--PIEPDVSLFGAFLHGC  610 (691)
Q Consensus       533 ~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~--~~~p~~~~~~~l~~~~  610 (691)
                      ..+..+...+...|++++|...++++.+.  .+.+...+..+...+...|++++|.+.++++  ..+.+...+..+...+
T Consensus        43 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~  120 (186)
T 3as5_A           43 DVALHLGIAYVKTGAVDRGTELLERSLAD--APDNVKVATVLGLTYVQVQKYDLAVPLLIKVAEANPINFNVRFRLGVAL  120 (186)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCcHhHHHHHHHHHHH
Confidence            34444444444455555555555444322  1112444555555666666666666666655  1234556777777888


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          611 GLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       611 ~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      ...|++++|...++++.+..|+++..+..++.++...|++++|.+.+++..+..
T Consensus       121 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  174 (186)
T 3as5_A          121 DNLGRFDEAIDSFKIALGLRPNEGKVHRAIAFSYEQMGRHEEALPHFKKANELD  174 (186)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHcCcHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC
Confidence            888888888888888888888888888888888888888888888888877643

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.24  E-value=5.8e-10  Score=99.87  Aligned_cols=162  Identities=10%  Similarity=0.018  Sum_probs=95.9

Q ss_pred             HHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCC
Q 040394          347 HVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNV  426 (691)
Q Consensus       347 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~  426 (691)
                      ...|..+...+...|++++|...++.+.+..|.+..++..+..+|.+.|++++|...+......               .
T Consensus         5 ~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~---------------~   69 (184)
T 3vtx_A            5 TTIYMDIGDKKRTKGDFDGAIRAYKKVLKADPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVL---------------D   69 (184)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------------C
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc---------------C
Confidence            3445555555555555555555555555555555555566666666666666666666554432               1


Q ss_pred             CCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHH
Q 040394          427 SPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAM  503 (691)
Q Consensus       427 ~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~l  503 (691)
                      +.+...+..+...+...++.+.+...+....+..  |.+...+..+...|.+.|++++|+..|++..+   .+..+|..+
T Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~--~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~l  147 (184)
T 3vtx_A           70 TTSAEAYYILGSANFMIDEKQAAIDALQRAIALN--TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPGFIRAYQSI  147 (184)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcchhhhHHHHH
Confidence            2233444455555556666666666666666655  55666666666666666666666666666553   245566666


Q ss_pred             HHHHhcCCChHHHHHHHHHHHH
Q 040394          504 IGGYGMQGDGGGSLALFSDMLN  525 (691)
Q Consensus       504 i~~~~~~~~~~~A~~~~~~m~~  525 (691)
                      ...|.+.|++++|++.|++..+
T Consensus       148 g~~~~~~g~~~~A~~~~~~al~  169 (184)
T 3vtx_A          148 GLAYEGKGLRDEAVKYFKKALE  169 (184)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHh
Confidence            6666666666666666666665

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.23  E-value=2.1e-09  Score=105.19  Aligned_cols=180  Identities=12%  Similarity=0.047  Sum_probs=114.4

Q ss_pred             hhHHHHHHHHHH-hCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCC-HH-HHHHHHHHH
Q 040394          364 NMGRMVHSLGIR-LGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPD-AV-TLVSVISAC  440 (691)
Q Consensus       364 ~~a~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~-~~-~~~~ll~~~  440 (691)
                      ++|..+++.+.+ ..+.+...+..++..+.+.|++++|..+|++..+.                .|+ .. .|..+...+
T Consensus        81 ~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~----------------~p~~~~~~~~~~~~~~  144 (308)
T 2ond_A           81 DEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI----------------EDIDPTLVYIQYMKFA  144 (308)
T ss_dssp             HHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS----------------SSSCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc----------------cccCccHHHHHHHHHH
Confidence            455555555555 34445555566666666666666666666665532                232 22 566666666


Q ss_pred             hccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHH-hcCCHHHHHHHHHhccc--C-CHhHHHHHHHHHhcCCChHHH
Q 040394          441 ASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYA-KCGDAQSARMVFDAMRE--K-NTVTWSAMIGGYGMQGDGGGS  516 (691)
Q Consensus       441 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~g~~~~A~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~A  516 (691)
                      .+.|+++.|..+|+...+..  |.+...|........ ..|++++|..+|+...+  | +...|..++..+.+.|++++|
T Consensus       145 ~~~~~~~~A~~~~~~a~~~~--p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~A  222 (308)
T 2ond_A          145 RRAEGIKSGRMIFKKAREDA--RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNT  222 (308)
T ss_dssp             HHHHCHHHHHHHHHHHHTST--TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHH
T ss_pred             HHhcCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHH
Confidence            66777777777777776655  444555544433322 25777788777777653  2 566777777777778888888


Q ss_pred             HHHHHHHHHCC-CCCC--HHHHHHHHHHhcccCCHHHHHHHHHHchhh
Q 040394          517 LALFSDMLNEE-VQPN--EVIFTTILSACSHTGMVGEGWKCFYSMCRD  561 (691)
Q Consensus       517 ~~~~~~m~~~g-~~p~--~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~  561 (691)
                      ..+|++..+.. +.|+  ...|..++......|+.+.|..+++++.+.
T Consensus       223 ~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a~~~  270 (308)
T 2ond_A          223 RVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             HHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            88888887753 3543  456666777777778888888888777544

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.22  E-value=1.6e-09  Score=109.56  Aligned_cols=196  Identities=9%  Similarity=0.062  Sum_probs=96.8

Q ss_pred             HHHHHHHHHhccCcHHHHHHHHHHHHHcCCC-----CCchhHHHHHHHHHHhcCCHHHHHHHHHhccc-----CC----H
Q 040394          432 TLVSVISACASLGAVQVGSSLHAYSTKQGLL-----SSNVYVGTALLNFYAKCGDAQSARMVFDAMRE-----KN----T  497 (691)
Q Consensus       432 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-----~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~----~  497 (691)
                      ++..+...+...|+++.|...+++..+....     +....+++.+...|...|++++|...|++..+     ++    .
T Consensus       143 ~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~  222 (378)
T 3q15_A          143 FHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIA  222 (378)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            4555556666666666666666655442110     01234455666666677777777666665442     11    2


Q ss_pred             hHHHHHHHHHhcCCChHHHHHHHHHHHHC----CCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC---hhH
Q 040394          498 VTWSAMIGGYGMQGDGGGSLALFSDMLNE----EVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS---MKH  570 (691)
Q Consensus       498 ~~~~~li~~~~~~~~~~~A~~~~~~m~~~----g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~---~~~  570 (691)
                      .++..+...|...|++++|+..+++..+.    +.+....++..+..++.+.|++++|...+++......-.++   ...
T Consensus       223 ~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  302 (378)
T 3q15_A          223 ISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKEL  302 (378)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            34555666666666666666666665541    11112344455555555666666666666554333221111   223


Q ss_pred             HHHHHHHHHhcCC---hHHHHHHHHhCCCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 040394          571 YVCMVDLLARAGR---LEEALEFMENMPIEPDV-SLFGAFLHGCGLYSRFDLGEVMIKKML  627 (691)
Q Consensus       571 ~~~li~~~~~~g~---~~~A~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~  627 (691)
                      +..+...+...|+   .++|+..+++.+..|+. ..+..+...|...|++++|...++++.
T Consensus       303 ~~~l~~ly~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al  363 (378)
T 3q15_A          303 FLFLQAVYKETVDERKIHDLLSYFEKKNLHAYIEACARSAAAVFESSCHFEQAAAFYRKVL  363 (378)
T ss_dssp             HHHHHHHHSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCcHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3333344444444   45555555544322222 233344444444555555555554444

>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=99.22  E-value=7.9e-10  Score=102.93  Aligned_cols=205  Identities=8%  Similarity=0.039  Sum_probs=154.8

Q ss_pred             CCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-CHhHHHHH
Q 040394          427 SPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--K-NTVTWSAM  503 (691)
Q Consensus       427 ~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~l  503 (691)
                      ..|+..+......+...|++++|...|+...+... +++...+..+...+...|++++|...|++..+  | +...|..+
T Consensus         4 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l   82 (228)
T 4i17_A            4 TTDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTN-NQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNYNLANAYIGK   82 (228)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT-TCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCSHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccC-CCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCcchHHHHHHH
Confidence            34667888888899999999999999999998873 37777777789999999999999999998774  3 45678889


Q ss_pred             HHHHhcCCChHHHHHHHHHHHHCCCCCC-H-------HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC---hhHHH
Q 040394          504 IGGYGMQGDGGGSLALFSDMLNEEVQPN-E-------VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS---MKHYV  572 (691)
Q Consensus       504 i~~~~~~~~~~~A~~~~~~m~~~g~~p~-~-------~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~---~~~~~  572 (691)
                      ...|...|++++|+..+++..+.  .|+ .       ..|..+-..+...|++++|.+.|++..   .+.|+   ...+.
T Consensus        83 ~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al---~~~p~~~~~~~~~  157 (228)
T 4i17_A           83 SAAYRDMKNNQEYIATLTEGIKA--VPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHAT---DVTSKKWKTDALY  157 (228)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT---TSSCHHHHHHHHH
T ss_pred             HHHHHHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHH---hcCCCcccHHHHH
Confidence            99999999999999999999885  444 3       346666667788899999999999664   45665   45677


Q ss_pred             HHHHHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHH
Q 040394          573 CMVDLLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLY  644 (691)
Q Consensus       573 ~li~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~  644 (691)
                      .+..+|...|+.     .++++ . ...+...+....  ....+.+++|...+++++++.|+++.+...+..+.
T Consensus       158 ~l~~~~~~~~~~-----~~~~a~~~~~~~~~~~~~~~--~~~~~~~~~A~~~~~~a~~l~p~~~~~~~~l~~i~  224 (228)
T 4i17_A          158 SLGVLFYNNGAD-----VLRKATPLASSNKEKYASEK--AKADAAFKKAVDYLGEAVTLSPNRTEIKQMQDQVK  224 (228)
T ss_dssp             HHHHHHHHHHHH-----HHHHHGGGTTTCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH-----HHHHHHhcccCCHHHHHHHH--HHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHH
Confidence            777777665543     22222 1 122333443332  33456789999999999999999988888777664

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.20  E-value=6.5e-10  Score=115.76  Aligned_cols=208  Identities=13%  Similarity=-0.019  Sum_probs=147.8

Q ss_pred             chhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCCh-hhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHh
Q 040394          328 PDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNL-NMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFET  406 (691)
Q Consensus       328 ~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  406 (691)
                      ++++++.+++.... ...+...+..+...+...|++ ++|...++.+.+..+.+..++..+..+|.+.|++++|...|++
T Consensus        84 ~~~al~~l~~~~~~-~~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~  162 (474)
T 4abn_A           84 MEKTLQQMEEVLGS-AQVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEPELVEAWNQLGEVYWKKGDVTSAHTCFSG  162 (474)
T ss_dssp             HHHHHHHHHHHHTT-CCCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcc-CchhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            45666666655443 223567777777788888998 9999999999888888888999999999999999999999999


Q ss_pred             CCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhcc---------CcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHH
Q 040394          407 TSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASL---------GAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYA  477 (691)
Q Consensus       407 ~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~---------~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~  477 (691)
                      ..+.                .|+...+..+...+...         |++++|...+++..+..  |.+...+..+...|.
T Consensus       163 al~~----------------~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~  224 (474)
T 4abn_A          163 ALTH----------------CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD--VLDGRSWYILGNAYL  224 (474)
T ss_dssp             HHTT----------------CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHH
T ss_pred             HHhh----------------CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHH
Confidence            8754                57778888888888888         89999999999988887  677788888888777


Q ss_pred             hc--------CCHHHHHHHHHhccc--C----CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhc
Q 040394          478 KC--------GDAQSARMVFDAMRE--K----NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACS  543 (691)
Q Consensus       478 ~~--------g~~~~A~~~~~~~~~--~----~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~  543 (691)
                      ..        |++++|...|++..+  |    +...|..+...|...|++++|+..|++..+.. +-+...+..+..++.
T Consensus       225 ~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~a~~~l~~~~~  303 (474)
T 4abn_A          225 SLYFNTGQNPKISQQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALD-PAWPEPQQREQQLLE  303 (474)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHhhccccchHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence            77        667777666666543  2    44455556666666666666666666655531 112233444444444


Q ss_pred             ccCCHHHHHHHH
Q 040394          544 HTGMVGEGWKCF  555 (691)
Q Consensus       544 ~~g~~~~A~~~~  555 (691)
                      ..|++++|.+.+
T Consensus       304 ~lg~~~eAi~~~  315 (474)
T 4abn_A          304 FLSRLTSLLESK  315 (474)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHh
Confidence            555555554433

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.20  E-value=5.6e-09  Score=105.40  Aligned_cols=264  Identities=9%  Similarity=-0.021  Sum_probs=188.4

Q ss_pred             HHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCH----HHHHHHHHHHhccCcHHHHHHHHHHHHHcC
Q 040394          385 NALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDA----VTLVSVISACASLGAVQVGSSLHAYSTKQG  460 (691)
Q Consensus       385 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~----~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  460 (691)
                      ......+...|++++|...+++.....              ...+.    .++..+...+...|+++.|...+++..+..
T Consensus        18 ~~~a~~~~~~g~~~~A~~~~~~al~~~--------------~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~   83 (373)
T 1hz4_A           18 ALRAQVAINDGNPDEAERLAKLALEEL--------------PPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMA   83 (373)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHTC--------------CTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHcC--------------CCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHH
Confidence            444556677899999988887754321              01111    245666677888999999999999877532


Q ss_pred             CCCCc----hhHHHHHHHHHHhcCCHHHHHHHHHhccc----------C-CHhHHHHHHHHHhcCCChHHHHHHHHHHHH
Q 040394          461 LLSSN----VYVGTALLNFYAKCGDAQSARMVFDAMRE----------K-NTVTWSAMIGGYGMQGDGGGSLALFSDMLN  525 (691)
Q Consensus       461 ~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----------~-~~~~~~~li~~~~~~~~~~~A~~~~~~m~~  525 (691)
                      ....+    ...+..+...+...|++++|...+++..+          + ....+..+...+...|++++|...+++..+
T Consensus        84 ~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  163 (373)
T 1hz4_A           84 RQHDVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIE  163 (373)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HhcCcHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            10111    23356678889999999999999987653          1 123566788889999999999999999886


Q ss_pred             CCCC--C--CHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHH-----HHHHHHHhcCChHHHHHHHHhC-C
Q 040394          526 EEVQ--P--NEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYV-----CMVDLLARAGRLEEALEFMENM-P  595 (691)
Q Consensus       526 ~g~~--p--~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~-----~li~~~~~~g~~~~A~~~~~~~-~  595 (691)
                      ....  +  ...++..+...+...|++++|...+++......-......+.     ..+..+...|++++|.+.+++. .
T Consensus       164 ~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~  243 (373)
T 1hz4_A          164 VLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAK  243 (373)
T ss_dssp             HTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCC
T ss_pred             HhhccCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCC
Confidence            4221  1  235677777788999999999999998754322111111121     2334577999999999999998 2


Q ss_pred             CCCC-----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC------chhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          596 IEPD-----VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK------ACYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       596 ~~p~-----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      ..|.     ...+..+...+...|++++|...++++.+..+..      ...+..++.++...|++++|.+.+++..+
T Consensus       244 ~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~  321 (373)
T 1hz4_A          244 PEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  321 (373)
T ss_dssp             CCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             CCCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            2222     2256677888899999999999999998753321      23677889999999999999999988765

>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=99.18  E-value=4.6e-10  Score=104.52  Aligned_cols=190  Identities=11%  Similarity=-0.038  Sum_probs=117.2

Q ss_pred             CCchhHHHHHHHHHHhcCCHHHHHHHHHhccc----CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCH-HHHHH
Q 040394          463 SSNVYVGTALLNFYAKCGDAQSARMVFDAMRE----KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNE-VIFTT  537 (691)
Q Consensus       463 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~-~~~~~  537 (691)
                      +.++..+......+...|++++|...|++..+    ++...+..+..++...|++++|+..+++..+.  .|+. ..+..
T Consensus         4 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~   81 (228)
T 4i17_A            4 TTDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKK--NYNLANAYIG   81 (228)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TCSHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHh--CcchHHHHHH
Confidence            34556666677777777777777777776553    45555655677777777777777777777763  4433 45555


Q ss_pred             HHHHhcccCCHHHHHHHHHHchhhcCCCCC-h-------hHHHHHHHHHHhcCChHHHHHHHHhC-CCCCC---HHHHHH
Q 040394          538 ILSACSHTGMVGEGWKCFYSMCRDFKFVPS-M-------KHYVCMVDLLARAGRLEEALEFMENM-PIEPD---VSLFGA  605 (691)
Q Consensus       538 ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~-------~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~---~~~~~~  605 (691)
                      +..++...|++++|.+.+++..+.   .|+ .       ..|..+...+...|++++|++.+++. ...|+   ...|..
T Consensus        82 l~~~~~~~~~~~~A~~~~~~al~~---~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~  158 (228)
T 4i17_A           82 KSAAYRDMKNNQEYIATLTEGIKA---VPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVTSKKWKTDALYS  158 (228)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSSCHHHHHHHHHH
T ss_pred             HHHHHHHcccHHHHHHHHHHHHHH---CCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcCCCcccHHHHHH
Confidence            666677777777777777766433   333 2       34555666666667777777766665 44554   235555


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          606 FLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       606 l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      +...+..     .+...++++..+.+.+...+...  .....|.+++|...+++..+..
T Consensus       159 l~~~~~~-----~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~~~~A~~~~~~a~~l~  210 (228)
T 4i17_A          159 LGVLFYN-----NGADVLRKATPLASSNKEKYASE--KAKADAAFKKAVDYLGEAVTLS  210 (228)
T ss_dssp             HHHHHHH-----HHHHHHHHHGGGTTTCHHHHHHH--HHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHH-----HHHHHHHHHHhcccCCHHHHHHH--HHHHHHHHHHHHHHHHHHhhcC
Confidence            5555533     33444555555555544333322  2344556699999999998754

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.18  E-value=7.9e-11  Score=115.62  Aligned_cols=246  Identities=11%  Similarity=-0.012  Sum_probs=166.0

Q ss_pred             chhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHc
Q 040394          380 DYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQ  459 (691)
Q Consensus       380 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  459 (691)
                      ...++..+...+...|++++|..+++++.+.-.       .......+....++..+...+...|++++|...++...+.
T Consensus        26 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~-------~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~   98 (311)
T 3nf1_A           26 RLRTLHNLVIQYASQGRYEVAVPLCKQALEDLE-------KTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAI   98 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH-------HHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH-------HHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            455567777778888888888887777653100       0000001223456788888999999999999999988765


Q ss_pred             ------CCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc-------C----CHhHHHHHHHHHhcCCChHHHHHHHHH
Q 040394          460 ------GLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE-------K----NTVTWSAMIGGYGMQGDGGGSLALFSD  522 (691)
Q Consensus       460 ------~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-------~----~~~~~~~li~~~~~~~~~~~A~~~~~~  522 (691)
                            +..+.....+..+...|...|++++|...+++..+       +    ....+..+...+...|++++|+.++++
T Consensus        99 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~  178 (311)
T 3nf1_A           99 REKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQR  178 (311)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHhCCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence                  22144567888899999999999999999998763       1    244688889999999999999999999


Q ss_pred             HHHC------CCCCCH-HHHHHHHHHhcccCCHHHHHHHHHHchhhc------CCCCChh-H------HHHHHHHHHhcC
Q 040394          523 MLNE------EVQPNE-VIFTTILSACSHTGMVGEGWKCFYSMCRDF------KFVPSMK-H------YVCMVDLLARAG  582 (691)
Q Consensus       523 m~~~------g~~p~~-~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~------~~~p~~~-~------~~~li~~~~~~g  582 (691)
                      +.+.      +-.|+. .++..+..++...|++++|.+.++++....      ...+... .      +..+...+...+
T Consensus       179 a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  258 (311)
T 3nf1_A          179 ALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGT  258 (311)
T ss_dssp             HHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-------C
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHH
Confidence            8874      223333 467778889999999999999999885421      1222211 1      222223334445


Q ss_pred             ChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040394          583 RLEEALEFMENMP-IEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPD  632 (691)
Q Consensus       583 ~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~  632 (691)
                      .+.+|...++... ..| +..++..+...|...|++++|...+++++++.|+
T Consensus       259 ~~~~a~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l~~~  310 (311)
T 3nf1_A          259 SFGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEEAAMRSRKQ  310 (311)
T ss_dssp             CSCCCC---------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhc
Confidence            5555666666662 333 3457888999999999999999999999988775

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.17  E-value=2.6e-09  Score=108.07  Aligned_cols=226  Identities=10%  Similarity=-0.017  Sum_probs=170.4

Q ss_pred             HHHHHhccCcHHHHHHHHHHHHHcCCC----CCchhHHHHHHHHHHhcCCHHHHHHHHHhccc-----CC-----HhHHH
Q 040394          436 VISACASLGAVQVGSSLHAYSTKQGLL----SSNVYVGTALLNFYAKCGDAQSARMVFDAMRE-----KN-----TVTWS  501 (691)
Q Consensus       436 ll~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~-----~~~~~  501 (691)
                      ....+...|+++.|...+++..+....    +....++..+...|...|+++.|...+++..+     ++     ..+++
T Consensus       107 ~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  186 (378)
T 3q15_A          107 RGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLF  186 (378)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHH
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHH
Confidence            344567899999999999998764210    12356778889999999999999999987653     12     34788


Q ss_pred             HHHHHHhcCCChHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHhcccCCHHHHHHHHHHchhhcC--CCCC-hhHHHH
Q 040394          502 AMIGGYGMQGDGGGSLALFSDMLNE----EVQP-NEVIFTTILSACSHTGMVGEGWKCFYSMCRDFK--FVPS-MKHYVC  573 (691)
Q Consensus       502 ~li~~~~~~~~~~~A~~~~~~m~~~----g~~p-~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~--~~p~-~~~~~~  573 (691)
                      .+...|...|++++|.+.+++..+.    +-.+ ...++..+..++...|++++|.+.+++...-..  ..|. ..++..
T Consensus       187 ~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  266 (378)
T 3q15_A          187 VIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFG  266 (378)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHH
Confidence            8999999999999999999988763    1111 124667777889999999999999998754111  2233 667888


Q ss_pred             HHHHHHhcCChHHHHHHHHhC----CC--CCC-HHHHHHHHHHHHhcCC---HHHHHHHHHHHHhcCCCCchhHHHHHHH
Q 040394          574 MVDLLARAGRLEEALEFMENM----PI--EPD-VSLFGAFLHGCGLYSR---FDLGEVMIKKMLELHPDKACYYVLVSNL  643 (691)
Q Consensus       574 li~~~~~~g~~~~A~~~~~~~----~~--~p~-~~~~~~l~~~~~~~g~---~~~A~~~~~~~~~~~p~~~~~~~~l~~~  643 (691)
                      +...+.+.|++++|.+.+++.    ..  .|. ...+..+...+...++   +.+|...+++. ...|.....+..++.+
T Consensus       267 la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~-~~~~~~~~~~~~la~~  345 (378)
T 3q15_A          267 LSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKK-NLHAYIEACARSAAAV  345 (378)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhC-CChhHHHHHHHHHHHH
Confidence            999999999999999999887    11  222 2345566666777788   77888777762 2334445677899999


Q ss_pred             HHhCCCcHHHHHHHHHHHh
Q 040394          644 YASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       644 ~~~~g~~~~A~~~~~~~~~  662 (691)
                      |...|++++|.+.+++..+
T Consensus       346 y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          346 FESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHH
Confidence            9999999999999998875

>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=99.16  E-value=2e-09  Score=96.29  Aligned_cols=168  Identities=13%  Similarity=0.019  Sum_probs=137.0

Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHh
Q 040394          466 VYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSAC  542 (691)
Q Consensus       466 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~  542 (691)
                      ...+..+...+...|++++|...++++.+   .+...+..+...+...|++++|...++++.+.. +.+...+..+...+
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~   86 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYDADAFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTY   86 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCCTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHH
Confidence            44566677788888899999998888774   366778888888899999999999999988753 44567777888888


Q ss_pred             cccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHH
Q 040394          543 SHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGE  620 (691)
Q Consensus       543 ~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~  620 (691)
                      ...|++++|.+.++++...  .+.+...+..+...+...|++++|.+.+++. . .+.+...+..+...+...|++++|.
T Consensus        87 ~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~  164 (186)
T 3as5_A           87 VQVQKYDLAVPLLIKVAEA--NPINFNVRFRLGVALDNLGRFDEAIDSFKIALGLRPNEGKVHRAIAFSYEQMGRHEEAL  164 (186)
T ss_dssp             HHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHhc--CcHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCHHHHH
Confidence            8999999999999987544  2334677888889999999999999999887 2 3345678899999999999999999


Q ss_pred             HHHHHHHhcCCCCchh
Q 040394          621 VMIKKMLELHPDKACY  636 (691)
Q Consensus       621 ~~~~~~~~~~p~~~~~  636 (691)
                      ..++++.+..|+++..
T Consensus       165 ~~~~~~~~~~~~~~~~  180 (186)
T 3as5_A          165 PHFKKANELDEGASVE  180 (186)
T ss_dssp             HHHHHHHHHHHCCCGG
T ss_pred             HHHHHHHHcCCCchhh
Confidence            9999999988886543

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.10  E-value=2.7e-08  Score=100.41  Aligned_cols=257  Identities=7%  Similarity=-0.070  Sum_probs=148.2

Q ss_pred             HHHHHhCCChhHHHHHHHHHHHcCCCCCcc----hHHHHHHHHcccCChhHHHHHHHHHHHhCCC--C----hhHHHHHH
Q 040394          118 IRWYFLNDLYKDIVEFYKCMRKRLKEHDNF----VFSKVLKACCELRDIDEGMKVHCEIVKVGGP--D----SFVLTGLV  187 (691)
Q Consensus       118 l~~~~~~~~~~~a~~~~~~m~~~~~~~~~~----~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~--~----~~~~~~l~  187 (691)
                      ...+...|++++|...+++........+..    ++..+...+...|++++|...+++.....+.  +    ..++..+.
T Consensus        21 a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la  100 (373)
T 1hz4_A           21 AQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQS  100 (373)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            334456677777777777766543111111    3444445566677777777777776653311  1    23355666


Q ss_pred             HHhHhcCChHHHHHHHhccCC----------C-ChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCC--C--ChhhHHHH
Q 040394          188 DMYAKCRDIGSSRQVFDETLD----------K-NVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVE--G--NQITLGSL  252 (691)
Q Consensus       188 ~~~~~~g~~~~A~~~~~~~~~----------~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~--p--~~~t~~~l  252 (691)
                      ..+...|++++|...+++...          | ....+..+...+...|++++|...+++.......  +  ...++..+
T Consensus       101 ~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l  180 (373)
T 1hz4_A          101 EILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAML  180 (373)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHH
Confidence            677777777777777765421          1 1234556667777888888888888777543211  1  22456666


Q ss_pred             HHHHHccCChhhHHHHHHHHHHHCCCCch-HHHH-----HHHHHHHhcCCHHHHHHHHHhcCCCC-------hhHHHHHH
Q 040394          253 VTACAKLRALHQGKWLHGYILKIGIEINS-HLVT-----ALLDMYVKCGNIRDARSVFDELCSID-------LVSWTAMI  319 (691)
Q Consensus       253 i~~~~~~~~~~~a~~~~~~~~~~g~~~~~-~~~~-----~li~~~~~~g~~~~A~~~~~~~~~~~-------~~~~~~li  319 (691)
                      ...+...|++++|...++........++. ..+.     ..+..+...|++++|...+++...+.       ...+..+.
T Consensus       181 a~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~la  260 (373)
T 1hz4_A          181 IQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIA  260 (373)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHHH
Confidence            66777788888888888777654222211 1111     23344667888888888888774322       11355666


Q ss_pred             HHHHhcCCchhHHHHHHHhhHC----CCCCcHH-HHHHHHHHHhcCCChhhHHHHHHHHH
Q 040394          320 VGYTQSGYPDKALKLFTDKKWA----DFFPNHV-TIASVLSASAQLGNLNMGRMVHSLGI  374 (691)
Q Consensus       320 ~~~~~~g~~~~a~~~~~~m~~~----g~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~~~  374 (691)
                      ..+...|++++|.+.+++....    |..++.. .+..+..++...|+.++|...+....
T Consensus       261 ~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al  320 (373)
T 1hz4_A          261 RAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDAL  320 (373)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            7777788888888777766432    2111221 33333444555555555555554443

>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=99.07  E-value=9.5e-10  Score=106.04  Aligned_cols=221  Identities=12%  Similarity=0.109  Sum_probs=151.6

Q ss_pred             ccCcHHHHHHHHHHHHH-------cCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc-------C----CHhHHHHH
Q 040394          442 SLGAVQVGSSLHAYSTK-------QGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE-------K----NTVTWSAM  503 (691)
Q Consensus       442 ~~~~~~~a~~~~~~~~~-------~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-------~----~~~~~~~l  503 (691)
                      ..|+++.|...+++..+       ... +....++..+...|...|++++|...+++..+       +    ...+|..+
T Consensus        13 ~~~~~~~A~~~~~~al~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l   91 (283)
T 3edt_B           13 GLVPRGSAVPLCKQALEDLEKTSGHDH-PDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNL   91 (283)
T ss_dssp             CCSCSSSHHHHHHHHHHHHHHHHCSSS-HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHhcCCCC-HHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHH
Confidence            34555556655555443       232 44567788899999999999999999987652       1    24578888


Q ss_pred             HHHHhcCCChHHHHHHHHHHHHC------CCCCC-HHHHHHHHHHhcccCCHHHHHHHHHHchhhc-----CCCCC-hhH
Q 040394          504 IGGYGMQGDGGGSLALFSDMLNE------EVQPN-EVIFTTILSACSHTGMVGEGWKCFYSMCRDF-----KFVPS-MKH  570 (691)
Q Consensus       504 i~~~~~~~~~~~A~~~~~~m~~~------g~~p~-~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~-----~~~p~-~~~  570 (691)
                      ...|...|++++|...+++..+.      .-.|+ ..++..+...+...|++++|...+++.....     +..|+ ..+
T Consensus        92 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  171 (283)
T 3edt_B           92 AVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKT  171 (283)
T ss_dssp             HHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence            99999999999999999988764      11232 4567777888999999999999998875431     11333 567


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhC-C---------CCCCH-HHHHHHHHHHHhcCC------HHHHHHHHHHHHhcCCCC
Q 040394          571 YVCMVDLLARAGRLEEALEFMENM-P---------IEPDV-SLFGAFLHGCGLYSR------FDLGEVMIKKMLELHPDK  633 (691)
Q Consensus       571 ~~~li~~~~~~g~~~~A~~~~~~~-~---------~~p~~-~~~~~l~~~~~~~g~------~~~A~~~~~~~~~~~p~~  633 (691)
                      +..+...|.+.|++++|.+.+++. .         ..+.. ..|..+.......+.      +..+...++......|..
T Consensus       172 ~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  251 (283)
T 3edt_B          172 KNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKVDSPTV  251 (283)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCCCCHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCCCCHHH
Confidence            888899999999999999998877 1         12222 344444433333222      333333343333345666


Q ss_pred             chhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          634 ACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       634 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      ..++..++.+|...|++++|.+.+++.++.
T Consensus       252 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~  281 (283)
T 3edt_B          252 NTTLRSLGALYRRQGKLEAAHTLEDCASRN  281 (283)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            778899999999999999999999988763

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=99.00  E-value=2.8e-08  Score=92.00  Aligned_cols=182  Identities=13%  Similarity=0.005  Sum_probs=120.0

Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhccc--CC----HhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHH----HH
Q 040394          466 VYVGTALLNFYAKCGDAQSARMVFDAMRE--KN----TVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEV----IF  535 (691)
Q Consensus       466 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~----~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~----~~  535 (691)
                      ...+..+...+.+.|++++|...|+++.+  |+    ...+..+..+|.+.|++++|+..|+++.+.  .|+..    .+
T Consensus         4 ~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~--~P~~~~~~~a~   81 (225)
T 2yhc_A            4 PNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRL--NPTHPNIDYVM   81 (225)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCTTHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--CcCCCcHHHHH
Confidence            34455566778888899999888888774  32    246777788888888888888888888874  34321    23


Q ss_pred             HHHHHHhcc------------------cCCHHHHHHHHHHchhhcCCCCCh-hHHHHHHHHHHhcCChHHHHHHHHhCCC
Q 040394          536 TTILSACSH------------------TGMVGEGWKCFYSMCRDFKFVPSM-KHYVCMVDLLARAGRLEEALEFMENMPI  596 (691)
Q Consensus       536 ~~ll~~~~~------------------~g~~~~A~~~~~~m~~~~~~~p~~-~~~~~li~~~~~~g~~~~A~~~~~~~~~  596 (691)
                      ..+..++..                  .|++++|...|+++++   ..|+. ..+......    +......        
T Consensus        82 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~---~~P~~~~a~~a~~~l----~~~~~~~--------  146 (225)
T 2yhc_A           82 YMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVR---GYPNSQYTTDATKRL----VFLKDRL--------  146 (225)
T ss_dssp             HHHHHHHHHHHC--------------CCHHHHHHHHHHHHHHT---TCTTCTTHHHHHHHH----HHHHHHH--------
T ss_pred             HHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHH---HCcCChhHHHHHHHH----HHHHHHH--------
Confidence            333333332                  3456666666665532   23332 111111100    0000000        


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc---hhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCcc
Q 040394          597 EPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKA---CYYVLVSNLYASDGRWIRVNQVRELMKQRGLSK  667 (691)
Q Consensus       597 ~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~---~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~~  667 (691)
                         ......+...+.+.|++++|+..++++++..|+++   ..+..++.+|.+.|++++|.+.++.+...+...
T Consensus       147 ---~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~~~~  217 (225)
T 2yhc_A          147 ---AKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNT  217 (225)
T ss_dssp             ---HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCCSCC
T ss_pred             ---HHHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCc
Confidence               00113456678899999999999999999999976   568899999999999999999999998876543

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=98.97  E-value=1.3e-08  Score=110.36  Aligned_cols=156  Identities=7%  Similarity=0.018  Sum_probs=91.7

Q ss_pred             hhhHHHHHHhcCCChHHHHHHhccCCC---CCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcc
Q 040394           82 CNTKLVSMYGSFGHVKYARSVFDSMPN---PDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCE  158 (691)
Q Consensus        82 ~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~  158 (691)
                      .++.+..+|.+.|++++|++.|++..+   .+..+|+.+..+|.+.|++++|+..|++..+.. +-+...|..+..++..
T Consensus        11 al~nLG~~~~~~G~~~eAi~~~~kAl~l~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~-P~~~~a~~nLg~~l~~   89 (723)
T 4gyw_A           11 SLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS-PTFADAYSNMGNTLKE   89 (723)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHH
Confidence            566666666666666666666665432   234456666666666666666666666665542 2234556666666666


Q ss_pred             cCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCC---CChhhHHHHHHHHHhCCChhHHHHHHH
Q 040394          159 LRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLD---KNVVSWTSMIAGYVQNDCAQEGLVLFN  235 (691)
Q Consensus       159 ~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~A~~~~~  235 (691)
                      .|++++|.+.|++.++..+.+..+|+.+..+|.+.|++++|++.|++..+   .+...|..+...+...|++++|.+.++
T Consensus        90 ~g~~~~A~~~~~kAl~l~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~~~g~~~~A~~~~~  169 (723)
T 4gyw_A           90 MQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMK  169 (723)
T ss_dssp             TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCCTTHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHHHhcccHHHHHHHHH
Confidence            66666666666666666555666666666666666666666666655422   234455556666666666666666555


Q ss_pred             HHH
Q 040394          236 RMR  238 (691)
Q Consensus       236 ~m~  238 (691)
                      +..
T Consensus       170 kal  172 (723)
T 4gyw_A          170 KLV  172 (723)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            554

>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=98.97  E-value=1.3e-08  Score=85.18  Aligned_cols=126  Identities=14%  Similarity=0.119  Sum_probs=85.3

Q ss_pred             HHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhc
Q 040394          536 TTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLY  613 (691)
Q Consensus       536 ~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~  613 (691)
                      ..+...+...|++++|..+++++.+.  .+.+...+..+...+...|++++|.+.++++ . .+.+...+..+...+...
T Consensus         5 ~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~   82 (136)
T 2fo7_A            5 YNLGNAYYKQGDYDEAIEYYQKALEL--DPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQ   82 (136)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHcCcHHHHHHHHHHHHHc--CCcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHh
Confidence            33444455555555555555555322  1122445555566666666666666666665 1 233456677777788888


Q ss_pred             CCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          614 SRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       614 g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      |++++|...++++.+..|+++..+..++.++...|++++|.+.++++.+.
T Consensus        83 ~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  132 (136)
T 2fo7_A           83 GDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALEL  132 (136)
T ss_dssp             TCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHccHHHHHHHHHHHHcc
Confidence            88888888888888888888888888888888888888888888887764

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.97  E-value=5.7e-09  Score=101.12  Aligned_cols=185  Identities=10%  Similarity=-0.014  Sum_probs=97.3

Q ss_pred             HHhcCCHHHHHHHHHhccc-----CC----HhHHHHHHHHHhcCCChHHHHHHHHHHHHCCC---CCC--HHHHHHHHHH
Q 040394          476 YAKCGDAQSARMVFDAMRE-----KN----TVTWSAMIGGYGMQGDGGGSLALFSDMLNEEV---QPN--EVIFTTILSA  541 (691)
Q Consensus       476 ~~~~g~~~~A~~~~~~~~~-----~~----~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~---~p~--~~~~~~ll~~  541 (691)
                      |...|++++|...|++..+     .+    ..+|+.+...|...|++++|+..+++..+...   .+.  ..+++.+...
T Consensus        47 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~  126 (292)
T 1qqe_A           47 YRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEI  126 (292)
T ss_dssp             HHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4445555555555544332     01    23555555566666666666666555544210   000  2345555556


Q ss_pred             hccc-CCHHHHHHHHHHchhhcCCCCC----hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCC---H-----HHHHHHH
Q 040394          542 CSHT-GMVGEGWKCFYSMCRDFKFVPS----MKHYVCMVDLLARAGRLEEALEFMENM-PIEPD---V-----SLFGAFL  607 (691)
Q Consensus       542 ~~~~-g~~~~A~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~---~-----~~~~~l~  607 (691)
                      |... |++++|+..|++..+-..-..+    ..++..+...|.+.|++++|++.+++. ...|+   .     ..|..+.
T Consensus       127 ~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg  206 (292)
T 1qqe_A          127 LENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKG  206 (292)
T ss_dssp             HHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHH
T ss_pred             HHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHH
Confidence            6664 7777777776655332110001    235666677777777777777777776 22221   1     1455666


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCchh-----HHHHHHHHH--hCCCcHHHHHHHHHH
Q 040394          608 HGCGLYSRFDLGEVMIKKMLELHPDKACY-----YVLVSNLYA--SDGRWIRVNQVRELM  660 (691)
Q Consensus       608 ~~~~~~g~~~~A~~~~~~~~~~~p~~~~~-----~~~l~~~~~--~~g~~~~A~~~~~~~  660 (691)
                      .++...|++++|...+++++++.|+....     +..++..+.  ..+++++|...++++
T Consensus       207 ~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~l~~l~~~~~~~~~~~~~~A~~~~~~~  266 (292)
T 1qqe_A          207 LCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNF  266 (292)
T ss_dssp             HHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTS
T ss_pred             HHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHhccC
Confidence            66777777777777777777777765432     233444443  345677776666544

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.96  E-value=5.1e-08  Score=92.26  Aligned_cols=181  Identities=10%  Similarity=0.052  Sum_probs=117.7

Q ss_pred             HHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC-----CHhHHHHHHHHHhcCCChHHHHHHHHHH
Q 040394          449 GSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK-----NTVTWSAMIGGYGMQGDGGGSLALFSDM  523 (691)
Q Consensus       449 a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~~~~~~~li~~~~~~~~~~~A~~~~~~m  523 (691)
                      +...+++..+.+  +++......+..++...|++++|++++.+....     +...+..++..+.+.|+.+.|.+.+++|
T Consensus        85 a~~~l~~l~~~~--~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~  162 (310)
T 3mv2_B           85 NIEELENLLKDK--QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNY  162 (310)
T ss_dssp             CCHHHHHTTTTS--CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC--CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            445555555444  344444456667777777777777777776432     3456666777888888888888888888


Q ss_pred             HHCCCCC-----CHHHHHHHHHH--hcc--cCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC
Q 040394          524 LNEEVQP-----NEVIFTTILSA--CSH--TGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM  594 (691)
Q Consensus       524 ~~~g~~p-----~~~~~~~ll~~--~~~--~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~  594 (691)
                      .+  ..|     +..+...+..+  ...  .+++.+|..+|+++...   .|+..+...+..++.+.|++++|.+.++.+
T Consensus       163 ~~--~~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~---~p~~~~~~lLln~~~~~g~~~eAe~~L~~l  237 (310)
T 3mv2_B          163 TN--AIEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT---FPTWKTQLGLLNLHLQQRNIAEAQGIVELL  237 (310)
T ss_dssp             HH--HSCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT---SCSHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             Hh--cCccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh---CCCcccHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            77  356     35555555554  222  33788888888887433   344333334444788888888888887765


Q ss_pred             -CC----------CC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHH
Q 040394          595 -PI----------EP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYV  638 (691)
Q Consensus       595 -~~----------~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~  638 (691)
                       ..          .| |..+...++......|+  .|.++++++.+..|+++.+..
T Consensus       238 ~~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~~P~hp~i~d  291 (310)
T 3mv2_B          238 LSDYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKLDHEHAFIKH  291 (310)
T ss_dssp             HSHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHTTCCCHHHHH
T ss_pred             HHhcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHhCCCChHHHH
Confidence             21          24 44555455555556676  889999999999999876554

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.96  E-value=1.3e-08  Score=96.79  Aligned_cols=184  Identities=10%  Similarity=-0.021  Sum_probs=125.6

Q ss_pred             CCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-C---HhHHHHHHHHHhcCCChHHHHHHHHHHHHCCC-CCC-HHH
Q 040394          463 SSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--K-N---TVTWSAMIGGYGMQGDGGGSLALFSDMLNEEV-QPN-EVI  534 (691)
Q Consensus       463 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~---~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~-~p~-~~~  534 (691)
                      +.+...+-.+...+.+.|++++|...|+.+.+  | +   ...+..+..+|.+.|++++|+..|++..+... .|. ...
T Consensus        12 ~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a   91 (261)
T 3qky_A           12 HSSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYGRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQA   91 (261)
T ss_dssp             CSSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGCSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHH
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHH
Confidence            45566666777778888888888888887764  2 3   45677777778888888888888888877421 112 234


Q ss_pred             HHHHHHHhcc--------cCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHH
Q 040394          535 FTTILSACSH--------TGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGA  605 (691)
Q Consensus       535 ~~~ll~~~~~--------~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~  605 (691)
                      +..+..++..        .|++++|...|++..+.   .|+ ......+.......+..               ...+..
T Consensus        92 ~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~---~p~~~~~~~a~~~~~~~~~~~---------------~~~~~~  153 (261)
T 3qky_A           92 EYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDR---YPNHELVDDATQKIRELRAKL---------------ARKQYE  153 (261)
T ss_dssp             HHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHH---CTTCTTHHHHHHHHHHHHHHH---------------HHHHHH
T ss_pred             HHHHHHHHHHhcccccccchhHHHHHHHHHHHHHH---CcCchhHHHHHHHHHHHHHHH---------------HHHHHH
Confidence            5555556666        77778888877776544   343 22222211111100000               012456


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCc---hhHHHHHHHHHhC----------CCcHHHHHHHHHHHhCC
Q 040394          606 FLHGCGLYSRFDLGEVMIKKMLELHPDKA---CYYVLVSNLYASD----------GRWIRVNQVRELMKQRG  664 (691)
Q Consensus       606 l~~~~~~~g~~~~A~~~~~~~~~~~p~~~---~~~~~l~~~~~~~----------g~~~~A~~~~~~~~~~g  664 (691)
                      +...+...|++++|+..++++++..|+++   ..+..++.+|...          |++++|...++++++..
T Consensus       154 la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~  225 (261)
T 3qky_A          154 AARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIF  225 (261)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHC
Confidence            77889999999999999999999999854   5788899999876          89999999999998754

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.96  E-value=1.5e-08  Score=98.11  Aligned_cols=205  Identities=6%  Similarity=-0.056  Sum_probs=149.6

Q ss_pred             HHHHhccCcHHHHHHHHHHHHHc----CCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC-----C----HhHHHHH
Q 040394          437 ISACASLGAVQVGSSLHAYSTKQ----GLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK-----N----TVTWSAM  503 (691)
Q Consensus       437 l~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~----~~~~~~l  503 (691)
                      ...+...|++++|...+.+..+.    +..+....+++.+...|.+.|++++|...+++..+-     +    ..+|+.+
T Consensus        44 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~l  123 (292)
T 1qqe_A           44 ATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFEL  123 (292)
T ss_dssp             HHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            44677889999999999887654    320112568889999999999999999999887641     2    3578889


Q ss_pred             HHHHhcC-CChHHHHHHHHHHHHCCCC-CC----HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCCh-----hHHH
Q 040394          504 IGGYGMQ-GDGGGSLALFSDMLNEEVQ-PN----EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSM-----KHYV  572 (691)
Q Consensus       504 i~~~~~~-~~~~~A~~~~~~m~~~g~~-p~----~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~-----~~~~  572 (691)
                      ...|... |++++|+..|++..+.... .+    ..++..+...+...|++++|+..|++......-.+..     ..+.
T Consensus       124 g~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  203 (292)
T 1qqe_A          124 GEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFL  203 (292)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHH
T ss_pred             HHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Confidence            9999996 9999999999998873111 01    3467788889999999999999999885432111221     1567


Q ss_pred             HHHHHHHhcCChHHHHHHHHhC-CCCCCHH------HHHHHHHHHH--hcCCHHHHHHHHHHHHhcCCCCchhHHHHH
Q 040394          573 CMVDLLARAGRLEEALEFMENM-PIEPDVS------LFGAFLHGCG--LYSRFDLGEVMIKKMLELHPDKACYYVLVS  641 (691)
Q Consensus       573 ~li~~~~~~g~~~~A~~~~~~~-~~~p~~~------~~~~l~~~~~--~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~  641 (691)
                      .+..++...|++++|+..+++. ...|+..      .+..++.++.  ..+++++|...++++..++|.+...+..+-
T Consensus       204 ~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~l~~l~~~~~~~~~~~~~~A~~~~~~~~~l~~~~~~~~~~~k  281 (292)
T 1qqe_A          204 KKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMRLDKWKITILNKIK  281 (292)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCccHHHHHHHHHHHH
Confidence            7888899999999999999998 5555432      3444555554  457799999999888888887655444443

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.94  E-value=2.6e-08  Score=94.79  Aligned_cols=203  Identities=12%  Similarity=0.062  Sum_probs=147.9

Q ss_pred             CCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCc---hhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-C---H
Q 040394          427 SPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSN---VYVGTALLNFYAKCGDAQSARMVFDAMRE--K-N---T  497 (691)
Q Consensus       427 ~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~---~  497 (691)
                      +.+...+..+...+.+.|++++|...|+.+.+..  |.+   ...+..+..+|.+.|++++|...|+...+  | +   .
T Consensus        12 ~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~   89 (261)
T 3qky_A           12 HSSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYG--RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVP   89 (261)
T ss_dssp             CSSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC--SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHH
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC--CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhH
Confidence            3456777888888999999999999999999886  455   67788899999999999999999999875  3 1   3


Q ss_pred             hHHHHHHHHHhc--------CCChHHHHHHHHHHHHCCCCCCHH-HHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCCh
Q 040394          498 VTWSAMIGGYGM--------QGDGGGSLALFSDMLNEEVQPNEV-IFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSM  568 (691)
Q Consensus       498 ~~~~~li~~~~~--------~~~~~~A~~~~~~m~~~g~~p~~~-~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~  568 (691)
                      ..+..+..++..        .|++++|+..|++..+.  .|+.. ....              ...+..+...     -.
T Consensus        90 ~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~--~p~~~~~~~a--------------~~~~~~~~~~-----~~  148 (261)
T 3qky_A           90 QAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDR--YPNHELVDDA--------------TQKIRELRAK-----LA  148 (261)
T ss_dssp             HHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHH--CTTCTTHHHH--------------HHHHHHHHHH-----HH
T ss_pred             HHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHH--CcCchhHHHH--------------HHHHHHHHHH-----HH
Confidence            467778888888        99999999999999985  45432 1111              1111111000     01


Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhC-CCCCC----HHHHHHHHHHHHhc----------CCHHHHHHHHHHHHhcCCCC
Q 040394          569 KHYVCMVDLLARAGRLEEALEFMENM-PIEPD----VSLFGAFLHGCGLY----------SRFDLGEVMIKKMLELHPDK  633 (691)
Q Consensus       569 ~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~----~~~~~~l~~~~~~~----------g~~~~A~~~~~~~~~~~p~~  633 (691)
                      ..+..+...|.+.|++++|+..|+++ ...|+    ...+..+..++...          |++++|...++++++..|++
T Consensus       149 ~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~p~~  228 (261)
T 3qky_A          149 RKQYEAARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIFPDS  228 (261)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHCCCC
Confidence            22456778888999999999998887 33333    34677777777755          89999999999999999998


Q ss_pred             chh---HHHHHHHHHhCCCcHH
Q 040394          634 ACY---YVLVSNLYASDGRWIR  652 (691)
Q Consensus       634 ~~~---~~~l~~~~~~~g~~~~  652 (691)
                      +..   ...+..++...|++++
T Consensus       229 ~~~~~a~~~l~~~~~~~~~~~~  250 (261)
T 3qky_A          229 PLLRTAEELYTRARQRLTELEG  250 (261)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHHHHHHhhh
Confidence            643   4445555555554443

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.94  E-value=7e-08  Score=91.32  Aligned_cols=239  Identities=9%  Similarity=0.021  Sum_probs=167.1

Q ss_pred             HHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhH
Q 040394          389 DMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYV  468 (691)
Q Consensus       389 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  468 (691)
                      +-..-.|.+..++.-...+...                .++ ....-+.+++...|+.+..         ... +|....
T Consensus        21 kn~fy~G~yq~~i~e~~~~~~~----------------~~~-~~~~~~~Rs~iAlg~~~~~---------~~~-~~~~~a   73 (310)
T 3mv2_B           21 KQNYYTGNFVQCLQEIEKFSKV----------------TDN-TLLFYKAKTLLALGQYQSQ---------DPT-SKLGKV   73 (310)
T ss_dssp             HHHHTTTCHHHHTHHHHTSSCC----------------CCH-HHHHHHHHHHHHTTCCCCC---------CSS-STTHHH
T ss_pred             HHHHHhhHHHHHHHHHHhcCcc----------------chH-HHHHHHHHHHHHcCCCccC---------CCC-CHHHHH
Confidence            3445568888887755554322                122 2333345666666665421         111 344334


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHhcc
Q 040394          469 GTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQP-NEVIFTTILSACSH  544 (691)
Q Consensus       469 ~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p-~~~~~~~ll~~~~~  544 (691)
                      +..+...+ ..+    |...|++..+   ++..++..+..++...|++++|++++.+.+..|-.+ +...+...+..+.+
T Consensus        74 ~~~la~~~-~~~----a~~~l~~l~~~~~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~  148 (310)
T 3mv2_B           74 LDLYVQFL-DTK----NIEELENLLKDKQNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALL  148 (310)
T ss_dssp             HHHHHHHH-TTT----CCHHHHHTTTTSCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHh-ccc----HHHHHHHHHhcCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHH
Confidence            44444433 322    7778887663   455666788899999999999999999987765323 44677788889999


Q ss_pred             cCCHHHHHHHHHHchhhcCCCC-----ChhHHHHHHHH--HHh--cCChHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcC
Q 040394          545 TGMVGEGWKCFYSMCRDFKFVP-----SMKHYVCMVDL--LAR--AGRLEEALEFMENM-PIEPDVSLFGAFLHGCGLYS  614 (691)
Q Consensus       545 ~g~~~~A~~~~~~m~~~~~~~p-----~~~~~~~li~~--~~~--~g~~~~A~~~~~~~-~~~p~~~~~~~l~~~~~~~g  614 (691)
                      .|+.+.|.+.+++|. .  ..|     +..+...|..+  ...  .++.++|..+|+++ ...|+..+-..++.++.+.|
T Consensus       149 ~~r~d~A~k~l~~~~-~--~~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~~p~~~~~~lLln~~~~~g  225 (310)
T 3mv2_B          149 NNNVSTASTIFDNYT-N--AIEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQTFPTWKTQLGLLNLHLQQR  225 (310)
T ss_dssp             TTCHHHHHHHHHHHH-H--HSCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTTSCSHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHH-h--cCccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhCCCcccHHHHHHHHHHcC
Confidence            999999999999994 3  466     34555555555  333  34999999999999 45566444445555888999


Q ss_pred             CHHHHHHHHHHHHhc----------CCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          615 RFDLGEVMIKKMLEL----------HPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       615 ~~~~A~~~~~~~~~~----------~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      ++++|+..++.+.+.          +|+++.++..++.+....|+  +|.++++++.+..
T Consensus       226 ~~~eAe~~L~~l~~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~~  283 (310)
T 3mv2_B          226 NIAEAQGIVELLLSDYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKLD  283 (310)
T ss_dssp             CHHHHHHHHHHHHSHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHhC
Confidence            999999999988775          48899999888888888897  8999999999864

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.91  E-value=4e-08  Score=94.76  Aligned_cols=175  Identities=8%  Similarity=-0.056  Sum_probs=135.9

Q ss_pred             HHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHhcccCCHHHHHHHHHHchhh
Q 040394          483 QSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQP-NEVIFTTILSACSHTGMVGEGWKCFYSMCRD  561 (691)
Q Consensus       483 ~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p-~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~  561 (691)
                      +.....+......+...+..+...+...|++++|...|++..+.  .| +...+..+...+...|++++|...+++... 
T Consensus       103 ~~l~~~l~~~lp~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~-  179 (287)
T 3qou_A          103 EAIRALLDXVLPREEELXAQQAMQLMQESNYTDALPLLXDAWQL--SNQNGEIGLLLAETLIALNRSEDAEAVLXTIPL-  179 (287)
T ss_dssp             HHHHHHHHHHSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--TTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCG-
T ss_pred             HHHHHHHHHHcCCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHh--CCcchhHHHHHHHHHHHCCCHHHHHHHHHhCch-
Confidence            34444444444445556677778888889999999999988875  44 456777778888999999999999987743 


Q ss_pred             cCCCCChhHHHH-HHHHHHhcCChHHHHHHHHhC-CC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC--chh
Q 040394          562 FKFVPSMKHYVC-MVDLLARAGRLEEALEFMENM-PI-EPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK--ACY  636 (691)
Q Consensus       562 ~~~~p~~~~~~~-li~~~~~~g~~~~A~~~~~~~-~~-~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~--~~~  636 (691)
                        ..|+...... ....+.+.++.++|++.+++. .. +.+...+..+...+...|++++|...++++++.+|++  ...
T Consensus       180 --~~p~~~~~~~~~~~~l~~~~~~~~a~~~l~~al~~~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a  257 (287)
T 3qou_A          180 --QDQDTRYQGLVAQIELLXQAADTPEIQQLQQQVAENPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQT  257 (287)
T ss_dssp             --GGCSHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHH
T ss_pred             --hhcchHHHHHHHHHHHHhhcccCccHHHHHHHHhcCCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchH
Confidence              3566433322 233466778888888888887 33 4466789999999999999999999999999999998  789


Q ss_pred             HHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          637 YVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       637 ~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      +..++.++...|+.++|...+++.+.
T Consensus       258 ~~~l~~~~~~~g~~~~a~~~~r~al~  283 (287)
T 3qou_A          258 RXTFQEILAALGTGDALASXYRRQLY  283 (287)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHHH
Confidence            99999999999999999999887654

>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=98.90  E-value=1.4e-09  Score=93.43  Aligned_cols=139  Identities=12%  Similarity=0.017  Sum_probs=90.7

Q ss_pred             HHhcCCChHHHHHHHHHHHHCCCCCCH-HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCC
Q 040394          506 GYGMQGDGGGSLALFSDMLNEEVQPNE-VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGR  583 (691)
Q Consensus       506 ~~~~~~~~~~A~~~~~~m~~~g~~p~~-~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~  583 (691)
                      .+...|++++|++.+++....  .|+. ..+..+...|.+.|++++|++.|++.++   +.|+ ...|..+..+|.+.|+
T Consensus         6 ~~~~~~~~e~ai~~~~~a~~~--~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~---~~p~~~~a~~~lg~~~~~~~~   80 (150)
T 4ga2_A            6 MRRSKADVERYIASVQGSTPS--PRQKSIKGFYFAKLYYEAKEYDLAKKYICTYIN---VQERDPKAHRFLGLLYELEEN   80 (150)
T ss_dssp             -CCCHHHHHHHHHHHHHHSCS--HHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHcChHHHHHHHHHHhccc--CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCc
Confidence            344456666666666665442  3332 2344455566677777777777776543   3454 5667777777777777


Q ss_pred             hHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHH-HHHHHHhcCCCCchhHHHHHHHHHhCCC
Q 040394          584 LEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEV-MIKKMLELHPDKACYYVLVSNLYASDGR  649 (691)
Q Consensus       584 ~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~-~~~~~~~~~p~~~~~~~~l~~~~~~~g~  649 (691)
                      +++|+..|++. ...| +...|..+...+.+.|++++|.. +++++++++|+++.++...+.++...|+
T Consensus        81 ~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P~~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A           81 TDKAVECYRRSVELNPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFPGSPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHSTTCHHHHHHHHHHHHTCCC
T ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCc
Confidence            77777777776 4444 45677777777777887765554 4578888888888888877777777775

>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=98.88  E-value=5.6e-08  Score=81.30  Aligned_cols=131  Identities=15%  Similarity=0.191  Sum_probs=97.7

Q ss_pred             HHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHH
Q 040394          499 TWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLL  578 (691)
Q Consensus       499 ~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~  578 (691)
                      .|..+...+...|++++|..+++++.+.+ +.+...+..+...+...|++++|...++++...  .+.+...+..+...+
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~   79 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALEL--DPRSAEAWYNLGNAY   79 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHH--CCCchHHHHHHHHHH
Confidence            45666777777777888888887777653 335566667777777788888888888877443  122356677778888


Q ss_pred             HhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040394          579 ARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPD  632 (691)
Q Consensus       579 ~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~  632 (691)
                      ...|++++|.+.++++ . .+.+...+..+...+...|++++|...++++.+..|+
T Consensus        80 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~  135 (136)
T 2fo7_A           80 YKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR  135 (136)
T ss_dssp             HTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHSTT
T ss_pred             HHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHccHHHHHHHHHHHHccCCC
Confidence            8888888888888877 2 2345677888888899999999999999999988886

>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=98.86  E-value=1.5e-07  Score=86.05  Aligned_cols=172  Identities=6%  Similarity=-0.056  Sum_probs=113.8

Q ss_pred             HHHHHHhccc-CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccC----CHHHHHHHHHHch
Q 040394          485 ARMVFDAMRE-KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTG----MVGEGWKCFYSMC  559 (691)
Q Consensus       485 A~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g----~~~~A~~~~~~m~  559 (691)
                      |.+.|++..+ .+...+..+...|...+++++|+..|++..+.|   +...+..+-..|.. +    ++++|.+.|++..
T Consensus         5 A~~~~~~aa~~g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~   80 (212)
T 3rjv_A            5 PGSQYQQQAEAGDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLAEKAV   80 (212)
T ss_dssp             TTHHHHHHHHTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHH
Confidence            3344443332 345556666666666666777777777666654   34445555555555 4    6777777777652


Q ss_pred             hhcCCCCChhHHHHHHHHHHh----cCChHHHHHHHHhC-CCCCC---HHHHHHHHHHHHh----cCCHHHHHHHHHHHH
Q 040394          560 RDFKFVPSMKHYVCMVDLLAR----AGRLEEALEFMENM-PIEPD---VSLFGAFLHGCGL----YSRFDLGEVMIKKML  627 (691)
Q Consensus       560 ~~~~~~p~~~~~~~li~~~~~----~g~~~~A~~~~~~~-~~~p~---~~~~~~l~~~~~~----~g~~~~A~~~~~~~~  627 (691)
                      +.    -+...+..|...|..    .+++++|+++|++. ...|+   ...+..|...|..    .+++++|...++++.
T Consensus        81 ~~----g~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~  156 (212)
T 3rjv_A           81 EA----GSKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSS  156 (212)
T ss_dssp             HT----TCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHH
T ss_pred             HC----CCHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHH
Confidence            21    235556666666665    67788888887776 33442   6677777777777    778888888888888


Q ss_pred             hcCCCCchhHHHHHHHHHhC-C-----CcHHHHHHHHHHHhCCC
Q 040394          628 ELHPDKACYYVLVSNLYASD-G-----RWIRVNQVRELMKQRGL  665 (691)
Q Consensus       628 ~~~p~~~~~~~~l~~~~~~~-g-----~~~~A~~~~~~~~~~g~  665 (691)
                      +. |+++..+..|+.+|... |     ++++|.+.+++..+.|.
T Consensus       157 ~~-~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g~  199 (212)
T 3rjv_A          157 SL-SRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEGF  199 (212)
T ss_dssp             HT-SCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHTC
T ss_pred             Hc-CCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcCC
Confidence            87 56677888888888754 3     88888888888887765

>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=98.86  E-value=7.1e-09  Score=113.01  Aligned_cols=190  Identities=11%  Similarity=0.002  Sum_probs=134.5

Q ss_pred             hccCcHHHHHHHHHHHH--------HcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhc
Q 040394          441 ASLGAVQVGSSLHAYST--------KQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGM  509 (691)
Q Consensus       441 ~~~~~~~~a~~~~~~~~--------~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~  509 (691)
                      ...|++++|...++...        +..  +.+...+..+...|...|++++|...|++..+   .+...|..+..+|..
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~--p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~  479 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDF--SESVELPLMEVRALLDLGDVAKATRKLDDLAERVGWRWRLVWYRAVAELL  479 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CC--TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhccccccccc--ccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCcchHHHHHHHHHHHHH
Confidence            67788888888888887        444  66777788888888888888888888887764   366788888888888


Q ss_pred             CCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHH
Q 040394          510 QGDGGGSLALFSDMLNEEVQP-NEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEA  587 (691)
Q Consensus       510 ~~~~~~A~~~~~~m~~~g~~p-~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A  587 (691)
                      .|++++|+..|++..+.  .| +...+..+..++...|++++ .+.|++..+   +.|+ ...|..+..++.+.|++++|
T Consensus       480 ~g~~~~A~~~~~~al~l--~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~---~~P~~~~a~~~lg~~~~~~g~~~~A  553 (681)
T 2pzi_A          480 TGDYDSATKHFTEVLDT--FPGELAPKLALAATAELAGNTDE-HKFYQTVWS---TNDGVISAAFGLARARSAEGDRVGA  553 (681)
T ss_dssp             HTCHHHHHHHHHHHHHH--STTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             cCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHcCChHH-HHHHHHHHH---hCCchHHHHHHHHHHHHHcCCHHHH
Confidence            88888888888888874  34 44667777778888888888 888886643   3554 56777888888888888888


Q ss_pred             HHHHHhC-CCCCCH-HHHHHHHHHHHhcCC-----HHHHHHHHHHHHhcCCCCchhHH
Q 040394          588 LEFMENM-PIEPDV-SLFGAFLHGCGLYSR-----FDLGEVMIKKMLELHPDKACYYV  638 (691)
Q Consensus       588 ~~~~~~~-~~~p~~-~~~~~l~~~~~~~g~-----~~~A~~~~~~~~~~~p~~~~~~~  638 (691)
                      ++.|++. ...|+. ..+..+..++...++     .+...+..+......++.+....
T Consensus       554 ~~~~~~al~l~P~~~~a~~~~~~~~~~~~~~~~~~~~~~~~A~~~l~~~~~~~~~~~~  611 (681)
T 2pzi_A          554 VRTLDEVPPTSRHFTTARLTSAVTLLSGRSTSEVTEEQIRDAARRVEALPPTEPRVLQ  611 (681)
T ss_dssp             HHHHHTSCTTSTTHHHHHHHHHHHTC-------CCHHHHHHHHHHHHTSCTTSTTHHH
T ss_pred             HHHHHhhcccCcccHHHHHHHHHHHHccCCCCCCCHHHHHHHHHHHhhCCCCcHHHHH
Confidence            8888887 566664 466666666655554     23344444444446666555443

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.86  E-value=1.9e-08  Score=85.78  Aligned_cols=102  Identities=13%  Similarity=0.072  Sum_probs=91.1

Q ss_pred             CCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHH
Q 040394          563 KFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVL  639 (691)
Q Consensus       563 ~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~  639 (691)
                      .+.|+ ...+..+...+.+.|++++|++.|++. ...| +...|..+..++...|++++|+..|+++++++|+++..+..
T Consensus        30 ~l~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~~~~~~~~  109 (151)
T 3gyz_A           30 AIPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFH  109 (151)
T ss_dssp             CSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSSCCHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCCCcHHHHH
Confidence            56676 567778888999999999999999998 4444 57789999999999999999999999999999999999999


Q ss_pred             HHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          640 VSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       640 l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      ++.+|...|++++|.+.|++.++..
T Consensus       110 lg~~~~~lg~~~eA~~~~~~al~l~  134 (151)
T 3gyz_A          110 TGQCQLRLKAPLKAKECFELVIQHS  134 (151)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            9999999999999999999998854

>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=98.86  E-value=1.9e-08  Score=96.80  Aligned_cols=194  Identities=11%  Similarity=0.024  Sum_probs=95.5

Q ss_pred             chHHHHHHHHcccCChhHHHHHHHHHHHh------C-CC-ChhHHHHHHHHhHhcCChHHHHHHHhccCC----------
Q 040394          147 FVFSKVLKACCELRDIDEGMKVHCEIVKV------G-GP-DSFVLTGLVDMYAKCRDIGSSRQVFDETLD----------  208 (691)
Q Consensus       147 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~------~-~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----------  208 (691)
                      .++..+...+...|++++|...+++..+.      + .+ ...++..+...|...|++++|...|++..+          
T Consensus        44 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  123 (283)
T 3edt_B           44 TMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFH  123 (283)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCC
Confidence            34444445555555555555555554443      1 11 344555555555555555555555544311          


Q ss_pred             C-ChhhHHHHHHHHHhCCChhHHHHHHHHHHhC------CCCC-ChhhHHHHHHHHHccCChhhHHHHHHHHHHH-----
Q 040394          209 K-NVVSWTSMIAGYVQNDCAQEGLVLFNRMREG------FVEG-NQITLGSLVTACAKLRALHQGKWLHGYILKI-----  275 (691)
Q Consensus       209 ~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~------~~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~-----  275 (691)
                      | ...+|..+...+...|++++|.+.+++..+.      +-.| ...++..+...+...|++++|...++...+.     
T Consensus       124 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~  203 (283)
T 3edt_B          124 PDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILTRAHEKE  203 (283)
T ss_dssp             HHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhc
Confidence            1 2334555555666666666666666655442      1111 2344555666666666666666666666543     


Q ss_pred             --CCCCc-hHHHHHHHHHHHhcC------CHHHHHHHHHhcCCC---ChhHHHHHHHHHHhcCCchhHHHHHHHhhH
Q 040394          276 --GIEIN-SHLVTALLDMYVKCG------NIRDARSVFDELCSI---DLVSWTAMIVGYTQSGYPDKALKLFTDKKW  340 (691)
Q Consensus       276 --g~~~~-~~~~~~li~~~~~~g------~~~~A~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  340 (691)
                        ...+. ...+..+...+...+      .+..+...++.....   ...++..+...|...|++++|.+++++..+
T Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          204 FGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKVDSPTVNTTLRSLGALYRRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             SSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCCCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             CCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence              11111 222222222222222      234444444444322   234677788888888888888888887654

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=98.84  E-value=1.7e-06  Score=89.83  Aligned_cols=124  Identities=14%  Similarity=0.142  Sum_probs=62.4

Q ss_pred             hHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHh-ccCcHHHHHHHHHHHHHcC
Q 040394          382 TVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACA-SLGAVQVGSSLHAYSTKQG  460 (691)
Q Consensus       382 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~-~~~~~~~a~~~~~~~~~~~  460 (691)
                      .+|...+..+.+.+..+.|..+|++....                ..+...|......-. ..++.+.|..+|+...+..
T Consensus       287 ~lw~~y~~~~~r~~~~~~AR~i~~~A~~~----------------~~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~~  350 (493)
T 2uy1_A          287 LLRINHLNYVLKKRGLELFRKLFIELGNE----------------GVGPHVFIYCAFIEYYATGSRATPYNIFSSGLLKH  350 (493)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHHHTTS----------------CCCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHhhCC----------------CCChHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC
Confidence            34455555555556666666666665211                112223322111111 1224666666666666543


Q ss_pred             CCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHH
Q 040394          461 LLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDML  524 (691)
Q Consensus       461 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~  524 (691)
                        +.++..+...++...+.|+.+.|..+|+.+. .....|...+.--...|+.+.+.++++++.
T Consensus       351 --~~~~~~~~~yid~e~~~~~~~~aR~l~er~~-k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~  411 (493)
T 2uy1_A          351 --PDSTLLKEEFFLFLLRIGDEENARALFKRLE-KTSRMWDSMIEYEFMVGSMELFRELVDQKM  411 (493)
T ss_dssp             --TTCHHHHHHHHHHHHHHTCHHHHHHHHHHSC-CBHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             --CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence              3344444555555566666666666666653 234455555554445555555555555544

>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=98.83  E-value=1.3e-08  Score=87.20  Aligned_cols=121  Identities=11%  Similarity=-0.012  Sum_probs=102.7

Q ss_pred             HHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCH
Q 040394          540 SACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRF  616 (691)
Q Consensus       540 ~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~  616 (691)
                      ..+...|++++|++.++...   ...|+ ...+-.+...|.+.|++++|++.|++. ...| +..+|..+..++...|++
T Consensus         5 ~~~~~~~~~e~ai~~~~~a~---~~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~   81 (150)
T 4ga2_A            5 SMRRSKADVERYIASVQGST---PSPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQERDPKAHRFLGLLYELEENT   81 (150)
T ss_dssp             --CCCHHHHHHHHHHHHHHS---CSHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHcChHHHHHHHHHHhc---ccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCch
Confidence            35567789999999998653   45565 556677899999999999999999998 4445 567999999999999999


Q ss_pred             HHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHH-HHHHHhC
Q 040394          617 DLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQV-RELMKQR  663 (691)
Q Consensus       617 ~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~-~~~~~~~  663 (691)
                      ++|+..++++++++|+++.++..++.+|.+.|++++|.+. +++.++.
T Consensus        82 ~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l  129 (150)
T 4ga2_A           82 DKAVECYRRSVELNPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKL  129 (150)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999887765 5887764

>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=98.81  E-value=5.1e-08  Score=104.40  Aligned_cols=159  Identities=11%  Similarity=0.059  Sum_probs=120.9

Q ss_pred             cCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHH
Q 040394          479 CGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCF  555 (691)
Q Consensus       479 ~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~  555 (691)
                      .|++++|...+++..+   .+...|..+...+...|++++|.+.+++..+.. +.+...+..+..++...|++++|.+.+
T Consensus         2 ~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~   80 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGRVRWTQQRHAEAAVLL   80 (568)
T ss_dssp             -------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            4788999999988774   357789999999999999999999999998853 334677888888999999999999999


Q ss_pred             HHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhc---CCHHHHHHHHHHHHhc
Q 040394          556 YSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLY---SRFDLGEVMIKKMLEL  629 (691)
Q Consensus       556 ~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~---g~~~~A~~~~~~~~~~  629 (691)
                      ++..+.   .|+ ...+..+..+|.+.|++++|.+.+++. ...| +...+..+...+...   |++++|...++++++.
T Consensus        81 ~~al~~---~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~~  157 (568)
T 2vsy_A           81 QQASDA---APEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQ  157 (568)
T ss_dssp             HHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHH
T ss_pred             HHHHhc---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhc
Confidence            987543   455 678888999999999999999999987 3334 567888888999999   9999999999999999


Q ss_pred             CCCCchhHHHHH
Q 040394          630 HPDKACYYVLVS  641 (691)
Q Consensus       630 ~p~~~~~~~~l~  641 (691)
                      +|++...+..++
T Consensus       158 ~p~~~~~~~~l~  169 (568)
T 2vsy_A          158 GVGAVEPFAFLS  169 (568)
T ss_dssp             TCCCSCHHHHTT
T ss_pred             CCcccChHHHhC
Confidence            999888887775

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.80  E-value=9.4e-08  Score=87.16  Aligned_cols=128  Identities=5%  Similarity=0.030  Sum_probs=95.0

Q ss_pred             HHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHH
Q 040394          501 SAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLA  579 (691)
Q Consensus       501 ~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~  579 (691)
                      +.+...|.+.|++++|+..|++..+.. +-+...+..+..++...|++++|...|++..+   +.|+ ...+..+..+|.
T Consensus        58 ~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~---~~P~~~~a~~~lg~~~~  133 (208)
T 3urz_A           58 TELALAYKKNRNYDKAYLFYKELLQKA-PNNVDCLEACAEMQVCRGQEKDALRMYEKILQ---LEADNLAANIFLGNYYY  133 (208)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---cCCCCHHHHHHHHHHHH
Confidence            347888889999999999999988852 33556777888888999999999999997754   4565 677888888876


Q ss_pred             hcCC--hHHHHHHHHhCC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040394          580 RAGR--LEEALEFMENMP-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPD  632 (691)
Q Consensus       580 ~~g~--~~~A~~~~~~~~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~  632 (691)
                      ..|+  .+.+...+++.. ..|....+.....++...|++++|+..|++++++.|+
T Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~l~P~  189 (208)
T 3urz_A          134 LTAEQEKKKLETDYKKLSSPTKMQYARYRDGLSKLFTTRYEKARNSLQKVILRFPS  189 (208)
T ss_dssp             HHHHHHHHHHHHHHC---CCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTTSCC
T ss_pred             HHhHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC
Confidence            6654  445566666662 2233334555666677889999999999999999998

>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=98.79  E-value=6.5e-08  Score=85.58  Aligned_cols=77  Identities=9%  Similarity=0.028  Sum_probs=63.1

Q ss_pred             HHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC--chhHHHHHHHHHhCCCcHHHHHHHHHHH
Q 040394          586 EALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK--ACYYVLVSNLYASDGRWIRVNQVRELMK  661 (691)
Q Consensus       586 ~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~  661 (691)
                      +|++.+++. ...| +...+..+...+...|++++|...++++++.+|+.  +..+..++.++...|+.++|...+++.+
T Consensus        92 ~a~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~~al  171 (176)
T 2r5s_A           92 PELKRLEQELAANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYRRQL  171 (176)
T ss_dssp             HHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHHHHH
Confidence            355556555 3344 56788889999999999999999999999999875  4588999999999999999999998876


Q ss_pred             h
Q 040394          662 Q  662 (691)
Q Consensus       662 ~  662 (691)
                      .
T Consensus       172 ~  172 (176)
T 2r5s_A          172 Y  172 (176)
T ss_dssp             H
T ss_pred             H
Confidence            4

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.79  E-value=3.9e-08  Score=81.24  Aligned_cols=100  Identities=11%  Similarity=0.080  Sum_probs=66.6

Q ss_pred             CCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHH
Q 040394          564 FVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLV  640 (691)
Q Consensus       564 ~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l  640 (691)
                      +.|+ ...+......|.+.|++++|++.|++. ...| +...|..+..++.+.|++++|+..++++++++|+++..|..+
T Consensus         8 inP~~a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~l   87 (126)
T 4gco_A            8 INPELAQEEKNKGNEYFKKGDYPTAMRHYNEAVKRDPENAILYSNRAACLTKLMEFQRALDDCDTCIRLDSKFIKGYIRK   87 (126)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhhhhHHHHHH
Confidence            4454 345556666677777777777777665 3233 455666666677777777777777777777777777777777


Q ss_pred             HHHHHhCCCcHHHHHHHHHHHhC
Q 040394          641 SNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       641 ~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      +.+|...|++++|++.+++.++.
T Consensus        88 g~~~~~~~~~~~A~~~~~~al~l  110 (126)
T 4gco_A           88 AACLVAMREWSKAQRAYEDALQV  110 (126)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHH
Confidence            77777777777777777766653

>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=98.75  E-value=8.8e-08  Score=84.71  Aligned_cols=156  Identities=10%  Similarity=-0.055  Sum_probs=120.9

Q ss_pred             hhhHHHHHHhcCCChHHHHHHhccCCC---CCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHH-Hc
Q 040394           82 CNTKLVSMYGSFGHVKYARSVFDSMPN---PDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKA-CC  157 (691)
Q Consensus        82 ~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~-~~  157 (691)
                      ....+...+.+.|++++|...|++..+   .+...+..+..++...|++++|+..|++..+..  |+...+...... +.
T Consensus         8 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~--p~~~~~~~~~~~~~~   85 (176)
T 2r5s_A            8 QLLKQVSELLQQGEHAQALNVIQTLSDELQSRGDVKLAKADCLLETKQFELAQELLATIPLEY--QDNSYKSLIAKLELH   85 (176)
T ss_dssp             THHHHHHHHHHTTCHHHHHHHHHTSCHHHHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGG--CCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhcc--CChHHHHHHHHHHHH
Confidence            556678889999999999999999874   456789999999999999999999999987653  344332222111 22


Q ss_pred             ccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCC--CC---hhhHHHHHHHHHhCCChhHHHH
Q 040394          158 ELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLD--KN---VVSWTSMIAGYVQNDCAQEGLV  232 (691)
Q Consensus       158 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~---~~~~~~li~~~~~~g~~~~A~~  232 (691)
                      ..+....|...++...+..|.+...+..+...+...|++++|...|++..+  |+   ...+..+...+...|+.++|..
T Consensus        86 ~~~~~~~a~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~  165 (176)
T 2r5s_A           86 QQAAESPELKRLEQELAANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIAS  165 (176)
T ss_dssp             HHHTSCHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHH
T ss_pred             hhcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHH
Confidence            223444578899999998888899999999999999999999999988744  32   4478888888888999999988


Q ss_pred             HHHHHHh
Q 040394          233 LFNRMRE  239 (691)
Q Consensus       233 ~~~~m~~  239 (691)
                      .|++...
T Consensus       166 ~y~~al~  172 (176)
T 2r5s_A          166 KYRRQLY  172 (176)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8887653

>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=98.75  E-value=2e-07  Score=85.36  Aligned_cols=129  Identities=12%  Similarity=0.018  Sum_probs=94.5

Q ss_pred             hHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHH
Q 040394          498 VTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVD  576 (691)
Q Consensus       498 ~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~  576 (691)
                      ..+..+...+...|++++|+..+++.    +.|+...+..+..++...|++++|.+.+++....   .|+ ...+..+..
T Consensus         7 ~~~~~~g~~~~~~~~~~~A~~~~~~a----~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~---~~~~~~~~~~lg~   79 (213)
T 1hh8_A            7 ISLWNEGVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINR---DKHLAVAYFQRGM   79 (213)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHH----cCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CccchHHHHHHHH
Confidence            34556677777888888888888766    3567777777777888888888888888876443   343 667777888


Q ss_pred             HHHhcCChHHHHHHHHhC-CCCC-C----------------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC
Q 040394          577 LLARAGRLEEALEFMENM-PIEP-D----------------VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK  633 (691)
Q Consensus       577 ~~~~~g~~~~A~~~~~~~-~~~p-~----------------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~  633 (691)
                      +|...|++++|++.+++. ...| +                ...+..+..++...|++++|...++++++..|++
T Consensus        80 ~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~  154 (213)
T 1hh8_A           80 LYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEP  154 (213)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSG
T ss_pred             HHHHcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcCccc
Confidence            888888888888887776 2122 1                2567777777888888888888888888888875

>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=3.1e-07  Score=100.07  Aligned_cols=168  Identities=10%  Similarity=-0.045  Sum_probs=134.8

Q ss_pred             HhcCCHHHHHHHHHhcc--------c---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhccc
Q 040394          477 AKCGDAQSARMVFDAMR--------E---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHT  545 (691)
Q Consensus       477 ~~~g~~~~A~~~~~~~~--------~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~  545 (691)
                      ...|++++|++.+++..        +   .+...|..+...+...|++++|+..+++..+.. +-+...+..+-.++...
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~  480 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAERV-GWRWRLVWYRAVAELLT  480 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-cchHHHHHHHHHHHHHc
Confidence            67889999999998876        2   356788888889999999999999999988852 33556777777788899


Q ss_pred             CCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHH
Q 040394          546 GMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVM  622 (691)
Q Consensus       546 g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~  622 (691)
                      |++++|.+.|++..+   +.|+ ...+..+..+|.+.|++++ ++.|++. ...| +...|..+..++.+.|++++|...
T Consensus       481 g~~~~A~~~~~~al~---l~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~  556 (681)
T 2pzi_A          481 GDYDSATKHFTEVLD---TFPGELAPKLALAATAELAGNTDE-HKFYQTVWSTNDGVISAAFGLARARSAEGDRVGAVRT  556 (681)
T ss_dssp             TCHHHHHHHHHHHHH---HSTTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CCHHHHHHHHHHHHH---hCCCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCCchHHHHHHHHHHHHHcCCHHHHHHH
Confidence            999999999987753   4565 6778888889999999999 8888887 4344 556888888899999999999999


Q ss_pred             HHHHHhcCCCCchhHHHHHHHHHhCCC
Q 040394          623 IKKMLELHPDKACYYVLVSNLYASDGR  649 (691)
Q Consensus       623 ~~~~~~~~p~~~~~~~~l~~~~~~~g~  649 (691)
                      ++++++++|++...+..++.++...|+
T Consensus       557 ~~~al~l~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          557 LDEVPPTSRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HHTSCTTSTTHHHHHHHHHHHTC----
T ss_pred             HHhhcccCcccHHHHHHHHHHHHccCC
Confidence            999999999988899888888876555

>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=98.72  E-value=3.1e-07  Score=89.50  Aligned_cols=212  Identities=8%  Similarity=-0.033  Sum_probs=150.4

Q ss_pred             ccCcHHHHHHHHHHHHHcC---CC--CCc----hhHHHHHHHHHHhcCCHHHHHHHHHhccc-----CC----HhHHHHH
Q 040394          442 SLGAVQVGSSLHAYSTKQG---LL--SSN----VYVGTALLNFYAKCGDAQSARMVFDAMRE-----KN----TVTWSAM  503 (691)
Q Consensus       442 ~~~~~~~a~~~~~~~~~~~---~~--~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~----~~~~~~l  503 (691)
                      ..|++++|..++++..+..   +.  .++    ...|......|...|++++|...|.+..+     .+    ..+|+.+
T Consensus         3 ~~~~~~eA~~~~~~a~k~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~l   82 (307)
T 2ifu_A            3 AAQKISEAHEHIAKAEKYLKTSFMKWKPDYDSAASEYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQA   82 (307)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCCCSSSCSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHccccccCCCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            3567778888887666531   10  122    23566677788899999999999987663     12    3478888


Q ss_pred             HHHHhcCCChHHHHHHHHHHHHCCC---CCC--HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC----hhHHHHH
Q 040394          504 IGGYGMQGDGGGSLALFSDMLNEEV---QPN--EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS----MKHYVCM  574 (691)
Q Consensus       504 i~~~~~~~~~~~A~~~~~~m~~~g~---~p~--~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~----~~~~~~l  574 (691)
                      ...|...|++++|+..+++..+.-.   .|.  ..++..+...|.. |++++|++.|++...-..-..+    ..++..+
T Consensus        83 g~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~l  161 (307)
T 2ifu_A           83 GMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKA  161 (307)
T ss_dssp             HHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHH
Confidence            9999999999999999998765311   122  3567777778888 9999999999877543211111    4578889


Q ss_pred             HHHHHhcCChHHHHHHHHhC-CC---CCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchh-----HHHHH
Q 040394          575 VDLLARAGRLEEALEFMENM-PI---EPD----VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACY-----YVLVS  641 (691)
Q Consensus       575 i~~~~~~g~~~~A~~~~~~~-~~---~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~-----~~~l~  641 (691)
                      ...|.+.|++++|++.+++. ..   .++    ...+..++..+...|++++|...+++++ ..|+....     ...++
T Consensus       162 g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al-~~p~~~~~~e~~~l~~l~  240 (307)
T 2ifu_A          162 SRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY-SIPGFSGSEDCAALEDLL  240 (307)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT-TSTTSTTSHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh-CCCCCCCCHHHHHHHHHH
Confidence            99999999999999999987 11   112    2256666777778899999999999999 99976543     33444


Q ss_pred             HHHHhCCCcHHHHHH
Q 040394          642 NLYASDGRWIRVNQV  656 (691)
Q Consensus       642 ~~~~~~g~~~~A~~~  656 (691)
                      ..+ ..|+.+.+.++
T Consensus       241 ~~~-~~~d~~~~~~~  254 (307)
T 2ifu_A          241 QAY-DEQDEEQLLRV  254 (307)
T ss_dssp             HHH-HTTCHHHHHHH
T ss_pred             HHH-HhcCHHHHHHH
Confidence            544 56777666553

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.72  E-value=2.5e-06  Score=81.65  Aligned_cols=216  Identities=10%  Similarity=0.084  Sum_probs=167.8

Q ss_pred             ccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcC--CHHHHHHHHHhccc---CCHhHHHHHHHHH----hcC--
Q 040394          442 SLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCG--DAQSARMVFDAMRE---KNTVTWSAMIGGY----GMQ--  510 (691)
Q Consensus       442 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g--~~~~A~~~~~~~~~---~~~~~~~~li~~~----~~~--  510 (691)
                      +....++|....+.+...+  |....+++.--..+...|  ++++++..++.+..   .+...|+.-...+    ...  
T Consensus        45 ~~e~s~~aL~~t~~~L~~n--P~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk~y~aW~~R~~iL~~~~~~l~~  122 (306)
T 3dra_A           45 AEEYSERALHITELGINEL--ASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNEKNYQIWNYRQLIIGQIMELNNN  122 (306)
T ss_dssp             TTCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHHHTTT
T ss_pred             cCCCCHHHHHHHHHHHHHC--cHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCcccHHHHHHHHHHHHHHHHhccc
Confidence            3445578999999999998  788888888888888888  99999999998875   2455666544444    444  


Q ss_pred             -CChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHH--HHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCC----
Q 040394          511 -GDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVG--EGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGR----  583 (691)
Q Consensus       511 -~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~--~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~----  583 (691)
                       +++++++.+++++.+.. +-|...|+.--.++.+.|.++  ++++.++++.+.  -.-|...|+.-..++.+.|+    
T Consensus       123 ~~~~~~EL~~~~~~l~~~-pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~--d~~N~sAW~~R~~ll~~l~~~~~~  199 (306)
T 3dra_A          123 DFDPYREFDILEAMLSSD-PKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDT--DLKNNSAWSHRFFLLFSKKHLATD  199 (306)
T ss_dssp             CCCTHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHSSGGGCCH
T ss_pred             cCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHhccccchh
Confidence             78999999999999863 446677777666667777777  999999988654  22346677766666666666    


Q ss_pred             --hHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCC-HHHHHHHHHHHHhcC---CCCchhHHHHHHHHHhCCCcHHHHH
Q 040394          584 --LEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSR-FDLGEVMIKKMLELH---PDKACYYVLVSNLYASDGRWIRVNQ  655 (691)
Q Consensus       584 --~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~-~~~A~~~~~~~~~~~---p~~~~~~~~l~~~~~~~g~~~~A~~  655 (691)
                        ++++++.++++ . .+-|...|+.+...+.+.|+ .+.+..+.+++.++.   |.++..+..++.+|.+.|+.++|.+
T Consensus       200 ~~~~eEl~~~~~aI~~~p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~  279 (306)
T 3dra_A          200 NTIDEELNYVKDKIVKCPQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRT  279 (306)
T ss_dssp             HHHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             hhHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHH
Confidence              88899998887 3 34577899888888888777 444666777777765   8888999999999999999999999


Q ss_pred             HHHHHHh
Q 040394          656 VRELMKQ  662 (691)
Q Consensus       656 ~~~~~~~  662 (691)
                      .++.+.+
T Consensus       280 ~~~~l~~  286 (306)
T 3dra_A          280 VYDLLKS  286 (306)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            9999876

>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=98.71  E-value=5.1e-08  Score=83.19  Aligned_cols=101  Identities=9%  Similarity=0.070  Sum_probs=74.2

Q ss_pred             CCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHH
Q 040394          563 KFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PI-EPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVL  639 (691)
Q Consensus       563 ~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~-~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~  639 (691)
                      .+.|+ ...+..+...+.+.|++++|++.|++. .. +.+...|..+..++...|++++|+..++++++++|+++..+..
T Consensus        15 ~~~p~~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~   94 (148)
T 2vgx_A           15 EISSDTLEQLYSLAFNQYQSGXYEDAHXVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIXEPRFPFH   94 (148)
T ss_dssp             TCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHH
T ss_pred             cCCHhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHcCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHH
Confidence            34454 455666677777778888887777776 33 3356677777777778888888888888888888888888888


Q ss_pred             HHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          640 VSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       640 l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      ++.+|...|++++|.+.+++.++.
T Consensus        95 lg~~~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           95 AAECLLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHH
Confidence            888888888888888888777664

>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=98.70  E-value=1.4e-06  Score=84.31  Aligned_cols=160  Identities=9%  Similarity=-0.020  Sum_probs=116.9

Q ss_pred             HHHHHhcCCChHHHHHHHHHHHHCC-CCCCHH----HHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC----hhHHHH
Q 040394          503 MIGGYGMQGDGGGSLALFSDMLNEE-VQPNEV----IFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS----MKHYVC  573 (691)
Q Consensus       503 li~~~~~~~~~~~A~~~~~~m~~~g-~~p~~~----~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~----~~~~~~  573 (691)
                      .+..+...|++++|..++++..+.. ..|+..    .+..+...+...|++++|...+++......-.++    ..+++.
T Consensus        81 ~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~  160 (293)
T 3u3w_A           81 QVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENA  160 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHH
Confidence            3667778888888888888887632 122221    2333555667778899999988887543222223    236888


Q ss_pred             HHHHHHhcCChHHHHHHHHhC-----CCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC------chhHH
Q 040394          574 MVDLLARAGRLEEALEFMENM-----PIEPD----VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK------ACYYV  638 (691)
Q Consensus       574 li~~~~~~g~~~~A~~~~~~~-----~~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~------~~~~~  638 (691)
                      +..+|...|++++|++.++++     ..+.+    ..++..+...|.+.|++++|...+++++++.+..      ..++.
T Consensus       161 lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~  240 (293)
T 3u3w_A          161 IANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYY  240 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHH
Confidence            888999999999998888876     12112    2377888999999999999999999999854332      56889


Q ss_pred             HHHHHHHhCCC-cHHHHHHHHHHHh
Q 040394          639 LVSNLYASDGR-WIRVNQVRELMKQ  662 (691)
Q Consensus       639 ~l~~~~~~~g~-~~~A~~~~~~~~~  662 (691)
                      .++.+|.+.|+ +++|.+.+++..+
T Consensus       241 ~lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          241 QRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            99999999995 6999999988765

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.69  E-value=5.7e-07  Score=87.01  Aligned_cols=164  Identities=10%  Similarity=-0.054  Sum_probs=117.6

Q ss_pred             HHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCH-----HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC----hh
Q 040394          499 TWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNE-----VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS----MK  569 (691)
Q Consensus       499 ~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~-----~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~----~~  569 (691)
                      .+...+..+...|++++|.+.+++..+.....+.     ..+..+...+...|++++|...+++......-..+    ..
T Consensus        77 ~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~  156 (293)
T 2qfc_A           77 QFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLY  156 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHH
Confidence            4445667778888888888888887764322111     12333444667788999999988876433211112    34


Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhC----CCCCC-----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC------Cc
Q 040394          570 HYVCMVDLLARAGRLEEALEFMENM----PIEPD-----VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPD------KA  634 (691)
Q Consensus       570 ~~~~li~~~~~~g~~~~A~~~~~~~----~~~p~-----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~------~~  634 (691)
                      +++.+...|...|++++|++.+++.    ...|+     ..++..+...|...|++++|...++++++..++      ..
T Consensus       157 ~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~  236 (293)
T 2qfc_A          157 IENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIG  236 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHH
Confidence            7888889999999999999888876    11222     257888889999999999999999999875432      15


Q ss_pred             hhHHHHHHHHHhCCCcHHH-HHHHHHHHh
Q 040394          635 CYYVLVSNLYASDGRWIRV-NQVRELMKQ  662 (691)
Q Consensus       635 ~~~~~l~~~~~~~g~~~~A-~~~~~~~~~  662 (691)
                      .++..++.+|.+.|++++| ...+++...
T Consensus       237 ~~~~~lg~~y~~~g~~~~Ai~~~~~~Al~  265 (293)
T 2qfc_A          237 QLYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence            6788899999999999999 777777653

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.69  E-value=7.2e-07  Score=85.86  Aligned_cols=163  Identities=4%  Similarity=-0.028  Sum_probs=113.2

Q ss_pred             CCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCC--CChhhHHH-HHH
Q 040394          143 EHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLD--KNVVSWTS-MIA  219 (691)
Q Consensus       143 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~~~~-li~  219 (691)
                      +.+...+..+...+...|++++|...+++..+..|.+...+..+...+.+.|++++|...+++...  |+...... ...
T Consensus       114 p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~~~~~  193 (287)
T 3qou_A          114 PREEELXAQQAMQLMQESNYTDALPLLXDAWQLSNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQDQDTRYQGLVAQI  193 (287)
T ss_dssp             CCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGGCSHHHHHHHHHH
T ss_pred             CCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHhCCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchhhcchHHHHHHHHH
Confidence            344556777777888899999999999999998888888999999999999999999999998865  44332222 223


Q ss_pred             HHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCC-chHHHHHHHHHHHhcCCHH
Q 040394          220 GYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEI-NSHLVTALLDMYVKCGNIR  298 (691)
Q Consensus       220 ~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~-~~~~~~~li~~~~~~g~~~  298 (691)
                      .+.+.++.++|.+.|++...... .+...+..+...+...|+.++|...+..+.+..... +...+..++..+...|+.+
T Consensus       194 ~l~~~~~~~~a~~~l~~al~~~P-~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~  272 (287)
T 3qou_A          194 ELLXQAADTPEIQQLQQQVAENP-EDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGD  272 (287)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTC
T ss_pred             HHHhhcccCccHHHHHHHHhcCC-ccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCC
Confidence            35667778888888888776432 245566666666677777777777777776654321 2445666666666666666


Q ss_pred             HHHHHHHh
Q 040394          299 DARSVFDE  306 (691)
Q Consensus       299 ~A~~~~~~  306 (691)
                      +|...+++
T Consensus       273 ~a~~~~r~  280 (287)
T 3qou_A          273 ALASXYRR  280 (287)
T ss_dssp             HHHHHHHH
T ss_pred             cHHHHHHH
Confidence            66555543

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.68  E-value=7.5e-07  Score=81.08  Aligned_cols=170  Identities=11%  Similarity=-0.022  Sum_probs=128.6

Q ss_pred             HHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHH----------------HHHHHHhcCCHHHHHHHHHhccc-
Q 040394          432 TLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTA----------------LLNFYAKCGDAQSARMVFDAMRE-  494 (691)
Q Consensus       432 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~----------------l~~~~~~~g~~~~A~~~~~~~~~-  494 (691)
                      .+......+...|+++.|...|+...+..  |.+...+..                +...|.+.|++++|...|++..+ 
T Consensus         6 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~   83 (208)
T 3urz_A            6 EMLQKVSAAIEAGQNGQAVSYFRQTIALN--IDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQK   83 (208)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC--HHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            34445556778999999999999999987  667777777                89999999999999999998874 


Q ss_pred             -C-CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHhcccCC--HHHHHHHHHHchhhcCCCCChh
Q 040394          495 -K-NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQP-NEVIFTTILSACSHTGM--VGEGWKCFYSMCRDFKFVPSMK  569 (691)
Q Consensus       495 -~-~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p-~~~~~~~ll~~~~~~g~--~~~A~~~~~~m~~~~~~~p~~~  569 (691)
                       | +...|..+...+...|++++|+..|++..+.  .| +...+..+..++...|.  .+.+...++...   ...|...
T Consensus        84 ~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~  158 (208)
T 3urz_A           84 APNNVDCLEACAEMQVCRGQEKDALRMYEKILQL--EADNLAANIFLGNYYYLTAEQEKKKLETDYKKLS---SPTKMQY  158 (208)
T ss_dssp             CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHC------CCCHHHH
T ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHh---CCCchhH
Confidence             3 6789999999999999999999999999985  45 45667777666655543  344555555441   2223333


Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhC-CCCCCHHHHHHHHH
Q 040394          570 HYVCMVDLLARAGRLEEALEFMENM-PIEPDVSLFGAFLH  608 (691)
Q Consensus       570 ~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~~~~~~l~~  608 (691)
                      .+..+..++...|++++|++.|++. ...|+......+..
T Consensus       159 a~~~~g~~~~~~~~~~~A~~~~~~al~l~P~~~~~~~l~~  198 (208)
T 3urz_A          159 ARYRDGLSKLFTTRYEKARNSLQKVILRFPSTEAQKTLDK  198 (208)
T ss_dssp             HHHHHHHHHHHHHTHHHHHHHHHHHTTTSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence            4445566777889999999999997 78888765555443

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=98.67  E-value=1.1e-05  Score=83.65  Aligned_cols=369  Identities=9%  Similarity=-0.010  Sum_probs=208.8

Q ss_pred             hHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCC-hhhHHHHHHHHHH
Q 040394          196 IGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRA-LHQGKWLHGYILK  274 (691)
Q Consensus       196 ~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~-~~~a~~~~~~~~~  274 (691)
                      ++.|..+|+...           ..+-. |+++.+..+|++....  .|+...|..-+....+.++ .+....+|+..+.
T Consensus        11 i~~aR~vyer~l-----------~~~P~-~~~e~~~~iferal~~--~ps~~LW~~Y~~f~~~~~~~~~~i~~~fe~al~   76 (493)
T 2uy1_A           11 LSSPSAIMEHAR-----------RLYMS-KDYRSLESLFGRCLKK--SYNLDLWMLYIEYVRKVSQKKFKLYEVYEFTLG   76 (493)
T ss_dssp             -CCHHHHHHHHH-----------HHHHT-TCHHHHHHHHHHHSTT--CCCHHHHHHHHHHHHHHC----CTHHHHHHHHH
T ss_pred             hHHHHHHHHHHH-----------HHCCC-CCHHHHHHHHHHHhcc--CCCHHHHHHHHHHHHHhCchHHHHHHHHHHHHH
Confidence            666666666542           22221 8899999999998773  4788888887777766663 4567778887776


Q ss_pred             H-CCCC-chHHHHHHHHHHH----hcCCHHHHHHHHHhcCC-CC--hh-HHHHHHHHHHhcCCchhHHHHHHHhhHCCCC
Q 040394          275 I-GIEI-NSHLVTALLDMYV----KCGNIRDARSVFDELCS-ID--LV-SWTAMIVGYTQSGYPDKALKLFTDKKWADFF  344 (691)
Q Consensus       275 ~-g~~~-~~~~~~~li~~~~----~~g~~~~A~~~~~~~~~-~~--~~-~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  344 (691)
                      . |..| +..+|...+..+.    ..|+++.+.++|++... |.  .. .|...... ........+.+++.+..     
T Consensus        77 ~vg~d~~s~~iW~~Yi~f~~~~~~~~~~~~~vR~iy~rAL~~P~~~~~~lw~~Y~~f-E~~~~~~~~~~~~~~~~-----  150 (493)
T 2uy1_A           77 QFENYWDSYGLYKEYIEEEGKIEDEQTRIEKIRNGYMRALQTPMGSLSELWKDFENF-ELELNKITGKKIVGDTL-----  150 (493)
T ss_dssp             HSTTCTTCHHHHHHHHHHTSSCSSHHHHHHHHHHHHHHHHTSCCTTHHHHHHHHHHH-HHHHCHHHHHHHHHHHH-----
T ss_pred             HcCCCcccHHHHHHHHHHHHhchhhhHHHHHHHHHHHHHHhChhhhHHHHHHHHHHH-HHHhccccHHHHHHHHh-----
Confidence            4 5433 5677777776654    34567888888888733 21  11 12222111 11111222222222211     


Q ss_pred             CcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCC-chhHHHHHHHHhHhc--CC-----hHHHHHHHHhCCCCCchhHH
Q 040394          345 PNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLE-DYTVINALVDMYAKC--HV-----IADARYIFETTSEKDVIAWN  416 (691)
Q Consensus       345 p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~--g~-----~~~a~~~~~~~~~~~~~~~~  416 (691)
                                      +.+..|+.++..+...-.. +...+...++.-...  |-     .+.+..+|+++...      
T Consensus       151 ----------------~~y~~ar~~y~~~~~~~~~~s~~~W~~y~~~E~~~~~~~~~~~~~~Rv~~~ye~al~~------  208 (493)
T 2uy1_A          151 ----------------PIFQSSFQRYQQIQPLIRGWSVKNAARLIDLEMENGMKLGGRPHESRMHFIHNYILDS------  208 (493)
T ss_dssp             ----------------HHHHHHHHHHHHHHHHHHTCSHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHH------
T ss_pred             ----------------HHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHhcCCccCcchhhHHHHHHHHHHHHHc------
Confidence                            1122233333322221111 222333333332211  00     23345566665432      


Q ss_pred             HHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHH-HHHHHhcc--
Q 040394          417 SIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSA-RMVFDAMR--  493 (691)
Q Consensus       417 ~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A-~~~~~~~~--  493 (691)
                               .+-+...|...+.-+.+.|+.+.|..+++..... .  .+...+..    |+...+.++. ..+.+...  
T Consensus       209 ---------~p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~-P--~~~~l~~~----y~~~~e~~~~~~~l~~~~~~~  272 (493)
T 2uy1_A          209 ---------FYYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM-S--DGMFLSLY----YGLVMDEEAVYGDLKRKYSMG  272 (493)
T ss_dssp             ---------TTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-C--CSSHHHHH----HHHHTTCTHHHHHHHHHTC--
T ss_pred             ---------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC-C--CcHHHHHH----HHhhcchhHHHHHHHHHHHhh
Confidence                     3445677777777788899999999999999988 3  33333322    2221111111 11221110  


Q ss_pred             ----------cCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhc-ccCCHHHHHHHHHHchhhc
Q 040394          494 ----------EKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACS-HTGMVGEGWKCFYSMCRDF  562 (691)
Q Consensus       494 ----------~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~-~~g~~~~A~~~~~~m~~~~  562 (691)
                                ......|...+..+.+.++.+.|..+|++. .. ..++...|......-. ..++.+.|..+|+...+.+
T Consensus       273 ~~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A-~~-~~~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~~  350 (493)
T 2uy1_A          273 EAESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIEL-GN-EGVGPHVFIYCAFIEYYATGSRATPYNIFSSGLLKH  350 (493)
T ss_dssp             --------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH-TT-SCCCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHC
T ss_pred             ccchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHh-hC-CCCChHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC
Confidence                      011245666677777778899999999988 32 1234444433222111 2336899999999886664


Q ss_pred             CCCCChhHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040394          563 KFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLE  628 (691)
Q Consensus       563 ~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  628 (691)
                      +-.  +..+...++...+.|+.+.|..+|+++.  .....|...+.--...|+.+.+..+++++.+
T Consensus       351 ~~~--~~~~~~yid~e~~~~~~~~aR~l~er~~--k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          351 PDS--TLLKEEFFLFLLRIGDEENARALFKRLE--KTSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             TTC--HHHHHHHHHHHHHHTCHHHHHHHHHHSC--CBHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             CCC--HHHHHHHHHHHHHcCCHHHHHHHHHHHH--HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            322  3455667777788899999999999983  3567787777777778999999988888875

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.62  E-value=2.6e-07  Score=78.26  Aligned_cols=100  Identities=6%  Similarity=-0.022  Sum_probs=72.5

Q ss_pred             CCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHH
Q 040394          564 FVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIE-PDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLV  640 (691)
Q Consensus       564 ~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~-p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l  640 (691)
                      +.|+ ...+..+...+.+.|++++|++.|++. ... .+...|..+..++...|++++|+..++++++++|+++..+..+
T Consensus        13 ~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l   92 (142)
T 2xcb_A           13 LSEDTLEQLYALGFNQYQAGKWDDAQKIFQALCMLDHYDARYFLGLGACRQSLGLYEQALQSYSYGALMDINEPRFPFHA   92 (142)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHH
Confidence            4444 445555666777777777777777776 323 3556777777777778888888888888888888888888888


Q ss_pred             HHHHHhCCCcHHHHHHHHHHHhC
Q 040394          641 SNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       641 ~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      +.+|...|++++|.+.+++.++.
T Consensus        93 g~~~~~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           93 AECHLQLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHh
Confidence            88888888888888887777654

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.62  E-value=1.8e-05  Score=75.68  Aligned_cols=229  Identities=9%  Similarity=0.015  Sum_probs=176.0

Q ss_pred             HhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCC-HHHHHHHHHHHhccC--cHHHHHHHHHHHHHcCCCCCchhH
Q 040394          392 AKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPD-AVTLVSVISACASLG--AVQVGSSLHAYSTKQGLLSSNVYV  468 (691)
Q Consensus       392 ~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~-~~~~~~ll~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~  468 (691)
                      .+....++|+..++.+...                .|+ ...|+.--..+...+  +++++..+++.+....  |.+..+
T Consensus        44 ~~~e~s~~aL~~t~~~L~~----------------nP~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~n--Pk~y~a  105 (306)
T 3dra_A           44 KAEEYSERALHITELGINE----------------LASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDN--EKNYQI  105 (306)
T ss_dssp             HTTCCSHHHHHHHHHHHHH----------------CTTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHC--TTCCHH
T ss_pred             HcCCCCHHHHHHHHHHHHH----------------CcHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHC--cccHHH
Confidence            3344456788888877643                354 445676667777777  9999999999999988  677777


Q ss_pred             HHHHHHHH----Hhc---CCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChH--HHHHHHHHHHHCCCCCCHHHHH
Q 040394          469 GTALLNFY----AKC---GDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGG--GSLALFSDMLNEEVQPNEVIFT  536 (691)
Q Consensus       469 ~~~l~~~~----~~~---g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~--~A~~~~~~m~~~g~~p~~~~~~  536 (691)
                      ++.-...+    ...   +++++++.+++.+.+   +|..+|+.-...+.+.|.++  ++++.++++++.. +-|...|+
T Consensus       106 W~~R~~iL~~~~~~l~~~~~~~~EL~~~~~~l~~~pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d-~~N~sAW~  184 (306)
T 3dra_A          106 WNYRQLIIGQIMELNNNDFDPYREFDILEAMLSSDPKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTD-LKNNSAWS  184 (306)
T ss_dssp             HHHHHHHHHHHHHHTTTCCCTHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             HHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhC-CCCHHHHH
Confidence            76665555    555   789999999999885   47778888777778888888  9999999999875 34556666


Q ss_pred             HHHHHhcccCC------HHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHH-HHHHHHhC-CC----CCCHHHH
Q 040394          537 TILSACSHTGM------VGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEE-ALEFMENM-PI----EPDVSLF  603 (691)
Q Consensus       537 ~ll~~~~~~g~------~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~-A~~~~~~~-~~----~p~~~~~  603 (691)
                      .-...+...+.      ++++++.++.++..   .|+ ...|+.+...+.+.|+..+ +.++..+. ..    ..+...+
T Consensus       185 ~R~~ll~~l~~~~~~~~~~eEl~~~~~aI~~---~p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al  261 (306)
T 3dra_A          185 HRFFLLFSKKHLATDNTIDEELNYVKDKIVK---CPQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFAL  261 (306)
T ss_dssp             HHHHHHHSSGGGCCHHHHHHHHHHHHHHHHH---CSSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHH
T ss_pred             HHHHHHHhccccchhhhHHHHHHHHHHHHHh---CCCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHH
Confidence            65555555565      88999999877543   555 7788888888888888544 56677776 22    3477889


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHh-cCCCCchhHHHHHH
Q 040394          604 GAFLHGCGLYSRFDLGEVMIKKMLE-LHPDKACYYVLVSN  642 (691)
Q Consensus       604 ~~l~~~~~~~g~~~~A~~~~~~~~~-~~p~~~~~~~~l~~  642 (691)
                      ..+...+.+.|+.++|.++++.+.+ .+|-...+|...+.
T Consensus       262 ~~la~~~~~~~~~~~A~~~~~~l~~~~Dpir~~yW~~~~~  301 (306)
T 3dra_A          262 ETLAKIYTQQKKYNESRTVYDLLKSKYNPIRSNFWDYQIS  301 (306)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHTTCGGGHHHHHHHHH
T ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhccChHHHHHHHHHHh
Confidence            9999999999999999999999997 79998888876654

>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=98.62  E-value=5e-07  Score=96.69  Aligned_cols=146  Identities=8%  Similarity=-0.042  Sum_probs=102.4

Q ss_pred             cCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHH
Q 040394          443 LGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLAL  519 (691)
Q Consensus       443 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~  519 (691)
                      .|+.++|...+++..+..  +.+...+..+...|...|++++|...+++..+   .+...|..+...|...|++++|.+.
T Consensus         2 ~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~   79 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHR--PQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVL   79 (568)
T ss_dssp             ---------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTSTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            467888888888888776  67788888888888889999999999888764   2567888888888899999999999


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhc---CChHHHHHHHHhC
Q 040394          520 FSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARA---GRLEEALEFMENM  594 (691)
Q Consensus       520 ~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~---g~~~~A~~~~~~~  594 (691)
                      +++..+.. +.+...+..+..++...|++++|.+.+++..+.   .|+ ...+..+...+...   |+.++|.+.+++.
T Consensus        80 ~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~a  154 (568)
T 2vsy_A           80 LQQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL---LPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAA  154 (568)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHH
T ss_pred             HHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHhhccccHHHHHHHHHHH
Confidence            98888753 334567777888888889999999988877543   454 66777888888888   8889998888887

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.59  E-value=6.5e-07  Score=73.78  Aligned_cols=112  Identities=10%  Similarity=0.023  Sum_probs=88.6

Q ss_pred             CCCH-HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHH
Q 040394          529 QPNE-VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFG  604 (691)
Q Consensus       529 ~p~~-~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~  604 (691)
                      .|+. ..+...-..+.+.|++++|++.|++.++   +.|+ ...|..+..+|.+.|++++|++.+++. ...| +...|.
T Consensus         9 nP~~a~~~~~~G~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~   85 (126)
T 4gco_A            9 NPELAQEEKNKGNEYFKKGDYPTAMRHYNEAVK---RDPENAILYSNRAACLTKLMEFQRALDDCDTCIRLDSKFIKGYI   85 (126)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhhhhHHHH
Confidence            3443 3455556677788888888888887643   3454 677888888888888998888888887 4334 567899


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHH
Q 040394          605 AFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNL  643 (691)
Q Consensus       605 ~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~  643 (691)
                      .+..++...|++++|...|+++++++|+++..+..++.+
T Consensus        86 ~lg~~~~~~~~~~~A~~~~~~al~l~P~~~~a~~~l~~~  124 (126)
T 4gco_A           86 RKAACLVAMREWSKAQRAYEDALQVDPSNEEAREGVRNC  124 (126)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCcCCHHHHHHHHHh
Confidence            999999999999999999999999999999988888765

>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=98.59  E-value=4.7e-06  Score=75.97  Aligned_cols=174  Identities=9%  Similarity=-0.104  Sum_probs=138.0

Q ss_pred             HHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccC-CHhHHHHHHHHHhcCC----ChHHHHHHHHH
Q 040394          448 VGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREK-NTVTWSAMIGGYGMQG----DGGGSLALFSD  522 (691)
Q Consensus       448 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~~~~~~~li~~~~~~~----~~~~A~~~~~~  522 (691)
                      +|...|++..+.|    ++..+..+...|...+++++|...|++..+. +...+..|...|.. +    ++++|+..|++
T Consensus         4 eA~~~~~~aa~~g----~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~   78 (212)
T 3rjv_A            4 EPGSQYQQQAEAG----DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQGDGDALALLAQLKIR-NPQQADYPQARQLAEK   78 (212)
T ss_dssp             CTTHHHHHHHHTT----CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCHHHHHHHHHHTTS-STTSCCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHCC----CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHc-CCCCCCHHHHHHHHHH
Confidence            4566777777654    4677778888898999999999999988764 67788888888887 6    89999999999


Q ss_pred             HHHCCCCCCHHHHHHHHHHhcc----cCCHHHHHHHHHHchhhcCCCCC---hhHHHHHHHHHHh----cCChHHHHHHH
Q 040394          523 MLNEEVQPNEVIFTTILSACSH----TGMVGEGWKCFYSMCRDFKFVPS---MKHYVCMVDLLAR----AGRLEEALEFM  591 (691)
Q Consensus       523 m~~~g~~p~~~~~~~ll~~~~~----~g~~~~A~~~~~~m~~~~~~~p~---~~~~~~li~~~~~----~g~~~~A~~~~  591 (691)
                      ..+.|   +...+..+-..|..    .+++++|.+.|++..   ...|.   ...+..|...|..    .+++++|+++|
T Consensus        79 A~~~g---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~---~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~  152 (212)
T 3rjv_A           79 AVEAG---SKSGEIVLARVLVNRQAGATDVAHAITLLQDAA---RDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYF  152 (212)
T ss_dssp             HHHTT---CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHT---SSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHH
T ss_pred             HHHCC---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHH---HcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Confidence            98865   55666667677766    889999999999763   34443   6788888899988    78999999999


Q ss_pred             HhC-CCCCCHHHHHHHHHHHHhc-C-----CHHHHHHHHHHHHhcCCC
Q 040394          592 ENM-PIEPDVSLFGAFLHGCGLY-S-----RFDLGEVMIKKMLELHPD  632 (691)
Q Consensus       592 ~~~-~~~p~~~~~~~l~~~~~~~-g-----~~~~A~~~~~~~~~~~p~  632 (691)
                      ++. ...++...+..|...|... |     +.++|...++++.+..+.
T Consensus       153 ~~A~~~~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g~~  200 (212)
T 3rjv_A          153 KGSSSLSRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEGFD  200 (212)
T ss_dssp             HHHHHTSCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcCCH
Confidence            998 3345666777888887653 3     899999999998887544

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.58  E-value=4e-07  Score=73.06  Aligned_cols=99  Identities=10%  Similarity=0.042  Sum_probs=86.5

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC--CchhHHHHHHH
Q 040394          568 MKHYVCMVDLLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPD--KACYYVLVSNL  643 (691)
Q Consensus       568 ~~~~~~li~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~--~~~~~~~l~~~  643 (691)
                      ...+..+...+.+.|++++|...+++. . .+.+...+..+...+...|++++|...++++++..|+  +...+..++.+
T Consensus         6 ~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l~~~   85 (112)
T 2kck_A            6 PEEYYLEGVLQYDAGNYTESIDLFEKAIQLDPEESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDVWAAKADA   85 (112)
T ss_dssp             TTGGGGHHHHHHSSCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHHHHHHHHH
Confidence            556777888888999999999998887 3 3345678888999999999999999999999999999  99999999999


Q ss_pred             HHhC-CCcHHHHHHHHHHHhCCCc
Q 040394          644 YASD-GRWIRVNQVRELMKQRGLS  666 (691)
Q Consensus       644 ~~~~-g~~~~A~~~~~~~~~~g~~  666 (691)
                      +... |++++|.+.+++..+....
T Consensus        86 ~~~~~~~~~~A~~~~~~~~~~~p~  109 (112)
T 2kck_A           86 LRYIEGKEVEAEIAEARAKLEHHH  109 (112)
T ss_dssp             HTTCSSCSHHHHHHHHHHGGGCCC
T ss_pred             HHHHhCCHHHHHHHHHHHhhcccC
Confidence            9999 9999999999999886553

>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=98.57  E-value=8.6e-07  Score=77.19  Aligned_cols=125  Identities=9%  Similarity=-0.041  Sum_probs=92.7

Q ss_pred             HHHHHHHhcccCCHHHHHHHHHHchhhcCCCC-ChhHHHHHHHHHHhcCChHHHHHHHHhC-CC-CCCHHHHHHHHHHHH
Q 040394          535 FTTILSACSHTGMVGEGWKCFYSMCRDFKFVP-SMKHYVCMVDLLARAGRLEEALEFMENM-PI-EPDVSLFGAFLHGCG  611 (691)
Q Consensus       535 ~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~-~p~~~~~~~l~~~~~  611 (691)
                      +..+...+...|++++|...+++....   .| +...+..+...+...|++++|++.+++. .. +.+...|..+...+.
T Consensus        16 ~~~~a~~~~~~~~~~~A~~~~~~al~~---~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~   92 (166)
T 1a17_A           16 LKTQANDYFKAKDYENAIKFYSQAIEL---NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNM   92 (166)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHh---CCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHH
Confidence            444455566667777777777665432   33 3566667777777788888888777776 22 335678888888999


Q ss_pred             hcCCHHHHHHHHHHHHhcCCCCchhHHHHHH--HHHhCCCcHHHHHHHHHHHh
Q 040394          612 LYSRFDLGEVMIKKMLELHPDKACYYVLVSN--LYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       612 ~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~--~~~~~g~~~~A~~~~~~~~~  662 (691)
                      ..|++++|...++++++..|++...+..+..  .+...|++++|.+.++...+
T Consensus        93 ~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  145 (166)
T 1a17_A           93 ALGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEHKRS  145 (166)
T ss_dssp             HTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHcccchHH
Confidence            9999999999999999999998887754444  48888999999999887654

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.56  E-value=1.2e-06  Score=80.79  Aligned_cols=55  Identities=9%  Similarity=-0.084  Sum_probs=30.4

Q ss_pred             HHHHHccCChhhHHHHHHHHHHHCCCC--chHHHHHHHHHHHhcCCHHHHHHHHHhc
Q 040394          253 VTACAKLRALHQGKWLHGYILKIGIEI--NSHLVTALLDMYVKCGNIRDARSVFDEL  307 (691)
Q Consensus       253 i~~~~~~~~~~~a~~~~~~~~~~g~~~--~~~~~~~li~~~~~~g~~~~A~~~~~~~  307 (691)
                      ...+.+.|++++|...|+.+++.....  ....+..+..++.+.|+.++|.+.++.+
T Consensus       154 a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l  210 (225)
T 2yhc_A          154 AEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKII  210 (225)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence            344555566666666666655543211  1234555666666666666666666655

>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=98.56  E-value=1.3e-07  Score=90.80  Aligned_cols=189  Identities=8%  Similarity=-0.055  Sum_probs=95.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhccc--C-CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcc
Q 040394          468 VGTALLNFYAKCGDAQSARMVFDAMRE--K-NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSH  544 (691)
Q Consensus       468 ~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~  544 (691)
                      .+..+...+.+.|++++|...|++..+  | +...|..+...|.+.|++++|+..+++..+.. +-+...+..+..++..
T Consensus         6 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~   84 (281)
T 2c2l_A            6 ELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQCQLE   84 (281)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHH
Confidence            333444444444444444444444332  2 34444444445555555555555555544421 1223344444445555


Q ss_pred             cCCHHHHHHHHHHchhhcCCCCCh-hHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 040394          545 TGMVGEGWKCFYSMCRDFKFVPSM-KHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMI  623 (691)
Q Consensus       545 ~g~~~~A~~~~~~m~~~~~~~p~~-~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~  623 (691)
                      .|++++|...|++..+.   .|+. ..+...+....+..+... ..........++......+.. + ..|++++|.+.+
T Consensus        85 ~g~~~~A~~~~~~al~l---~p~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~i~~~l~~-l-~~~~~~~A~~~~  158 (281)
T 2c2l_A           85 MESYDEAIANLQRAYSL---AKEQRLNFGDDIPSALRIAKKKR-WNSIEERRIHQESELHSYLTR-L-IAAERERELEEC  158 (281)
T ss_dssp             TTCHHHHHHHHHHHHHH---HHHTTCCCCSHHHHHHHHHHHHH-HHHHHHTCCCCCCHHHHHHHH-H-HHHHHHHHHTTT
T ss_pred             cCCHHHHHHHHHHHHHh---CccchhhHHHHHHHHHHHHHHHH-HHHHHHHHHhhhHHHHHHHHH-H-HHHHHHHHHHHH
Confidence            55555555555544221   2210 011111111111111111 111222233344444443422 2 368899999999


Q ss_pred             HHHHhcCCCCchhHHHHHHHHHhC-CCcHHHHHHHHHHHhC
Q 040394          624 KKMLELHPDKACYYVLVSNLYASD-GRWIRVNQVRELMKQR  663 (691)
Q Consensus       624 ~~~~~~~p~~~~~~~~l~~~~~~~-g~~~~A~~~~~~~~~~  663 (691)
                      +++++.+|++......+...+.+. +.+++|.++|+++.+.
T Consensus       159 ~~al~~~p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~~  199 (281)
T 2c2l_A          159 QRNHEGHEDDGHIRAQQACIEAKHDKYMADMDELFSQVDEK  199 (281)
T ss_dssp             SGGGTTTSCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSCT
T ss_pred             HhhhccccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            999999998877777777777766 7788999999888763

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.55  E-value=1e-06  Score=72.18  Aligned_cols=114  Identities=14%  Similarity=0.123  Sum_probs=79.8

Q ss_pred             HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHH
Q 040394          533 VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGC  610 (691)
Q Consensus       533 ~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~  610 (691)
                      ..+..+...+...|++++|.+.++++....  +.+...+..+...+.+.|++++|...++++ . .+.+..++..+...+
T Consensus        10 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~   87 (125)
T 1na0_A           10 EAWYNLGNAYYKQGDYDEAIEYYQKALELD--PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAY   87 (125)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHH
Confidence            445555556666667777776666664331  123556666777777777777777777766 2 234566777888888


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCC
Q 040394          611 GLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDG  648 (691)
Q Consensus       611 ~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g  648 (691)
                      ...|++++|...++++.+..|+++..+..++.++...|
T Consensus        88 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  125 (125)
T 1na0_A           88 YKQGDYDEAIEYYQKALELDPNNAEAKQNLGNAKQKQG  125 (125)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHC
T ss_pred             HHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhcc
Confidence            88899999999999988888888888888877776543

>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=98.55  E-value=3.3e-07  Score=81.06  Aligned_cols=124  Identities=6%  Similarity=0.127  Sum_probs=63.2

Q ss_pred             hcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCC-ChhHHHHHHHH-HHhcCCh-
Q 040394          508 GMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVP-SMKHYVCMVDL-LARAGRL-  584 (691)
Q Consensus       508 ~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~-~~~~g~~-  584 (691)
                      ...|++++|+..+++..+.. +.+...+..+...+...|++++|...|++..+.   .| +...+..+..+ +...|++ 
T Consensus        21 ~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~---~p~~~~~~~~la~~l~~~~~~~~   96 (177)
T 2e2e_A           21 ASQQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQL---RGENAELYAALATVLYYQASQHM   96 (177)
T ss_dssp             C-----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---HCSCHHHHHHHHHHHHHHTTTCC
T ss_pred             hhccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc---CCCCHHHHHHHHHHHHHhcCCcc
Confidence            34555666666666655532 234455555555666666666666666655322   23 24444455555 4455555 


Q ss_pred             -HHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCch
Q 040394          585 -EEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKAC  635 (691)
Q Consensus       585 -~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~  635 (691)
                       ++|++.+++. ...| +...+..+...+...|++++|...++++++..|+++.
T Consensus        97 ~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~  150 (177)
T 2e2e_A           97 TAQTRAMIDKALALDSNEITALMLLASDAFMQANYAQAIELWQKVMDLNSPRIN  150 (177)
T ss_dssp             CHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTSC
T ss_pred             hHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhhCCCCcc
Confidence             5665555554 2222 3445555555555566666666666666665555443

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.53  E-value=1.1e-06  Score=72.79  Aligned_cols=116  Identities=13%  Similarity=0.018  Sum_probs=86.1

Q ss_pred             HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCC-ChhHHHHHHHHHHhcCChHHHHHHHHhC-CC-CCCHHHHHHHHHH
Q 040394          533 VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVP-SMKHYVCMVDLLARAGRLEEALEFMENM-PI-EPDVSLFGAFLHG  609 (691)
Q Consensus       533 ~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~-~p~~~~~~~l~~~  609 (691)
                      ..+..+...+...|++++|...+++....   .| +...+..+...+...|++++|++.+++. .. +.+...+..+...
T Consensus        13 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~   89 (131)
T 2vyi_A           13 ERLKTEGNEQMKVENFEAAVHFYGKAIEL---NPANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPAYSKAYGRMGLA   89 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHc---CCCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcCccCHHHHHHHHHH
Confidence            44555555666667777777777665433   23 3556667777777777888887777776 22 3346678888888


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcH
Q 040394          610 CGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWI  651 (691)
Q Consensus       610 ~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~  651 (691)
                      +...|++++|...++++.+..|+++..+..++.++...|+++
T Consensus        90 ~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~  131 (131)
T 2vyi_A           90 LSSLNKHVEAVAYYKKALELDPDNETYKSNLKIAELKLREAP  131 (131)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTTCC
T ss_pred             HHHhCCHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHhcCC
Confidence            999999999999999999999998999999999988888763

>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=98.53  E-value=1.1e-06  Score=80.22  Aligned_cols=123  Identities=13%  Similarity=-0.001  Sum_probs=87.3

Q ss_pred             hhHHHHHHhcCCChHHHHHHhccCCCCCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCCh
Q 040394           83 NTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDI  162 (691)
Q Consensus        83 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~  162 (691)
                      +..+...+...|++++|...|++..+|+...|..+...+...|++++|+..|++..+.. +.+...+..+..++...|++
T Consensus         9 ~~~~g~~~~~~~~~~~A~~~~~~a~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~   87 (213)
T 1hh8_A            9 LWNEGVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKY   87 (213)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHcCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcccH
Confidence            34567777888888888888888877777788888888888888888888888887763 34556777777888888888


Q ss_pred             hHHHHHHHHHHHhCCCCh----------------hHHHHHHHHhHhcCChHHHHHHHhcc
Q 040394          163 DEGMKVHCEIVKVGGPDS----------------FVLTGLVDMYAKCRDIGSSRQVFDET  206 (691)
Q Consensus       163 ~~a~~~~~~~~~~~~~~~----------------~~~~~l~~~~~~~g~~~~A~~~~~~~  206 (691)
                      ++|...++...+..+.+.                .++..+..+|.+.|++++|...|++.
T Consensus        88 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a  147 (213)
T 1hh8_A           88 DLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALA  147 (213)
T ss_dssp             HHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            888888888887655433                44444444444444444444444443

>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=98.52  E-value=8.3e-07  Score=73.25  Aligned_cols=95  Identities=8%  Similarity=0.006  Sum_probs=67.4

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhC-CC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHh
Q 040394          569 KHYVCMVDLLARAGRLEEALEFMENM-PI-EPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYAS  646 (691)
Q Consensus       569 ~~~~~li~~~~~~g~~~~A~~~~~~~-~~-~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~  646 (691)
                      ..+..+...+.+.|++++|++.|++. .. +.+...|..+..++...|++++|+..++++++.+|+++..+..++.++..
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~   84 (126)
T 3upv_A            5 EEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQIA   84 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHH
Confidence            34555666667777777777777766 22 23456677777777777777777777777777777777777777777777


Q ss_pred             CCCcHHHHHHHHHHHhC
Q 040394          647 DGRWIRVNQVRELMKQR  663 (691)
Q Consensus       647 ~g~~~~A~~~~~~~~~~  663 (691)
                      .|++++|.+.+++..+.
T Consensus        85 ~~~~~~A~~~~~~al~~  101 (126)
T 3upv_A           85 VKEYASALETLDAARTK  101 (126)
T ss_dssp             TTCHHHHHHHHHHHHHH
T ss_pred             HhCHHHHHHHHHHHHHh
Confidence            77777777777777654

>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=98.52  E-value=4e-07  Score=88.74  Aligned_cols=162  Identities=7%  Similarity=-0.013  Sum_probs=125.0

Q ss_pred             HHHHHHHHHhcCCChHHHHHHHHHHHHCCC---CC-C-HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCC--CCC--hh
Q 040394          499 TWSAMIGGYGMQGDGGGSLALFSDMLNEEV---QP-N-EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKF--VPS--MK  569 (691)
Q Consensus       499 ~~~~li~~~~~~~~~~~A~~~~~~m~~~g~---~p-~-~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~--~p~--~~  569 (691)
                      .|+.....|...|++++|...+.+..+...   .+ . ..+|+.+...|...|++++|+..+++...-..-  .|.  ..
T Consensus        38 ~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~  117 (307)
T 2ifu_A           38 EYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAM  117 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            455567788899999999999998776311   11 1 346777888899999999999999876443211  111  45


Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhC-CCC---CC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc------h
Q 040394          570 HYVCMVDLLARAGRLEEALEFMENM-PIE---PD----VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKA------C  635 (691)
Q Consensus       570 ~~~~li~~~~~~g~~~~A~~~~~~~-~~~---p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~------~  635 (691)
                      ++..+..+|.. |++++|++.+++. ...   .+    ..++..+...+...|++++|+..+++++++.|++.      .
T Consensus       118 ~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  196 (307)
T 2ifu_A          118 ALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYK  196 (307)
T ss_dssp             HHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHH
Confidence            77888889988 9999999999887 111   11    35788889999999999999999999999766543      3


Q ss_pred             hHHHHHHHHHhCCCcHHHHHHHHHHH
Q 040394          636 YYVLVSNLYASDGRWIRVNQVRELMK  661 (691)
Q Consensus       636 ~~~~l~~~~~~~g~~~~A~~~~~~~~  661 (691)
                      ++..++.++...|++++|.+.+++.+
T Consensus       197 ~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          197 KCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            66778888899999999999999988

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.52  E-value=9.3e-07  Score=73.56  Aligned_cols=114  Identities=11%  Similarity=0.037  Sum_probs=69.5

Q ss_pred             HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCC-ChhHHHHHHHHHHhcCChHHHHHHHHhC-CC-CCCHHHHHHHHHH
Q 040394          533 VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVP-SMKHYVCMVDLLARAGRLEEALEFMENM-PI-EPDVSLFGAFLHG  609 (691)
Q Consensus       533 ~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~-~p~~~~~~~l~~~  609 (691)
                      ..+..+...+...|++++|...+++..   ...| +...+..+...+...|++++|++.+++. .. +.+...+..+...
T Consensus        17 ~~~~~~~~~~~~~~~~~~A~~~~~~al---~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~   93 (133)
T 2lni_A           17 LMVKNKGNECFQKGDYPQAMKHYTEAI---KRNPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPTFIKGYTRKAAA   93 (133)
T ss_dssp             HHHHHHHHHHHHTTCSHHHHHHHHHHH---TTCTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHH---HcCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCchHHHHHHHHH
Confidence            344444445555555555555555442   1233 2445555555566666666666665555 22 2345667777777


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCC
Q 040394          610 CGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGR  649 (691)
Q Consensus       610 ~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  649 (691)
                      +...|++++|...++++++..|++...+..++.++...|+
T Consensus        94 ~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~  133 (133)
T 2lni_A           94 LEAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCMMAQYN  133 (133)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCGGGTHHHHHHHHHHHHHTC
T ss_pred             HHHHhhHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhcC
Confidence            7777888888888888887777777777777777766553

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.49  E-value=4.9e-07  Score=73.89  Aligned_cols=95  Identities=9%  Similarity=-0.043  Sum_probs=84.1

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhC
Q 040394          570 HYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASD  647 (691)
Q Consensus       570 ~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~  647 (691)
                      .+..+...+.+.|++++|+..+++. ...| +...|..+..++...|++++|+..++++++++|+++..+..++.+|...
T Consensus        19 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~la~~~~~~   98 (121)
T 1hxi_A           19 NPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNE   98 (121)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc
Confidence            4556777889999999999999998 4444 6778889999999999999999999999999999999999999999999


Q ss_pred             CCcHHHHHHHHHHHhCC
Q 040394          648 GRWIRVNQVRELMKQRG  664 (691)
Q Consensus       648 g~~~~A~~~~~~~~~~g  664 (691)
                      |++++|.+.+++.++..
T Consensus        99 g~~~~A~~~~~~al~~~  115 (121)
T 1hxi_A           99 HNANAALASLRAWLLSQ  115 (121)
T ss_dssp             HHHHHHHHHHHHHHC--
T ss_pred             CCHHHHHHHHHHHHHhC
Confidence            99999999999998754

>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=98.48  E-value=1.1e-06  Score=86.65  Aligned_cols=95  Identities=11%  Similarity=0.074  Sum_probs=81.7

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHH
Q 040394          568 MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYA  645 (691)
Q Consensus       568 ~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~  645 (691)
                      ...|..+..+|.+.|++++|++.+++. ...| +...|..+..++...|++++|+..|+++++++|++..++..++.++.
T Consensus       196 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~  275 (336)
T 1p5q_A          196 LASHLNLAMCHLKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQ  275 (336)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
Confidence            357778888889999999999988887 3334 66789999999999999999999999999999999999999999999


Q ss_pred             hCCCcHHH-HHHHHHHHh
Q 040394          646 SDGRWIRV-NQVRELMKQ  662 (691)
Q Consensus       646 ~~g~~~~A-~~~~~~~~~  662 (691)
                      ..|++++| ...++.|.+
T Consensus       276 ~~~~~~~a~~~~~~~~~~  293 (336)
T 1p5q_A          276 RIRRQLAREKKLYANMFE  293 (336)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            99999999 456666643

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.47  E-value=1.9e-06  Score=80.41  Aligned_cols=192  Identities=6%  Similarity=-0.129  Sum_probs=134.2

Q ss_pred             ccCcHHHHHHHHHHHHHcCCCCCchhHHHHH-------HHHHHhcCCHHHHHHHHHhccc--C-------C---------
Q 040394          442 SLGAVQVGSSLHAYSTKQGLLSSNVYVGTAL-------LNFYAKCGDAQSARMVFDAMRE--K-------N---------  496 (691)
Q Consensus       442 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l-------~~~~~~~g~~~~A~~~~~~~~~--~-------~---------  496 (691)
                      ..++.+.|.+.|.++.+..  |.....|..+       ...+.+.++..++...+..-.+  |       +         
T Consensus        18 ~~~d~~~A~~~F~~a~~~d--P~~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~l~p~~l~a~~~~~g~y~~~~   95 (282)
T 4f3v_A           18 LPMSEARSLDLFTEITNYD--ESACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQISMSTLNARIAIGGLYGDIT   95 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTTCCGGGGCCEEECCTTTCCCE
T ss_pred             cCCCHHHHHHHHHHHHHhC--hhhhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhccCCcccccc
Confidence            5789999999999999998  7888888877       4666666666666655554443  1       1         


Q ss_pred             ------HhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC--h
Q 040394          497 ------TVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS--M  568 (691)
Q Consensus       497 ------~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~--~  568 (691)
                            ...+-.+...+...|++++|.++|+.+...  .|+......+...+.+.+++++|+..|+... ... .|.  .
T Consensus        96 ~~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~~--~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~-~~~-d~~~~~  171 (282)
T 4f3v_A           96 YPVTSPLAITMGFAACEAAQGNYADAMEALEAAPVA--GSEHLVAWMKAVVYGAAERWTDVIDQVKSAG-KWP-DKFLAG  171 (282)
T ss_dssp             EECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCCT--TCHHHHHHHHHHHHHHTTCHHHHHHHHTTGG-GCS-CHHHHH
T ss_pred             cccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCchHHHHHHHHHHHHcCCHHHHHHHHHHhh-ccC-CcccHH
Confidence                  112344567778888888888888887764  3555444444557778888888888887552 111 111  2


Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhC--C-CCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHH
Q 040394          569 KHYVCMVDLLARAGRLEEALEFMENM--P-IEPD--VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLV  640 (691)
Q Consensus       569 ~~~~~li~~~~~~g~~~~A~~~~~~~--~-~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l  640 (691)
                      ..+..+..++.+.|++++|++.|++.  + ..|.  ...+.....++.+.|+.++|...|+++...+|+ ......|
T Consensus       172 ~a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~P~-~~~~~aL  247 (282)
T 4f3v_A          172 AAGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTHPE-PKVAAAL  247 (282)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSCC-HHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCc-HHHHHHH
Confidence            35667788888888888888888887  2 2143  235666777788888888888888888888888 6665555

>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=98.45  E-value=1.7e-06  Score=72.44  Aligned_cols=96  Identities=6%  Similarity=-0.129  Sum_probs=66.5

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhC-CC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHH
Q 040394          568 MKHYVCMVDLLARAGRLEEALEFMENM-PI-EPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYA  645 (691)
Q Consensus       568 ~~~~~~li~~~~~~g~~~~A~~~~~~~-~~-~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~  645 (691)
                      ...+..+...+...|++++|++.|++. .. +.+...|..+..++...|++++|...++++++..|+++..+..++.+|.
T Consensus         9 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~   88 (137)
T 3q49_B            9 AQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQL   88 (137)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCchhHHHHHHHHHHHH
Confidence            455666666667777777777766665 22 2345566677777777777777777777777777777777777777777


Q ss_pred             hCCCcHHHHHHHHHHHhC
Q 040394          646 SDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       646 ~~g~~~~A~~~~~~~~~~  663 (691)
                      ..|++++|.+.+++..+.
T Consensus        89 ~~~~~~~A~~~~~~a~~~  106 (137)
T 3q49_B           89 EMESYDEAIANLQRAYSL  106 (137)
T ss_dssp             HTTCHHHHHHHHHHHHHH
T ss_pred             HHhhHHHHHHHHHHHHHH
Confidence            777777777777776653

>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=98.45  E-value=3.9e-05  Score=73.99  Aligned_cols=193  Identities=12%  Similarity=-0.067  Sum_probs=137.0

Q ss_pred             CCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHH---HHHHHHHHhcCCHHHHHHHHHhcccC-----C-
Q 040394          426 VSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVG---TALLNFYAKCGDAQSARMVFDAMREK-----N-  496 (691)
Q Consensus       426 ~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~---~~l~~~~~~~g~~~~A~~~~~~~~~~-----~-  496 (691)
                      ..|+..++..+...+.-.-+         .+..... .......   ...+..+...|++++|...+++..+.     + 
T Consensus        42 ~~~~~~~l~~i~~~l~~~~~---------~~~~~~~-~~~~~~~~~l~~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~  111 (293)
T 3u3w_A           42 VYPSMDILQGIAAKLQIPII---------HFYEVLI-YSDIERKKQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEF  111 (293)
T ss_dssp             CCCCHHHHHHHHHHHTCCTH---------HHHHTTT-SSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHH
T ss_pred             CCCCHHHHHHHHHHhCcCHH---------HHhCCCC-CCcchhHHHHHHHHHHHHHHhhHHHHHHHHHHHhccccCChHH
Confidence            46777777777666543211         1111111 2222222   33467788999999999999987652     1 


Q ss_pred             ---HhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCC-CC----HHHHHHHHHHhcccCCHHHHHHHHHHchhhc----CC
Q 040394          497 ---TVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQ-PN----EVIFTTILSACSHTGMVGEGWKCFYSMCRDF----KF  564 (691)
Q Consensus       497 ---~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~-p~----~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~----~~  564 (691)
                         ...+..+...+...+++++|+..+++..+.... ++    ..+++.+..+|...|++++|..++++..+..    +.
T Consensus       112 ~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~  191 (293)
T 3u3w_A          112 QQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDN  191 (293)
T ss_dssp             HHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCC
T ss_pred             HHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccc
Confidence               113445777778888999999999999984322 22    2368888889999999999999999886422    22


Q ss_pred             CCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-------CCCCC-HHHHHHHHHHHHhcCC-HHHHHHHHHHHHh
Q 040394          565 VPS-MKHYVCMVDLLARAGRLEEALEFMENM-------PIEPD-VSLFGAFLHGCGLYSR-FDLGEVMIKKMLE  628 (691)
Q Consensus       565 ~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-------~~~p~-~~~~~~l~~~~~~~g~-~~~A~~~~~~~~~  628 (691)
                      .+. ..++..+...|.+.|++++|++.+++.       +..+. ..+|..+..++.+.|+ +++|...+++++.
T Consensus       192 ~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          192 EEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            222 347888999999999999999998877       22233 5688889999999994 6999999999886

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.44  E-value=1.2e-06  Score=76.33  Aligned_cols=109  Identities=9%  Similarity=-0.040  Sum_probs=90.0

Q ss_pred             CHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCC-ChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHH
Q 040394          531 NEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVP-SMKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFL  607 (691)
Q Consensus       531 ~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~  607 (691)
                      +...+..+...+...|++++|++.|++..+.   .| +...|..+..+|.+.|++++|++.+++. ...| +...|..+.
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg   86 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSI---APANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPKYSKAWSRLG   86 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence            4456777778889999999999999987543   45 4778888999999999999999999988 4344 467888999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHH
Q 040394          608 HGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSN  642 (691)
Q Consensus       608 ~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~  642 (691)
                      .++...|++++|...+++++++.|++...+...+.
T Consensus        87 ~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l  121 (164)
T 3sz7_A           87 LARFDMADYKGAKEAYEKGIEAEGNGGSDAMKRGL  121 (164)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHSSSCCHHHHHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHHhCCCchHHHHHHHH
Confidence            99999999999999999999999998886655543

>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=98.41  E-value=2.4e-06  Score=69.11  Aligned_cols=92  Identities=12%  Similarity=0.026  Sum_probs=46.1

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCC
Q 040394          571 YVCMVDLLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDG  648 (691)
Q Consensus       571 ~~~li~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g  648 (691)
                      +..+...+...|++++|.+.+++. . .+.+...+..+...+...|++++|...++++.+..|+++..+..++.++...|
T Consensus         7 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~   86 (118)
T 1elw_A            7 LKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLN   86 (118)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHh
Confidence            333444444455555555554444 1 12234444445555555555555555555555555555555555555555555


Q ss_pred             CcHHHHHHHHHHHh
Q 040394          649 RWIRVNQVRELMKQ  662 (691)
Q Consensus       649 ~~~~A~~~~~~~~~  662 (691)
                      ++++|.+.+++..+
T Consensus        87 ~~~~A~~~~~~~~~  100 (118)
T 1elw_A           87 RFEEAKRTYEEGLK  100 (118)
T ss_dssp             CHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHH
Confidence            55555555555544

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.41  E-value=2.3e-06  Score=71.10  Aligned_cols=97  Identities=11%  Similarity=0.062  Sum_probs=88.6

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHH
Q 040394          568 MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYA  645 (691)
Q Consensus       568 ~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~  645 (691)
                      ...+..+...+.+.|++++|++.+++. ...| +...+..+...+...|++++|...++++.+..|+++..+..++.++.
T Consensus        16 ~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~   95 (133)
T 2lni_A           16 ALMVKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPTFIKGYTRKAAALE   95 (133)
T ss_dssp             HHHHHHHHHHHHHTTCSHHHHHHHHHHHTTCTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCchHHHHHHHHHHH
Confidence            667888999999999999999999997 4444 67789999999999999999999999999999999999999999999


Q ss_pred             hCCCcHHHHHHHHHHHhCC
Q 040394          646 SDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       646 ~~g~~~~A~~~~~~~~~~g  664 (691)
                      ..|++++|.+.+++..+..
T Consensus        96 ~~~~~~~A~~~~~~~~~~~  114 (133)
T 2lni_A           96 AMKDYTKAMDVYQKALDLD  114 (133)
T ss_dssp             HTTCHHHHHHHHHHHHHHC
T ss_pred             HHhhHHHHHHHHHHHHHhC
Confidence            9999999999999988753

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.40  E-value=8.4e-06  Score=78.70  Aligned_cols=163  Identities=12%  Similarity=-0.057  Sum_probs=119.9

Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-C------HhHHHHHHHHHhcCCChHHHHHHHHHHHHCCC---CCC--
Q 040394          466 VYVGTALLNFYAKCGDAQSARMVFDAMRE--K-N------TVTWSAMIGGYGMQGDGGGSLALFSDMLNEEV---QPN--  531 (691)
Q Consensus       466 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~------~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~---~p~--  531 (691)
                      ...+...+..+...|++++|...+.+..+  + .      ...+..+...+...|++++|+..+++..+...   .+.  
T Consensus        75 ~~~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~  154 (293)
T 2qfc_A           75 KKQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQN  154 (293)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHH
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHH
Confidence            33445567778889999999888876553  1 1      12344466677888999999999999876321   222  


Q ss_pred             HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-----hhHHHHHHHHHHhcCChHHHHHHHHhC-------CCCCC
Q 040394          532 EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-----MKHYVCMVDLLARAGRLEEALEFMENM-------PIEPD  599 (691)
Q Consensus       532 ~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-----~~~~~~li~~~~~~g~~~~A~~~~~~~-------~~~p~  599 (691)
                      ..+++.+...|...|++++|...+++........|+     ..++..+...|.+.|++++|++.+++.       +....
T Consensus       155 ~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~  234 (293)
T 2qfc_A          155 LYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMAL  234 (293)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSS
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHH
Confidence            347778888999999999999999987632222232     257888999999999999999998886       11111


Q ss_pred             -HHHHHHHHHHHHhcCCHHHH-HHHHHHHHh
Q 040394          600 -VSLFGAFLHGCGLYSRFDLG-EVMIKKMLE  628 (691)
Q Consensus       600 -~~~~~~l~~~~~~~g~~~~A-~~~~~~~~~  628 (691)
                       ..+|..+...+...|++++| ...+++++.
T Consensus       235 ~~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al~  265 (293)
T 2qfc_A          235 IGQLYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence             56788899999999999999 888998776

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.40  E-value=4.2e-06  Score=75.66  Aligned_cols=94  Identities=12%  Similarity=0.043  Sum_probs=52.7

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhC----CCCC-C----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC--CCc---
Q 040394          569 KHYVCMVDLLARAGRLEEALEFMENM----PIEP-D----VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHP--DKA---  634 (691)
Q Consensus       569 ~~~~~li~~~~~~g~~~~A~~~~~~~----~~~p-~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p--~~~---  634 (691)
                      ..+..+...+...|++++|.+.+++.    ...+ +    ...+..+...+...|++++|...++++++..+  +++   
T Consensus        67 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  146 (203)
T 3gw4_A           67 RALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAI  146 (203)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHH
Confidence            34445555555666666665555554    0011 1    23455566666667777777777777665321  111   


Q ss_pred             -hhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          635 -CYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       635 -~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                       ..+..++.++...|++++|.+.+++..+
T Consensus       147 ~~~~~~la~~~~~~g~~~~A~~~~~~al~  175 (203)
T 3gw4_A          147 ACAFRGLGDLAQQEKNLLEAQQHWLRARD  175 (203)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence             2345666777777777777777666554

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.39  E-value=6.2e-06  Score=76.97  Aligned_cols=183  Identities=8%  Similarity=-0.037  Sum_probs=138.2

Q ss_pred             hcCCHHHHHHHHHhccc--C-CHhHHHHH-------HHHHhcCCChHHHHHHHHHHHHCCCCCCH---------------
Q 040394          478 KCGDAQSARMVFDAMRE--K-NTVTWSAM-------IGGYGMQGDGGGSLALFSDMLNEEVQPNE---------------  532 (691)
Q Consensus       478 ~~g~~~~A~~~~~~~~~--~-~~~~~~~l-------i~~~~~~~~~~~A~~~~~~m~~~g~~p~~---------------  532 (691)
                      ..++...|.+.|.+..+  | ....|..+       ...+...++..+++..+++-..  +.|+.               
T Consensus        18 ~~~d~~~A~~~F~~a~~~dP~~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~--l~p~~l~a~~~~~g~y~~~~   95 (282)
T 4f3v_A           18 LPMSEARSLDLFTEITNYDESACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQ--ISMSTLNARIAIGGLYGDIT   95 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTT--CCGGGGCCEEECCTTTCCCE
T ss_pred             cCCCHHHHHHHHHHHHHhChhhhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhc--CChhhhhhhhccCCcccccc
Confidence            57999999999999885  3 45678777       4555555555555555555443  22221               


Q ss_pred             -------HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhCCCCCCH----H
Q 040394          533 -------VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDV----S  601 (691)
Q Consensus       533 -------~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~----~  601 (691)
                             .....+...+...|++++|.++|+.+..   ..|+......+...+.+.|++++|+..|+.....|+.    .
T Consensus        96 ~~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~---~~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~d~~~~~~  172 (282)
T 4f3v_A           96 YPVTSPLAITMGFAACEAAQGNYADAMEALEAAPV---AGSEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWPDKFLAGA  172 (282)
T ss_dssp             EECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCC---TTCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCSCHHHHHH
T ss_pred             cccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHh---cCCchHHHHHHHHHHHHcCCHHHHHHHHHHhhccCCcccHHH
Confidence                   2233455677889999999999997742   3565446666777899999999999999987544433    3


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcC--CC-CchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          602 LFGAFLHGCGLYSRFDLGEVMIKKMLELH--PD-KACYYVLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       602 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      .+..+..++...|++++|+..|+++..-.  |. .+......+.++.+.|+.++|...|+++.....
T Consensus       173 a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~P  239 (282)
T 4f3v_A          173 AGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTHP  239 (282)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC
Confidence            67788889999999999999999998633  55 456788999999999999999999999988654

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.39  E-value=2.9e-06  Score=69.44  Aligned_cols=97  Identities=14%  Similarity=0.182  Sum_probs=87.6

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHH
Q 040394          568 MKHYVCMVDLLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYA  645 (691)
Q Consensus       568 ~~~~~~li~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~  645 (691)
                      ...+..+...+...|++++|.+.++++ . .+.+..++..+...+...|++++|...++++.+..|+++..+..++.++.
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~   88 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYY   88 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHH
Confidence            467788889999999999999999998 2 33467788999999999999999999999999999999999999999999


Q ss_pred             hCCCcHHHHHHHHHHHhCC
Q 040394          646 SDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       646 ~~g~~~~A~~~~~~~~~~g  664 (691)
                      ..|++++|.+.++++.+..
T Consensus        89 ~~~~~~~A~~~~~~~~~~~  107 (125)
T 1na0_A           89 KQGDYDEAIEYYQKALELD  107 (125)
T ss_dssp             HTTCHHHHHHHHHHHHHHC
T ss_pred             HhcCHHHHHHHHHHHHHhC
Confidence            9999999999999998754

>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=98.37  E-value=1.4e-06  Score=71.87  Aligned_cols=95  Identities=8%  Similarity=0.018  Sum_probs=69.5

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCch-------hHHH
Q 040394          569 KHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKAC-------YYVL  639 (691)
Q Consensus       569 ~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~-------~~~~  639 (691)
                      ..+..+...+.+.|++++|++.|++. ...| +...|..+..+|...|++++|+..+++++++.|++..       ++..
T Consensus         9 ~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~   88 (127)
T 4gcn_A            9 IAEKDLGNAAYKQKDFEKAHVHYDKAIELDPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSR   88 (127)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHH
Confidence            34556777777888888888887776 3334 4567777778888888888888888888887766542       5666


Q ss_pred             HHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          640 VSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       640 l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      ++.++...|++++|++.+++.++.
T Consensus        89 lg~~~~~~~~~~~A~~~~~kal~~  112 (127)
T 4gcn_A           89 AGNAFQKQNDLSLAVQWFHRSLSE  112 (127)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhh
Confidence            777788888888888888877663

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.35  E-value=4.3e-06  Score=70.97  Aligned_cols=109  Identities=9%  Similarity=0.032  Sum_probs=57.6

Q ss_pred             HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC----hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHH
Q 040394          532 EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS----MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGA  605 (691)
Q Consensus       532 ~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~  605 (691)
                      ...+..+...+...|++++|.+.|++..   ...|+    ...+..+...|...|++++|++.+++. ...| +...+..
T Consensus        28 ~~~~~~~a~~~~~~~~~~~A~~~~~~a~---~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~  104 (148)
T 2dba_A           28 VEQLRKEGNELFKCGDYGGALAAYTQAL---GLDATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDGGDVKALYR  104 (148)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHH---TSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSCCHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHH---HHcccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCccCHHHHHH
Confidence            3445555555555666666666665443   23444    344555555555555666655555554 2222 3445555


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHH
Q 040394          606 FLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNL  643 (691)
Q Consensus       606 l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~  643 (691)
                      +..++...|++++|...++++++..|++...+..+..+
T Consensus       105 ~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~  142 (148)
T 2dba_A          105 RSQALEKLGRLDQAVLDLQRCVSLEPKNKVFQEALRNI  142 (148)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCSSCHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHH
Confidence            55555555566666666665555555555555444443

>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=98.34  E-value=1.1e-06  Score=74.88  Aligned_cols=105  Identities=9%  Similarity=0.029  Sum_probs=82.0

Q ss_pred             HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCC-ChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHH
Q 040394          533 VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVP-SMKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHG  609 (691)
Q Consensus       533 ~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~  609 (691)
                      ..+..+...+...|++++|...|+....   ..| +...|..+..+|...|++++|++.+++. ...| +...+..+..+
T Consensus        22 ~~~~~~g~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~   98 (148)
T 2vgx_A           22 EQLYSLAFNQYQSGXYEDAHXVFQALCV---LDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIXEPRFPFHAAEC   98 (148)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHH---cCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHH
Confidence            4455566677788888888888887643   345 3667778888888899999999888887 3334 55788888999


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCchhHHHH
Q 040394          610 CGLYSRFDLGEVMIKKMLELHPDKACYYVLV  640 (691)
Q Consensus       610 ~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l  640 (691)
                      +...|++++|...+++++++.|+++......
T Consensus        99 ~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~  129 (148)
T 2vgx_A           99 LLQXGELAEAESGLFLAQELIANXPEFXELS  129 (148)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHTTCGGGHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHCcCCCcchHHH
Confidence            9999999999999999999999877665433

>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=98.34  E-value=3.2e-06  Score=74.60  Aligned_cols=122  Identities=10%  Similarity=0.104  Sum_probs=96.4

Q ss_pred             hcccCCHHHHHHHHHHchhhcCCCC-ChhHHHHHHHHHHhcCChHHHHHHHHhC-CCC-CCHHHHHHHHHH-HHhcCCH-
Q 040394          542 CSHTGMVGEGWKCFYSMCRDFKFVP-SMKHYVCMVDLLARAGRLEEALEFMENM-PIE-PDVSLFGAFLHG-CGLYSRF-  616 (691)
Q Consensus       542 ~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~-p~~~~~~~l~~~-~~~~g~~-  616 (691)
                      +...|++++|...++.....   .| +...+..+...|...|++++|++.+++. ... .+...+..+... +...|++ 
T Consensus        20 ~~~~~~~~~A~~~~~~al~~---~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~l~~~~~~~~   96 (177)
T 2e2e_A           20 FASQQNPEAQLQALQDKIRA---NPQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGENAELYAALATVLYYQASQHM   96 (177)
T ss_dssp             CC-----CCCCHHHHHHHHH---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHTTTCC
T ss_pred             hhhccCHHHHHHHHHHHHHh---CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCcc
Confidence            45678888888888876543   34 4678888899999999999999999887 333 356677778877 7788998 


Q ss_pred             -HHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCc
Q 040394          617 -DLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLS  666 (691)
Q Consensus       617 -~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~  666 (691)
                       ++|...++++++..|+++..+..++.+|...|++++|...++++.+....
T Consensus        97 ~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~  147 (177)
T 2e2e_A           97 TAQTRAMIDKALALDSNEITALMLLASDAFMQANYAQAIELWQKVMDLNSP  147 (177)
T ss_dssp             CHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCT
T ss_pred             hHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhhCCC
Confidence             99999999999999999999999999999999999999999998886543

>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=98.33  E-value=8.6e-06  Score=65.74  Aligned_cols=109  Identities=12%  Similarity=0.104  Sum_probs=79.2

Q ss_pred             HHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCC-ChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHH
Q 040394          533 VIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVP-SMKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHG  609 (691)
Q Consensus       533 ~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~  609 (691)
                      ..+..+...+...|++++|...++.....   .| +...+..+...+...|++++|.+.+++. ...| +...+..+..+
T Consensus         5 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~   81 (118)
T 1elw_A            5 NELKEKGNKALSVGNIDDALQCYSEAIKL---DPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAA   81 (118)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHH---CCCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCcccHHHHHHHHHH
Confidence            34455555666667777777777665432   33 3556666777777778888887777776 2233 56778888889


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHH
Q 040394          610 CGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLY  644 (691)
Q Consensus       610 ~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~  644 (691)
                      +...|++++|...++++.+..|+++..+..++.+.
T Consensus        82 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~  116 (118)
T 1elw_A           82 LEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNME  116 (118)
T ss_dssp             HHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHhh
Confidence            99999999999999999999999888887776654

>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=98.32  E-value=3.8e-06  Score=75.71  Aligned_cols=168  Identities=7%  Similarity=0.001  Sum_probs=102.5

Q ss_pred             HHhcCCHHHHHHHHHhcccC---CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHH
Q 040394          476 YAKCGDAQSARMVFDAMREK---NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGW  552 (691)
Q Consensus       476 ~~~~g~~~~A~~~~~~~~~~---~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~  552 (691)
                      ....|+++.+.+.++.-.+.   ....+..+...+...|++++|+..|++..+.  .|+...+...        ..+.-.
T Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~~~~~~~~~~--------~~~~~~   83 (198)
T 2fbn_A           14 RENLYFQGAKKSIYDYTDEEKVQSAFDIKEEGNEFFKKNEINEAIVKYKEALDF--FIHTEEWDDQ--------ILLDKK   83 (198)
T ss_dssp             --------CCCSGGGCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TTTCTTCCCH--------HHHHHH
T ss_pred             hhhhhhccccCchhhCCHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--Hhcccccchh--------hHHHHH
Confidence            34445555555555433321   3445666777777788888888888877763  2221100000        000000


Q ss_pred             HHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC
Q 040394          553 KCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PI-EPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELH  630 (691)
Q Consensus       553 ~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~-~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  630 (691)
                         ..        .....+..+..+|.+.|++++|++.+++. .. +.+...+..+..++...|++++|...++++++..
T Consensus        84 ---~~--------~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~  152 (198)
T 2fbn_A           84 ---KN--------IEISCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAASLN  152 (198)
T ss_dssp             ---HH--------HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             ---HH--------HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC
Confidence               00        01245667778888888888888888887 33 3456788889999999999999999999999999


Q ss_pred             CCCchhHHHHHHHHHhCCCcHHHH-HHHHHHHhCC
Q 040394          631 PDKACYYVLVSNLYASDGRWIRVN-QVRELMKQRG  664 (691)
Q Consensus       631 p~~~~~~~~l~~~~~~~g~~~~A~-~~~~~~~~~g  664 (691)
                      |++...+..++.++...|+.+++. ..+..|...|
T Consensus       153 p~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~f~~~  187 (198)
T 2fbn_A          153 PNNLDIRNSYELCVNKLKEARKKDKLTFGGMFDKG  187 (198)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHHC-------------
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            999999999999999999888887 5566665544

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.32  E-value=2.1e-06  Score=72.98  Aligned_cols=92  Identities=4%  Similarity=-0.042  Sum_probs=43.0

Q ss_pred             hHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHh
Q 040394          113 SFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAK  192 (691)
Q Consensus       113 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~  192 (691)
                      .+..+...+.+.|++++|+..|++..... +.+...|..+..++...|++++|...|+...+..|.++..|..+..+|.+
T Consensus        38 ~~~~lg~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~~~~~~~~lg~~~~~  116 (151)
T 3gyz_A           38 DIYSYAYDFYNKGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFHTGQCQLR  116 (151)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSSCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHH
Confidence            44444445555555555555555554442 22334444444444455555555555555554444444444444444444


Q ss_pred             cCChHHHHHHHhc
Q 040394          193 CRDIGSSRQVFDE  205 (691)
Q Consensus       193 ~g~~~~A~~~~~~  205 (691)
                      .|++++|...|++
T Consensus       117 lg~~~eA~~~~~~  129 (151)
T 3gyz_A          117 LKAPLKAKECFEL  129 (151)
T ss_dssp             TTCHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHH
Confidence            4444444444433

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.32  E-value=1e-05  Score=68.65  Aligned_cols=98  Identities=13%  Similarity=-0.010  Sum_probs=83.2

Q ss_pred             ChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHH
Q 040394          567 SMKHYVCMVDLLARAGRLEEALEFMENM-PIEPD----VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVS  641 (691)
Q Consensus       567 ~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~  641 (691)
                      +...+..+...+...|++++|++.+++. ...|+    ...|..+...+...|++++|...++++++..|+++..+..++
T Consensus        27 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a  106 (148)
T 2dba_A           27 SVEQLRKEGNELFKCGDYGGALAAYTQALGLDATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDGGDVKALYRRS  106 (148)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCccCHHHHHHHH
Confidence            3667777888888999999999998887 66676    567888888888899999999999999999998888888999


Q ss_pred             HHHHhCCCcHHHHHHHHHHHhCC
Q 040394          642 NLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       642 ~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      .+|...|++++|.+.+++..+..
T Consensus       107 ~~~~~~~~~~~A~~~~~~al~~~  129 (148)
T 2dba_A          107 QALEKLGRLDQAVLDLQRCVSLE  129 (148)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHcCCHHHHHHHHHHHHHcC
Confidence            99999999999999998887743

>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=98.32  E-value=0.0004  Score=67.11  Aligned_cols=222  Identities=10%  Similarity=-0.026  Sum_probs=141.3

Q ss_pred             HHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccC-ChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhc-
Q 040394          116 VMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELR-DIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKC-  193 (691)
Q Consensus       116 ~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~-  193 (691)
                      .+.......+..++|+++++.++... +-+..+|+.--..+...| +++++...++.++...+.+..+|+.-...+.+. 
T Consensus        59 ~~r~~~~~~e~se~AL~lt~~~L~~n-P~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPKny~aW~hR~wlL~~l~  137 (349)
T 3q7a_A           59 YFRAIAAKEEKSERALELTEIIVRMN-PAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLKSYQVWHHRLLLLDRIS  137 (349)
T ss_dssp             HHHHHHHTTCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhc
Confidence            33333445556678888888888763 223345666555666666 588888999888888888888888888777776 


Q ss_pred             C-ChHHHHHHHhccCCC---ChhhHHHHHHHHHhCCChh--------HHHHHHHHHHhCCCCCChhhHHHHHHHHHccCC
Q 040394          194 R-DIGSSRQVFDETLDK---NVVSWTSMIAGYVQNDCAQ--------EGLVLFNRMREGFVEGNQITLGSLVTACAKLRA  261 (691)
Q Consensus       194 g-~~~~A~~~~~~~~~~---~~~~~~~li~~~~~~g~~~--------~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~  261 (691)
                      + +++++++.++++.+.   |..+|+--.-.+.+.|.++        ++++.++++.+..+. |...|+.....+.+.++
T Consensus       138 ~~~~~~EL~~~~k~L~~dpkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp~-N~SAW~~R~~lL~~l~~  216 (349)
T 3q7a_A          138 PQDPVSEIEYIHGSLLPDPKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDGR-NNSAWGWRWYLRVSRPG  216 (349)
T ss_dssp             CSCCHHHHHHHHHHTSSCTTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHTTSTT
T ss_pred             CCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhccc
Confidence            6 788888888887664   4556665555555555555        888888888776543 66677777777666665


Q ss_pred             -------hhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCH--------------------HHHHHHHHhcC------
Q 040394          262 -------LHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNI--------------------RDARSVFDELC------  308 (691)
Q Consensus       262 -------~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~--------------------~~A~~~~~~~~------  308 (691)
                             ++++.+.+..++... +-|...|+-+-..+.+.|..                    ....++..++.      
T Consensus       217 ~~~~~~~~~eELe~~~~aI~~~-P~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  295 (349)
T 3q7a_A          217 AETSSRSLQDELIYILKSIHLI-PHNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDPLPE  295 (349)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCCC-CCCS
T ss_pred             cccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHHhccccc
Confidence                   566777777777664 23566666666556555543                    22333333331      


Q ss_pred             ---CCChhHHHHHHHHHHhcCCchhHHHHHHHhhH
Q 040394          309 ---SIDLVSWTAMIVGYTQSGYPDKALKLFTDKKW  340 (691)
Q Consensus       309 ---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  340 (691)
                         .++...+..|+..|...|+.++|.++++.+.+
T Consensus       296 ~~~~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~  330 (349)
T 3q7a_A          296 DTPLPVPLALEYLADSFIEQNRVDDAAKVFEKLSS  330 (349)
T ss_dssp             SCCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ccCCCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Confidence               13444556666666666666666666666543

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.30  E-value=5.1e-06  Score=68.61  Aligned_cols=97  Identities=7%  Similarity=0.011  Sum_probs=87.6

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHH
Q 040394          568 MKHYVCMVDLLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYA  645 (691)
Q Consensus       568 ~~~~~~li~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~  645 (691)
                      ...+..+...+...|++++|.+.+++. . .+.+...+..+...+...|++++|...++++.+..|+++..+..++.++.
T Consensus        12 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~   91 (131)
T 2vyi_A           12 AERLKTEGNEQMKVENFEAAVHFYGKAIELNPANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPAYSKAYGRMGLALS   91 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHccCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcCccCHHHHHHHHHHHH
Confidence            567778888999999999999999997 3 33467788899999999999999999999999999999999999999999


Q ss_pred             hCCCcHHHHHHHHHHHhCC
Q 040394          646 SDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       646 ~~g~~~~A~~~~~~~~~~g  664 (691)
                      ..|++++|.+.+++..+..
T Consensus        92 ~~~~~~~A~~~~~~~~~~~  110 (131)
T 2vyi_A           92 SLNKHVEAVAYYKKALELD  110 (131)
T ss_dssp             HTTCHHHHHHHHHHHHHHS
T ss_pred             HhCCHHHHHHHHHHHHhcC
Confidence            9999999999999998754

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.29  E-value=3e-06  Score=70.06  Aligned_cols=94  Identities=7%  Similarity=0.000  Sum_probs=44.1

Q ss_pred             HHhcccCCHHHHHHHHHHchhhcCCCCC-h---hHHHHHHHHHHhcCChHHHHHHHHhC-CCCCC----HHHHHHHHHHH
Q 040394          540 SACSHTGMVGEGWKCFYSMCRDFKFVPS-M---KHYVCMVDLLARAGRLEEALEFMENM-PIEPD----VSLFGAFLHGC  610 (691)
Q Consensus       540 ~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~---~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~----~~~~~~l~~~~  610 (691)
                      ..+...|++++|...|+...+.   .|+ .   ..+..+..++.+.|++++|++.+++. ...|+    ...+..+..++
T Consensus        10 ~~~~~~~~~~~A~~~~~~~~~~---~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~la~~~   86 (129)
T 2xev_A           10 FDALKNGKYDDASQLFLSFLEL---YPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPTHDKAAGGLLKLGLSQ   86 (129)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH---CSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHH
T ss_pred             HHHHHhCCHHHHHHHHHHHHHH---CCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHH
Confidence            3444555555555555554332   122 1   24444445555555555555555544 11222    23344444455


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCchh
Q 040394          611 GLYSRFDLGEVMIKKMLELHPDKACY  636 (691)
Q Consensus       611 ~~~g~~~~A~~~~~~~~~~~p~~~~~  636 (691)
                      ...|++++|...++++++..|+++..
T Consensus        87 ~~~g~~~~A~~~~~~~~~~~p~~~~~  112 (129)
T 2xev_A           87 YGEGKNTEAQQTLQQVATQYPGSDAA  112 (129)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSTTSHHH
T ss_pred             HHcCCHHHHHHHHHHHHHHCCCChHH
Confidence            55555555555555555555554433

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.29  E-value=6.3e-06  Score=74.46  Aligned_cols=132  Identities=10%  Similarity=0.013  Sum_probs=70.7

Q ss_pred             hHHHHHHHHHhcCCChHHHHHHHHHHHH----CCCCC-CHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCC-C----
Q 040394          498 VTWSAMIGGYGMQGDGGGSLALFSDMLN----EEVQP-NEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVP-S----  567 (691)
Q Consensus       498 ~~~~~li~~~~~~~~~~~A~~~~~~m~~----~g~~p-~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p-~----  567 (691)
                      ..+..+...+...|++++|...+++..+    .|..| ....+..+...+...|++++|.+.+++......-.+ +    
T Consensus        27 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  106 (203)
T 3gw4_A           27 GARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLAA  106 (203)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHHH
Confidence            3444444445555555555555544443    11111 123344444455566666666666555433211111 1    


Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhC----CCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 040394          568 MKHYVCMVDLLARAGRLEEALEFMENM----PIEPD----VSLFGAFLHGCGLYSRFDLGEVMIKKMLEL  629 (691)
Q Consensus       568 ~~~~~~li~~~~~~g~~~~A~~~~~~~----~~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  629 (691)
                      ...+..+...+...|++++|.+.+++.    ...++    ..++..+...+...|++++|...+++++++
T Consensus       107 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  176 (203)
T 3gw4_A          107 SANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRARDI  176 (203)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            234556666677777777776666665    11112    124566777788888888888888887764

>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=98.27  E-value=0.00041  Score=67.09  Aligned_cols=125  Identities=13%  Similarity=0.075  Sum_probs=67.2

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCC-------HHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCCh--
Q 040394          515 GSLALFSDMLNEEVQPNEVIFTTILSACSHTGM-------VGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRL--  584 (691)
Q Consensus       515 ~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~-------~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~--  584 (691)
                      ++++.++++++.. +-|...|+..-..+.+.+.       ++++++.+++.+.   ..|+ ...|+-+-..+.+.|+.  
T Consensus       185 eELe~~~k~I~~d-p~N~SAW~~R~~lL~~l~~~~~~~~~~~eELe~~~~aI~---~~P~n~SaW~Ylr~Ll~~~~~~~~  260 (349)
T 3q7a_A          185 SELDWCNEMLRVD-GRNNSAWGWRWYLRVSRPGAETSSRSLQDELIYILKSIH---LIPHNVSAWNYLRGFLKHFSLPLV  260 (349)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHTTSTTCCCCHHHHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCCSG
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHhcCCCcc
Confidence            5666666666643 2344445544444444443       4566666655432   2443 44555544445444442  


Q ss_pred             ------------------HHHHHHHHhC-CC-------CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-hcCCCCchhH
Q 040394          585 ------------------EEALEFMENM-PI-------EPDVSLFGAFLHGCGLYSRFDLGEVMIKKML-ELHPDKACYY  637 (691)
Q Consensus       585 ------------------~~A~~~~~~~-~~-------~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~p~~~~~~  637 (691)
                                        .+..++...+ +.       .++...+..|+..|...|+.++|.++++.+. +.+|-...+|
T Consensus       261 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~~~dpir~~yw  340 (349)
T 3q7a_A          261 PILPAILPYTASKLNPDIETVEAFGFPMPSDPLPEDTPLPVPLALEYLADSFIEQNRVDDAAKVFEKLSSEYDQMRAGYW  340 (349)
T ss_dssp             GGHHHHGGGTC--------------CCCCC-CCCSSCCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCGGGHHHH
T ss_pred             cccccccccccccccccchhHHHHHHHHHhcccccccCCCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhhChHHHHHH
Confidence                              2333343333 11       2566677777788888888888888888876 4677766666


Q ss_pred             HHHHHH
Q 040394          638 VLVSNL  643 (691)
Q Consensus       638 ~~l~~~  643 (691)
                      ...+..
T Consensus       341 ~~~~~~  346 (349)
T 3q7a_A          341 EFRRRE  346 (349)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            655443

>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=98.26  E-value=3.9e-06  Score=70.47  Aligned_cols=91  Identities=13%  Similarity=0.030  Sum_probs=69.4

Q ss_pred             HHHHHHHHhcCChHHHHHHHHhC-CCCCC-------------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhc-------C
Q 040394          572 VCMVDLLARAGRLEEALEFMENM-PIEPD-------------VSLFGAFLHGCGLYSRFDLGEVMIKKMLEL-------H  630 (691)
Q Consensus       572 ~~li~~~~~~g~~~~A~~~~~~~-~~~p~-------------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-------~  630 (691)
                      ......+.+.|++++|++.|++. .+.|+             ...|..+..++.+.|++++|+..+++++++       +
T Consensus        15 ~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~~   94 (159)
T 2hr2_A           15 LSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELN   94 (159)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTT
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCC
Confidence            33445555666666666666665 22222             237888888888889999999999999988       9


Q ss_pred             CCCchhH----HHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          631 PDKACYY----VLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       631 p~~~~~~----~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      |++...|    +..+.++...|++++|+..|++.++
T Consensus        95 pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A           95 QDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             STHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence            9988888    8999999999999999999988876

>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=98.25  E-value=1.5e-05  Score=69.12  Aligned_cols=124  Identities=6%  Similarity=0.003  Sum_probs=68.6

Q ss_pred             hHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHh
Q 040394          113 SFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAK  192 (691)
Q Consensus       113 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~  192 (691)
                      .|..+...+...|++++|...|++..+.. +.+...+..+...+...|++++|...++...+..+.+..++..+..++..
T Consensus        15 ~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~   93 (166)
T 1a17_A           15 ELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMA   93 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHH
Confidence            34555555666666666666666665542 23445555555666666666666666666666655555566666666666


Q ss_pred             cCChHHHHHHHhccCC---CChhhHHH--HHHHHHhCCChhHHHHHHHHH
Q 040394          193 CRDIGSSRQVFDETLD---KNVVSWTS--MIAGYVQNDCAQEGLVLFNRM  237 (691)
Q Consensus       193 ~g~~~~A~~~~~~~~~---~~~~~~~~--li~~~~~~g~~~~A~~~~~~m  237 (691)
                      .|++++|...|++..+   .+...+..  ++..+...|++++|++.+...
T Consensus        94 ~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~  143 (166)
T 1a17_A           94 LGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEHK  143 (166)
T ss_dssp             TTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHcccch
Confidence            6666666666655422   12233322  222244555666666655544

>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=98.24  E-value=1e-05  Score=66.52  Aligned_cols=109  Identities=10%  Similarity=-0.037  Sum_probs=80.1

Q ss_pred             HHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHH
Q 040394          534 IFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGC  610 (691)
Q Consensus       534 ~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~  610 (691)
                      .+......+...|++++|...|++..+.   .|+ ...|..+..+|.+.|++++|++.+++. ...| +...|..+..++
T Consensus         6 ~~~~~g~~~~~~~~~~~A~~~~~~al~~---~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~   82 (126)
T 3upv_A            6 EARLEGKEYFTKSDWPNAVKAYTEMIKR---APEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQ   82 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHh---CCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHH
Confidence            4445555666777777777777765432   343 567777777888888888888887776 3334 466888888899


Q ss_pred             HhcCCHHHHHHHHHHHHhcC------CCCchhHHHHHHHHH
Q 040394          611 GLYSRFDLGEVMIKKMLELH------PDKACYYVLVSNLYA  645 (691)
Q Consensus       611 ~~~g~~~~A~~~~~~~~~~~------p~~~~~~~~l~~~~~  645 (691)
                      ...|++++|...+++++++.      |++..+...+..+..
T Consensus        83 ~~~~~~~~A~~~~~~al~~~p~~~~~p~~~~~~~~l~~~~~  123 (126)
T 3upv_A           83 IAVKEYASALETLDAARTKDAEVNNGSSAREIDQLYYKASQ  123 (126)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHHHTTTTHHHHHHHHHHHHH
T ss_pred             HHHhCHHHHHHHHHHHHHhCcccCCchhHHHHHHHHHHHHH
Confidence            99999999999999999988      887777777766543

>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=98.24  E-value=4.8e-06  Score=79.74  Aligned_cols=95  Identities=6%  Similarity=-0.171  Sum_probs=49.4

Q ss_pred             HHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCC
Q 040394          349 TIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSP  428 (691)
Q Consensus       349 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p  428 (691)
                      .+..+...+...|++++|...++.+.+..+.+...+..+..+|.+.|++++|...+++..+.+               +.
T Consensus         6 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~---------------p~   70 (281)
T 2c2l_A            6 ELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELD---------------GQ   70 (281)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC---------------TT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC---------------CC
Confidence            333444444455555555555555555555455555556666666666666666666555431               12


Q ss_pred             CHHHHHHHHHHHhccCcHHHHHHHHHHHHH
Q 040394          429 DAVTLVSVISACASLGAVQVGSSLHAYSTK  458 (691)
Q Consensus       429 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  458 (691)
                      +...+..+..++...|++++|...++...+
T Consensus        71 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  100 (281)
T 2c2l_A           71 SVKAHFFLGQCQLEMESYDEAIANLQRAYS  100 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            334444555555555555555555555444

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.22  E-value=7.1e-06  Score=69.21  Aligned_cols=106  Identities=11%  Similarity=0.002  Sum_probs=80.6

Q ss_pred             HHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHH
Q 040394          534 IFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGC  610 (691)
Q Consensus       534 ~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~  610 (691)
                      .+..+...+...|++++|...|+.....   .|+ ...|..+..+|.+.|++++|++.+++. ...| +...+..+..++
T Consensus        20 ~~~~~a~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~   96 (142)
T 2xcb_A           20 QLYALGFNQYQAGKWDDAQKIFQALCML---DHYDARYFLGLGACRQSLGLYEQALQSYSYGALMDINEPRFPFHAAECH   96 (142)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccHHHHHHHHHHHHHh---CCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHH
Confidence            3444555677788888888888876433   443 667777888888888888888888887 3333 556788888899


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCchhHHHHHH
Q 040394          611 GLYSRFDLGEVMIKKMLELHPDKACYYVLVSN  642 (691)
Q Consensus       611 ~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~  642 (691)
                      ...|++++|...++++++..|+++........
T Consensus        97 ~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~  128 (142)
T 2xcb_A           97 LQLGDLDGAESGFYSARALAAAQPAHEALAAR  128 (142)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHTCGGGHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhCCCCcchHHHHHH
Confidence            99999999999999999999988777655433

>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=98.22  E-value=0.00035  Score=67.19  Aligned_cols=216  Identities=13%  Similarity=0.009  Sum_probs=143.5

Q ss_pred             ccCcH-HHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCC----------HHHHHHHHHhccc---CCHhHHHHHHHHH
Q 040394          442 SLGAV-QVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGD----------AQSARMVFDAMRE---KNTVTWSAMIGGY  507 (691)
Q Consensus       442 ~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~----------~~~A~~~~~~~~~---~~~~~~~~li~~~  507 (691)
                      +.|.. ++|..+...+...+  |.+..+++.--..+...+.          +++++.+++.+..   ++..+|+.-...+
T Consensus        41 ~~~e~s~eaL~~t~~~L~~n--P~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~PKny~aW~hR~wlL  118 (331)
T 3dss_A           41 QAGELDESVLELTSQILGAN--PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLL  118 (331)
T ss_dssp             HTTCCSHHHHHHHHHHHTTC--TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HcCCCCHHHHHHHHHHHHHC--chhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            34443 47788888888777  5666666655444444333          5677777777664   3666777766666


Q ss_pred             hcCC--ChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCC-HHHHHHHHHHchhhcCCCC-ChhHHHHHHHHHHhc--
Q 040394          508 GMQG--DGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGM-VGEGWKCFYSMCRDFKFVP-SMKHYVCMVDLLARA--  581 (691)
Q Consensus       508 ~~~~--~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~-~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~--  581 (691)
                      ...+  ++++++.+++++.+.. +-|...|+.--.++...|. ++++++.++.+++.   .| |...|+....++.+.  
T Consensus       119 ~~l~~~~~~~EL~~~~k~l~~d-prNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~---~p~N~SAW~~R~~ll~~l~~  194 (331)
T 3dss_A          119 SRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITR---NFSNYSSWHYRSCLLPQLHP  194 (331)
T ss_dssp             HHCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH---CSCCHHHHHHHHHHHHHHSC
T ss_pred             hccCcccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHH---CCCCHHHHHHHHHHHHHhhh
Confidence            6666  4788888888888864 3455666665555666666 58888888877543   34 355666655555444  


Q ss_pred             ------------CChHHHHHHHHhC--CCCCCHHHHHHHHHHHHhc-----------CCHHHHHHHHHHHHhcCCCCchh
Q 040394          582 ------------GRLEEALEFMENM--PIEPDVSLFGAFLHGCGLY-----------SRFDLGEVMIKKMLELHPDKACY  636 (691)
Q Consensus       582 ------------g~~~~A~~~~~~~--~~~p~~~~~~~l~~~~~~~-----------g~~~~A~~~~~~~~~~~p~~~~~  636 (691)
                                  +.++++++.+.+.  ..+-|...|+-+-..+.+.           +.++++++.++++++..|++.-.
T Consensus       195 ~~~~~~~~~~~~~~~~eEle~~~~ai~~~P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~~~~elle~~pd~~w~  274 (331)
T 3dss_A          195 QPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELESCKELQELEPENKWC  274 (331)
T ss_dssp             CC------CCCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHHHHHHHHHHCTTCHHH
T ss_pred             ccccccccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhccCccccchHHHHHHHHHHHHHHHHHhhCcccchH
Confidence                        4577888888777  3344667777666666554           45788999999999999998655


Q ss_pred             HHHHHHH---HHhCCCcHHHHHHHHHHHhC
Q 040394          637 YVLVSNL---YASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       637 ~~~l~~~---~~~~g~~~~A~~~~~~~~~~  663 (691)
                      +..++.+   ....|..+++...++++.+.
T Consensus       275 l~~~~~~~~~~~~~~~~~~~~~~l~~l~~~  304 (331)
T 3dss_A          275 LLTIILLMRALDPLLYEKETLQYFSTLKAV  304 (331)
T ss_dssp             HHHHHHHHHHHCTTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcccccHHHHHHHHHHHHHh
Confidence            5444332   22467788888888888764

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.20  E-value=1.4e-05  Score=69.32  Aligned_cols=95  Identities=5%  Similarity=-0.017  Sum_probs=56.1

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHH
Q 040394          568 MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYA  645 (691)
Q Consensus       568 ~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~  645 (691)
                      ...+..+...+.+.|++++|++.|++. ...| +...|..+..++...|++++|+..++++++++|+++..+..++.+|.
T Consensus        11 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~   90 (164)
T 3sz7_A           11 SDKLKSEGNAAMARKEYSKAIDLYTQALSIAPANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPKYSKAWSRLGLARF   90 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            344555555566666666666666655 2222 44555556666666666666666666666666666666666666666


Q ss_pred             hCCCcHHHHHHHHHHHh
Q 040394          646 SDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       646 ~~g~~~~A~~~~~~~~~  662 (691)
                      ..|++++|.+.+++.++
T Consensus        91 ~~g~~~~A~~~~~~al~  107 (164)
T 3sz7_A           91 DMADYKGAKEAYEKGIE  107 (164)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HccCHHHHHHHHHHHHH
Confidence            66666666666665554

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.19  E-value=1.4e-06  Score=70.73  Aligned_cols=91  Identities=12%  Similarity=0.093  Sum_probs=43.9

Q ss_pred             cCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHH
Q 040394          545 TGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEV  621 (691)
Q Consensus       545 ~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~  621 (691)
                      .|++++|+..|++..+...-.|+ ...+..+..+|.+.|++++|++.+++. ...| +...+..+..++...|++++|..
T Consensus         3 ~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~   82 (117)
T 3k9i_A            3 LGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPNHQALRVFYAMVLYNLGRYEQGVE   82 (117)
T ss_dssp             ----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHcCCHHHHHH
Confidence            45556666666654321000232 344555555555555555555555555 2222 33455555555555555555555


Q ss_pred             HHHHHHhcCCCCch
Q 040394          622 MIKKMLELHPDKAC  635 (691)
Q Consensus       622 ~~~~~~~~~p~~~~  635 (691)
                      .++++++..|+++.
T Consensus        83 ~~~~al~~~p~~~~   96 (117)
T 3k9i_A           83 LLLKIIAETSDDET   96 (117)
T ss_dssp             HHHHHHHHHCCCHH
T ss_pred             HHHHHHHhCCCcHH
Confidence            55555555555543

>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=98.18  E-value=6.6e-06  Score=67.93  Aligned_cols=96  Identities=8%  Similarity=0.039  Sum_probs=76.9

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC-------chhHHH
Q 040394          569 KHYVCMVDLLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK-------ACYYVL  639 (691)
Q Consensus       569 ~~~~~li~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~-------~~~~~~  639 (691)
                      ..+..+...+...|++++|...+++. . .+.+...+..+...+...|++++|...++++.+..|++       +.++..
T Consensus         5 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (131)
T 1elr_A            5 LKEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYAR   84 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHHH
Confidence            45666777778888888888888776 2 33456778888888888999999999999998887766       778888


Q ss_pred             HHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          640 VSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       640 l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      ++.++...|++++|.+.+++..+..
T Consensus        85 la~~~~~~~~~~~A~~~~~~~~~~~  109 (131)
T 1elr_A           85 IGNSYFKEEKYKDAIHFYNKSLAEH  109 (131)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhccHHHHHHHHHHHHHhC
Confidence            8899999999999999998888743

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.15  E-value=4.8e-05  Score=78.08  Aligned_cols=120  Identities=8%  Similarity=-0.095  Sum_probs=64.3

Q ss_pred             hcccCCHHHHHHHHHHchhh---cCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-----C--CCCC-HHHHHHHHHH
Q 040394          542 CSHTGMVGEGWKCFYSMCRD---FKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-----P--IEPD-VSLFGAFLHG  609 (691)
Q Consensus       542 ~~~~g~~~~A~~~~~~m~~~---~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-----~--~~p~-~~~~~~l~~~  609 (691)
                      +...|+++.|..+++.....   .+..+. ..++..+...|...|++++|.+++++.     +  .++. ..++..++..
T Consensus       105 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  184 (434)
T 4b4t_Q          105 EQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDDKPSLVDVHLLESKV  184 (434)
T ss_dssp             CSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCSTHHHHHHHHHHHH
T ss_pred             HhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHH
Confidence            33455566665555543221   122222 334555666666666666666666554     1  1111 2355666666


Q ss_pred             HHhcCCHHHHHHHHHHHHhcC---CCC----chhHHHHHHHHHhCCCcHHHHHHHHHHH
Q 040394          610 CGLYSRFDLGEVMIKKMLELH---PDK----ACYYVLVSNLYASDGRWIRVNQVRELMK  661 (691)
Q Consensus       610 ~~~~g~~~~A~~~~~~~~~~~---p~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~  661 (691)
                      |...|++++|..+++++....   |+.    ..++..++.++...|++++|...+....
T Consensus       185 ~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~  243 (434)
T 4b4t_Q          185 YHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESF  243 (434)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHH
T ss_pred             HHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            666777777777776666532   221    1344555666666677777766655554

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.15  E-value=7.3e-06  Score=71.01  Aligned_cols=101  Identities=16%  Similarity=0.053  Sum_probs=53.2

Q ss_pred             HHHHHHHHhcccCCHHHHHHHHHHchhhcCC---------------CCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CC
Q 040394          534 IFTTILSACSHTGMVGEGWKCFYSMCRDFKF---------------VPS-MKHYVCMVDLLARAGRLEEALEFMENM-PI  596 (691)
Q Consensus       534 ~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~---------------~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~  596 (691)
                      .+...-..+.+.|++++|+..|.+.+.....               .|. ...|..+..+|.+.|++++|+..+++. ..
T Consensus        13 ~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al~~   92 (162)
T 3rkv_A           13 ALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVLKR   92 (162)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhc
Confidence            4445555666677777777777665332000               111 234555555555555555555555554 22


Q ss_pred             CC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040394          597 EP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKA  634 (691)
Q Consensus       597 ~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~  634 (691)
                      .| +...|..+..++...|++++|...++++++++|+++
T Consensus        93 ~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~p~~~  131 (162)
T 3rkv_A           93 EETNEKALFRRAKARIAAWKLDEAEEDLKLLLRNHPAAA  131 (162)
T ss_dssp             STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCGGGH
T ss_pred             CCcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhcCCCCH
Confidence            22 344555555555555555555555555555555554

>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=98.11  E-value=4.3e-06  Score=75.35  Aligned_cols=151  Identities=11%  Similarity=0.036  Sum_probs=85.5

Q ss_pred             HHHHHhcCCChHHHHHHhccCCC---CCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCc----------------
Q 040394           86 LVSMYGSFGHVKYARSVFDSMPN---PDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDN----------------  146 (691)
Q Consensus        86 l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~----------------  146 (691)
                      .+......|.++.|.+.++...+   .....+..+...+...|++++|+..|++..+.. +.+.                
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~   88 (198)
T 2fbn_A           10 HSSGRENLYFQGAKKSIYDYTDEEKVQSAFDIKEEGNEFFKKNEINEAIVKYKEALDFF-IHTEEWDDQILLDKKKNIEI   88 (198)
T ss_dssp             ------------CCCSGGGCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT-TTCTTCCCHHHHHHHHHHHH
T ss_pred             hhhhhhhhhhccccCchhhCCHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH-hcccccchhhHHHHHHHHHH
Confidence            34445556677777777654332   234467777888888999999999999888752 1122                


Q ss_pred             chHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCC---CChhhHHHHHHHHHh
Q 040394          147 FVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLD---KNVVSWTSMIAGYVQ  223 (691)
Q Consensus       147 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~  223 (691)
                      ..+..+..++...|++++|...++...+..+.+..++..+..+|...|++++|...|++..+   .+...+..+..++..
T Consensus        89 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~  168 (198)
T 2fbn_A           89 SCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSYELCVNK  168 (198)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHH
Confidence            45666666677777777777777777777666666777777777777777777766665422   244455555555555


Q ss_pred             CCChhHHH-HHHHHH
Q 040394          224 NDCAQEGL-VLFNRM  237 (691)
Q Consensus       224 ~g~~~~A~-~~~~~m  237 (691)
                      .++..++. ..+..|
T Consensus       169 ~~~~~~~~~~~~~~~  183 (198)
T 2fbn_A          169 LKEARKKDKLTFGGM  183 (198)
T ss_dssp             HHHHHC---------
T ss_pred             HHHHHHHHHHHHHHH
Confidence            55544444 334443

>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=98.11  E-value=1.9e-05  Score=65.95  Aligned_cols=111  Identities=10%  Similarity=-0.033  Sum_probs=78.9

Q ss_pred             CCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHH
Q 040394          530 PNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAF  606 (691)
Q Consensus       530 p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l  606 (691)
                      .+...+..+...+...|++++|...|+.....   .|+ ...+..+..++...|++++|+..+++. ...| +...|..+
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~---~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l   83 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITR---NPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFL   83 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhh---CcCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCchhHHHHHHH
Confidence            34556666666777777777777777766433   343 566777777788888888888877776 3233 56688888


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCC-----CchhHHHHHHH
Q 040394          607 LHGCGLYSRFDLGEVMIKKMLELHPD-----KACYYVLVSNL  643 (691)
Q Consensus       607 ~~~~~~~g~~~~A~~~~~~~~~~~p~-----~~~~~~~l~~~  643 (691)
                      ..++...|++++|...++++++..|+     +......+..+
T Consensus        84 ~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~l~~~  125 (137)
T 3q49_B           84 GQCQLEMESYDEAIANLQRAYSLAKEQRLNFGDDIPSALRIA  125 (137)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCCCTTHHHHHHHHH
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHHChhHHHHHHHHHHHHHHHH
Confidence            88888999999999999999988777     44455544443

>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=98.10  E-value=1.8e-05  Score=81.54  Aligned_cols=144  Identities=10%  Similarity=0.015  Sum_probs=98.7

Q ss_pred             HhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHH
Q 040394          497 TVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVD  576 (691)
Q Consensus       497 ~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~  576 (691)
                      ...|..+...+.+.|++++|+..|++.++.  .|+...+          . .+...+ ...        -....|..+..
T Consensus       268 a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~--~p~~~~~----------~-~~~~~~-~~~--------~~~~~~~nla~  325 (457)
T 1kt0_A          268 AAIVKEKGTVYFKGGKYMQAVIQYGKIVSW--LEMEYGL----------S-EKESKA-SES--------FLLAAFLNLAM  325 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--HTTCCSC----------C-HHHHHH-HHH--------HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHH--hcccccC----------C-hHHHHH-HHH--------HHHHHHHHHHH
Confidence            446666777777777777777777777663  2221000          0 000000 000        01356777888


Q ss_pred             HHHhcCChHHHHHHHHhC-CCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHH
Q 040394          577 LLARAGRLEEALEFMENM-PIE-PDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVN  654 (691)
Q Consensus       577 ~~~~~g~~~~A~~~~~~~-~~~-p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~  654 (691)
                      +|.+.|++++|++.+++. ... .+...|..+..+|...|++++|+..|+++++++|++...+..++.++.+.|+++++.
T Consensus       326 ~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~~a~  405 (457)
T 1kt0_A          326 CYLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQISMCQKKAKEHNERD  405 (457)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC----CHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            888999999999888887 333 356788899999999999999999999999999999999999999999999998886


Q ss_pred             H-HHHHHHh
Q 040394          655 Q-VRELMKQ  662 (691)
Q Consensus       655 ~-~~~~~~~  662 (691)
                      + .++.|..
T Consensus       406 ~~~~~~~f~  414 (457)
T 1kt0_A          406 RRIYANMFK  414 (457)
T ss_dssp             HHHHHHC--
T ss_pred             HHHHHHHHh
Confidence            4 4565544

>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=98.08  E-value=1e-05  Score=83.89  Aligned_cols=115  Identities=10%  Similarity=-0.041  Sum_probs=91.7

Q ss_pred             HhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHH
Q 040394          541 ACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFD  617 (691)
Q Consensus       541 ~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~  617 (691)
                      .+.+.|++++|.+.+++..+.   .|+ ...+..+..+|.+.|++++|++.+++. ...| +...|..+..++...|+++
T Consensus        15 ~~~~~g~~~~A~~~~~~Al~~---~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~~~~g~~~   91 (477)
T 1wao_1           15 DYFKAKDYENAIKFYSQAIEL---NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALGKFR   91 (477)
T ss_dssp             STTTTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHh---CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHH
Confidence            456678888888888876433   454 677888888888899999998888887 4444 5678888999999999999


Q ss_pred             HHHHHHHHHHhcCCCCchhHHHHHHH--HHhCCCcHHHHHHHH
Q 040394          618 LGEVMIKKMLELHPDKACYYVLVSNL--YASDGRWIRVNQVRE  658 (691)
Q Consensus       618 ~A~~~~~~~~~~~p~~~~~~~~l~~~--~~~~g~~~~A~~~~~  658 (691)
                      +|...++++++..|++...+..++.+  +.+.|++++|.+.++
T Consensus        92 eA~~~~~~al~~~p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           92 AALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHHHHSTTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            99999999999999999999888888  888899999999987

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.08  E-value=1.1e-05  Score=69.56  Aligned_cols=93  Identities=14%  Similarity=0.087  Sum_probs=63.8

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhC----CCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC------CCch
Q 040394          570 HYVCMVDLLARAGRLEEALEFMENM----PIEPD----VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHP------DKAC  635 (691)
Q Consensus       570 ~~~~li~~~~~~g~~~~A~~~~~~~----~~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p------~~~~  635 (691)
                      .+..+...+...|++++|.+.+++.    ...++    ...+..+...+...|++++|...++++++..+      ....
T Consensus        51 ~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~  130 (164)
T 3ro3_A           51 AYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGR  130 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHH
Confidence            4445555666666666666665554    11111    34566777778888899999888888887422      1235


Q ss_pred             hHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          636 YYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       636 ~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      .+..++.++...|++++|.+.+++..+
T Consensus       131 ~~~~la~~~~~~g~~~~A~~~~~~a~~  157 (164)
T 3ro3_A          131 ACWSLGNAYTALGNHDQAMHFAEKHLE  157 (164)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            677888899999999999999888765

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.06  E-value=6.6e-06  Score=81.06  Aligned_cols=150  Identities=7%  Similarity=-0.034  Sum_probs=86.5

Q ss_pred             HhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHH
Q 040394          497 TVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVD  576 (691)
Q Consensus       497 ~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~  576 (691)
                      ...|..+...+.+.|++++|+..|++....  .|+...       +...++.+++...+.           ...|..+..
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~-------~~~~~~~~~~~~~l~-----------~~~~~nla~  238 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFM-------FQLYGKYQDMALAVK-----------NPCHLNIAA  238 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHH-------HTCCHHHHHHHHHHH-----------THHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchh-------hhhcccHHHHHHHHH-----------HHHHHHHHH
Confidence            456777888888999999999999998873  565442       233444444443322           136778889


Q ss_pred             HHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHH-HHhCCCcHHH
Q 040394          577 LLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNL-YASDGRWIRV  653 (691)
Q Consensus       577 ~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~-~~~~g~~~~A  653 (691)
                      +|.+.|++++|++.+++. ...| +...|..+..+|...|++++|+..|++++++.|+++..+..+..+ ....+..+++
T Consensus       239 ~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p~~~~a~~~L~~l~~~~~~~~~~a  318 (338)
T 2if4_A          239 CLIKLKRYDEAIGHCNIVLTEEEKNPKALFRRGKAKAELGQMDSARDDFRKAQKYAPDDKAIRRELRALAEQEKALYQKQ  318 (338)
T ss_dssp             HHHTTTCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC--------------------------
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999987 4344 667899999999999999999999999999999999999888887 4455778888


Q ss_pred             HHHHHHHHhCCCc
Q 040394          654 NQVRELMKQRGLS  666 (691)
Q Consensus       654 ~~~~~~~~~~g~~  666 (691)
                      ...+++|.+....
T Consensus       319 ~~~~~~~l~~~p~  331 (338)
T 2if4_A          319 KEMYKGIFKGKDE  331 (338)
T ss_dssp             -------------
T ss_pred             HHHHHHhhCCCCC
Confidence            8899888775443

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.06  E-value=5.5e-05  Score=62.24  Aligned_cols=93  Identities=12%  Similarity=0.124  Sum_probs=76.4

Q ss_pred             HHHHHHHHhcCChHHHHHHHHhC-CCCCC-H---HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC---chhHHHHHHH
Q 040394          572 VCMVDLLARAGRLEEALEFMENM-PIEPD-V---SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK---ACYYVLVSNL  643 (691)
Q Consensus       572 ~~li~~~~~~g~~~~A~~~~~~~-~~~p~-~---~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~---~~~~~~l~~~  643 (691)
                      ..+...+.+.|++++|.+.+++. ...|+ .   ..+..+..++...|++++|...++++++..|++   +..+..++.+
T Consensus         6 ~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~la~~   85 (129)
T 2xev_A            6 YNVAFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPTHDKAAGGLLKLGLS   85 (129)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCCCcccHHHHHHHHHH
Confidence            34567788899999999998887 32333 2   477778888889999999999999999999998   6778889999


Q ss_pred             HHhCCCcHHHHHHHHHHHhCC
Q 040394          644 YASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       644 ~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      +...|++++|...++++.+..
T Consensus        86 ~~~~g~~~~A~~~~~~~~~~~  106 (129)
T 2xev_A           86 QYGEGKNTEAQQTLQQVATQY  106 (129)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHcCCHHHHHHHHHHHHHHC
Confidence            999999999999999888754

>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=98.03  E-value=4.1e-05  Score=75.33  Aligned_cols=145  Identities=12%  Similarity=0.079  Sum_probs=99.5

Q ss_pred             CChHHHHHHhccCCC--C-CcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCC--------------cchHHHHHHHH
Q 040394           94 GHVKYARSVFDSMPN--P-DFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHD--------------NFVFSKVLKAC  156 (691)
Q Consensus        94 g~~~~A~~~~~~~~~--~-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~--------------~~~~~~ll~~~  156 (691)
                      +++++|...|+...+  | +...|..+...+.+.|++++|+..|++..+......              ...|..+..++
T Consensus       127 ~~~~~A~~~~~~a~~~~p~~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~  206 (336)
T 1p5q_A          127 KSFEKAKESWEMNSEEKLEQSTIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCH  206 (336)
T ss_dssp             EEEECCCCGGGCCHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eecccccchhcCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555544432  2 345778888888889999999999998887632211              35677777777


Q ss_pred             cccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCC---CChhhHHHHHHHHHhCCChhHH-HH
Q 040394          157 CELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLD---KNVVSWTSMIAGYVQNDCAQEG-LV  232 (691)
Q Consensus       157 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~A-~~  232 (691)
                      .+.|++++|...++..++..+.+..++..+..+|...|++++|...|++..+   .+..++..+..++.+.|+.++| ..
T Consensus       207 ~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~~a~~~  286 (336)
T 1p5q_A          207 LKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIRRQLAREKK  286 (336)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7788888888888888777766777777777777777777777777776532   3555667777777777777766 34


Q ss_pred             HHHHHH
Q 040394          233 LFNRMR  238 (691)
Q Consensus       233 ~~~~m~  238 (691)
                      +|+.|.
T Consensus       287 ~~~~~~  292 (336)
T 1p5q_A          287 LYANMF  292 (336)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            555553

>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=98.03  E-value=5e-05  Score=62.44  Aligned_cols=109  Identities=8%  Similarity=-0.042  Sum_probs=66.4

Q ss_pred             HHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-C----CCCC----HHHHHH
Q 040394          535 FTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-P----IEPD----VSLFGA  605 (691)
Q Consensus       535 ~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~----~~p~----~~~~~~  605 (691)
                      +..+...+...|++++|...+++....  .+.+...+..+...+...|++++|.+.+++. .    ..++    ..++..
T Consensus         7 ~~~l~~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (131)
T 1elr_A            7 EKELGNDAYKKKDFDTALKHYDKAKEL--DPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYAR   84 (131)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHhc--CCccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHHH
Confidence            334444445555555555555544322  1122445555555666666666666666555 1    1222    556777


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHh
Q 040394          606 FLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYAS  646 (691)
Q Consensus       606 l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~  646 (691)
                      +...+...|++++|...++++.+..|+ +.....+..+...
T Consensus        85 la~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~l~~~~~~  124 (131)
T 1elr_A           85 IGNSYFKEEKYKDAIHFYNKSLAEHRT-PDVLKKCQQAEKI  124 (131)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHH
T ss_pred             HHHHHHHhccHHHHHHHHHHHHHhCCC-HHHHHHHHHHHHH
Confidence            888888899999999999999998884 6666666655443

>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=98.02  E-value=0.0016  Score=62.56  Aligned_cols=230  Identities=9%  Similarity=0.010  Sum_probs=158.6

Q ss_pred             hcCCh-HHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHH-HHHHHHHHHhccCc----------HHHHHHHHHHHHHcC
Q 040394          393 KCHVI-ADARYIFETTSEKDVIAWNSIISGLDDNVSPDAV-TLVSVISACASLGA----------VQVGSSLHAYSTKQG  460 (691)
Q Consensus       393 ~~g~~-~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~-~~~~ll~~~~~~~~----------~~~a~~~~~~~~~~~  460 (691)
                      +.|.+ ++|+..++.+...                .|+.. +|+.--..+...+.          ++.+..+++.+....
T Consensus        41 ~~~e~s~eaL~~t~~~L~~----------------nP~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~  104 (331)
T 3dss_A           41 QAGELDESVLELTSQILGA----------------NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN  104 (331)
T ss_dssp             HTTCCSHHHHHHHHHHHTT----------------CTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HcCCCCHHHHHHHHHHHHH----------------CchhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhC
Confidence            44544 4788888888754                34433 34332222222222          678889999999887


Q ss_pred             CCCCchhHHHHHHHHHHhcC--CHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCC-hHHHHHHHHHHHHCCCCCCHHH
Q 040394          461 LLSSNVYVGTALLNFYAKCG--DAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGD-GGGSLALFSDMLNEEVQPNEVI  534 (691)
Q Consensus       461 ~~~~~~~~~~~l~~~~~~~g--~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~-~~~A~~~~~~m~~~g~~p~~~~  534 (691)
                        |.+..+++.-...+.+.+  .+++++.+++.+.+   .|...|+.-...+...|. ++++++.++++++.. +-|...
T Consensus       105 --PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~dprNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~-p~N~SA  181 (331)
T 3dss_A          105 --PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSS  181 (331)
T ss_dssp             --TTCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-SCCHHH
T ss_pred             --CCCHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHC-CCCHHH
Confidence              788889888888888888  48999999999885   477788877777777887 589999999999864 345555


Q ss_pred             HHHHHHHhccc--------------CCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhc-----------CChHHHH
Q 040394          535 FTTILSACSHT--------------GMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARA-----------GRLEEAL  588 (691)
Q Consensus       535 ~~~ll~~~~~~--------------g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~-----------g~~~~A~  588 (691)
                      |+.....+...              +.++++++.+.....   ..|+ ...|+-+-..+.+.           +.+++++
T Consensus       182 W~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~---~~P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el  258 (331)
T 3dss_A          182 WHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFF---TDPNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSEL  258 (331)
T ss_dssp             HHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHH---HSTTCHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHhccCccccchHHHHHHHHHH
Confidence            55544433332              457889998887653   4666 55666554555444           4578888


Q ss_pred             HHHHhC-CCCCCH-HHHHHHHH---HHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHH
Q 040394          589 EFMENM-PIEPDV-SLFGAFLH---GCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLY  644 (691)
Q Consensus       589 ~~~~~~-~~~p~~-~~~~~l~~---~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~  644 (691)
                      +.++++ ...||. ..+.+++.   +....|..++....+.++.+++|-....|.-+..-+
T Consensus       259 ~~~~elle~~pd~~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~~Dp~r~~~y~d~~~~~  319 (331)
T 3dss_A          259 ESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYLDDLRSKF  319 (331)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHCGGGHHHHHHHHHHH
T ss_pred             HHHHHHHhhCcccchHHHHHHHHHHhhcccccHHHHHHHHHHHHHhCcchhhHHHHHHHHH
Confidence            888888 556665 23322222   122467888999999999999999888887765543

>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=98.01  E-value=0.0001  Score=60.55  Aligned_cols=101  Identities=11%  Similarity=0.022  Sum_probs=73.9

Q ss_pred             HHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-C-------HhHH
Q 040394          431 VTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--K-N-------TVTW  500 (691)
Q Consensus       431 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~-------~~~~  500 (691)
                      .++..+...+.+.|++++|...|++..+..  |.+...+..+..+|.+.|++++|+..+++..+  | +       ..+|
T Consensus         9 ~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~--p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~   86 (127)
T 4gcn_A            9 IAEKDLGNAAYKQKDFEKAHVHYDKAIELD--PSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAM   86 (127)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHH
Confidence            456677778888888888888888888877  67788888888888888888888888877653  1 1       1256


Q ss_pred             HHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHH
Q 040394          501 SAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIF  535 (691)
Q Consensus       501 ~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~  535 (691)
                      ..+..++...|++++|++.|++..+.  .||..+.
T Consensus        87 ~~lg~~~~~~~~~~~A~~~~~kal~~--~~~~~~~  119 (127)
T 4gcn_A           87 SRAGNAFQKQNDLSLAVQWFHRSLSE--FRDPELV  119 (127)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH--SCCHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhh--CcCHHHH
Confidence            66667777777777777777777663  4555443

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.99  E-value=0.00031  Score=72.00  Aligned_cols=192  Identities=7%  Similarity=-0.055  Sum_probs=141.9

Q ss_pred             HHHHhccCcHHHHHHHHHHHHHcCCCCCc---------------hhHHHHHHHHHHhcCCHHHHHHHHHhccc-----CC
Q 040394          437 ISACASLGAVQVGSSLHAYSTKQGLLSSN---------------VYVGTALLNFYAKCGDAQSARMVFDAMRE-----KN  496 (691)
Q Consensus       437 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~---------------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~  496 (691)
                      ...+.+.|++++|.+.+..+.+......+               ...+..+...|...|++++|.+.+....+     ++
T Consensus        11 a~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~   90 (434)
T 4b4t_Q           11 ARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFAK   90 (434)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence            34567889999999999999886531111               12467789999999999999999988764     11


Q ss_pred             H----hHHHHHHHHHhcCCChHHHHHHHHHHHH----CCCCCC-HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC
Q 040394          497 T----VTWSAMIGGYGMQGDGGGSLALFSDMLN----EEVQPN-EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS  567 (691)
Q Consensus       497 ~----~~~~~li~~~~~~~~~~~A~~~~~~m~~----~g~~p~-~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~  567 (691)
                      .    ...+.+...+...|+.+.|..++++...    .+..+. ..++..+...+...|++++|..++++......-..+
T Consensus        91 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~  170 (434)
T 4b4t_Q           91 SKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDD  170 (434)
T ss_dssp             HHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSC
T ss_pred             hHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhccc
Confidence            1    2334444555668899999999888764    333444 356777888999999999999999887554322222


Q ss_pred             ----hhHHHHHHHHHHhcCChHHHHHHHHhC-------CCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040394          568 ----MKHYVCMVDLLARAGRLEEALEFMENM-------PIEPD--VSLFGAFLHGCGLYSRFDLGEVMIKKMLE  628 (691)
Q Consensus       568 ----~~~~~~li~~~~~~g~~~~A~~~~~~~-------~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  628 (691)
                          ...+..++..|...|++++|..++++.       +.+|.  ...+..+...+...|++++|...+.++++
T Consensus       171 ~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~~  244 (434)
T 4b4t_Q          171 KPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESFE  244 (434)
T ss_dssp             STHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence                457888999999999999999998876       11222  23566677777889999999999999886

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.98  E-value=9.5e-06  Score=65.69  Aligned_cols=84  Identities=10%  Similarity=0.095  Sum_probs=66.5

Q ss_pred             hcCChHHHHHHHHhC-CC---CC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHH
Q 040394          580 RAGRLEEALEFMENM-PI---EP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVN  654 (691)
Q Consensus       580 ~~g~~~~A~~~~~~~-~~---~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~  654 (691)
                      ..|++++|++.|++. ..   .| +...+..+...+...|++++|+..++++++..|+++.++..++.++...|++++|.
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~   81 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPNHQALRVFYAMVLYNLGRYEQGV   81 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHcCCHHHHH
Confidence            357788888888887 44   24 34578888888889999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhC
Q 040394          655 QVRELMKQR  663 (691)
Q Consensus       655 ~~~~~~~~~  663 (691)
                      +.+++.++.
T Consensus        82 ~~~~~al~~   90 (117)
T 3k9i_A           82 ELLLKIIAE   90 (117)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            998888764

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.98  E-value=2.6e-05  Score=80.17  Aligned_cols=123  Identities=12%  Similarity=0.038  Sum_probs=90.9

Q ss_pred             hcccCCHHHHHHHHHHchhhcC--CC---CC-hhHHHHHHHHHHhcCChHHHHHHHHhC---------CCCCCH-HHHHH
Q 040394          542 CSHTGMVGEGWKCFYSMCRDFK--FV---PS-MKHYVCMVDLLARAGRLEEALEFMENM---------PIEPDV-SLFGA  605 (691)
Q Consensus       542 ~~~~g~~~~A~~~~~~m~~~~~--~~---p~-~~~~~~li~~~~~~g~~~~A~~~~~~~---------~~~p~~-~~~~~  605 (691)
                      +...|++++|+.++++......  +.   |+ ..+++.|..+|...|++++|+.++++.         ...|+. .+++.
T Consensus       319 ~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~n  398 (490)
T 3n71_A          319 ARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMR  398 (490)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            3455666666666655433221  22   22 456778888888888888888877776         234544 47899


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHh-----cCCCCchhH---HHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          606 FLHGCGLYSRFDLGEVMIKKMLE-----LHPDKACYY---VLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       606 l~~~~~~~g~~~~A~~~~~~~~~-----~~p~~~~~~---~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      |...|...|++++|+.+++++++     +.|+++.+-   ..+..++.+.|++++|...+.+++++-
T Consensus       399 La~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~~  465 (490)
T 3n71_A          399 AGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREAA  465 (490)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999987     577776544   577888889999999999999998754

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.98  E-value=6.5e-05  Score=59.73  Aligned_cols=92  Identities=7%  Similarity=0.000  Sum_probs=42.7

Q ss_pred             hHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCC---C--ChhhHHHHHHHHH
Q 040394          148 VFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLD---K--NVVSWTSMIAGYV  222 (691)
Q Consensus       148 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~--~~~~~~~li~~~~  222 (691)
                      .+..+...+...|++++|...++...+..+.+..++..+...+...|++++|...|++..+   .  +...|..+...+.
T Consensus         8 ~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l~~~~~   87 (112)
T 2kck_A            8 EYYLEGVLQYDAGNYTESIDLFEKAIQLDPEESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDVWAAKADALR   87 (112)
T ss_dssp             GGGGHHHHHHSSCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHHHHHHHHHHH
Confidence            3444444444444555555555544444444444444444444444444444444443311   1  2334444444555


Q ss_pred             hC-CChhHHHHHHHHHHh
Q 040394          223 QN-DCAQEGLVLFNRMRE  239 (691)
Q Consensus       223 ~~-g~~~~A~~~~~~m~~  239 (691)
                      .. |++++|.+.+++...
T Consensus        88 ~~~~~~~~A~~~~~~~~~  105 (112)
T 2kck_A           88 YIEGKEVEAEIAEARAKL  105 (112)
T ss_dssp             TCSSCSHHHHHHHHHHGG
T ss_pred             HHhCCHHHHHHHHHHHhh
Confidence            55 555555555555444

>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=97.97  E-value=3.5e-05  Score=76.72  Aligned_cols=138  Identities=9%  Similarity=0.070  Sum_probs=103.2

Q ss_pred             HhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHH
Q 040394          497 TVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMV  575 (691)
Q Consensus       497 ~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li  575 (691)
                      ...|..+...+.+.|++++|+..|++.++.  .|+..          .....+++          ....|. ...|..+.
T Consensus       223 a~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~--~~~~~----------~~~~~~~~----------~~~~~~~~~~~~nla  280 (370)
T 1ihg_A          223 SEDLKNIGNTFFKSQNWEMAIKKYTKVLRY--VEGSR----------AAAEDADG----------AKLQPVALSCVLNIG  280 (370)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--HHHHH----------HHSCHHHH----------GGGHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHH--hhcCc----------cccChHHH----------HHHHHHHHHHHHHHH
Confidence            345667777777888888888888777652  11100          00001110          012333 56788889


Q ss_pred             HHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHH
Q 040394          576 DLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRV  653 (691)
Q Consensus       576 ~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A  653 (691)
                      .+|.+.|++++|++.+++. ...| +...|..+..++...|++++|...+++++++.|++..++..++.++...++.+++
T Consensus       281 ~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~P~~~~~~~~l~~~~~~~~~~~~a  360 (370)
T 1ihg_A          281 ACKLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLKVKQKIKAQKDK  360 (370)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999988 5555 5678899999999999999999999999999999999999999999998888877


Q ss_pred             HHH
Q 040394          654 NQV  656 (691)
Q Consensus       654 ~~~  656 (691)
                      .+.
T Consensus       361 ~k~  363 (370)
T 1ihg_A          361 EKA  363 (370)
T ss_dssp             HHC
T ss_pred             HHH
Confidence            654

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.96  E-value=3.5e-05  Score=60.14  Aligned_cols=65  Identities=14%  Similarity=0.009  Sum_probs=55.0

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          599 DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       599 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      +...+..+...+...|++++|+..++++++.+|+++..+..++.+|...|++++|.+.+++.++.
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l   70 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETDPDYVGTYYHLGKLYERLDRTDDAIDTYAQGIEV   70 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            55677888888888888888888888888888888888888888888888888888888877653

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.96  E-value=3.7e-06  Score=67.26  Aligned_cols=93  Identities=8%  Similarity=-0.039  Sum_probs=76.0

Q ss_pred             ChhHHHHHHHHHHhcCChHHHHHHHHhC-CCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC------chhHH
Q 040394          567 SMKHYVCMVDLLARAGRLEEALEFMENM-PIE-PDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK------ACYYV  638 (691)
Q Consensus       567 ~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~-p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~------~~~~~  638 (691)
                      +...+..+...+.+.|++++|++.+++. ... .+...|..+..++...|++++|+..++++++..|++      ...+.
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~   82 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLITAQPQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYTSTAEHVAIRSKLQY   82 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCSSTTSHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCccHHHHHHHHHH
Confidence            3456677788888889999998888887 333 356788889999999999999999999999999998      77788


Q ss_pred             HHHHHHHhCCCcHHHHHHHHH
Q 040394          639 LVSNLYASDGRWIRVNQVREL  659 (691)
Q Consensus       639 ~l~~~~~~~g~~~~A~~~~~~  659 (691)
                      .++.++...|++++|.+.+++
T Consensus        83 ~~~~~~~~~~~~~~a~~~~~~  103 (111)
T 2l6j_A           83 RLELAQGAVGSVQIPVVEVDE  103 (111)
T ss_dssp             HHHHHHHHHHCCCCCSSSSSS
T ss_pred             HHHHHHHHHHhHhhhHhHHHH
Confidence            888888888888877665543

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.87  E-value=3.7e-05  Score=61.89  Aligned_cols=63  Identities=13%  Similarity=0.093  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          600 VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       600 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      ...+..+...+...|++++|+..++++++..|++...+..++.+|...|++++|...+++..+
T Consensus        19 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~   81 (115)
T 2kat_A           19 MLLRFTLGKTYAEHEQFDAALPHLRAALDFDPTYSVAWKWLGKTLQGQGDRAGARQAWESGLA   81 (115)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            344444555555555555555555555555555555555555555555555555555555443

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.87  E-value=3.1e-05  Score=66.95  Aligned_cols=94  Identities=7%  Similarity=0.001  Sum_probs=67.7

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhC-CC------------------CC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC
Q 040394          571 YVCMVDLLARAGRLEEALEFMENM-PI------------------EP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELH  630 (691)
Q Consensus       571 ~~~li~~~~~~g~~~~A~~~~~~~-~~------------------~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  630 (691)
                      +......+.+.|++++|++.|++. ..                  .| +...|..+..++.+.|++++|+..++++++++
T Consensus        14 ~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al~~~   93 (162)
T 3rkv_A           14 LRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVLKRE   93 (162)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcC
Confidence            344566677778888887777765 21                  12 12466777777777888888888888888888


Q ss_pred             CCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          631 PDKACYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       631 p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      |+++..+..++.+|...|++++|...+++.++..
T Consensus        94 p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~  127 (162)
T 3rkv_A           94 ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRNH  127 (162)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhcC
Confidence            8888888888888888888888888887776643

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=97.87  E-value=4.7e-05  Score=61.93  Aligned_cols=92  Identities=4%  Similarity=-0.143  Sum_probs=49.8

Q ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhc
Q 040394          114 FQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKC  193 (691)
Q Consensus       114 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~  193 (691)
                      +..+...+.+.|++++|+..|++..+.. +.+...+..+..++...|+.++|...+++.++..+.+...+..+..+|...
T Consensus        20 ~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~la~~~~~~   98 (121)
T 1hxi_A           20 PMEEGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNE   98 (121)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc
Confidence            4444455555566666666665555542 224445555555555555666666666555555555555555555555555


Q ss_pred             CChHHHHHHHhcc
Q 040394          194 RDIGSSRQVFDET  206 (691)
Q Consensus       194 g~~~~A~~~~~~~  206 (691)
                      |++++|...|++.
T Consensus        99 g~~~~A~~~~~~a  111 (121)
T 1hxi_A           99 HNANAALASLRAW  111 (121)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH
Confidence            5555555555543

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=97.85  E-value=0.0001  Score=56.20  Aligned_cols=73  Identities=12%  Similarity=0.060  Sum_probs=63.1

Q ss_pred             CCCHHHHHHHHHHHHhcCC---HHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCccCCC
Q 040394          597 EPDVSLFGAFLHGCGLYSR---FDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLSKSPG  670 (691)
Q Consensus       597 ~p~~~~~~~l~~~~~~~g~---~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~~~~~  670 (691)
                      ++|...+..+..++...++   .++|..+++++++.+|+++.....++..+.+.|++++|++.|+++++.... .|.
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~p~-~~~   78 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSNDP-NLD   78 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCCCT-TCC
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-Ccc
Confidence            4566777788888765444   799999999999999999999999999999999999999999999998765 554

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.85  E-value=4.6e-05  Score=65.50  Aligned_cols=61  Identities=10%  Similarity=0.037  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhC-------CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC
Q 040394          570 HYVCMVDLLARAGRLEEALEFMENM-------PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELH  630 (691)
Q Consensus       570 ~~~~li~~~~~~g~~~~A~~~~~~~-------~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  630 (691)
                      .+..+...+...|++++|.+.+++.       +..+ ...++..+...+...|++++|...++++++..
T Consensus        91 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~  159 (164)
T 3ro3_A           91 SCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEIS  159 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHH
Confidence            4455556666666666666665554       1111 12356677777888888888888888887653

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.82  E-value=8.2e-05  Score=56.60  Aligned_cols=81  Identities=16%  Similarity=0.215  Sum_probs=62.3

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhC-CC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHH
Q 040394          568 MKHYVCMVDLLARAGRLEEALEFMENM-PI-EPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYA  645 (691)
Q Consensus       568 ~~~~~~li~~~~~~g~~~~A~~~~~~~-~~-~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~  645 (691)
                      ...+..+...+...|++++|++.+++. .. +.+...+..+...+...|++++|...++++.+..|+++..+..++.++.
T Consensus         9 ~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~   88 (91)
T 1na3_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAKQNLGNAKQ   88 (91)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence            445666777777888888888887776 22 3356677888888888889999999999988888888888888888776


Q ss_pred             hCC
Q 040394          646 SDG  648 (691)
Q Consensus       646 ~~g  648 (691)
                      ..|
T Consensus        89 ~~g   91 (91)
T 1na3_A           89 KQG   91 (91)
T ss_dssp             HHC
T ss_pred             hcC
Confidence            544

>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=97.82  E-value=8.7e-05  Score=76.81  Aligned_cols=114  Identities=12%  Similarity=0.066  Sum_probs=66.3

Q ss_pred             HHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHH
Q 040394          475 FYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEG  551 (691)
Q Consensus       475 ~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A  551 (691)
                      .+.+.|++++|.+.|++..+   .+...|..+..+|.+.|++++|++.+++..+.. +-+...+..+..++...|++++|
T Consensus        15 ~~~~~g~~~~A~~~~~~Al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~eA   93 (477)
T 1wao_1           15 DYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAA   93 (477)
T ss_dssp             STTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHH
Confidence            45566777777777776553   245666667777777777777777777776642 22345566666666677777777


Q ss_pred             HHHHHHchhhcCCCCC-hhHHHHHHHH--HHhcCChHHHHHHHH
Q 040394          552 WKCFYSMCRDFKFVPS-MKHYVCMVDL--LARAGRLEEALEFME  592 (691)
Q Consensus       552 ~~~~~~m~~~~~~~p~-~~~~~~li~~--~~~~g~~~~A~~~~~  592 (691)
                      .+.+++..+.   .|+ ...+..+..+  +.+.|++++|++.++
T Consensus        94 ~~~~~~al~~---~p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           94 LRDYETVVKV---KPHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHH---STTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHHHh---CCCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            7777665433   333 3344444444  566666666666666

>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=97.79  E-value=0.0011  Score=69.95  Aligned_cols=136  Identities=8%  Similarity=-0.051  Sum_probs=88.8

Q ss_pred             hHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccC--CHHHHHHHHHHchhhcCCCC-ChhHHHHHHHHHHhcC-ChHHHH
Q 040394          513 GGGSLALFSDMLNEEVQPNEVIFTTILSACSHTG--MVGEGWKCFYSMCRDFKFVP-SMKHYVCMVDLLARAG-RLEEAL  588 (691)
Q Consensus       513 ~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g--~~~~A~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g-~~~~A~  588 (691)
                      ++++++.++++.+.. +-+...|..--.++.+.+  +++++++.++++.+.   .| |...|+.-..++.+.| .+++++
T Consensus        89 ~~~eL~~~~~~l~~~-pK~y~aW~hR~w~l~~l~~~~~~~el~~~~k~l~~---d~~N~~aW~~R~~~l~~l~~~~~~el  164 (567)
T 1dce_A           89 VKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEA---DERNFHCWDYRRFVAAQAAVAPAEEL  164 (567)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTCCCHHHHH
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcccccHHHHHHHHHHHHhh---ccccccHHHHHHHHHHHcCCChHHHH
Confidence            555666666665532 223344444444445555  456666666666432   33 3555555555556666 667777


Q ss_pred             HHHHhC-CCCC-CHHHHHHHHHHHHhc--------------CCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHH
Q 040394          589 EFMENM-PIEP-DVSLFGAFLHGCGLY--------------SRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIR  652 (691)
Q Consensus       589 ~~~~~~-~~~p-~~~~~~~l~~~~~~~--------------g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  652 (691)
                      +.++++ ...| |...|+.....+.+.              +.++++.+.+++++..+|++...|..+..++.+.|+.++
T Consensus       165 ~~~~~~I~~~p~n~saW~~r~~ll~~l~~~~~~~~~~~~~~~~~~eel~~~~~ai~~~P~~~saW~y~~~ll~~~~~~~~  244 (567)
T 1dce_A          165 AFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEPHDV  244 (567)
T ss_dssp             HHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCCCCCSC
T ss_pred             HHHHHHHHHCCCCccHHHHHHHHHHhhcccccccccccccHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHHhcCCCccc
Confidence            777776 3333 456666666655442              568999999999999999999999999999999888655

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.74  E-value=0.00012  Score=72.06  Aligned_cols=152  Identities=9%  Similarity=-0.055  Sum_probs=80.0

Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcc
Q 040394          465 NVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSH  544 (691)
Q Consensus       465 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~  544 (691)
                      ....+..+...+.+.|++++|...|++....+....     .+...++.+++...+.          ...|..+..++.+
T Consensus       178 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~-----~~~~~~~~~~~~~~l~----------~~~~~nla~~~~~  242 (338)
T 2if4_A          178 AADRRKMDGNSLFKEEKLEEAMQQYEMAIAYMGDDF-----MFQLYGKYQDMALAVK----------NPCHLNIAACLIK  242 (338)
T ss_dssp             HHHHHHHHHHHTCSSSCCHHHHHHHHHHHHHSCHHH-----HHTCCHHHHHHHHHHH----------THHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhccch-----hhhhcccHHHHHHHHH----------HHHHHHHHHHHHH
Confidence            355677788888999999999999998764221111     1223344444433221          1356777778888


Q ss_pred             cCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCH-HHHHHHHHH-HHhcCCHHHHH
Q 040394          545 TGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEPDV-SLFGAFLHG-CGLYSRFDLGE  620 (691)
Q Consensus       545 ~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~-~~~~~l~~~-~~~~g~~~~A~  620 (691)
                      .|++++|+..+++.++   +.|+ ...|..+..+|...|++++|++.|++. ...|+. ..+..+... ....+..+.+.
T Consensus       243 ~g~~~~A~~~~~~al~---~~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p~~~~a~~~L~~l~~~~~~~~~~a~  319 (338)
T 2if4_A          243 LKRYDEAIGHCNIVLT---EEEKNPKALFRRGKAKAELGQMDSARDDFRKAQKYAPDDKAIRRELRALAEQEKALYQKQK  319 (338)
T ss_dssp             TTCCHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC---------------------------
T ss_pred             cCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999987754   3454 678888899999999999999999988 555644 345555444 23467788889


Q ss_pred             HHHHHHHhcCCCCc
Q 040394          621 VMIKKMLELHPDKA  634 (691)
Q Consensus       621 ~~~~~~~~~~p~~~  634 (691)
                      ..++++++..|+++
T Consensus       320 ~~~~~~l~~~p~~~  333 (338)
T 2if4_A          320 EMYKGIFKGKDEGG  333 (338)
T ss_dssp             --------------
T ss_pred             HHHHHhhCCCCCCC
Confidence            99999999888864

>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=97.73  E-value=8.6e-05  Score=76.50  Aligned_cols=98  Identities=7%  Similarity=-0.101  Sum_probs=81.1

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCC----------------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC
Q 040394          568 MKHYVCMVDLLARAGRLEEALEFMENM-PIEPD----------------VSLFGAFLHGCGLYSRFDLGEVMIKKMLELH  630 (691)
Q Consensus       568 ~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~----------------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  630 (691)
                      ...+..+...|.+.|++++|+..|++. ...|+                ...|..+..++.+.|++++|+..++++++++
T Consensus       268 a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  347 (457)
T 1kt0_A          268 AAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD  347 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC
Confidence            345556666777777777777777766 22222                4788889999999999999999999999999


Q ss_pred             CCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          631 PDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       631 p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      |++...+..++.+|...|++++|+..|++.++...
T Consensus       348 p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P  382 (457)
T 1kt0_A          348 SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNP  382 (457)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-
T ss_pred             CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC
Confidence            99999999999999999999999999999988643

>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=97.72  E-value=4.6e-05  Score=63.98  Aligned_cols=72  Identities=15%  Similarity=0.040  Sum_probs=56.2

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhC-CC-------CCCH-HHH----HHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchh
Q 040394          570 HYVCMVDLLARAGRLEEALEFMENM-PI-------EPDV-SLF----GAFLHGCGLYSRFDLGEVMIKKMLELHPDKACY  636 (691)
Q Consensus       570 ~~~~li~~~~~~g~~~~A~~~~~~~-~~-------~p~~-~~~----~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~  636 (691)
                      .|..+..++.+.|++++|+..+++. ..       .|+. ..|    .....++...|++++|+..|++++++.|++...
T Consensus        59 a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~p~d~~~  138 (159)
T 2hr2_A           59 CHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGE  138 (159)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCCSC
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHH
Confidence            6666777777777777777766665 33       7765 477    889999999999999999999999999998766


Q ss_pred             HHHHH
Q 040394          637 YVLVS  641 (691)
Q Consensus       637 ~~~l~  641 (691)
                      ..-+.
T Consensus       139 ~~~~~  143 (159)
T 2hr2_A          139 TPGKE  143 (159)
T ss_dssp             CTTHH
T ss_pred             HHHHH
Confidence            55443

>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=97.65  E-value=0.00012  Score=72.77  Aligned_cols=65  Identities=8%  Similarity=-0.120  Sum_probs=60.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          600 VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       600 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      ...|..+..++.+.|++++|+..++++++.+|+++..+..++.+|...|++++|.+.+++.++..
T Consensus       273 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~  337 (370)
T 1ihg_A          273 LSCVLNIGACKLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIA  337 (370)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHhccCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC
Confidence            46788899999999999999999999999999999999999999999999999999999998753

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.63  E-value=0.00019  Score=56.97  Aligned_cols=67  Identities=6%  Similarity=-0.070  Sum_probs=62.0

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          599 DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       599 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      +...|..+...+...|++++|...++++++..|+++..+..++.++...|++++|++.+++.++...
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p   69 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLITAQPQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYTS   69 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCS
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC
Confidence            4567888889999999999999999999999999999999999999999999999999999988643

>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=97.61  E-value=0.00027  Score=58.88  Aligned_cols=112  Identities=4%  Similarity=-0.123  Sum_probs=71.4

Q ss_pred             CCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHH
Q 040394          546 GMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGL----YSRFDLGEV  621 (691)
Q Consensus       546 g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~A~~  621 (691)
                      +++++|.+.|++..+. + .|+  ..  |...|...+..++|+++|++.-..-+...+..|...|..    .+|+++|..
T Consensus         9 ~d~~~A~~~~~~aa~~-g-~~~--a~--lg~~y~~g~~~~~A~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~~A~~   82 (138)
T 1klx_A            9 KDLKKAIQYYVKACEL-N-EMF--GC--LSLVSNSQINKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQ   82 (138)
T ss_dssp             HHHHHHHHHHHHHHHT-T-CTT--HH--HHHHTCTTSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHH
T ss_pred             cCHHHHHHHHHHHHcC-C-CHh--hh--HHHHHHcCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCccHHHHHH
Confidence            3455666666655222 2 111  22  555555555666666666665222455666666666666    677888888


Q ss_pred             HHHHHHhcCCCCchhHHHHHHHHHh----CCCcHHHHHHHHHHHhCCC
Q 040394          622 MIKKMLELHPDKACYYVLVSNLYAS----DGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       622 ~~~~~~~~~p~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~g~  665 (691)
                      .++++.+.  .++.....|+.+|..    .+++++|.+++++..+.|.
T Consensus        83 ~~~~Aa~~--g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           83 YYSKACGL--NDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             HHHHHHHT--TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHcC--CCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence            88877765  456777778888877    7788888888888777765

>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=97.57  E-value=5.2e-05  Score=63.47  Aligned_cols=86  Identities=16%  Similarity=0.052  Sum_probs=63.6

Q ss_pred             hcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCC----------HHHHHHHHHHHHhcCCCCchhHHHHHHHHHhC
Q 040394          580 RAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSR----------FDLGEVMIKKMLELHPDKACYYVLVSNLYASD  647 (691)
Q Consensus       580 ~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~----------~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~  647 (691)
                      +.+.+++|++.+++. ...| +...|..+..++...++          +++|+..|+++++++|++...|+.++.+|...
T Consensus        14 r~~~feeA~~~~~~Ai~l~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~~~~A~~~LG~ay~~l   93 (158)
T 1zu2_A           14 RILLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYTSF   93 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH
T ss_pred             HHhHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHh
Confidence            334555555555555 2222 44455555555555443          67999999999999999999999999999987


Q ss_pred             C-----------CcHHHHHHHHHHHhCCC
Q 040394          648 G-----------RWIRVNQVRELMKQRGL  665 (691)
Q Consensus       648 g-----------~~~~A~~~~~~~~~~g~  665 (691)
                      |           ++++|++.|++.++...
T Consensus        94 g~l~P~~~~a~g~~~eA~~~~~kAl~l~P  122 (158)
T 1zu2_A           94 AFLTPDETEAKHNFDLATQFFQQAVDEQP  122 (158)
T ss_dssp             HHHCCCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             cccCcchhhhhccHHHHHHHHHHHHHhCC
Confidence            5           89999999999988543

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=97.51  E-value=1.2e-05  Score=78.64  Aligned_cols=438  Identities=13%  Similarity=0.084  Sum_probs=263.8

Q ss_pred             HHhhccCchhHHHHHHHHHHhCCCCch-hhhHHHHHHhcCCChHHHHHHhccCCCCCcchHHHHHHHHHhCCChhHHHHH
Q 040394           55 LLGLCKSTGSLKAFHALLIVDGLTNDK-CNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEF  133 (691)
Q Consensus        55 ll~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~  133 (691)
                      |+...++++.|..+.+.      .+.+ +|..|..++.+.|++.+|...|-+.  .|...|..++.+..+.|.+++-+..
T Consensus        34 L~e~i~~ldRa~eyA~~------~n~p~VWs~LgkAqL~~~~v~eAIdsyIkA--~Dps~y~eVi~~A~~~~~~edLv~y  105 (624)
T 3lvg_A           34 LIEHIGNLDRAYEFAER------CNEPAVWSQLAKAQLQKGMVKEAIDSYIKA--DDPSSYMEVVQAANTSGNWEELVKY  105 (624)
T ss_dssp             CCGGGCCSTTTTTSSSS------CCCCCCSSSHHHHTTTSSSCTTTTTSSCCC--SCCCSSSHHHHHTTTSSCCTTHHHH
T ss_pred             HHHhccccHHHHHHHHH------hCCccHHHHHHHHHHccCchHHHHHHHHhC--CChHHHHHHHHHHHhCCCHHHHHHH
Confidence            34444555555444331      3444 9999999999999999998877544  4666789999999999999999999


Q ss_pred             HHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccC------
Q 040394          134 YKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETL------  207 (691)
Q Consensus       134 ~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~------  207 (691)
                      +.-.++..  -++..=+.++-+|++.+++.+-++.+.      .|+..-...+.+-|...|.++.|.-+|..+.      
T Consensus       106 L~MaRk~~--ke~~IDteLi~ayAk~~rL~elEefl~------~~N~A~iq~VGDrcf~e~lYeAAKilys~isN~akLA  177 (624)
T 3lvg_A          106 LQMARKKA--RESYVETELIFALAKTNRLAELEEFIN------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLA  177 (624)
T ss_dssp             HHTTSTTC--CSTTTTHHHHHHHHTSCSSSTTTSTTS------CCSSSCTHHHHHHHHHSCCSTTSSTTGGGSCCCTTTS
T ss_pred             HHHHHHHh--cccccHHHHHHHHHhhCcHHHHHHHHc------CCCcccHHHHHHHHHHccCHHHHHHHHHhCccHHHHH
Confidence            88666653  344455688899999998876555432      2455555667788888888888888887652      


Q ss_pred             ------------------CCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHH
Q 040394          208 ------------------DKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLH  269 (691)
Q Consensus       208 ------------------~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~  269 (691)
                                        ..++.+|..+-.+|...+.+.-|.-.--.+.-.   ||  ....++.-|-..|.+++...++
T Consensus       178 stLV~L~~yq~AVdaArKAns~ktWKeV~~ACvd~~EfrLAqicGLniIvh---ad--eL~elv~~YE~~G~f~ELIsLl  252 (624)
T 3lvg_A          178 STLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVH---AD--ELEELINYYQDRGYFEELITML  252 (624)
T ss_dssp             SSSSSCSGGGSSTTTTTTCCSSCSHHHHTHHHHHSCTTTTTTHHHHHHHCC---SS--CCSGGGSSSSTTCCCTTSTTTH
T ss_pred             HHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHhCchHHHHHHHhcchhccc---HH--HHHHHHHHHHhCCCHHHHHHHH
Confidence                              147789999999999999988776654444321   22  2334566677888888888877


Q ss_pred             HHHHHHCC-CCchHHHHHHHHHHHhcCCHHHHHHHHHhc----CCC-------ChhHHHHHHHHHHhcCCchhHHHHHHH
Q 040394          270 GYILKIGI-EINSHLVTALLDMYVKCGNIRDARSVFDEL----CSI-------DLVSWTAMIVGYTQSGYPDKALKLFTD  337 (691)
Q Consensus       270 ~~~~~~g~-~~~~~~~~~li~~~~~~g~~~~A~~~~~~~----~~~-------~~~~~~~li~~~~~~g~~~~a~~~~~~  337 (691)
                      +.-.  |. .....+++-|.-.|+|- +.++..+-++..    .-|       ....|.-++-.|....++|.|...   
T Consensus       253 Eagl--glErAHmGmFTELaILYsKY-~PeKlmEHlklf~sriNipKviracE~ahLW~ElvfLY~~ydE~DnA~lt---  326 (624)
T 3lvg_A          253 EAAL--GLERAHMGMFTELAILYSKF-KPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIIT---  326 (624)
T ss_dssp             HHHT--TSTTCCHHHHHHHHHHHHSS-CTTHHHHHHTTSSSSSCCTTTHHHHTTTTCHHHHHHHHHHHTCHHHHHHT---
T ss_pred             HHHh--CCCchhHHHHHHHHHHHHhc-CHHHHHHHHHHHHHhccHHHHHHHHHHHhhHHHHHHHHhcchhHHHHHHH---
Confidence            7655  33 34667888888888775 455555555443    112       344688899889988888877543   


Q ss_pred             hhHC-----------C---CCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHH
Q 040394          338 KKWA-----------D---FFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYI  403 (691)
Q Consensus       338 m~~~-----------g---~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~  403 (691)
                      |.+.           .   -.++...|-..|..|....-.- -..++..+ ...+ |.   +..++.+.+.|++.-....
T Consensus       327 Mi~h~~~Aw~h~~Fkdii~KVaN~EiyYKAi~FYL~e~P~l-L~DLL~vL-~prl-Dh---~RvV~~~~k~~~LpLIkpY  400 (624)
T 3lvg_A          327 MMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYLEFKPLL-LNDLLMVL-SPRL-DH---TRAVNYFSKVKQLPLVKPY  400 (624)
T ss_dssp             TTSCHHHHCCGGGGTTTGGGCSCSHHHHHHHHHHTTSCCTT-SHHHHHHH-CTTC-CS---TTTHHHHHTTTCGGGGTGG
T ss_pred             HHhCChhhccHHHHHHHHHHcchHHHHHHHHHHHHHhChHH-HHHHHHhc-cccC-Ch---HHHHHHHHhcCCchhhHHH
Confidence            2211           0   1234455555555544332211 00111100 0000 11   1233444445555544444


Q ss_pred             HHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHH------------HHHHHHHHcCCCCCchhHHHH
Q 040394          404 FETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGS------------SLHAYSTKQGLLSSNVYVGTA  471 (691)
Q Consensus       404 ~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~------------~~~~~~~~~~~~~~~~~~~~~  471 (691)
                      +......+....|                 .++-..+....|++.-.            .+-+++.++    +-...-..
T Consensus       401 L~~Vq~~N~~aVN-----------------eAln~L~IEEEDy~~LR~SId~ydNFD~i~LA~rLEkH----eL~eFRrI  459 (624)
T 3lvg_A          401 LRSVQNHNNKSVN-----------------ESLNNLFITEEDYQALRTSIDAYDNFDNISLAQRLEKH----ELIEFRRI  459 (624)
T ss_dssp             GTSCCCSCCHHHH-----------------HHHHHHHHHTTCCHHHHHTTSSCCCSCTTHHHHHHHTC----SSHHHHHH
T ss_pred             HHHHHHhhHHHHH-----------------HHHHHHHhhhhhHHHHHHHHHHhccccHHHHHHHHhhC----chHHHHHH
Confidence            4444443322111                 12222233333332211            122222322    22334444


Q ss_pred             HHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHH
Q 040394          472 LLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEG  551 (691)
Q Consensus       472 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A  551 (691)
                      -...|.+.++|+++..+..+=     ..|.-.|......|+.+-|.++++-..+.|   +...|...+-.|...=++|-+
T Consensus       460 AA~LYkkn~rw~qsi~l~KkD-----klykDAietAa~S~~~elaeeLL~yFv~~g---~~EcF~a~LytCYdLlrpDvV  531 (624)
T 3lvg_A          460 AAYLFKGNNRWKQSVELCKKD-----SLYKDAMQYASESKDTELAEELLQWFLQEE---KRECFGACLFTCYDLLRPDVV  531 (624)
T ss_dssp             HHHHHHTTCHHHHHSSCSSTT-----CCTTGGGTTTTTCCCTTHHHHHHHHHHHHC---STHHHHHHHHHTSSSSSCHHH
T ss_pred             HHHHHHhcccHHHHHHHHHhc-----ccHHHHHHHHHHcCCHHHHHHHHHHHHHcC---chHHHHHHHHHHhhccChHHH
Confidence            456677778888776654322     233334556677888888888888888765   445677777777776677777


Q ss_pred             HHH
Q 040394          552 WKC  554 (691)
Q Consensus       552 ~~~  554 (691)
                      +++
T Consensus       532 lEl  534 (624)
T 3lvg_A          532 LET  534 (624)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            665

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.45  E-value=0.00043  Score=52.43  Aligned_cols=65  Identities=15%  Similarity=0.136  Sum_probs=60.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          600 VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       600 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      ...+..+...+...|++++|...++++++..|+++..+..++.++...|++++|.+.+++..+..
T Consensus         9 ~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~   73 (91)
T 1na3_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD   73 (91)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence            45778888889999999999999999999999999999999999999999999999999998753

>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=97.35  E-value=9.9e-05  Score=61.81  Aligned_cols=92  Identities=14%  Similarity=0.186  Sum_probs=61.1

Q ss_pred             CCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCC----------hHHHHHHHHhC-CCCCC-HHHHHHHHHHHHh
Q 040394          546 GMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGR----------LEEALEFMENM-PIEPD-VSLFGAFLHGCGL  612 (691)
Q Consensus       546 g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~----------~~~A~~~~~~~-~~~p~-~~~~~~l~~~~~~  612 (691)
                      +.+++|.+.++...+   +.|+ ...|..+..++...++          +++|+..|++. .+.|+ ..+|..+..+|..
T Consensus        16 ~~feeA~~~~~~Ai~---l~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~~~~A~~~LG~ay~~   92 (158)
T 1zu2_A           16 LLFEQIRQDAENTYK---SNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYTS   92 (158)
T ss_dssp             HHHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHH
Confidence            345566666664432   3443 5555556666665554          34777777776 44553 4577777777766


Q ss_pred             c-----------CCHHHHHHHHHHHHhcCCCCchhHHHH
Q 040394          613 Y-----------SRFDLGEVMIKKMLELHPDKACYYVLV  640 (691)
Q Consensus       613 ~-----------g~~~~A~~~~~~~~~~~p~~~~~~~~l  640 (691)
                      .           |++++|+..|+++++++|++..+...+
T Consensus        93 lg~l~P~~~~a~g~~~eA~~~~~kAl~l~P~~~~y~~al  131 (158)
T 1zu2_A           93 FAFLTPDETEAKHNFDLATQFFQQAVDEQPDNTHYLKSL  131 (158)
T ss_dssp             HHHHCCCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             hcccCcchhhhhccHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence            5           589999999999999999987665544

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.26  E-value=0.00048  Score=70.72  Aligned_cols=86  Identities=9%  Similarity=0.023  Sum_probs=71.4

Q ss_pred             HHHhcCChHHHHHHHHhC---------CCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHh-----cCCCCc---hhHH
Q 040394          577 LLARAGRLEEALEFMENM---------PIEPDV-SLFGAFLHGCGLYSRFDLGEVMIKKMLE-----LHPDKA---CYYV  638 (691)
Q Consensus       577 ~~~~~g~~~~A~~~~~~~---------~~~p~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~p~~~---~~~~  638 (691)
                      .+...|++++|+.++++.         ...|+. .+++.|...|...|++++|+.+++++++     +.|+++   ..+.
T Consensus       318 ~~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~  397 (490)
T 3n71_A          318 KARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVM  397 (490)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            456789999999888776         133433 4889999999999999999999999987     455554   5678


Q ss_pred             HHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          639 LVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       639 ~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      .|+.+|..+|++++|..++++.++
T Consensus       398 nLa~~~~~~G~~~eA~~~~~~Al~  421 (490)
T 3n71_A          398 RAGLTNWHAGHIEVGHGMICKAYA  421 (490)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHH
Confidence            899999999999999999998875

>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=97.22  E-value=0.00045  Score=69.65  Aligned_cols=95  Identities=15%  Similarity=0.042  Sum_probs=54.3

Q ss_pred             ccCCHHHHHHHHHHchhhcC--CCCC----hhHHHHHHHHHHhcCChHHHHHHHHhC---------CCCCCH-HHHHHHH
Q 040394          544 HTGMVGEGWKCFYSMCRDFK--FVPS----MKHYVCMVDLLARAGRLEEALEFMENM---------PIEPDV-SLFGAFL  607 (691)
Q Consensus       544 ~~g~~~~A~~~~~~m~~~~~--~~p~----~~~~~~li~~~~~~g~~~~A~~~~~~~---------~~~p~~-~~~~~l~  607 (691)
                      ..|++++|+.++++......  +.|+    ..+++.|..+|...|++++|+.++++.         +..|+. .+++.|.
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa  389 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLG  389 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHH
Confidence            34677777777765533211  2222    345666666666666666666666555         123333 3566666


Q ss_pred             HHHHhcCCHHHHHHHHHHHHh-----cCCCCchhHH
Q 040394          608 HGCGLYSRFDLGEVMIKKMLE-----LHPDKACYYV  638 (691)
Q Consensus       608 ~~~~~~g~~~~A~~~~~~~~~-----~~p~~~~~~~  638 (691)
                      ..|...|++++|+.+++++++     +.|+++.+-.
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~  425 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAIAIMEVAHGKDHPYISE  425 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHHHHHHHHHcCCCChHHHH
Confidence            666666666666666666666     3566554443

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.15  E-value=0.0015  Score=52.10  Aligned_cols=79  Identities=9%  Similarity=-0.074  Sum_probs=57.9

Q ss_pred             HHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 040394          551 GWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKML  627 (691)
Q Consensus       551 A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  627 (691)
                      |++.+++..   ...|+ ...+..+...|...|++++|++.+++. ...| +...|..+..++...|++++|...+++++
T Consensus         4 a~~~~~~al---~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al   80 (115)
T 2kat_A            4 ITERLEAML---AQGTDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPTYSVAWKWLGKTLQGQGDRAGARQAWESGL   80 (115)
T ss_dssp             HHHHHHHHH---TTTCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHH---HhCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            455555443   34454 567777778888888888888888776 3333 45678888888888999999999999988


Q ss_pred             hcCCC
Q 040394          628 ELHPD  632 (691)
Q Consensus       628 ~~~p~  632 (691)
                      +..|+
T Consensus        81 ~~~~~   85 (115)
T 2kat_A           81 AAAQS   85 (115)
T ss_dssp             HHHHH
T ss_pred             Hhccc
Confidence            87775

>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=97.15  E-value=0.0083  Score=63.17  Aligned_cols=149  Identities=12%  Similarity=0.027  Sum_probs=116.2

Q ss_pred             CChHHHHHHHHHHHHCCCCCCHH-HHHHHHHHhcccCC----------HHHHHHHHHHchhhcCCCCC-hhHHHHHHHHH
Q 040394          511 GDGGGSLALFSDMLNEEVQPNEV-IFTTILSACSHTGM----------VGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLL  578 (691)
Q Consensus       511 ~~~~~A~~~~~~m~~~g~~p~~~-~~~~ll~~~~~~g~----------~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~  578 (691)
                      ...++|++.++++...  .|+.. .|+.--.++...|+          ++++++.++.+.+.   .|+ ..+|..-..++
T Consensus        43 ~~~eeal~~~~~~l~~--nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~---~pK~y~aW~hR~w~l  117 (567)
T 1dce_A           43 ELDESVLELTSQILGA--NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRV---NPKSYGTWHHRCWLL  117 (567)
T ss_dssp             CCSHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHH---CTTCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH--CchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHh---CCCCHHHHHHHHHHH
Confidence            3446789999999884  56553 44444344444555          89999999988654   454 67788878888


Q ss_pred             HhcC--ChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhC------
Q 040394          579 ARAG--RLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYS-RFDLGEVMIKKMLELHPDKACYYVLVSNLYASD------  647 (691)
Q Consensus       579 ~~~g--~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~------  647 (691)
                      .+.|  +++++++.++++ . .+-+...|+.-...+.+.| .++++.+.++++++.+|++..+|...+.++.+.      
T Consensus       118 ~~l~~~~~~~el~~~~k~l~~d~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~n~saW~~r~~ll~~l~~~~~~  197 (567)
T 1dce_A          118 SRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDS  197 (567)
T ss_dssp             HTCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCCS
T ss_pred             HHcccccHHHHHHHHHHHHhhccccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCCCccHHHHHHHHHHhhcccccc
Confidence            8889  779999999999 3 3447789988888888888 899999999999999999999999999988774      


Q ss_pred             --------CCcHHHHHHHHHHHhCC
Q 040394          648 --------GRWIRVNQVRELMKQRG  664 (691)
Q Consensus       648 --------g~~~~A~~~~~~~~~~g  664 (691)
                              +.++++.+.+++..+..
T Consensus       198 ~~~~~~~~~~~~eel~~~~~ai~~~  222 (567)
T 1dce_A          198 GPQGRLPENVLLKELELVQNAFFTD  222 (567)
T ss_dssp             SSCCSSCHHHHHHHHHHHHHHHHHC
T ss_pred             cccccccHHHHHHHHHHHHHHHhhC
Confidence                    55788888887777643

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=97.13  E-value=0.033  Score=43.98  Aligned_cols=140  Identities=9%  Similarity=-0.014  Sum_probs=100.7

Q ss_pred             hcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHH
Q 040394          508 GMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEA  587 (691)
Q Consensus       508 ~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A  587 (691)
                      .-.|..++..++..+...   +.+..-||.+|--....-+-+-..++++.+    |--.|          ...+|+....
T Consensus        18 ildG~v~qGveii~k~~~---ssni~E~NW~ICNiiD~a~C~y~v~vLd~I----GkiFD----------is~C~NlKrV   80 (172)
T 1wy6_A           18 LLDGYIDEGVKIVLEITK---SSTKSEYNWFICNLLESIDCRYMFQVLDKI----GSYFD----------LDKCQNLKSV   80 (172)
T ss_dssp             HHTTCHHHHHHHHHHHHH---HSCHHHHTHHHHHHHHHCCHHHHHHHHHHH----GGGSC----------GGGCSCTHHH
T ss_pred             HHhhhHHHHHHHHHHHcC---CCCccccceeeeecchhhchhHHHHHHHHH----hhhcC----------cHhhhcHHHH
Confidence            346778888888887776   334455555554444444445555555555    22223          2356777777


Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCc
Q 040394          588 LEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLS  666 (691)
Q Consensus       588 ~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~  666 (691)
                      ...+-.++  .+....+..+..+..+|.-++-.+++..++...|.++.....++.+|.+.|+..+|.+++.+.-+.|++
T Consensus        81 i~C~~~~n--~~se~vd~ALd~lv~~~KkDqLdki~~~~l~n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           81 VECGVINN--TLNEHVNKALDILVIQGKRDKLEEIGREILKNNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             HHHHHHTT--CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHhc--chHHHHHHHHHHHHHhccHhHHHHHHHHHhccCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            77777775  244556677888899999999999999977777666999999999999999999999999999999985

>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=97.11  E-value=0.0022  Score=64.67  Aligned_cols=81  Identities=10%  Similarity=0.014  Sum_probs=51.2

Q ss_pred             CChHHHHHHHHhC---------CCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHh-----cCCCCc---hhHHHHHHH
Q 040394          582 GRLEEALEFMENM---------PIEPDV-SLFGAFLHGCGLYSRFDLGEVMIKKMLE-----LHPDKA---CYYVLVSNL  643 (691)
Q Consensus       582 g~~~~A~~~~~~~---------~~~p~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~p~~~---~~~~~l~~~  643 (691)
                      |++++|+.++++.         ...|+. .+++.|..+|...|++++|+.+++++++     +.|+++   ..+..|+.+
T Consensus       312 g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~  391 (433)
T 3qww_A          312 KSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRL  391 (433)
T ss_dssp             SCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHH
Confidence            4555555555443         122332 4667777777777777777777777775     334443   456677777


Q ss_pred             HHhCCCcHHHHHHHHHHHh
Q 040394          644 YASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       644 ~~~~g~~~~A~~~~~~~~~  662 (691)
                      |..+|++++|..++++.++
T Consensus       392 ~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          392 YMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHhccCHHHHHHHHHHHHH
Confidence            7777777777777776654

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=97.10  E-value=0.0012  Score=50.93  Aligned_cols=79  Identities=15%  Similarity=0.187  Sum_probs=59.8

Q ss_pred             HHHHHHhcCChHHHHHHHHhC-CCCC-CHH-HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCc
Q 040394          574 MVDLLARAGRLEEALEFMENM-PIEP-DVS-LFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRW  650 (691)
Q Consensus       574 li~~~~~~g~~~~A~~~~~~~-~~~p-~~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~  650 (691)
                      ....+.+.|++++|++.+++. ...| +.. .+..+..++...|++++|...++++++.+|+++..+..        +.+
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~--------~~~   77 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELNPDSPALQAR--------KMV   77 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTHHHHH--------HHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHH--------HHH
Confidence            456778889999999999887 3344 456 78888888889999999999999999999998776632        344


Q ss_pred             HHHHHHHHHH
Q 040394          651 IRVNQVRELM  660 (691)
Q Consensus       651 ~~A~~~~~~~  660 (691)
                      .++...+++.
T Consensus        78 ~~a~~~~~~~   87 (99)
T 2kc7_A           78 MDILNFYNKD   87 (99)
T ss_dssp             HHHHHHHCCT
T ss_pred             HHHHHHHHHH
Confidence            5555555433

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=97.09  E-value=0.00076  Score=52.12  Aligned_cols=57  Identities=14%  Similarity=0.163  Sum_probs=35.1

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCch-hHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          607 LHGCGLYSRFDLGEVMIKKMLELHPDKAC-YYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       607 ~~~~~~~g~~~~A~~~~~~~~~~~p~~~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      ...+...|++++|...++++++..|+++. .+..++.+|...|++++|.+.+++.++.
T Consensus         7 a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A            7 IKELINQGDIENALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            34455566666666666666666666665 6666666666666666666666666554

>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=97.07  E-value=0.0087  Score=49.54  Aligned_cols=112  Identities=8%  Similarity=-0.073  Sum_probs=87.6

Q ss_pred             CChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHh----cCChHH
Q 040394          511 GDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLAR----AGRLEE  586 (691)
Q Consensus       511 ~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~----~g~~~~  586 (691)
                      +++++|++.|++..+.| .|+..    +-..|...+.+++|.+.|++..+.    -+...+..|...|..    .+++++
T Consensus         9 ~d~~~A~~~~~~aa~~g-~~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~----g~~~a~~~Lg~~y~~G~g~~~d~~~   79 (138)
T 1klx_A            9 KDLKKAIQYYVKACELN-EMFGC----LSLVSNSQINKQKLFQYLSKACEL----NSGNGCRFLGDFYENGKYVKKDLRK   79 (138)
T ss_dssp             HHHHHHHHHHHHHHHTT-CTTHH----HHHHTCTTSCHHHHHHHHHHHHHT----TCHHHHHHHHHHHHHCSSSCCCHHH
T ss_pred             cCHHHHHHHHHHHHcCC-CHhhh----HHHHHHcCCCHHHHHHHHHHHHcC----CCHHHHHHHHHHHHcCCCCCccHHH
Confidence            46788999999998887 44444    555677777888899999877432    356777788888887    789999


Q ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhcCC
Q 040394          587 ALEFMENMPIEPDVSLFGAFLHGCGL----YSRFDLGEVMIKKMLELHP  631 (691)
Q Consensus       587 A~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~p  631 (691)
                      |.++|++.-..-+...+..|...|..    .+|.++|...++++.+...
T Consensus        80 A~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           80 AAQYYSKACGLNDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence            99999998333567788888888888    8999999999999888744

>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=97.06  E-value=0.001  Score=67.22  Aligned_cols=103  Identities=12%  Similarity=-0.017  Sum_probs=74.1

Q ss_pred             HHHhcccCCHHHHHHHHHHchhhcC--CCCC----hhHHHHHHHHHHhcCChHHHHHHHHhC---------CCCCCH-HH
Q 040394          539 LSACSHTGMVGEGWKCFYSMCRDFK--FVPS----MKHYVCMVDLLARAGRLEEALEFMENM---------PIEPDV-SL  602 (691)
Q Consensus       539 l~~~~~~g~~~~A~~~~~~m~~~~~--~~p~----~~~~~~li~~~~~~g~~~~A~~~~~~~---------~~~p~~-~~  602 (691)
                      +..+...|++++|+.++++......  +.|+    ..+++.|..+|...|++++|+.++++.         +..|+. .+
T Consensus       294 ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~  373 (429)
T 3qwp_A          294 IEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQ  373 (429)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHH
T ss_pred             HHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHH
Confidence            5566677888888888887643321  2233    456778888888888888888887766         233443 46


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHh-----cCCCCchhHHHHH
Q 040394          603 FGAFLHGCGLYSRFDLGEVMIKKMLE-----LHPDKACYYVLVS  641 (691)
Q Consensus       603 ~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~p~~~~~~~~l~  641 (691)
                      ++.|...|...|++++|+.+++++++     ..|+++.+-..+.
T Consensus       374 l~nLa~~~~~~g~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~  417 (429)
T 3qwp_A          374 VMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLIL  417 (429)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhcCCCChHHHHHHH
Confidence            78888888888888888888888888     5788776666553

>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=97.05  E-value=0.0043  Score=62.65  Aligned_cols=87  Identities=10%  Similarity=0.125  Sum_probs=56.1

Q ss_pred             HHHHhcCChHHHHHHHHhC------CCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHh-----cCCCCc---hhH
Q 040394          576 DLLARAGRLEEALEFMENM------PIEPD----VSLFGAFLHGCGLYSRFDLGEVMIKKMLE-----LHPDKA---CYY  637 (691)
Q Consensus       576 ~~~~~~g~~~~A~~~~~~~------~~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~p~~~---~~~  637 (691)
                      ..+.+.|++++|++++++.      -..|+    ..+++.|...|...|++++|+.+++++++     ..|+++   ..+
T Consensus       295 e~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~l  374 (429)
T 3qwp_A          295 EELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQV  374 (429)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHH
T ss_pred             HHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHHH
Confidence            3345667777777776655      01122    23667777777777777777777777775     334443   456


Q ss_pred             HHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          638 VLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       638 ~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      ..|+.+|..+|++++|..++++.++
T Consensus       375 ~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          375 MKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            6777777777777777777776654

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=96.91  E-value=0.003  Score=58.21  Aligned_cols=88  Identities=5%  Similarity=0.032  Sum_probs=70.8

Q ss_pred             hHHHHHHHHhC-CCCCC---HHHHHHHHHHHHh-----cCCHHHHHHHHHHHHhcCCCC-chhHHHHHHHHHhC-CCcHH
Q 040394          584 LEEALEFMENM-PIEPD---VSLFGAFLHGCGL-----YSRFDLGEVMIKKMLELHPDK-ACYYVLVSNLYASD-GRWIR  652 (691)
Q Consensus       584 ~~~A~~~~~~~-~~~p~---~~~~~~l~~~~~~-----~g~~~~A~~~~~~~~~~~p~~-~~~~~~l~~~~~~~-g~~~~  652 (691)
                      ...|...+++. ...|+   ...|..|...|.+     .|+.++|.++|+++++++|+. ...++..+..++.. |++++
T Consensus       179 l~~A~a~lerAleLDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~  258 (301)
T 3u64_A          179 VHAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAG  258 (301)
T ss_dssp             HHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHH
T ss_pred             HHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHH
Confidence            34556666665 56666   4578888888877     599999999999999999975 88999999988884 99999


Q ss_pred             HHHHHHHHHhCCCccCCCe
Q 040394          653 VNQVRELMKQRGLSKSPGC  671 (691)
Q Consensus       653 A~~~~~~~~~~g~~~~~~~  671 (691)
                      |.+.+++.+.......|+.
T Consensus       259 a~~~L~kAL~a~p~~~P~~  277 (301)
T 3u64_A          259 FDEALDRALAIDPESVPHN  277 (301)
T ss_dssp             HHHHHHHHHHCCGGGCSSC
T ss_pred             HHHHHHHHHcCCCCCCCCh
Confidence            9999999999877765664

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=96.84  E-value=0.022  Score=54.97  Aligned_cols=68  Identities=9%  Similarity=-0.032  Sum_probs=45.1

Q ss_pred             ChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040394          567 SMKHYVCMVDLLARAGRLEEALEFMENM-PIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKA  634 (691)
Q Consensus       567 ~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~  634 (691)
                      +...|..+...+...|++++|...++++ ...|+...|..+...+.-.|++++|.+.+++++.++|..+
T Consensus       276 ~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL~P~~~  344 (372)
T 3ly7_A          276 LSIIYQIKAVSALVKGKTDESYQAINTGIDLEMSWLNYVLLGKVYEMKGMNREAADAYLTAFNLRPGAN  344 (372)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCSHH
T ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcC
Confidence            3556666655566667777777777776 3346666666666666677777777777777777777643

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=96.64  E-value=0.016  Score=55.95  Aligned_cols=69  Identities=12%  Similarity=0.028  Sum_probs=60.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          596 IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       596 ~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      .+.+..++..+...+...|++++|...++++++++|+ ...|..++.++.-.|++++|.+.+++....+.
T Consensus       273 ~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln~s-~~a~~llG~~~~~~G~~~eA~e~~~~AlrL~P  341 (372)
T 3ly7_A          273 LNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLEMS-WLNYVLLGKVYEMKGMNREAADAYLTAFNLRP  341 (372)
T ss_dssp             GTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSC
T ss_pred             CCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCC-HHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC
Confidence            3557778888887788889999999999999999986 77888999999999999999999999988654

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=96.56  E-value=0.016  Score=44.55  Aligned_cols=63  Identities=11%  Similarity=0.010  Sum_probs=46.2

Q ss_pred             CHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040394          429 DAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMR  493 (691)
Q Consensus       429 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  493 (691)
                      +...+..+...+...|++++|...|+...+..  |.+...+..+..+|...|++++|...|++..
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al   68 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETD--PDYVGTYYHLGKLYERLDRTDDAIDTYAQGI   68 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            45566677777777777888877777777776  5666677777777777777777777777654

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=96.54  E-value=0.0065  Score=50.19  Aligned_cols=93  Identities=13%  Similarity=0.037  Sum_probs=69.4

Q ss_pred             CCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcC---ChHHHHHHHHhC-CCC-C--CHHHHHHHHHHHHhcCCHHH
Q 040394          546 GMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAG---RLEEALEFMENM-PIE-P--DVSLFGAFLHGCGLYSRFDL  618 (691)
Q Consensus       546 g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g---~~~~A~~~~~~~-~~~-p--~~~~~~~l~~~~~~~g~~~~  618 (691)
                      +....+.+.|.+.... + .++..+.-.+..++++.+   +.++++.+++.. ... |  +...+-.|.-++.+.|++++
T Consensus        12 ~~l~~~~~~y~~e~~~-~-~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~LAv~~~kl~~Y~~   89 (152)
T 1pc2_A           12 EDLLKFEKKFQSEKAA-G-SVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEK   89 (152)
T ss_dssp             HHHHHHHHHHHHHHHT-T-CCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTSCHHH
T ss_pred             HHHHHHHHHHHHHHcc-C-CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHccCHHH
Confidence            4566677777765332 2 367777778888999988   666899888887 323 5  34566667778899999999


Q ss_pred             HHHHHHHHHhcCCCCchhHHHH
Q 040394          619 GEVMIKKMLELHPDKACYYVLV  640 (691)
Q Consensus       619 A~~~~~~~~~~~p~~~~~~~~l  640 (691)
                      |.+.++.+++.+|++.......
T Consensus        90 A~~y~~~lL~ieP~n~QA~~Lk  111 (152)
T 1pc2_A           90 ALKYVRGLLQTEPQNNQAKELE  111 (152)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCHHHHHHH
Confidence            9999999999999987666544

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.53  E-value=0.12  Score=57.53  Aligned_cols=153  Identities=12%  Similarity=0.132  Sum_probs=96.1

Q ss_pred             HHHhCCChhHHHH-HHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHH
Q 040394          120 WYFLNDLYKDIVE-FYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGS  198 (691)
Q Consensus       120 ~~~~~~~~~~a~~-~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  198 (691)
                      .....+++++|.+ ++..+      |+......++..+.+.|..+.|.++.+.-.           .-.......|++++
T Consensus       608 ~~~~~~~~~~a~~~~l~~i------~~~~~~~~~~~~l~~~~~~~~a~~~~~~~~-----------~~f~~~l~~~~~~~  670 (814)
T 3mkq_A          608 TLTLRGEIEEAIENVLPNV------EGKDSLTKIARFLEGQEYYEEALNISPDQD-----------QKFELALKVGQLTL  670 (814)
T ss_dssp             HHHHTTCHHHHHHHTGGGC------CCHHHHHHHHHHHHHTTCHHHHHHHCCCHH-----------HHHHHHHHHTCHHH
T ss_pred             HHHHhCCHHHHHHHHHhcC------CchHHHHHHHHHHHhCCChHHheecCCCcc-----------hheehhhhcCCHHH
Confidence            3345677777765 44211      101223566666777777777776553211           11344567899999


Q ss_pred             HHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCC
Q 040394          199 SRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIE  278 (691)
Q Consensus       199 A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~  278 (691)
                      |.++.+.+.  +...|..|...+.+.|+++.|.+.|.++..         |..+...+...|+.+...++-+.....|. 
T Consensus       671 A~~~~~~~~--~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~~~~~a~~~~~-  738 (814)
T 3mkq_A          671 ARDLLTDES--AEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVTLAKDAETTGK-  738 (814)
T ss_dssp             HHHHHTTCC--CHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHHHHHHHHHTTC-
T ss_pred             HHHHHHhhC--cHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHHHHHHHHHcCc-
Confidence            999988774  457899999999999999999999998853         34455555556766665555555444432 


Q ss_pred             CchHHHHHHHHHHHhcCCHHHHHHHHHh
Q 040394          279 INSHLVTALLDMYVKCGNIRDARSVFDE  306 (691)
Q Consensus       279 ~~~~~~~~li~~~~~~g~~~~A~~~~~~  306 (691)
                           ++.-..+|.+.|++++|.+++.+
T Consensus       739 -----~~~A~~~~~~~g~~~~a~~~~~~  761 (814)
T 3mkq_A          739 -----FNLAFNAYWIAGDIQGAKDLLIK  761 (814)
T ss_dssp             -----HHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             -----hHHHHHHHHHcCCHHHHHHHHHH
Confidence                 23333445566777777665544

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=96.51  E-value=0.017  Score=44.93  Aligned_cols=74  Identities=15%  Similarity=0.103  Sum_probs=56.7

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhC-----C----CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHH
Q 040394          568 MKHYVCMVDLLARAGRLEEALEFMENM-----P----IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYV  638 (691)
Q Consensus       568 ~~~~~~li~~~~~~g~~~~A~~~~~~~-----~----~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~  638 (691)
                      ...+-.|...+.+.|+++.|...++..     +    ..+...++..|..++.+.|+++.|...+++++++.|++..+..
T Consensus         5 a~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~   84 (104)
T 2v5f_A            5 AEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRANG   84 (104)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             HHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCCCHHHHh
Confidence            334556777777888888887777765     1    1234568889999999999999999999999999999877755


Q ss_pred             HHH
Q 040394          639 LVS  641 (691)
Q Consensus       639 ~l~  641 (691)
                      .+.
T Consensus        85 n~~   87 (104)
T 2v5f_A           85 NLK   87 (104)
T ss_dssp             HHH
T ss_pred             hHH
Confidence            553

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=96.49  E-value=0.00035  Score=68.61  Aligned_cols=119  Identities=12%  Similarity=0.051  Sum_probs=86.7

Q ss_pred             CChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHH
Q 040394          178 PDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACA  257 (691)
Q Consensus       178 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~  257 (691)
                      ..+.+|..|..+..+.+++.+|++-|-+  ..|+..|..+|....+.|.+++-...+...++..-.|  ..=+.++-+|+
T Consensus        52 n~p~VWs~LgkAqL~~~~v~eAIdsyIk--A~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~ke~--~IDteLi~ayA  127 (624)
T 3lvg_A           52 NEPAVWSQLAKAQLQKGMVKEAIDSYIK--ADDPSSYMEVVQAANTSGNWEELVKYLQMARKKARES--YVETELIFALA  127 (624)
T ss_dssp             CCCCCSSSHHHHTTTSSSCTTTTTSSCC--CSCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTCCST--TTTHHHHHHHH
T ss_pred             CCccHHHHHHHHHHccCchHHHHHHHHh--CCChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccc--ccHHHHHHHHH
Confidence            3677888888888888888887655533  3466778888888888999988888877766553333  34457888888


Q ss_pred             ccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhc
Q 040394          258 KLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDEL  307 (691)
Q Consensus       258 ~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~  307 (691)
                      +.+++.+.++.+       -.||..-...+.+-|...|.++.|.-+|..+
T Consensus       128 k~~rL~elEefl-------~~~N~A~iq~VGDrcf~e~lYeAAKilys~i  170 (624)
T 3lvg_A          128 KTNRLAELEEFI-------NGPNNAHIQQVGDRCYDEKMYDAAKLLYNNV  170 (624)
T ss_dssp             TSCSSSTTTSTT-------SCCSSSCTHHHHHHHHHSCCSTTSSTTGGGS
T ss_pred             hhCcHHHHHHHH-------cCCCcccHHHHHHHHHHccCHHHHHHHHHhC
Confidence            888877654443       2466666677778888888888888877766

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=96.16  E-value=2  Score=46.98  Aligned_cols=260  Identities=11%  Similarity=0.020  Sum_probs=131.5

Q ss_pred             HHHccCChhhHHHHHHHHHHHC--CCCchHHHHHHHHHHHhcCCHHHHHHHHHhcC-CCC----------hhHHHHHHHH
Q 040394          255 ACAKLRALHQGKWLHGYILKIG--IEINSHLVTALLDMYVKCGNIRDARSVFDELC-SID----------LVSWTAMIVG  321 (691)
Q Consensus       255 ~~~~~~~~~~a~~~~~~~~~~g--~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~-~~~----------~~~~~~li~~  321 (691)
                      +....|+.+++..+++..+..+  -.+....-..+.-+...+|.-+++..++.... ..+          +..-.++.-+
T Consensus       383 GlIh~g~~~~gl~~L~~yL~~~~s~~~~ik~GAllaLGli~ag~~~~~~~lL~~~L~~~~~~~~~~~~~~ir~gAaLGLG  462 (963)
T 4ady_A          383 GVIHKGNLLEGKKVMAPYLPGSRASSRFIKGGSLYGLGLIYAGFGRDTTDYLKNIIVENSGTSGDEDVDVLLHGASLGIG  462 (963)
T ss_dssp             HHHTSSCTTTHHHHHTTTSTTSCCSCHHHHHHHHHHHHHHTTTTTHHHHHHHHHHHHHHSSCCSCHHHHHHHHHHHHHHH
T ss_pred             hhhccCchHHHHHHHHHhccccCCCcHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHcCccccccccccHHHHHHHHHHHH
Confidence            4556778887777776654421  11222333344445556666556666665541 112          1112233333


Q ss_pred             HHhcCCc-hhHHHHHHHhhHCCCCCcHHHHH--HHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChH
Q 040394          322 YTQSGYP-DKALKLFTDKKWADFFPNHVTIA--SVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIA  398 (691)
Q Consensus       322 ~~~~g~~-~~a~~~~~~m~~~g~~p~~~t~~--~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  398 (691)
                      ++-.|.- +++.+.+..+....- +......  .+--.+...|+.+....++..+.+....+..-...+.-++...|+.+
T Consensus       463 la~~GS~~eev~e~L~~~L~dd~-~~~~~~AalALGli~vGTgn~~ai~~LL~~~~e~~~e~vrR~aalgLGll~~g~~e  541 (963)
T 4ady_A          463 LAAMGSANIEVYEALKEVLYNDS-ATSGEAAALGMGLCMLGTGKPEAIHDMFTYSQETQHGNITRGLAVGLALINYGRQE  541 (963)
T ss_dssp             HHSTTCCCHHHHHHHHHHHHTCC-HHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHTTTCGG
T ss_pred             HHhcCCCCHHHHHHHHHHHhcCC-HHHHHHHHHHHhhhhcccCCHHHHHHHHHHHhccCcHHHHHHHHHHHHhhhCCChH
Confidence            4334432 456666666554321 1111122  22223456677776677766665432223333333333344567777


Q ss_pred             HHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHH--HHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHH
Q 040394          399 DARYIFETTSEKDVIAWNSIISGLDDNVSPDAVT--LVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFY  476 (691)
Q Consensus       399 ~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~--~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~  476 (691)
                      .+..+++.+...               ..|....  ...+.-+|+..|+.....+++..+....  ..+......+.-++
T Consensus       542 ~~~~li~~L~~~---------------~dp~vRygaa~alglAyaGTGn~~aIq~LL~~~~~d~--~d~VRraAViaLGl  604 (963)
T 4ady_A          542 LADDLITKMLAS---------------DESLLRYGGAFTIALAYAGTGNNSAVKRLLHVAVSDS--NDDVRRAAVIALGF  604 (963)
T ss_dssp             GGHHHHHHHHHC---------------SCHHHHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHCS--CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC---------------CCHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccCC--cHHHHHHHHHHHHh
Confidence            666666655432               1121111  1233446778888888888888887654  33344333344444


Q ss_pred             HhcCCHHHHHHHHHhccc-CCHhH--HHHHHHHHhcCCCh-HHHHHHHHHHHHCCCCCCHHHH
Q 040394          477 AKCGDAQSARMVFDAMRE-KNTVT--WSAMIGGYGMQGDG-GGSLALFSDMLNEEVQPNEVIF  535 (691)
Q Consensus       477 ~~~g~~~~A~~~~~~~~~-~~~~~--~~~li~~~~~~~~~-~~A~~~~~~m~~~g~~p~~~~~  535 (691)
                      ...|+.+.+.++++.+.+ .|...  -.++..+....|.. .+++.++..+..   .+|..+-
T Consensus       605 I~~g~~e~v~rlv~~L~~~~d~~VR~gAalALGli~aGn~~~~aid~L~~L~~---D~d~~Vr  664 (963)
T 4ady_A          605 VLLRDYTTVPRIVQLLSKSHNAHVRCGTAFALGIACAGKGLQSAIDVLDPLTK---DPVDFVR  664 (963)
T ss_dssp             HTSSSCSSHHHHTTTGGGCSCHHHHHHHHHHHHHHTSSSCCHHHHHHHHHHHT---CSSHHHH
T ss_pred             hccCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhccCCCcHHHHHHHHHHcc---CCCHHHH
Confidence            456666666777765543 23333  23344444444444 567888888875   4555443

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=95.93  E-value=0.033  Score=45.99  Aligned_cols=67  Identities=9%  Similarity=-0.036  Sum_probs=47.9

Q ss_pred             CCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhcC-C-CCchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          597 EPDVSLFGAFLHGCGLYS---RFDLGEVMIKKMLELH-P-DKACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       597 ~p~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~~~~-p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      .++..+.-.+.+++.+++   +.++++.++++..+.+ | ++..+++.|+-.|.+.|++++|.++++.+++.
T Consensus        29 ~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~LAv~~~kl~~Y~~A~~y~~~lL~i  100 (152)
T 1pc2_A           29 SVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQT  100 (152)
T ss_dssp             CCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            456666667777777766   5667777777777766 6 44667777777777777777777777777764

>1qsa_A Protein (soluble lytic transglycosylase SLT70); alpha-superhelix, transferase; HET: GOL; 1.65A {Escherichia coli} SCOP: a.118.5.1 d.2.1.6 PDB: 1qte_A* 1sly_A*

Probab=95.92  E-value=2.1  Score=45.03  Aligned_cols=114  Identities=11%  Similarity=-0.018  Sum_probs=70.4

Q ss_pred             CChHHHHHHHHHHHHCCCCCCHHH----HHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHH
Q 040394          511 GDGGGSLALFSDMLNEEVQPNEVI----FTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEE  586 (691)
Q Consensus       511 ~~~~~A~~~~~~m~~~g~~p~~~~----~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~  586 (691)
                      .+.+.|...+....+.+ ..+...    ...+.......+...++...+.....   ..++.......+....+.|+++.
T Consensus       228 ~d~~~A~~~~~~~~~~~-~~~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~e~~~r~Alr~~d~~~  303 (618)
T 1qsa_A          228 QDAENARLMIPSLAQAQ-QLNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIM---RSQSTSLIERRVRMALGTGDRRG  303 (618)
T ss_dssp             HCHHHHHHHHHHHHHHT-TCCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHH---TCCCHHHHHHHHHHHHHHTCHHH
T ss_pred             cCHHHHHHHHHhhhhcc-CCCHHHHHHHHHHHHHHHHHcCCChHHHHHHHhccc---cCCChHHHHHHHHHHHHCCCHHH
Confidence            37788999998887543 223322    22333344555534556666665422   22333334445555567899999


Q ss_pred             HHHHHHhCCCCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040394          587 ALEFMENMPIEP--DVSLFGAFLHGCGLYSRFDLGEVMIKKMLE  628 (691)
Q Consensus       587 A~~~~~~~~~~p--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  628 (691)
                      |...|+.|...+  ...-.--+.+++...|+.++|..+|+++.+
T Consensus       304 a~~~~~~l~~~~~~~~r~~YW~~ra~~~~g~~~~a~~~~~~~a~  347 (618)
T 1qsa_A          304 LNTWLARLPMEAKEKDEWRYWQADLLLERGREAEAKEILHQLMQ  347 (618)
T ss_dssp             HHHHHHHSCTTGGGSHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHccccccccHhHHHHHHHHHHHcCCHHHHHHHHHHHhc
Confidence            999999995432  233333456677788999999999999875

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=95.86  E-value=0.037  Score=42.88  Aligned_cols=65  Identities=9%  Similarity=-0.053  Sum_probs=55.8

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC-------CCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          599 DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELH-------PDKACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       599 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-------p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      +...+..+...+...|+++.|...++++++..       +..+.++..|+.+|.+.|++++|..+++++.+.
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l   75 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            45566788899999999999999999999842       344678899999999999999999999999874

>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=95.85  E-value=0.027  Score=45.67  Aligned_cols=54  Identities=13%  Similarity=0.018  Sum_probs=36.3

Q ss_pred             cCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCc
Q 040394          613 YSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLS  666 (691)
Q Consensus       613 ~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~  666 (691)
                      .+|.++|.++|+.+++.+..-+.+|...+..-.++|+.+.|.+++.+.+..+..
T Consensus        73 i~D~d~aR~vy~~a~~~hKkFAKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k  126 (161)
T 4h7y_A           73 IQEPDDARDYFQMARANCKKFAFVHISFAQFELSQGNVKKSKQLLQKAVERGAV  126 (161)
T ss_dssp             HHCGGGCHHHHHHHHHHCTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCB
T ss_pred             hcCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcccHHHHHHHHHHHhccCCC
Confidence            367777777777776665555566666666677777777777777776665543

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=95.83  E-value=0.073  Score=40.11  Aligned_cols=69  Identities=12%  Similarity=0.100  Sum_probs=52.9

Q ss_pred             CChhHHHHHHHHHHhcCC---hHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040394          566 PSMKHYVCMVDLLARAGR---LEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKA  634 (691)
Q Consensus       566 p~~~~~~~li~~~~~~g~---~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~  634 (691)
                      .+...+..+..++...++   .++|..++++. ...| +......+...+.+.|++++|+..|+++++..|+++
T Consensus         4 ~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~p~~~   77 (93)
T 3bee_A            4 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSNDPNL   77 (93)
T ss_dssp             CCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCCCTTC
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCc
Confidence            346667777777765544   68888888887 4444 456777788888999999999999999999988843

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=95.52  E-value=0.098  Score=58.21  Aligned_cols=153  Identities=10%  Similarity=0.007  Sum_probs=88.2

Q ss_pred             HHhccCcHHHHHH-HHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHH
Q 040394          439 ACASLGAVQVGSS-LHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSL  517 (691)
Q Consensus       439 ~~~~~~~~~~a~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~  517 (691)
                      .....++++.|.+ ++..       .++......++..+.+.|.+++|.++.+...        .-.......|+++.|.
T Consensus       608 ~~~~~~~~~~a~~~~l~~-------i~~~~~~~~~~~~l~~~~~~~~a~~~~~~~~--------~~f~~~l~~~~~~~A~  672 (814)
T 3mkq_A          608 TLTLRGEIEEAIENVLPN-------VEGKDSLTKIARFLEGQEYYEEALNISPDQD--------QKFELALKVGQLTLAR  672 (814)
T ss_dssp             HHHHTTCHHHHHHHTGGG-------CCCHHHHHHHHHHHHHTTCHHHHHHHCCCHH--------HHHHHHHHHTCHHHHH
T ss_pred             HHHHhCCHHHHHHHHHhc-------CCchHHHHHHHHHHHhCCChHHheecCCCcc--------hheehhhhcCCHHHHH
Confidence            3345677777765 4421       1212233677778888888888876653211        1123345678888888


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhCCCC
Q 040394          518 ALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIE  597 (691)
Q Consensus       518 ~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~  597 (691)
                      ++.+.      ..+...|..+...+.+.++++.|.+.|..+ ++         |..+...+...|+.+...++-+.....
T Consensus       673 ~~~~~------~~~~~~W~~la~~al~~~~~~~A~~~y~~~-~d---------~~~l~~l~~~~~~~~~~~~~~~~a~~~  736 (814)
T 3mkq_A          673 DLLTD------ESAEMKWRALGDASLQRFNFKLAIEAFTNA-HD---------LESLFLLHSSFNNKEGLVTLAKDAETT  736 (814)
T ss_dssp             HHHTT------CCCHHHHHHHHHHHHHTTCHHHHHHHHHHH-TC---------HHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHh------hCcHhHHHHHHHHHHHcCCHHHHHHHHHHc-cC---------hhhhHHHHHHcCCHHHHHHHHHHHHHc
Confidence            87543      346678888888888889999998888876 32         334444455555555444333322111


Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 040394          598 PDVSLFGAFLHGCGLYSRFDLGEVMIKK  625 (691)
Q Consensus       598 p~~~~~~~l~~~~~~~g~~~~A~~~~~~  625 (691)
                      .+   ++....++.+.|++++|++++.+
T Consensus       737 ~~---~~~A~~~~~~~g~~~~a~~~~~~  761 (814)
T 3mkq_A          737 GK---FNLAFNAYWIAGDIQGAKDLLIK  761 (814)
T ss_dssp             TC---HHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             Cc---hHHHHHHHHHcCCHHHHHHHHHH
Confidence            11   12233334455666666665554

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=95.38  E-value=4.1  Score=44.66  Aligned_cols=269  Identities=10%  Similarity=-0.005  Sum_probs=140.0

Q ss_pred             HHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHH--HHHHHhcCCChhhHHHHHHHHHHhCC--------CchhHHHHHHH
Q 040394          320 VGYTQSGYPDKALKLFTDKKWADFFPNHVTIAS--VLSASAQLGNLNMGRMVHSLGIRLGL--------EDYTVINALVD  389 (691)
Q Consensus       320 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~--ll~~~~~~~~~~~a~~~~~~~~~~~~--------~~~~~~~~l~~  389 (691)
                      -+....|+.++++.++......+-..+..+-..  +.-+....|..+++..++........        +....-.++.-
T Consensus       382 LGlIh~g~~~~gl~~L~~yL~~~~s~~~~ik~GAllaLGli~ag~~~~~~~lL~~~L~~~~~~~~~~~~~~ir~gAaLGL  461 (963)
T 4ady_A          382 LGVIHKGNLLEGKKVMAPYLPGSRASSRFIKGGSLYGLGLIYAGFGRDTTDYLKNIIVENSGTSGDEDVDVLLHGASLGI  461 (963)
T ss_dssp             HHHHTSSCTTTHHHHHTTTSTTSCCSCHHHHHHHHHHHHHHTTTTTHHHHHHHHHHHHHHSSCCSCHHHHHHHHHHHHHH
T ss_pred             hhhhccCchHHHHHHHHHhccccCCCcHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHcCccccccccccHHHHHHHHHHH
Confidence            356677888888888877654321223332222  22245555555566666655554332        11122223333


Q ss_pred             Hh--HhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchh
Q 040394          390 MY--AKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVY  467 (691)
Q Consensus       390 ~~--~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  467 (691)
                      ++  .-.++ +++.+.+..+...+.             -......-.++...+...|+.+....+++.+.+..  ..+..
T Consensus       462 Gla~~GS~~-eev~e~L~~~L~dd~-------------~~~~~~AalALGli~vGTgn~~ai~~LL~~~~e~~--~e~vr  525 (963)
T 4ady_A          462 GLAAMGSAN-IEVYEALKEVLYNDS-------------ATSGEAAALGMGLCMLGTGKPEAIHDMFTYSQETQ--HGNIT  525 (963)
T ss_dssp             HHHSTTCCC-HHHHHHHHHHHHTCC-------------HHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHCS--CHHHH
T ss_pred             HHHhcCCCC-HHHHHHHHHHHhcCC-------------HHHHHHHHHHHhhhhcccCCHHHHHHHHHHHhccC--cHHHH
Confidence            33  33333 344444444332210             00001112233344557788888888888777643  22222


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhccc-CCHh-HHH---HHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHh
Q 040394          468 VGTALLNFYAKCGDAQSARMVFDAMRE-KNTV-TWS---AMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSAC  542 (691)
Q Consensus       468 ~~~~l~~~~~~~g~~~~A~~~~~~~~~-~~~~-~~~---~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~  542 (691)
                      -...+.-++.-.|+.+.+..+.+.+.. .+.. -|.   ++..+|+-.|+.....++++.+.+. ...+......+--++
T Consensus       526 R~aalgLGll~~g~~e~~~~li~~L~~~~dp~vRygaa~alglAyaGTGn~~aIq~LL~~~~~d-~~d~VRraAViaLGl  604 (963)
T 4ady_A          526 RGLAVGLALINYGRQELADDLITKMLASDESLLRYGGAFTIALAYAGTGNNSAVKRLLHVAVSD-SNDDVRRAAVIALGF  604 (963)
T ss_dssp             HHHHHHHHHHTTTCGGGGHHHHHHHHHCSCHHHHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHC-SCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhCCChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccC-CcHHHHHHHHHHHHh
Confidence            233333344467888888888777764 3333 333   3456778889987777799888874 122222222222244


Q ss_pred             cccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCCh-HHHHHHHHhCCCCCCHHHHHHHH
Q 040394          543 SHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRL-EEALEFMENMPIEPDVSLFGAFL  607 (691)
Q Consensus       543 ~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~-~~A~~~~~~~~~~p~~~~~~~l~  607 (691)
                      ...|+.+.+.++++.+.+.  ..|.+..-..+.-+....|.. .+|++.+..+...+|..+-...+
T Consensus       605 I~~g~~e~v~rlv~~L~~~--~d~~VR~gAalALGli~aGn~~~~aid~L~~L~~D~d~~Vrq~Ai  668 (963)
T 4ady_A          605 VLLRDYTTVPRIVQLLSKS--HNAHVRCGTAFALGIACAGKGLQSAIDVLDPLTKDPVDFVRQAAM  668 (963)
T ss_dssp             HTSSSCSSHHHHTTTGGGC--SCHHHHHHHHHHHHHHTSSSCCHHHHHHHHHHHTCSSHHHHHHHH
T ss_pred             hccCCHHHHHHHHHHHHhc--CCHHHHHHHHHHHHHhccCCCcHHHHHHHHHHccCCCHHHHHHHH
Confidence            4566666667777655332  245544444455555555554 67888888885556655443333

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=94.75  E-value=1.7  Score=36.84  Aligned_cols=129  Identities=10%  Similarity=0.114  Sum_probs=76.7

Q ss_pred             HHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHH
Q 040394          188 DMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKW  267 (691)
Q Consensus       188 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~  267 (691)
                      ......|+++.|.++.+++  .+...|..|.......|+++-|.+.|.+...         +..+.-.|...|+.+....
T Consensus        13 ~LAL~lg~l~~A~e~a~~l--~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~tg~~e~L~k   81 (177)
T 3mkq_B           13 DLALEYGNLDAALDEAKKL--NDSITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVTGDVNKLSK   81 (177)
T ss_dssp             HHHHHTTCHHHHHHHHHHH--CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHhcCCHHHHHHHHHHh--CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHhCCHHHHHH
Confidence            3445677888887777765  4566788888888888888888888887643         3444445555666666555


Q ss_pred             HHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHh
Q 040394          268 LHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDK  338 (691)
Q Consensus       268 ~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  338 (691)
                      +-+.....|-      ++.-...+.-.|+++++.++|.+....+...     ......|..+.|.++.+++
T Consensus        82 la~iA~~~g~------~n~af~~~l~lGdv~~~i~lL~~~~r~~eA~-----~~A~t~g~~~~a~~~~~~~  141 (177)
T 3mkq_B           82 MQNIAQTRED------FGSMLLNTFYNNSTKERSSIFAEGGSLPLAY-----AVAKANGDEAAASAFLEQA  141 (177)
T ss_dssp             HHHHHHHTTC------HHHHHHHHHHHTCHHHHHHHHHHTTCHHHHH-----HHHHHTTCHHHHHHHHHHT
T ss_pred             HHHHHHHCcc------HHHHHHHHHHcCCHHHHHHHHHHCCChHHHH-----HHHHHcCcHHHHHHHHHHh
Confidence            5444444442      2333444556678888877776653321111     1112245555666665554

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=94.74  E-value=0.77  Score=38.92  Aligned_cols=129  Identities=12%  Similarity=0.075  Sum_probs=67.2

Q ss_pred             HHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHH
Q 040394          474 NFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWK  553 (691)
Q Consensus       474 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~  553 (691)
                      +.....|+++.|.++.+.+  .+...|..|.......|+++-|.+.|.+..+         +..+.-.|.-.|+.+.-.+
T Consensus        13 ~LAL~lg~l~~A~e~a~~l--~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~tg~~e~L~k   81 (177)
T 3mkq_B           13 DLALEYGNLDAALDEAKKL--NDSITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVTGDVNKLSK   81 (177)
T ss_dssp             HHHHHTTCHHHHHHHHHHH--CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHhcCCHHHHHHHHHHh--CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHhCCHHHHHH
Confidence            3345667777777776655  3566777777777777777777777766543         2223333344455544433


Q ss_pred             HHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040394          554 CFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKM  626 (691)
Q Consensus       554 ~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~  626 (691)
                      +-+.. ...      .-++.-...+.-.|+++++.+++.+.+.-|....+      ....|-.+.|.++.+++
T Consensus        82 la~iA-~~~------g~~n~af~~~l~lGdv~~~i~lL~~~~r~~eA~~~------A~t~g~~~~a~~~~~~~  141 (177)
T 3mkq_B           82 MQNIA-QTR------EDFGSMLLNTFYNNSTKERSSIFAEGGSLPLAYAV------AKANGDEAAASAFLEQA  141 (177)
T ss_dssp             HHHHH-HHT------TCHHHHHHHHHHHTCHHHHHHHHHHTTCHHHHHHH------HHHTTCHHHHHHHHHHT
T ss_pred             HHHHH-HHC------ccHHHHHHHHHHcCCHHHHHHHHHHCCChHHHHHH------HHHcCcHHHHHHHHHHh
Confidence            32222 110      12334444555667777777776666432221111      11245555555555543

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=94.37  E-value=0.11  Score=41.22  Aligned_cols=94  Identities=13%  Similarity=0.016  Sum_probs=63.9

Q ss_pred             cCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHH---HHHHHHhC-CCC-C--CHHHHHHHHHHHHhcCCHH
Q 040394          545 TGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEE---ALEFMENM-PIE-P--DVSLFGAFLHGCGLYSRFD  617 (691)
Q Consensus       545 ~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~---A~~~~~~~-~~~-p--~~~~~~~l~~~~~~~g~~~  617 (691)
                      ...+..+.+-|.+.... +. |+..+--.+..++.+..+..+   ++.+++.. ... |  .....-.|.-++.+.|+++
T Consensus        14 ~~~l~~~~~~y~~e~~~-~~-~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~yklg~Y~   91 (126)
T 1nzn_A           14 VEDLLKFEKKFQSEKAA-GS-VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYE   91 (126)
T ss_dssp             HHHHHHHHHHHHHHHHH-SC-CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHHhcc-CC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHhhhHH
Confidence            34455566666654332 22 666666677788888877666   78888876 322 4  2234455667788999999


Q ss_pred             HHHHHHHHHHhcCCCCchhHHHH
Q 040394          618 LGEVMIKKMLELHPDKACYYVLV  640 (691)
Q Consensus       618 ~A~~~~~~~~~~~p~~~~~~~~l  640 (691)
                      +|...++.+++.+|+|.....+.
T Consensus        92 ~A~~~~~~lL~~eP~n~QA~~Lk  114 (126)
T 1nzn_A           92 KALKYVRGLLQTEPQNNQAKELE  114 (126)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHH
Confidence            99999999999999887666544

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=94.10  E-value=0.4  Score=37.94  Aligned_cols=67  Identities=10%  Similarity=-0.050  Sum_probs=43.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCHHH---HHHHHHHHHhcC-C-CCchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          597 EPDVSLFGAFLHGCGLYSRFDL---GEVMIKKMLELH-P-DKACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       597 ~p~~~~~~~l~~~~~~~g~~~~---A~~~~~~~~~~~-p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      .|+..+--.+.+++.++.+...   ++.++++..... | ..-.+.+.|+-.+.+.|+|++|.+.++.+++.
T Consensus        32 ~~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~yklg~Y~~A~~~~~~lL~~  103 (126)
T 1nzn_A           32 SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQT  103 (126)
T ss_dssp             CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            3556665566666766655444   777777766655 4 33456666777777777777777777777663

>2wpv_A GET4, UPF0363 protein YOR164C; golgi-ER trafficking, tail-anchored protein, protein binding GET4; 1.99A {Saccharomyces cerevisiae} PDB: 3lku_A

Probab=92.89  E-value=6.3  Score=37.09  Aligned_cols=114  Identities=11%  Similarity=0.116  Sum_probs=79.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHH----HHHHhhHCCCCCcHHHHHHHHHHH
Q 040394          282 HLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALK----LFTDKKWADFFPNHVTIASVLSAS  357 (691)
Q Consensus       282 ~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~----~~~~m~~~g~~p~~~t~~~ll~~~  357 (691)
                      ..|.++..-|.+.+++++|.+++..-           ...+.+.|+...|-+    +++...+.+++++..+...++..+
T Consensus        34 Q~~Rtl~~Ry~~~~~~~eAidlL~~g-----------a~~ll~~~Q~~sa~DLa~llvev~~~~~~~~~~~~~~rl~~l~  102 (312)
T 2wpv_A           34 QTLRTIANRYVRSKSYEHAIELISQG-----------ALSFLKAKQGGSGTDLIFYLLEVYDLAEVKVDDISVARLVRLI  102 (312)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHH-----------HHHHHHTTCHHHHHHHHHHHHHHHHHTTCCCSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHH-----------HHHHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence            35566666788889999998887653           345667787766555    456666778899988888888777


Q ss_pred             hcCCChh-hHHHHHHHHH----HhCC-C--chhHHHHHHHHhHhcCChHHHHHHHHh
Q 040394          358 AQLGNLN-MGRMVHSLGI----RLGL-E--DYTVINALVDMYAKCHVIADARYIFET  406 (691)
Q Consensus       358 ~~~~~~~-~a~~~~~~~~----~~~~-~--~~~~~~~l~~~~~~~g~~~~a~~~~~~  406 (691)
                      ..-..-+ .-.++.+.++    +.|. +  ++..+..+...|.+.|++.+|...|-.
T Consensus       103 ~~~p~~~~~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~~a~~~~~e~~~~~A~~H~i~  159 (312)
T 2wpv_A          103 AELDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGSKLLEGDFVYEAERYFML  159 (312)
T ss_dssp             TTCCTTCTTHHHHHHHHHHHHHHTSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHHT
T ss_pred             HHCCCCCchHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHh
Confidence            6543222 2233333333    3332 2  889999999999999999999988864

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=92.85  E-value=1.1  Score=36.24  Aligned_cols=76  Identities=7%  Similarity=0.110  Sum_probs=53.8

Q ss_pred             CCChhHHHHHHHHHHhcCChH---HHHHHHHhC-CCCC-CH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHH
Q 040394          565 VPSMKHYVCMVDLLARAGRLE---EALEFMENM-PIEP-DV-SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYV  638 (691)
Q Consensus       565 ~p~~~~~~~li~~~~~~g~~~---~A~~~~~~~-~~~p-~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~  638 (691)
                      .|+..+--.+..++.+..+.+   +++.+++.. ...| +. ...-.|.-++.+.|++++|.++.+.+++.+|+|.....
T Consensus        36 ~vs~~t~F~YAw~Lv~S~~~~di~~GI~LLe~l~~~~~~~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL~~eP~n~QA~~  115 (144)
T 1y8m_A           36 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERNNKQVGA  115 (144)
T ss_dssp             TSCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHTCCCCHHHHH
T ss_pred             CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCCCcHHHHH
Confidence            566666666777888877554   567777776 2233 22 34455667788999999999999999999999766554


Q ss_pred             HH
Q 040394          639 LV  640 (691)
Q Consensus       639 ~l  640 (691)
                      +.
T Consensus       116 Lk  117 (144)
T 1y8m_A          116 LK  117 (144)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=92.44  E-value=0.97  Score=37.61  Aligned_cols=60  Identities=7%  Similarity=-0.093  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHh---cC----------------------CCCchhHHHHHHHHHhCCCcHHHHHH
Q 040394          602 LFGAFLHGCGLYSRFDLGEVMIKKMLE---LH----------------------PDKACYYVLVSNLYASDGRWIRVNQV  656 (691)
Q Consensus       602 ~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~----------------------p~~~~~~~~l~~~~~~~g~~~~A~~~  656 (691)
                      ++..+..++...|++.+|...|+++++   .-                      +.+....+.++.||.+.|++++|+.+
T Consensus        65 ~l~~ladalf~~~eyrrA~~~y~qALq~~k~l~k~~s~~~~~~~~ss~p~s~~~~~e~Elkykia~C~~~l~~~~~Ai~~  144 (167)
T 3ffl_A           65 LLVYHADSLFHDKEYRNAVSKYTMALQQKKALSKTSKVRPSTGNSASTPQSQCLPSEIEVKYKLAECYTVLKQDKDAIAI  144 (167)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHCC--------------------CCCCHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHhcCCCccccccccCCCcccccccchHHHHHHHHHHHHHHCCHHHHHHH
Confidence            344455566666666666666666543   11                      11124667899999999999999999


Q ss_pred             HHHHH
Q 040394          657 RELMK  661 (691)
Q Consensus       657 ~~~~~  661 (691)
                      ++.+.
T Consensus       145 Le~Ip  149 (167)
T 3ffl_A          145 LDGIP  149 (167)
T ss_dssp             HHTSC
T ss_pred             HhcCC
Confidence            97653

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=92.41  E-value=0.87  Score=48.85  Aligned_cols=52  Identities=10%  Similarity=-0.040  Sum_probs=48.8

Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHH
Q 040394          610 CGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMK  661 (691)
Q Consensus       610 ~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  661 (691)
                      |...|+++.|..+.+++....|.+..+|..|+.+|...|+|+.|.-.++.+.
T Consensus       347 Ll~K~~~elAL~~Ak~AV~~aPseF~tW~~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          347 LLNRGDYELALGVSNTSTELALDSFESWYNLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             HhccCcHHHHHHHHHHHHhcCchhhHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence            5678999999999999999999999999999999999999999999998874

>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=92.40  E-value=0.76  Score=42.50  Aligned_cols=86  Identities=8%  Similarity=-0.011  Sum_probs=68.3

Q ss_pred             hhHHHHHHHHHHHhCCC--ChhHHHHHHHHhHh-----cCChHHHHHHHhccC--CC--ChhhHHHHHHHHHhC-CChhH
Q 040394          162 IDEGMKVHCEIVKVGGP--DSFVLTGLVDMYAK-----CRDIGSSRQVFDETL--DK--NVVSWTSMIAGYVQN-DCAQE  229 (691)
Q Consensus       162 ~~~a~~~~~~~~~~~~~--~~~~~~~l~~~~~~-----~g~~~~A~~~~~~~~--~~--~~~~~~~li~~~~~~-g~~~~  229 (691)
                      ...|+..+++.++..+.  +...|..|...|.+     .|+.++|.+.|++..  .|  +..++......++.. |+.++
T Consensus       179 l~~A~a~lerAleLDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~  258 (301)
T 3u64_A          179 VHAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAG  258 (301)
T ss_dssp             HHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHH
T ss_pred             HHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHH
Confidence            46788888999998887  77899999999988     489999999998863  34  477777888888874 88888


Q ss_pred             HHHHHHHHHhCCCC--CChh
Q 040394          230 GLVLFNRMREGFVE--GNQI  247 (691)
Q Consensus       230 A~~~~~~m~~~~~~--p~~~  247 (691)
                      +.+.+++.......  |+..
T Consensus       259 a~~~L~kAL~a~p~~~P~~~  278 (301)
T 3u64_A          259 FDEALDRALAIDPESVPHNK  278 (301)
T ss_dssp             HHHHHHHHHHCCGGGCSSCH
T ss_pred             HHHHHHHHHcCCCCCCCChh
Confidence            89999888887665  5543

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=91.44  E-value=9.8  Score=36.07  Aligned_cols=113  Identities=12%  Similarity=0.062  Sum_probs=79.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHH----HHHhhHCCCCCcHHHHHHHHHHH
Q 040394          282 HLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKL----FTDKKWADFFPNHVTIASVLSAS  357 (691)
Q Consensus       282 ~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~----~~~m~~~g~~p~~~t~~~ll~~~  357 (691)
                      .+|.++..-|.+.+++++|.+++..-           ...+.+.|+...+.++    ++...+.++++|..+...++..+
T Consensus        36 Q~~RTi~~Ry~~~k~y~eAidLL~~G-----------A~~ll~~~Q~~sg~DL~~llvevy~~~~~~~~~~~~~rL~~L~  104 (336)
T 3lpz_A           36 QETRLVAARYSKQGNWAAAVDILASV-----------SQTLLRSGQGGSGGDLAVLLVDTFRQAGQRVDGASRGKLLGCL  104 (336)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHH-----------HHHHHHTTCHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCHHHHHHHHHHH-----------HHHHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence            45666777789999999999887653           3456677777665544    46666778889998888888877


Q ss_pred             hcCCChhh-HHHHHH----HHHHhC--CC-chhHHHHHHHHhHhcCChHHHHHHHH
Q 040394          358 AQLGNLNM-GRMVHS----LGIRLG--LE-DYTVINALVDMYAKCHVIADARYIFE  405 (691)
Q Consensus       358 ~~~~~~~~-a~~~~~----~~~~~~--~~-~~~~~~~l~~~~~~~g~~~~a~~~~~  405 (691)
                      .....-+- -..+.+    ...+.|  +. ++.....+...|.+.+++.+|...|-
T Consensus       105 ~~~~~~~p~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~ig~~~~~e~~~~~Ae~H~i  160 (336)
T 3lpz_A          105 RLFQPGEPVRKRFVKEMIDWSKKFGDYPAGDPELHHVVGTLYVEEGEFEAAEKHLV  160 (336)
T ss_dssp             TTSCTTCHHHHHHHHHHHHHHHHHSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHT
T ss_pred             HhCCCCCcHHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHccCCHHHHHHHHH
Confidence            76554221 122222    223334  23 89999999999999999999999884

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=90.91  E-value=11  Score=35.72  Aligned_cols=167  Identities=10%  Similarity=0.026  Sum_probs=105.1

Q ss_pred             hhhHHHHHHhcCCChHHHHHHhccCCCCCcchHHHHHHHHHhCCChhHHHHHH----HHHHHcCCCCCcchHHHHHHHHc
Q 040394           82 CNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFY----KCMRKRLKEHDNFVFSKVLKACC  157 (691)
Q Consensus        82 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~----~~m~~~~~~~~~~~~~~ll~~~~  157 (691)
                      .+..+..-|.+++++++|.+++-           .-...+.+.|+...|.++-    +-+.+.++++|......++..+.
T Consensus        37 ~~RTi~~Ry~~~k~y~eAidLL~-----------~GA~~ll~~~Q~~sg~DL~~llvevy~~~~~~~~~~~~~rL~~L~~  105 (336)
T 3lpz_A           37 ETRLVAARYSKQGNWAAAVDILA-----------SVSQTLLRSGQGGSGGDLAVLLVDTFRQAGQRVDGASRGKLLGCLR  105 (336)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHH-----------HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhhcCHHHHHHHHH-----------HHHHHHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            45567777899999999998763           2334556678777666554    55567788999988888888887


Q ss_pred             ccCChh-HHHHHHHHH----HHhC-CC--ChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhH
Q 040394          158 ELRDID-EGMKVHCEI----VKVG-GP--DSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQE  229 (691)
Q Consensus       158 ~~~~~~-~a~~~~~~~----~~~~-~~--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  229 (691)
                      ....-+ .=..+.+.+    .+.| .+  |+.....+...|.+.+++.+|+..|---.++....+..++.-+...+...+
T Consensus       106 ~~~~~~p~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~ig~~~~~e~~~~~Ae~H~ilg~~~s~~~~a~mL~ew~~~~~~~e  185 (336)
T 3lpz_A          106 LFQPGEPVRKRFVKEMIDWSKKFGDYPAGDPELHHVVGTLYVEEGEFEAAEKHLVLGTKESPEVLARMEYEWYKQDESHT  185 (336)
T ss_dssp             TSCTTCHHHHHHHHHHHHHHHHHSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHTTSCTTHHHHHHHHHHHHHHTSCGGG
T ss_pred             hCCCCCcHHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHhcCCchHHHHHHHHHHHHHhcCCcc
Confidence            655322 112233333    3444 33  899999999999999999999988853233333566555544444433222


Q ss_pred             HHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHH
Q 040394          230 GLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILK  274 (691)
Q Consensus       230 A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~  274 (691)
                      +--.+-              . .+-.|.-.+++..|...++...+
T Consensus       186 ~dlfia--------------R-aVL~yL~l~n~~~A~~~~~~f~~  215 (336)
T 3lpz_A          186 APLYCA--------------R-AVLPYLLVANVRAANTAYRIFTS  215 (336)
T ss_dssp             HHHHHH--------------H-HHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHH--------------H-HHHHHHHhCCHHHHHHHHHHHHH
Confidence            221111              1 22234456677777777666554

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=90.87  E-value=5.2  Score=31.87  Aligned_cols=140  Identities=9%  Similarity=-0.025  Sum_probs=93.6

Q ss_pred             HhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHH
Q 040394          222 VQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDAR  301 (691)
Q Consensus       222 ~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~  301 (691)
                      .-.|..++..++..+....   .+..-||.+|--....-+-+...+.++.+-+   --|.          ..+|++....
T Consensus        18 ildG~v~qGveii~k~~~s---sni~E~NW~ICNiiD~a~C~y~v~vLd~IGk---iFDi----------s~C~NlKrVi   81 (172)
T 1wy6_A           18 LLDGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGS---YFDL----------DKCQNLKSVV   81 (172)
T ss_dssp             HHTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGG---GSCG----------GGCSCTHHHH
T ss_pred             HHhhhHHHHHHHHHHHcCC---CCccccceeeeecchhhchhHHHHHHHHHhh---hcCc----------HhhhcHHHHH
Confidence            4567778888888777653   3556677777666665555555555544422   1121          2345555555


Q ss_pred             HHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCC
Q 040394          302 SVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLE  379 (691)
Q Consensus       302 ~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  379 (691)
                      ..+-.+.. +....+.-+..+...|+-|+-.+++.++.. +.+|++.....+..+|.+.|+..++..++.++.+.|.+
T Consensus        82 ~C~~~~n~-~se~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           82 ECGVINNT-LNEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             HHHHHTTC-CCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHhcc-hHHHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            55544422 444556667788889999999999888543 35778888888888999999999998888888887765

>3o48_A Mitochondria fission 1 protein; tetratricopeptide repeat fold, TPR, scaffold, peroxisome, membrane fission, protein binding; 1.75A {Saccharomyces cerevisiae} PDB: 2pqr_A 2pqn_A 3uux_A

Probab=90.58  E-value=1  Score=35.86  Aligned_cols=76  Identities=7%  Similarity=0.099  Sum_probs=48.0

Q ss_pred             CCCChhHHHHHHHHHHhcCCh---HHHHHHHHhC-CCCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhH
Q 040394          564 FVPSMKHYVCMVDLLARAGRL---EEALEFMENM-PIEP--DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYY  637 (691)
Q Consensus       564 ~~p~~~~~~~li~~~~~~g~~---~~A~~~~~~~-~~~p--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~  637 (691)
                      -.|+..+--.+..++.+..+.   .+++.+++.. ...|  ....+-.|.-++.+.|+++.|.+..+.+++..|+|....
T Consensus        36 ~~vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~~eP~N~QA~  115 (134)
T 3o48_A           36 PTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERNNKQVG  115 (134)
T ss_dssp             GGSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTCTTCHHHH
T ss_pred             CCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhCCCCHHHH
Confidence            345555555566667766654   3456666665 2224  233555566677788888888888888888888876554


Q ss_pred             HH
Q 040394          638 VL  639 (691)
Q Consensus       638 ~~  639 (691)
                      .+
T Consensus       116 ~L  117 (134)
T 3o48_A          116 AL  117 (134)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>2wpv_A GET4, UPF0363 protein YOR164C; golgi-ER trafficking, tail-anchored protein, protein binding GET4; 1.99A {Saccharomyces cerevisiae} PDB: 3lku_A

Probab=90.21  E-value=12  Score=35.12  Aligned_cols=167  Identities=8%  Similarity=0.040  Sum_probs=105.6

Q ss_pred             hhhHHHHHHhcCCChHHHHHHhccCCCCCcchHHHHHHHHHhCCChhHHHHH----HHHHHHcCCCCCcchHHHHHHHHc
Q 040394           82 CNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEF----YKCMRKRLKEHDNFVFSKVLKACC  157 (691)
Q Consensus        82 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~----~~~m~~~~~~~~~~~~~~ll~~~~  157 (691)
                      .+..+..-|.+++++++|.+++.           .-...+.+.|+...|.++    ++-..+.+.+++......++..+.
T Consensus        35 ~~Rtl~~Ry~~~~~~~eAidlL~-----------~ga~~ll~~~Q~~sa~DLa~llvev~~~~~~~~~~~~~~rl~~l~~  103 (312)
T 2wpv_A           35 TLRTIANRYVRSKSYEHAIELIS-----------QGALSFLKAKQGGSGTDLIFYLLEVYDLAEVKVDDISVARLVRLIA  103 (312)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHH-----------HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCCSHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHH-----------HHHHHHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            55667888889999999998863           233455677887777665    555566788888888888888776


Q ss_pred             ccCChh-----HHHHHHHHHHHhCC-C--ChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhC---CC
Q 040394          158 ELRDID-----EGMKVHCEIVKVGG-P--DSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQN---DC  226 (691)
Q Consensus       158 ~~~~~~-----~a~~~~~~~~~~~~-~--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~---g~  226 (691)
                      ....-+     -..+......+.|. +  ++..+..+...|.+.|++.+|+..|---...+...+..++.-+...   |.
T Consensus       104 ~~p~~~~~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~~a~~~~~e~~~~~A~~H~i~~~~~s~~~~a~~l~~w~~~~~~~~  183 (312)
T 2wpv_A          104 ELDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGSKLLEGDFVYEAERYFMLGTHDSMIKYVDLLWDWLCQVDDIE  183 (312)
T ss_dssp             TCCTTCTTHHHHHHHHHHHHHHTSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTCCC
T ss_pred             HCCCCCchHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHhCCCccHHHHHHHHHHHHHhcCCCC
Confidence            533211     22333333334442 3  8999999999999999999999887633222455555555444443   43


Q ss_pred             hhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHH
Q 040394          227 AQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILK  274 (691)
Q Consensus       227 ~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~  274 (691)
                      ..++--.+-+               .+-.+.-.+++..|..+++...+
T Consensus       184 ~~e~dlf~~R---------------aVL~yL~l~n~~~A~~~~~~f~~  216 (312)
T 2wpv_A          184 DSTVAEFFSR---------------LVFNYLFISNISFAHESKDIFLE  216 (312)
T ss_dssp             HHHHHHHHHH---------------HHHHHHHTTBHHHHHHHHHHHHH
T ss_pred             cchHHHHHHH---------------HHHHHHHhcCHHHHHHHHHHHHH
Confidence            3332221111               12234456788888888776654

>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=90.02  E-value=5.2  Score=32.61  Aligned_cols=97  Identities=8%  Similarity=0.145  Sum_probs=51.5

Q ss_pred             CCChhhHHHHHHHHHhCCCh------hHHHHHHHHHHhCCCCCChhh-HHHHHHH------HHccCChhhHHHHHHHHHH
Q 040394          208 DKNVVSWTSMIAGYVQNDCA------QEGLVLFNRMREGFVEGNQIT-LGSLVTA------CAKLRALHQGKWLHGYILK  274 (691)
Q Consensus       208 ~~~~~~~~~li~~~~~~g~~------~~A~~~~~~m~~~~~~p~~~t-~~~li~~------~~~~~~~~~a~~~~~~~~~  274 (691)
                      ..|..+|-..+...-+.|++      ++..++|++.... ++|+... +..-+..      +...++.+.|.++|+.+++
T Consensus        10 p~~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~-~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~~   88 (161)
T 4h7y_A           10 ANNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEA-LPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARA   88 (161)
T ss_dssp             CCSHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHH-SCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHc-CCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            34677888878777777888      7777888877653 5554311 1111110      1122566666666666655


Q ss_pred             HCCCCchHHHHHHHHHHHhcCCHHHHHHHHHh
Q 040394          275 IGIEINSHLVTALLDMYVKCGNIRDARSVFDE  306 (691)
Q Consensus       275 ~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~  306 (691)
                      .+-. -..+|......-.+.|+++.|.+++..
T Consensus        89 ~hKk-FAKiwi~~AqFEiRqgnl~kARkILg~  119 (161)
T 4h7y_A           89 NCKK-FAFVHISFAQFELSQGNVKKSKQLLQK  119 (161)
T ss_dssp             HCTT-BHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HhHH-HHHHHHHHHHHHHHcccHHHHHHHHHH
Confidence            4211 144444444444444555555444443

>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=89.40  E-value=0.83  Score=45.21  Aligned_cols=54  Identities=11%  Similarity=0.075  Sum_probs=25.7

Q ss_pred             HHHHHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040394          573 CMVDLLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKM  626 (691)
Q Consensus       573 ~li~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~  626 (691)
                      .++..+...|++++|+..+... . .+-+...|..++.++.+.|+..+|...|++.
T Consensus       176 ~~~~~~l~~g~~~~a~~~l~~~~~~~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~  231 (388)
T 2ff4_A          176 AKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRV  231 (388)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            3444444555555555444443 1 2224445555555555555555555555544

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=89.37  E-value=4.7  Score=32.53  Aligned_cols=78  Identities=5%  Similarity=-0.045  Sum_probs=57.4

Q ss_pred             HHHHHHhC-CCCCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhcCCC-CchhHHHHHHHHHhCCCcHHHHHHHHHHH
Q 040394          587 ALEFMENM-PIEPDVSLFGAFLHGCGLYS---RFDLGEVMIKKMLELHPD-KACYYVLVSNLYASDGRWIRVNQVRELMK  661 (691)
Q Consensus       587 A~~~~~~~-~~~p~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~~~~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  661 (691)
                      ..+-+.+- +..|+..+--.+.+++.++.   +..+++.+++++....|. .-.+.+.|+-.+.+.|+|++|.++.+.++
T Consensus        25 lr~qY~~E~~~~vs~~t~F~YAw~Lv~S~~~~di~~GI~LLe~l~~~~~~~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL  104 (144)
T 1y8m_A           25 LRQQVVSEGGPTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLF  104 (144)
T ss_dssp             HHHHHHHTTSTTSCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhccCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            33334333 33567777667777887765   456788899998888884 34677888888999999999999998888


Q ss_pred             hCC
Q 040394          662 QRG  664 (691)
Q Consensus       662 ~~g  664 (691)
                      +..
T Consensus       105 ~~e  107 (144)
T 1y8m_A          105 EHE  107 (144)
T ss_dssp             HTC
T ss_pred             hcC
Confidence            754

>2p58_C Putative type III secretion protein YSCG; type III secretion system, structure, needle protein, YSCE, YSCF, transport protein/chaperone complex; 1.80A {Yersinia pestis}

Probab=89.17  E-value=5.4  Score=29.58  Aligned_cols=86  Identities=14%  Similarity=0.123  Sum_probs=62.2

Q ss_pred             ChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhH
Q 040394          261 ALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKW  340 (691)
Q Consensus       261 ~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  340 (691)
                      .-++|.-|-+.+...|.  ...+--.-+..+...|++++|..+.+.++-||...|-+|-.  .+.|..+++...+.++..
T Consensus        22 ~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce--~rlGl~s~le~rL~~la~   97 (116)
T 2p58_C           22 YHEEANCIAEWLHLKGE--EEAVQLIRLSSLMNRGDYASALQQGNKLAYPDLEPWLALCE--YRLGLGSALESRLNRLAR   97 (116)
T ss_dssp             CHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHHHHTTSCCGGGHHHHHHHH--HHHTCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHH--HhcccHHHHHHHHHHHHh
Confidence            45677777777666554  33333334556889999999999999999999999988765  466888888888877776


Q ss_pred             CCCCCcHHHHH
Q 040394          341 ADFFPNHVTIA  351 (691)
Q Consensus       341 ~g~~p~~~t~~  351 (691)
                      .| .|....|.
T Consensus        98 sg-~p~~q~Fa  107 (116)
T 2p58_C           98 SQ-DPRIQTFV  107 (116)
T ss_dssp             CC-CHHHHHHH
T ss_pred             CC-CHHHHHHH
Confidence            65 45555553

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=88.33  E-value=5.1  Score=29.66  Aligned_cols=86  Identities=10%  Similarity=0.073  Sum_probs=62.5

Q ss_pred             ChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhH
Q 040394          261 ALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKW  340 (691)
Q Consensus       261 ~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  340 (691)
                      .-++|.-|-+.+...|.  ...+--.-+..+...|++++|..+.+.++-||...|-+|-.  .+.|..+++...+.++..
T Consensus        21 ~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce--~rlGl~s~le~rL~~la~   96 (115)
T 2uwj_G           21 CHEEALCIAEWLERLGQ--DEAARLIRISSLANQGRYQEALAFAHGNPWPALEPWFALCE--WHLGLGAALDRRLAGLGG   96 (115)
T ss_dssp             CHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHGGGTTCCCGGGHHHHHHHH--HHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHH--HhcccHHHHHHHHHHHHh
Confidence            45677777776666554  33333334556789999999999999999999999988765  577888888888878777


Q ss_pred             CCCCCcHHHHH
Q 040394          341 ADFFPNHVTIA  351 (691)
Q Consensus       341 ~g~~p~~~t~~  351 (691)
                      .| .|....|.
T Consensus        97 sg-~p~~q~Fa  106 (115)
T 2uwj_G           97 SS-DPALADFA  106 (115)
T ss_dssp             CS-SHHHHHHH
T ss_pred             CC-CHHHHHHH
Confidence            65 45555553

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=88.27  E-value=1.4  Score=36.72  Aligned_cols=40  Identities=10%  Similarity=0.079  Sum_probs=26.8

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHH
Q 040394          604 GAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLY  644 (691)
Q Consensus       604 ~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~  644 (691)
                      -.+..+|.+.|++++|+..++.+....-. +.+...|+++|
T Consensus       126 ykia~C~~~l~~~~~Ai~~Le~Ip~k~Rt-~kvnm~LakLy  165 (167)
T 3ffl_A          126 YKLAECYTVLKQDKDAIAILDGIPSRQRT-PKINMLLANLY  165 (167)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHTSCGGGCC-HHHHHHHHHHC
T ss_pred             HHHHHHHHHHCCHHHHHHHHhcCCchhcC-HHHHHHHHHHh
Confidence            33566677888888888888765444333 55666676665

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=87.96  E-value=11  Score=37.75  Aligned_cols=25  Identities=8%  Similarity=0.017  Sum_probs=11.6

Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHH
Q 040394          465 NVYVGTALLNFYAKCGDAQSARMVF  489 (691)
Q Consensus       465 ~~~~~~~l~~~~~~~g~~~~A~~~~  489 (691)
                      +......++..|...|+++...+.+
T Consensus        55 ~~r~l~~iv~l~~~~~~~~~l~e~i   79 (445)
T 4b4t_P           55 SKEVLAKIVDLLASRNKWDDLNEQL   79 (445)
T ss_dssp             CHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHH
Confidence            3444444445555555554444333

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=87.76  E-value=22  Score=34.81  Aligned_cols=128  Identities=11%  Similarity=0.003  Sum_probs=58.5

Q ss_pred             HHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC---chhHHHHHHHHHHhc-CCHHHHHHHHHhccc---CCHhHH---
Q 040394          431 VTLVSVISACASLGAVQVGSSLHAYSTKQGLLSS---NVYVGTALLNFYAKC-GDAQSARMVFDAMRE---KNTVTW---  500 (691)
Q Consensus       431 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~-g~~~~A~~~~~~~~~---~~~~~~---  500 (691)
                      .....|...|.+.|+.++...++......-...+   .......+++.+... +..+.-.++..+..+   .+-.+|   
T Consensus        20 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~kak~~k~v~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~~~r~flr~   99 (394)
T 3txn_A           20 QGILQQGELYKQEGKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMDAGTGIEVQLCKDCIEWAKQEKRTFLRQ   99 (394)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHTTTGGGGSCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455566666666666666666655432110011   122334455555443 222222233322221   111122   


Q ss_pred             ---HHHHHHHhcCCChHHHHHHHHHHHHCCCCCCH-----HHHHHHHHHhcccCCHHHHHHHHHHc
Q 040394          501 ---SAMIGGYGMQGDGGGSLALFSDMLNEEVQPNE-----VIFTTILSACSHTGMVGEGWKCFYSM  558 (691)
Q Consensus       501 ---~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~-----~~~~~ll~~~~~~g~~~~A~~~~~~m  558 (691)
                         .-++..|...|++.+|.+++.++.+.=-..|.     ..+..-++.|...+++.++...+...
T Consensus       100 ~l~~kL~~l~~~~~~y~~a~~~i~~l~~~~~~~dd~~~llev~lle~~~~~~~~n~~k~k~~l~~a  165 (394)
T 3txn_A          100 SLEARLIALYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSA  165 (394)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSSCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence               13556666666666666666666552111111     22333344555566666666666544

>1qsa_A Protein (soluble lytic transglycosylase SLT70); alpha-superhelix, transferase; HET: GOL; 1.65A {Escherichia coli} SCOP: a.118.5.1 d.2.1.6 PDB: 1qte_A* 1sly_A*

Probab=87.14  E-value=32  Score=36.09  Aligned_cols=390  Identities=7%  Similarity=-0.092  Sum_probs=186.0

Q ss_pred             hhhHHHHHHhcCCChHHHHHHhccCCCCCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCC
Q 040394           82 CNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRD  161 (691)
Q Consensus        82 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~  161 (691)
                      +-..-+..+++.+++......+.. +..+...--....+....|+..+|......+-..| ...+..+..++..+.+.|.
T Consensus        74 Lr~~~l~~l~~~~~w~~~l~~~~~-~p~~~~~~c~~~~A~~~~G~~~~a~~~~~~lW~~~-~~~p~~c~~l~~~~~~~g~  151 (618)
T 1qsa_A           74 LQSRFVNELARREDWRGLLAFSPE-KPGTTEAQCNYYYAKWNTGQSEEAWQGAKELWLTG-KSQPNACDKLFSVWRASGK  151 (618)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHCCS-CCSSHHHHHHHHHHHHHTTCHHHHHHHHHHHHSCS-SCCCTHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHhCCCHHHHHHhccC-CCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHhCC-CCCcHHHHHHHHHHHHCCC
Confidence            566678888889999998887776 43344444445666777888888877777776654 3345566666666665554


Q ss_pred             hhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCC
Q 040394          162 IDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGF  241 (691)
Q Consensus       162 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~  241 (691)
                      +....                .-.-+......|+...|..+...+..........++....   +...+......     
T Consensus       152 lt~~~----------------~~~R~~~al~~~~~~~a~~l~~~l~~~~~~~a~~~~al~~---~p~~~~~~~~~-----  207 (618)
T 1qsa_A          152 QDPLA----------------YLERIRLAMKAGNTGLVTVLAGQMPADYQTIASAIISLAN---NPNTVLTFART-----  207 (618)
T ss_dssp             SCHHH----------------HHHHHHHHHHTTCHHHHHHHHHTCCGGGHHHHHHHHHHHH---CGGGHHHHHHH-----
T ss_pred             CCHHH----------------HHHHHHHHHHCCCHHHHHHHHHhCCHHHHHHHHHHHHHHh---ChHhHHHHHhc-----
Confidence            43221                1112233445566666666666552221112222222221   22222222221     


Q ss_pred             CCCChhh---HHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHH----HHHHHHHHHhcCCHHHHHHHHHhc--CCCCh
Q 040394          242 VEGNQIT---LGSLVTACAKLRALHQGKWLHGYILKIGIEINSHL----VTALLDMYVKCGNIRDARSVFDEL--CSIDL  312 (691)
Q Consensus       242 ~~p~~~t---~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~----~~~li~~~~~~g~~~~A~~~~~~~--~~~~~  312 (691)
                      +.|+...   +...+.-+.+. +.+.|...+....+.+. .+...    ...+...+...+...++...+...  ...+.
T Consensus       208 ~~~~~~~~~~~~~~~~rlar~-d~~~A~~~~~~~~~~~~-~~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~~~~~~~~  285 (618)
T 1qsa_A          208 TGATDFTRQMAAVAFASVARQ-DAENARLMIPSLAQAQQ-LNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRSQST  285 (618)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHH-CHHHHHHHHHHHHHHTT-CCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHTCCCH
T ss_pred             cCCChhhHHHHHHHHHHHHhc-CHHHHHHHHHhhhhccC-CCHHHHHHHHHHHHHHHHHcCCChHHHHHHHhccccCCCh
Confidence            1122221   11122222222 55667777666654432 12221    222222222333233444444443  12222


Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhH
Q 040394          313 VSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYA  392 (691)
Q Consensus       313 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~  392 (691)
                      ....-.+....+.|+++.|...|+.|..... ......--+..++...|+.++|..++..+.+.  .  ..|..+..  .
T Consensus       286 ~~~e~~~r~Alr~~d~~~a~~~~~~l~~~~~-~~~r~~YW~~ra~~~~g~~~~a~~~~~~~a~~--~--~fYg~lAa--~  358 (618)
T 1qsa_A          286 SLIERRVRMALGTGDRRGLNTWLARLPMEAK-EKDEWRYWQADLLLERGREAEAKEILHQLMQQ--R--GFYPMVAA--Q  358 (618)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHSCTTGG-GSHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--C--SHHHHHHH--H
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHcccccc-ccHhHHHHHHHHHHHcCCHHHHHHHHHHHhcC--C--ChHHHHHH--H
Confidence            2222233334456777777777777655321 12333334445666667777777777666542  1  22332211  1


Q ss_pred             hcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCC---CHH---HHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCch
Q 040394          393 KCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSP---DAV---TLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNV  466 (691)
Q Consensus       393 ~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p---~~~---~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  466 (691)
                      +.|..-       .....              .+.+   ...   .-...+..+...|....|...+..+.+..  +  .
T Consensus       359 ~Lg~~~-------~~~~~--------------~~~~~~~~~~~~~~~~~r~~~L~~~g~~~~a~~ew~~~~~~~--~--~  413 (618)
T 1qsa_A          359 RIGEEY-------ELKID--------------KAPQNVDSALTQGPEMARVRELMYWNLDNTARSEWANLVKSK--S--K  413 (618)
T ss_dssp             HTTCCC-------CCCCC--------------CCCSCCCCHHHHSHHHHHHHHHHHTTCHHHHHHHHHHHHTTC--C--H
T ss_pred             HcCCCC-------CCCCC--------------CCChhHHhhhccChHHHHHHHHHHCCChhhHHHHHHHHHhcC--C--H
Confidence            122100       00000              0001   000   11223445667888888888888776542  2  2


Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHhcccCCH------hHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCC
Q 040394          467 YVGTALLNFYAKCGDAQSARMVFDAMREKNT------VTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPN  531 (691)
Q Consensus       467 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~------~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~  531 (691)
                      .-...+.......|..+.+..........+.      ..|..++..+++.-.++..+-.---..+.++.|+
T Consensus       414 ~~~~~la~~a~~~~~~~~~v~~~~~~~~~~~~~~~~P~~y~~~i~~~a~~~gv~~~ll~Ai~~~ES~f~p~  484 (618)
T 1qsa_A          414 TEQAQLARYAFNNQWWDLSVQATIAGKLWDHLEERFPLAYNDLFKRYTSGKEIPQSYAMAIARQESAWNPK  484 (618)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHTTCTTCHHHHSCCTTHHHHHHHHTTSSSCHHHHHHHHHHHHTTCTT
T ss_pred             HHHHHHHHHHHHCCChHHHHHHHHHHHhhcchhhhCCcchHHHHHHHHHHcCCCHHHHHHHHHHhCCCCCC
Confidence            3333455556677777777666554443321      1344455555554444443332222334445554

>3o48_A Mitochondria fission 1 protein; tetratricopeptide repeat fold, TPR, scaffold, peroxisome, membrane fission, protein binding; 1.75A {Saccharomyces cerevisiae} PDB: 2pqr_A 2pqn_A 3uux_A

Probab=87.06  E-value=2.6  Score=33.54  Aligned_cols=69  Identities=6%  Similarity=-0.020  Sum_probs=45.6

Q ss_pred             CCCCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhcCCC-CchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          595 PIEPDVSLFGAFLHGCGLYS---RFDLGEVMIKKMLELHPD-KACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       595 ~~~p~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~~~~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      +..|+..+--.+.+++.++.   +..+++.+++++.+..|. ...+++.|+-.+.+.|++++|.+..+.+++.
T Consensus        35 ~~~vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~~  107 (134)
T 3o48_A           35 GPTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEH  107 (134)
T ss_dssp             GGGSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHTT
T ss_pred             CCCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh
Confidence            44556665555666666554   344677777777776663 3456677777777777777777777777764

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=85.03  E-value=33  Score=34.32  Aligned_cols=51  Identities=10%  Similarity=0.046  Sum_probs=32.5

Q ss_pred             CChhHHHHHHHHHHHc-----CCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHh
Q 040394          125 DLYKDIVEFYKCMRKR-----LKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKV  175 (691)
Q Consensus       125 ~~~~~a~~~~~~m~~~-----~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  175 (691)
                      |++++|++.+-.+.+.     ....+......++..|...|+++...+.+..+.+.
T Consensus        30 ~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskk   85 (445)
T 4b4t_P           30 NDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKK   85 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            6777887777665542     12333445666777777888888777766655543

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=84.04  E-value=4.6  Score=30.12  Aligned_cols=63  Identities=13%  Similarity=0.174  Sum_probs=48.1

Q ss_pred             ChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHH
Q 040394          512 DGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVD  576 (691)
Q Consensus       512 ~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~  576 (691)
                      |.=+..+-+..+....+.|++......+++|-+..++..|.++++.+..+  +.+...+|..++.
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K--~~~~~~iY~~~lq   87 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK--AGPHKEIYPYVIQ   87 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--TTTCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH--hcCchhhHHHHHH
Confidence            34456667777777888999999999999999999999999999988544  3344556776654

>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=83.83  E-value=11  Score=32.58  Aligned_cols=50  Identities=18%  Similarity=0.246  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHHh--cCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          616 FDLGEVMIKKMLE--LHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       616 ~~~A~~~~~~~~~--~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      ...+..+|..|..  +.-..+..|...+..+...|++++|.++|+.=++++-
T Consensus        95 ~~~p~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~~Vy~~GI~~~A  146 (202)
T 3esl_A           95 FHESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAKVLLELGAENNC  146 (202)
T ss_dssp             HHHHHHHHHHHHHHTSSTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC
T ss_pred             cCCHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC
Confidence            4455555555554  3444445555555556666666666666555555444

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=83.63  E-value=3.8  Score=30.58  Aligned_cols=59  Identities=12%  Similarity=0.209  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHH
Q 040394          129 DIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLV  187 (691)
Q Consensus       129 ~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~  187 (691)
                      +..+-++.+....+.|++......+++|.+.+++..|.++++-++..-.....+|..++
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~~~~~~iY~~~l   86 (109)
T 1v54_E           28 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVI   86 (109)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCchhhHHHHH
Confidence            44455556666677888888888888888888888888888877765433344555554

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=83.33  E-value=8.5  Score=41.34  Aligned_cols=54  Identities=13%  Similarity=0.142  Sum_probs=50.0

Q ss_pred             HHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCC
Q 040394          355 SASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTS  408 (691)
Q Consensus       355 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  408 (691)
                      ..|...|+++.|..+-+......|.+..+|..|..+|...|+++.|+-.++.++
T Consensus       345 ~FLl~K~~~elAL~~Ak~AV~~aPseF~tW~~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          345 NFLLNRGDYELALGVSNTSTELALDSFESWYNLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             HHHhccCcHHHHHHHHHHHHhcCchhhHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence            356778999999999999999999999999999999999999999999999997

>2p58_C Putative type III secretion protein YSCG; type III secretion system, structure, needle protein, YSCE, YSCF, transport protein/chaperone complex; 1.80A {Yersinia pestis}

Probab=83.06  E-value=12  Score=27.89  Aligned_cols=79  Identities=11%  Similarity=0.011  Sum_probs=56.5

Q ss_pred             CChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHh
Q 040394          160 RDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMRE  239 (691)
Q Consensus       160 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  239 (691)
                      ...++|..+-+.+...+. ...+--.-+..+...|++++|..+.+.+.-||...|-+|-.  .+.|..+++..-+.++..
T Consensus        21 H~HqEA~tIAdwL~~~~~-~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce--~rlGl~s~le~rL~~la~   97 (116)
T 2p58_C           21 HYHEEANCIAEWLHLKGE-EEAVQLIRLSSLMNRGDYASALQQGNKLAYPDLEPWLALCE--YRLGLGSALESRLNRLAR   97 (116)
T ss_dssp             TCHHHHHHHHHHHHHTTC-HHHHHHHHHHHHHHTTCHHHHHHHHTTSCCGGGHHHHHHHH--HHHTCHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHHHhCCc-HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHH--HhcccHHHHHHHHHHHHh
Confidence            356667666666666554 33344444567788899999999999999999999988765  366777777777767765


Q ss_pred             CC
Q 040394          240 GF  241 (691)
Q Consensus       240 ~~  241 (691)
                      +|
T Consensus        98 sg   99 (116)
T 2p58_C           98 SQ   99 (116)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=82.69  E-value=11  Score=27.98  Aligned_cols=79  Identities=6%  Similarity=-0.060  Sum_probs=57.3

Q ss_pred             CChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHh
Q 040394          160 RDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMRE  239 (691)
Q Consensus       160 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  239 (691)
                      ...++|..+-+.+...+. ...+--.-+..+...|++++|..+.+.+.-||...|-+|-.  .+.|..+++..-+.++..
T Consensus        20 H~HqEA~tIAdwL~~~~~-~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce--~rlGl~s~le~rL~~la~   96 (115)
T 2uwj_G           20 HCHEEALCIAEWLERLGQ-DEAARLIRISSLANQGRYQEALAFAHGNPWPALEPWFALCE--WHLGLGAALDRRLAGLGG   96 (115)
T ss_dssp             TCHHHHHHHHHHHHHTTC-HHHHHHHHHHHHHHTTCHHHHHGGGTTCCCGGGHHHHHHHH--HHTTCHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHhCCc-HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHH--HhcccHHHHHHHHHHHHh
Confidence            355666666666665554 33344444567788999999999999999999999988765  467887887777777766


Q ss_pred             CC
Q 040394          240 GF  241 (691)
Q Consensus       240 ~~  241 (691)
                      +|
T Consensus        97 sg   98 (115)
T 2uwj_G           97 SS   98 (115)
T ss_dssp             CS
T ss_pred             CC
Confidence            54

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=82.29  E-value=77  Score=36.39  Aligned_cols=61  Identities=7%  Similarity=-0.113  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHhcCCChhhHHHHHHHHHHhCCC-c----hhHHHHHHHHhHhcCChHHHHHHHHhCC
Q 040394          348 VTIASVLSASAQLGNLNMGRMVHSLGIRLGLE-D----YTVINALVDMYAKCHVIADARYIFETTS  408 (691)
Q Consensus       348 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~----~~~~~~l~~~~~~~g~~~~a~~~~~~~~  408 (691)
                      .-|..++..+.+.+.++.+.++-..+.+.... +    ...|..+.+.+...|++++|...+-.++
T Consensus       900 ~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~p  965 (1139)
T 4fhn_B          900 CYYLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAHVALMVLS  965 (1139)
T ss_dssp             HHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCC
Confidence            34555566666666666666665555544332 1    1245566666666677766666665544

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=81.65  E-value=10  Score=34.48  Aligned_cols=121  Identities=10%  Similarity=0.116  Sum_probs=71.1

Q ss_pred             HHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChh----HHHHHHHHHHh
Q 040394          505 GGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMK----HYVCMVDLLAR  580 (691)
Q Consensus       505 ~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~----~~~~li~~~~~  580 (691)
                      ..+.+.|+.+++++....-++.. +-|...=..+++.+|-.|++++|.+-++...   .+.|+..    .|..+|.+-  
T Consensus         5 ~~ll~~g~L~~al~~~~~~VR~~-P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a---~l~p~~~~~a~~yr~lI~aE--   78 (273)
T 1zbp_A            5 KNALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSI---KLFPEYLPGASQLRHLVKAA--   78 (273)
T ss_dssp             HHHTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH---HHCGGGHHHHHHHHHHHHHH--
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH---HhCchhhHHHHHHHHHHHHH--
Confidence            34567788888888877777752 4455555667778888888888888777663   2456532    333333221  


Q ss_pred             cCChHHHHHHHHhC---C-CCCCHHHHHHHHHHHH--hcCCHHHHHHHHHHHHhcCCCCch
Q 040394          581 AGRLEEALEFMENM---P-IEPDVSLFGAFLHGCG--LYSRFDLGEVMIKKMLELHPDKAC  635 (691)
Q Consensus       581 ~g~~~~A~~~~~~~---~-~~p~~~~~~~l~~~~~--~~g~~~~A~~~~~~~~~~~p~~~~  635 (691)
                        ...  .++|..-   + ......-...++.+..  ..|+.++|..+-.++.+..|..+.
T Consensus        79 --~~R--~~vfaG~~~P~~~g~~~~w~~~ll~Al~~~~~G~~~~A~~lr~~A~e~ap~~~G  135 (273)
T 1zbp_A           79 --QAR--KDFAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELRQEKGF  135 (273)
T ss_dssp             --HHH--HHHTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCCE
T ss_pred             --HHH--HHHHcCCCCCCCCCCCHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhcCcccCC
Confidence              111  1122221   0 1112223344445443  468999999999988888777543

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=81.29  E-value=3.3  Score=37.62  Aligned_cols=59  Identities=20%  Similarity=0.313  Sum_probs=42.7

Q ss_pred             HHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040394          576 DLLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKA  634 (691)
Q Consensus       576 ~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~  634 (691)
                      ..+.+.|++++|++.+..- + .+-|...-..|+..+|-.|++++|.+-++...+++|+..
T Consensus         5 ~~ll~~g~L~~al~~~~~~VR~~P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l~p~~~   65 (273)
T 1zbp_A            5 KNALSEGQLQQALELLIEAIKASPKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYL   65 (273)
T ss_dssp             HHHTTTTCHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGGGH
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCchhh
Confidence            3456778888887776665 3 334555666777888888888888888888888888843

>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=81.26  E-value=8.1  Score=38.04  Aligned_cols=70  Identities=13%  Similarity=0.128  Sum_probs=47.9

Q ss_pred             HHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchh----hcCCCCChhH
Q 040394          500 WSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCR----DFKFVPSMKH  570 (691)
Q Consensus       500 ~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~----~~~~~p~~~~  570 (691)
                      ...++..+...|++++++..++.+.... +-+...+..++.++...|+..+|.+.|+.+.+    +.|+.|...+
T Consensus       174 ~~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l  247 (388)
T 2ff4_A          174 HTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  247 (388)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHH
Confidence            3445666777788888887777776642 44666777778888888888888777776532    4567776554

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=80.34  E-value=85  Score=36.01  Aligned_cols=28  Identities=18%  Similarity=0.240  Sum_probs=14.9

Q ss_pred             ChhHHHHHHHHhHhcCChHHHHHHHhcc
Q 040394          179 DSFVLTGLVDMYAKCRDIGSSRQVFDET  206 (691)
Q Consensus       179 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~  206 (691)
                      ++...-.+..+|..+|++++|...|.+.
T Consensus       841 ~~~~~yl~g~~~L~~ge~~~A~~~F~ka  868 (1139)
T 4fhn_B          841 DPIAVYLKALIYLKSKEAVKAVRCFKTT  868 (1139)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHTC
T ss_pred             CcHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            3333344455555666666666666543

---

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	691
d1w3ba_	388	a.118.8.1 (A:) O-GlcNAc transferase p110 subunit,	0.002

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]} Length = 388

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]

 Score = 38.5 bits (88), Expect = 0.002
 Identities = 45/384 (11%), Positives = 102/384 (26%), Gaps = 39/384 (10%)

Query: 291 YVKCGNIRDARSVFDELCSID---LVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNH 347
             + G+   A     +L   +         +   + Q    D++             P  
Sbjct: 9   EYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDRSAHFS--TLAIKQNPLL 66

Query: 348 VTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETT 407
               S L    +        + H         D+      +          +       +
Sbjct: 67  AEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVS 126

Query: 408 SEKDVIAWNSIISGLDDNVSPDAVTLV-------------SVISACASLGAV--QVGSSL 452
           + +       + S L + +                     +   A ++LG V    G   
Sbjct: 127 ALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIW 186

Query: 453 HAYSTKQGLLSSNVYVGTALLN---FYAKCGDAQSARMVFDAMREKNTVTWSAMIG---G 506
            A    +  ++ +     A +N      +      A   +      +             
Sbjct: 187 LAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACV 246

Query: 507 YGMQGDGGGSLALFSDMLNEEVQPNEV-IFTTILSACSHTGMVGEGWKCFYSMCRDFKFV 565
           Y  QG    ++  +   +  E+QP+    +  + +A    G V E   C+ +  R     
Sbjct: 247 YYEQGLIDLAIDTYRRAI--ELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTH 304

Query: 566 PSMKHYVCMVDLLARAGRLEEALEFMEN-MPIEPDVSLF----GAFLHGCGLYSRFDLGE 620
                   + ++    G +EEA+      + + P+ +       + L   G   +     
Sbjct: 305 --ADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQG---KLQEAL 359

Query: 621 VMIKKMLELHPDKACYYVLVSNLY 644
           +  K+ + + P  A  Y  + N  
Sbjct: 360 MHYKEAIRISPTFADAYSNMGNTL 383

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	691
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.91
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.89
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.58
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.48
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.11
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.98
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	98.97
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	98.94
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.93
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.92
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.91
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.9
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.86
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	98.86
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.58
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.57
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.53
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.48
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.47
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.45
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.44
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.42
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.37
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.37
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.25
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.24
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.22
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	98.19
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.16
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	98.12
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.08
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.03
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	98.02
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.96
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.95
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.92
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.9
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	97.89
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	97.88
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.87
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.84
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.83
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	97.79
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	97.59
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.57
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.57
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.47
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.36
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.35
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	97.25
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	97.16
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.08
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	96.99
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	96.88
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	96.87
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	96.32
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	95.16
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	94.9
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	93.58
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	93.54
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	93.11
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	91.27
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	84.32
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	83.11

>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=99.91  E-value=1.7e-20  Score=189.16  Aligned_cols=375  Identities=12%  Similarity=0.087  Sum_probs=245.2

Q ss_pred             HHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCCCchHHHHHHHHHHHhcCCH
Q 040394          218 IAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIEINSHLVTALLDMYVKCGNI  297 (691)
Q Consensus       218 i~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~  297 (691)
                      ...+.+.|++++|.+.++++.+... -+...+..+...+.+.|++++|...++..++.. +-+..++..+..+|.+.|++
T Consensus         6 a~~~~~~G~~~~A~~~~~~~l~~~p-~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~~~~~g~~   83 (388)
T d1w3ba_           6 AHREYQAGDFEAAERHCMQLWRQEP-DNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQL   83 (388)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHhhhhccc
Confidence            3445566666666666666655321 134445555555555555555555555555543 11334455555555555555


Q ss_pred             HHHHHHHHhc---CCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHH
Q 040394          298 RDARSVFDEL---CSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGI  374 (691)
Q Consensus       298 ~~A~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~  374 (691)
                      ++|...+...   ...+...+..........+....+..                                   ......
T Consensus        84 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------------------------~~~~~~  128 (388)
T d1w3ba_          84 QEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQ-----------------------------------AYVSAL  128 (388)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHH-----------------------------------HHHHHH
T ss_pred             ccccccccccccccccccccccccccccccccccccccc-----------------------------------cccccc
Confidence            5555555444   11222222223333333333333333                                   333333


Q ss_pred             HhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHH
Q 040394          375 RLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHA  454 (691)
Q Consensus       375 ~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~  454 (691)
                      ....................+....+...+......               .+-+...+..+...+...|+.+.|...++
T Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~~~~~~l~~~~~~~~~~~~A~~~~~  193 (388)
T d1w3ba_         129 QYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIET---------------QPNFAVAWSNLGCVFNAQGEIWLAIHHFE  193 (388)
T ss_dssp             HHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHH---------------CTTCHHHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             ccccccccccccccccccccchhhhhHHHHHHhhcc---------------CcchhHHHHhhcccccccCcHHHHHHHHH
Confidence            333333333334444444455555555544443321               12234555666666777777777777777


Q ss_pred             HHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCC
Q 040394          455 YSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPN  531 (691)
Q Consensus       455 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~  531 (691)
                      ...+..  |.+...+..+...+...|++++|...++....   .+...+..+...+.+.|++++|+..|++..+.. +-+
T Consensus       194 ~al~~~--p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~  270 (388)
T d1w3ba_         194 KAVTLD--PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHF  270 (388)
T ss_dssp             HHHHHC--TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSC
T ss_pred             HHHHhC--cccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCC
Confidence            777766  66777788888888888888888888877653   356677778888888899999999998888742 234


Q ss_pred             HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCC-HHHHHHHHHH
Q 040394          532 EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM-PIEPD-VSLFGAFLHG  609 (691)
Q Consensus       532 ~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~-~~~~~~l~~~  609 (691)
                      ..++..+..++...|++++|.+.++.....  .+.+...+..+...+.+.|++++|++.+++. ...|+ ..++..+...
T Consensus       271 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~  348 (388)
T d1w3ba_         271 PDAYCNLANALKEKGSVAEAEDCYNTALRL--CPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASV  348 (388)
T ss_dssp             HHHHHHHHHHHHHHSCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHhhhcc--CCccchhhhHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            567777888888999999999999877443  3344677888888999999999999999986 55564 5678889999


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCC
Q 040394          610 CGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGR  649 (691)
Q Consensus       610 ~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  649 (691)
                      +.+.|++++|...++++++++|+++.++..++.+|.+.||
T Consensus       349 ~~~~g~~~~A~~~~~~al~l~P~~~~a~~~lg~~~~~~~D  388 (388)
T d1w3ba_         349 LQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             HHTTTCCHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTCC
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCC
Confidence            9999999999999999999999999999999999998886

>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=99.89  E-value=6.1e-20  Score=185.04  Aligned_cols=329  Identities=9%  Similarity=0.003  Sum_probs=239.9

Q ss_pred             hHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhH
Q 040394          313 VSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYA  392 (691)
Q Consensus       313 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~  392 (691)
                      .++..+...|.+.|++++|...+++..+.. +-+..++..+...+...|++++|...+....+..+..............
T Consensus        34 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~  112 (388)
T d1w3ba_          34 GVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAALV  112 (388)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHhhhhcccccccccccccccccccccccccccccccc
Confidence            344444444444444444444444443331 1122344444444444455555555554444444443333333333333


Q ss_pred             hcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHH
Q 040394          393 KCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTAL  472 (691)
Q Consensus       393 ~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  472 (691)
                      ..+....+..........               ..................+....+...+.......  |.....+..+
T Consensus       113 ~~~~~~~~~~~~~~~~~~---------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~l  175 (388)
T d1w3ba_         113 AAGDMEGAVQAYVSALQY---------------NPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQ--PNFAVAWSNL  175 (388)
T ss_dssp             HHSCSSHHHHHHHHHHHH---------------CTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHC--TTCHHHHHHH
T ss_pred             cccccccccccccccccc---------------ccccccccccccccccccchhhhhHHHHHHhhccC--cchhHHHHhh
Confidence            334333333333322211               23344455556666777888888888888888777  6788888999


Q ss_pred             HHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHH
Q 040394          473 LNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVG  549 (691)
Q Consensus       473 ~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~  549 (691)
                      ...+...|++++|...+++..+   .+...|..+...+...|++++|+..+++....+ +.+...+..+...+.+.|+++
T Consensus       176 ~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~  254 (388)
T d1w3ba_         176 GCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVVHGNLACVYYEQGLID  254 (388)
T ss_dssp             HHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             cccccccCcHHHHHHHHHHHHHhCcccHHHHHHHhhhhhccccHHHHHHHHHHhHHHh-hhHHHHHHHHHHHHHHCCCHH
Confidence            9999999999999999998764   366789999999999999999999999998864 455677777888999999999


Q ss_pred             HHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC--CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040394          550 EGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM--PIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKM  626 (691)
Q Consensus       550 ~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~--~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~  626 (691)
                      +|...|++..+   +.|+ ..++..+...+...|++++|++.++..  ..+.+...+..+...+...|++++|+..++++
T Consensus       255 ~A~~~~~~al~---~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a  331 (388)
T d1w3ba_         255 LAIDTYRRAIE---LQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKA  331 (388)
T ss_dssp             HHHHHHHHHHH---TCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCCccchhhhHHHHHHHHCCCHHHHHHHHHHH
Confidence            99999998743   4566 678889999999999999999999988  34567788899999999999999999999999


Q ss_pred             HhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          627 LELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       627 ~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      ++..|+++.++..++.+|.+.|++++|++.+++.++.
T Consensus       332 l~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l  368 (388)
T d1w3ba_         332 LEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI  368 (388)
T ss_dssp             TTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT
T ss_pred             HHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999875

>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=99.58  E-value=1.1e-13  Score=134.87  Aligned_cols=225  Identities=12%  Similarity=0.006  Sum_probs=187.0

Q ss_pred             HHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-CHhHHHHHHHHHhcCC
Q 040394          435 SVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--K-NTVTWSAMIGGYGMQG  511 (691)
Q Consensus       435 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~li~~~~~~~  511 (691)
                      .....+.+.|++++|...|+.+.+..  |.+...+..+...|...|++++|...|++..+  | +...|..+...|...|
T Consensus        24 ~~g~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~  101 (323)
T d1fcha_          24 EEGLRRLQEGDLPNAVLLFEAAVQQD--PKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNES  101 (323)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHSC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccccccccccccccccccccc
Confidence            44556789999999999999999988  78899999999999999999999999998764  3 6778999999999999


Q ss_pred             ChHHHHHHHHHHHHCCCCCCHHH----------------HHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHH
Q 040394          512 DGGGSLALFSDMLNEEVQPNEVI----------------FTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMV  575 (691)
Q Consensus       512 ~~~~A~~~~~~m~~~g~~p~~~~----------------~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li  575 (691)
                      ++++|.+.+++....  .|+...                ....+..+...+..++|.+.+.+..+...-.++...+..+.
T Consensus       102 ~~~~A~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~  179 (323)
T d1fcha_         102 LQRQACEILRDWLRY--TPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLG  179 (323)
T ss_dssp             CHHHHHHHHHHHHHT--STTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHH
T ss_pred             cccccccchhhHHHh--ccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhH
Confidence            999999999998874  332111                11112223345667888888887755433344567788899


Q ss_pred             HHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHH
Q 040394          576 DLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRV  653 (691)
Q Consensus       576 ~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A  653 (691)
                      ..+...|++++|+..+++. ...| +..+|..+...+...|++++|...++++++.+|+++.++..++.+|.+.|++++|
T Consensus       180 ~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A  259 (323)
T d1fcha_         180 VLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREA  259 (323)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHhhhhcccccccccccccccchhhhhhcccccccchhHHHHHHHHHHHhhccHHHHHHHHHHHHHCCCHHHH
Confidence            9999999999999999997 3344 5678999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhC
Q 040394          654 NQVRELMKQR  663 (691)
Q Consensus       654 ~~~~~~~~~~  663 (691)
                      ++.|++.++.
T Consensus       260 ~~~~~~al~l  269 (323)
T d1fcha_         260 VEHFLEALNM  269 (323)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            9999998873

>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=99.48  E-value=1.5e-12  Score=126.51  Aligned_cols=251  Identities=10%  Similarity=-0.015  Sum_probs=196.6

Q ss_pred             HHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCc
Q 040394          386 ALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSN  465 (691)
Q Consensus       386 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~  465 (691)
                      .....+.+.|++++|...|+++.+.+               +-+..+|..+..++...|+++.|...+.+..+..  |.+
T Consensus        24 ~~g~~~~~~g~~~~A~~~~~~al~~~---------------P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~   86 (323)
T d1fcha_          24 EEGLRRLQEGDLPNAVLLFEAAVQQD---------------PKHMEAWQYLGTTQAENEQELLAISALRRCLELK--PDN   86 (323)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHSC---------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTC
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhC---------------CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc--ccc
Confidence            34566788999999999999987642               3356788999999999999999999999999987  788


Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhccc--CCH----------------hHHHHHHHHHhcCCChHHHHHHHHHHHHCC
Q 040394          466 VYVGTALLNFYAKCGDAQSARMVFDAMRE--KNT----------------VTWSAMIGGYGMQGDGGGSLALFSDMLNEE  527 (691)
Q Consensus       466 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~----------------~~~~~li~~~~~~~~~~~A~~~~~~m~~~g  527 (691)
                      ...+..+...|...|++++|.+.++....  |+.                ......+..+...+...+|...+.+..+..
T Consensus        87 ~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~  166 (323)
T d1fcha_          87 QTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLD  166 (323)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             ccccccccccccccccccccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHh
Confidence            89999999999999999999999998763  110                011112233445567788888888887643


Q ss_pred             C-CCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHH
Q 040394          528 V-QPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLF  603 (691)
Q Consensus       528 ~-~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~  603 (691)
                      . .++...+..+...+...|++++|...+++....   .|+ ...|..+...|.+.|++++|++.+++. ...| +..+|
T Consensus       167 p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~---~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~  243 (323)
T d1fcha_         167 PTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSV---RPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSR  243 (323)
T ss_dssp             TTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             hcccccccchhhHHHHHHHHHHhhhhccccccccc---ccccccchhhhhhcccccccchhHHHHHHHHHHHhhccHHHH
Confidence            2 345667777888899999999999999987543   555 778889999999999999999999987 4445 46689


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchh-----------HHHHHHHHHhCCCcHHHHHH
Q 040394          604 GAFLHGCGLYSRFDLGEVMIKKMLELHPDKACY-----------YVLVSNLYASDGRWIRVNQV  656 (691)
Q Consensus       604 ~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~-----------~~~l~~~~~~~g~~~~A~~~  656 (691)
                      ..+..+|.+.|++++|+..|++++++.|++...           +..+..++...|+.+.+...
T Consensus       244 ~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~~~~~~~~~~l~~al~~~~~~d~~~~~  307 (323)
T d1fcha_         244 YNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAA  307 (323)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhCCcChhhhhhhHHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            999999999999999999999999988876543           34566677777777665433

>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=99.11  E-value=7e-09  Score=101.44  Aligned_cols=267  Identities=10%  Similarity=-0.032  Sum_probs=191.4

Q ss_pred             HHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCC-CHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCC--
Q 040394          385 NALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSP-DAVTLVSVISACASLGAVQVGSSLHAYSTKQGL--  461 (691)
Q Consensus       385 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~--  461 (691)
                      ......+...|++++|..++++.......           +..+ ...++..+...+...|++++|...++...+...  
T Consensus        16 ~lrA~~~~~~g~~~~A~~~~~~aL~~~~~-----------~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~   84 (366)
T d1hz4a_          16 ALRAQVAINDGNPDEAERLAKLALEELPP-----------GWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQH   84 (366)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHTCCT-----------TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHhhCcC-----------CCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            44566678889999999998876543100           0000 124566778889999999999999998765321  


Q ss_pred             --CCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc-------C----CHhHHHHHHHHHhcCCChHHHHHHHHHHHHCC-
Q 040394          462 --LSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE-------K----NTVTWSAMIGGYGMQGDGGGSLALFSDMLNEE-  527 (691)
Q Consensus       462 --~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-------~----~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g-  527 (691)
                        .+.....+..+...+...|++..+...+.....       +    ....+..+...+...|+++.+...+....... 
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~  164 (366)
T d1hz4a_          85 DVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLS  164 (366)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhh
Confidence              011234556677788899999999998887542       1    12355667788899999999999999887642 


Q ss_pred             ---CCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-----hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC
Q 040394          528 ---VQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-----MKHYVCMVDLLARAGRLEEALEFMENM-PIEP  598 (691)
Q Consensus       528 ---~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-----~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p  598 (691)
                         .......+......+...++...+...+........-..+     ...+..+...+...|++++|.+.+++. ...|
T Consensus       165 ~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~  244 (366)
T d1hz4a_         165 SYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEF  244 (366)
T ss_dssp             TSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCC
T ss_pred             hhhhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhcc
Confidence               2223345555666777888998888877765433222221     234566677888999999999999987 2222


Q ss_pred             -----CHHHHHHHHHHHHhcCCHHHHHHHHHHHHh------cCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          599 -----DVSLFGAFLHGCGLYSRFDLGEVMIKKMLE------LHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       599 -----~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~------~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                           ....+..+...+...|++++|...+++++.      ..|.....+..++.+|...|++++|.+.+++.++
T Consensus       245 ~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         245 ANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  319 (366)
T ss_dssp             TTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                 234566678889999999999999999875      3455567889999999999999999999998765

>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=98.98  E-value=1.3e-08  Score=97.05  Aligned_cols=209  Identities=11%  Similarity=0.073  Sum_probs=167.7

Q ss_pred             HHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcC-CHHHHHHHHHhccc---CCHhHHHHHHHH
Q 040394          431 VTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCG-DAQSARMVFDAMRE---KNTVTWSAMIGG  506 (691)
Q Consensus       431 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~---~~~~~~~~li~~  506 (691)
                      ..++.+...+.+.+..++|..+++.+++..  |.+...|+.....+...| ++++|+..++...+   .+..+|+.+...
T Consensus        44 ~a~~~~~~~~~~~e~~~~Al~~~~~ai~ln--P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~~~~a~~~~~~~  121 (315)
T d2h6fa1          44 DVYDYFRAVLQRDERSERAFKLTRDAIELN--AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVL  121 (315)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHHHHC--CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHhhhhHHHHHhHH
Confidence            456667677888899999999999999998  889999999999988876 59999999998764   478899999999


Q ss_pred             HhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCC--
Q 040394          507 YGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGR--  583 (691)
Q Consensus       507 ~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~--  583 (691)
                      +.+.|++++|+..++++.+.. +-+...|..+...+...|++++|++.++.+++   +.|+ ...|+.+..++.+.+.  
T Consensus       122 ~~~l~~~~eAl~~~~kal~~d-p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~---~~p~n~~a~~~r~~~l~~~~~~~  197 (315)
T d2h6fa1         122 VEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLK---EDVRNNSVWNQRYFVISNTTGYN  197 (315)
T ss_dssp             HHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCSC
T ss_pred             HHhhccHHHHHHHHhhhhhhh-hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHH---HCCccHHHHHHHHHHHHHccccc
Confidence            999999999999999999853 44578888899999999999999999998854   4665 6678877777666655  


Q ss_pred             ----hHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc--hhHHHHHHHHHh
Q 040394          584 ----LEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKA--CYYVLVSNLYAS  646 (691)
Q Consensus       584 ----~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~--~~~~~l~~~~~~  646 (691)
                          +++|++.+.+. ...| +...|..+...+. ....+++.+.++.+.++.|+..  ..+..++.+|..
T Consensus       198 ~~~~~~~ai~~~~~al~~~P~~~~~~~~l~~ll~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~y~~  267 (315)
T d2h6fa1         198 DRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQ-DRGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYED  267 (315)
T ss_dssp             SHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHT-TTCGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHHH
T ss_pred             hhhhhHHhHHHHHHHHHhCCCchHHHHHHHHHHH-hcChHHHHHHHHHHHHhCCCcCCHHHHHHHHHHHHH
Confidence                57888888776 4444 5677877766654 4456888999999998887754  445566666654

>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=98.97  E-value=4.7e-07  Score=87.90  Aligned_cols=168  Identities=14%  Similarity=-0.058  Sum_probs=99.2

Q ss_pred             HHHHHHHHHhcCCchhHHHHHHHhhHC----CCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCC-------chhH
Q 040394          315 WTAMIVGYTQSGYPDKALKLFTDKKWA----DFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLE-------DYTV  383 (691)
Q Consensus       315 ~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-------~~~~  383 (691)
                      +..+...+...|+++.+...+......    +......++......+...++...+...+.........       ....
T Consensus       136 ~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~  215 (366)
T d1hz4a_         136 VRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNA  215 (366)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHH
T ss_pred             HHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHH
Confidence            334445555666666666655554432    11222333444444555556666655555444332111       2334


Q ss_pred             HHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHc----
Q 040394          384 INALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQ----  459 (691)
Q Consensus       384 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~----  459 (691)
                      +..+...+...|+.++|...++........           ........+..+...+...|+.+.|...++.....    
T Consensus       216 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~-----------~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~  284 (366)
T d1hz4a_         216 NKVRVIYWQMTGDKAAAANWLRHTAKPEFA-----------NNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSL  284 (366)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHSCCCCCT-----------TCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhcccHHHHHHHHHHHHHhccc-----------cchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhc
Confidence            566677888899999999999887654210           11222345566777788888888888888876532    


Q ss_pred             CCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040394          460 GLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMR  493 (691)
Q Consensus       460 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  493 (691)
                      +..+.....+..+...|.+.|++++|.+.+++..
T Consensus       285 ~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al  318 (366)
T d1hz4a_         285 RLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDAL  318 (366)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             ccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3212334566667778888888888888877654

>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=98.94  E-value=2.3e-09  Score=103.91  Aligned_cols=260  Identities=8%  Similarity=-0.099  Sum_probs=180.7

Q ss_pred             hhhHHHHHHHHHHhCCCchhHHHHHHHH----------hHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHH
Q 040394          363 LNMGRMVHSLGIRLGLEDYTVINALVDM----------YAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVT  432 (691)
Q Consensus       363 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~----------~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~  432 (691)
                      .++|..+++.+.+..|.+..+|+..-..          +...|.+++|+..++...+.               .+-+...
T Consensus        45 ~~~al~~~~~~l~~~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~---------------~pk~~~~  109 (334)
T d1dcea1          45 DESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRV---------------NPKSYGT  109 (334)
T ss_dssp             SHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHH---------------CTTCHHH
T ss_pred             cHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHh---------------CCCcHHH
Confidence            3555555555555555544444322222          23344577888888877643               2335556


Q ss_pred             HHHHHHHHhccC--cHHHHHHHHHHHHHcCCCCCchhHHH-HHHHHHHhcCCHHHHHHHHHhcccC---CHhHHHHHHHH
Q 040394          433 LVSVISACASLG--AVQVGSSLHAYSTKQGLLSSNVYVGT-ALLNFYAKCGDAQSARMVFDAMREK---NTVTWSAMIGG  506 (691)
Q Consensus       433 ~~~ll~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~li~~  506 (691)
                      |..+..++...+  +.+.+...++.+.+..  +.+...+. .....+...+.+++|+..++...+.   +...|+.+...
T Consensus       110 ~~~~~~~~~~~~~~~~~~a~~~~~~al~~~--~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p~~~~a~~~l~~~  187 (334)
T d1dcea1         110 WHHRCWLLSRLPEPNWARELELCARFLEAD--ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCL  187 (334)
T ss_dssp             HHHHHHHHHTCSSCCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHH
T ss_pred             HHHhhHHHHHhccccHHHHHHHHHHHHhhC--chhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            666666666554  5899999999999887  56666554 4556777889999999999988853   67789999999


Q ss_pred             HhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHH
Q 040394          507 YGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEE  586 (691)
Q Consensus       507 ~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~  586 (691)
                      +.+.|++++|...+++..+.  .|+..   .....+...+..+++...+......  -.++...+..++..+...|+.++
T Consensus       188 ~~~~~~~~~A~~~~~~~~~~--~~~~~---~~~~~~~~l~~~~~a~~~~~~~l~~--~~~~~~~~~~l~~~~~~~~~~~~  260 (334)
T d1dcea1         188 LPQLHPQPDSGPQGRLPENV--LLKEL---ELVQNAFFTDPNDQSAWFYHRWLLG--RAEPLFRCELSVEKSTVLQSELE  260 (334)
T ss_dssp             HHHHSCCCCSSSCCSSCHHH--HHHHH---HHHHHHHHHCSSCSHHHHHHHHHHS--CCCCSSSCCCCHHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHhHHh--HHHHH---HHHHHHHHhcchhHHHHHHHHHHHh--CcchhhHHHHHHHHHHHHhhHHH
Confidence            99999988887666554442  22221   1222334455666677777655332  22335566677778888899999


Q ss_pred             HHHHHHhC-CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHh
Q 040394          587 ALEFMENM-PIEPD-VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYAS  646 (691)
Q Consensus       587 A~~~~~~~-~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~  646 (691)
                      |.+.+.+. ...|+ ..+|..+...+...|++++|.+.++++++++|++..+|..|+..+.-
T Consensus       261 a~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~ldP~~~~y~~~L~~~~~~  322 (334)
T d1dcea1         261 SCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYLDDLRSKFLL  322 (334)
T ss_dssp             HHHHHHHHCTTCHHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCcccHHHHHHHHHHHhH
Confidence            99988887 45554 45788888999999999999999999999999999999988777654

>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=98.93  E-value=9.8e-09  Score=95.29  Aligned_cols=200  Identities=9%  Similarity=-0.104  Sum_probs=137.4

Q ss_pred             HHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-CHhHHHHHHHHH
Q 040394          431 VTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--K-NTVTWSAMIGGY  507 (691)
Q Consensus       431 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~li~~~  507 (691)
                      .++..+..++.+.|+++.|...|++..+..  |.++.++..+..+|.+.|++++|...|++..+  | +..+|..+...|
T Consensus        38 ~~~~~~G~~y~~~g~~~~A~~~~~~al~l~--p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~  115 (259)
T d1xnfa_          38 QLLYERGVLYDSLGLRALARNDFSQALAIR--PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIAL  115 (259)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHhhccC--CCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHHhhhhhhHHHHHHHH
Confidence            466677788999999999999999999988  78899999999999999999999999998874  3 566888899999


Q ss_pred             hcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCCh---
Q 040394          508 GMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRL---  584 (691)
Q Consensus       508 ~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~---  584 (691)
                      ...|++++|...+++..+.. +.+......+..++.+.+..+.+..+.... ..  ..++...++ ++..+......   
T Consensus       116 ~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~--~~~~~~~~~-~~~~~~~~~~~~~~  190 (259)
T d1xnfa_         116 YYGGRDKLAQDDLLAFYQDD-PNDPFRSLWLYLAEQKLDEKQAKEVLKQHF-EK--SDKEQWGWN-IVEFYLGNISEQTL  190 (259)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCHHHHHHHHHHHH-HH--SCCCSTHHH-HHHHHTTSSCHHHH
T ss_pred             HHHhhHHHHHHHHHHHHhhc-cccHHHHHHHHHHHHHhhhHHHHHHHHHHh-hc--cchhhhhhh-HHHHHHHHHHHHHH
Confidence            99999999999999998853 223333333333445555555555554444 22  222222222 22222222222   


Q ss_pred             -HHHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhH
Q 040394          585 -EEALEFMENM-PIEPD-VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYY  637 (691)
Q Consensus       585 -~~A~~~~~~~-~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~  637 (691)
                       +.+...+... ...|+ ..+|..+...+...|++++|...++++++.+|++...|
T Consensus       191 ~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~  246 (259)
T d1xnfa_         191 MERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNVHNFVEH  246 (259)
T ss_dssp             HHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCTTCHHH
T ss_pred             HHHHHHHHHHhhhcCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHH
Confidence             2222221111 12232 24667788888899999999999999999999865444

>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=98.92  E-value=1e-08  Score=95.23  Aligned_cols=214  Identities=9%  Similarity=-0.039  Sum_probs=148.1

Q ss_pred             HHHHHHHHHHHHHcCCC--CCchhHHHHHHHHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHHH
Q 040394          446 VQVGSSLHAYSTKQGLL--SSNVYVGTALLNFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLALF  520 (691)
Q Consensus       446 ~~~a~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~~  520 (691)
                      .+.+..-+++.......  +....++..+...|.+.|++++|...|++..+   .+..+|+.+..+|.+.|++++|+..|
T Consensus        15 ~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~~~~a~~~lg~~~~~~g~~~~A~~~~   94 (259)
T d1xnfa_          15 QEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAF   94 (259)
T ss_dssp             HHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccCCCCHHHHhhhchHHHHHHHHHHhhhhh
Confidence            34455555555543310  11334666778899999999999999998874   47889999999999999999999999


Q ss_pred             HHHHHCCCCCC-HHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCC
Q 040394          521 SDMLNEEVQPN-EVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIE  597 (691)
Q Consensus       521 ~~m~~~g~~p~-~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~  597 (691)
                      ++..+.  .|+ ..++..+..++...|++++|.+.|+...+.   .|+ ......+...+.+.+..+.+..+.... ...
T Consensus        95 ~~al~~--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  169 (259)
T d1xnfa_          95 DSVLEL--DPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD---DPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSD  169 (259)
T ss_dssp             HHHHHH--CTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSC
T ss_pred             hHHHHH--HhhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhh---ccccHHHHHHHHHHHHHhhhHHHHHHHHHHhhccc
Confidence            999985  444 467777888899999999999999987544   454 334334444555556555554444433 122


Q ss_pred             CCHHHHHHHHHHHH----hcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          598 PDVSLFGAFLHGCG----LYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       598 p~~~~~~~l~~~~~----~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      ++...+. ++..+.    ..+..+.+...+.......|+....+..++.+|...|++++|.+.+++.++..+
T Consensus       170 ~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p  240 (259)
T d1xnfa_         170 KEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNV  240 (259)
T ss_dssp             CCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCC
T ss_pred             hhhhhhh-HHHHHHHHHHHHHHHHHHHHHHHHhhhcCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCC
Confidence            2222222 222222    223344445555555556777778889999999999999999999999987654

>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=98.91  E-value=8.5e-08  Score=91.21  Aligned_cols=187  Identities=8%  Similarity=0.063  Sum_probs=142.1

Q ss_pred             CcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-C-HhHHHHHHHHHhcCCChHHHHHH
Q 040394          444 GAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--K-N-TVTWSAMIGGYGMQGDGGGSLAL  519 (691)
Q Consensus       444 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~-~~~~~~li~~~~~~~~~~~A~~~  519 (691)
                      +..+.+..+++...+... |.+...+...+..+.+.|+++.|..+|+.+.+  | + ...|...+..+.+.|+.+.|.++
T Consensus        78 ~~~~~a~~i~~ral~~~~-p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i  156 (308)
T d2onda1          78 LFSDEAANIYERAISTLL-KKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMI  156 (308)
T ss_dssp             HHHHHHHHHHHHHHTTTT-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHH
Confidence            345788889988887654 67777888888889999999999999998764  2 2 34688888888899999999999


Q ss_pred             HHHHHHCCCCCCHHHHHHHHH-HhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHHHHHHHhC----
Q 040394          520 FSDMLNEEVQPNEVIFTTILS-ACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEALEFMENM----  594 (691)
Q Consensus       520 ~~~m~~~g~~p~~~~~~~ll~-~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~~----  594 (691)
                      |+++.+.+ +.+...|..... -+...|+.+.|..+|+.+.+.  .+.+...|...++.+.+.|+.+.|..+|++.    
T Consensus       157 ~~~al~~~-~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~--~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~  233 (308)
T d2onda1         157 FKKAREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKK--YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSG  233 (308)
T ss_dssp             HHHHHTST-TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH--HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSS
T ss_pred             HHHHHHhC-CCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh--hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC
Confidence            99988764 223333433332 234568899999999988654  2333677888888889999999999999886    


Q ss_pred             CCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040394          595 PIEPD--VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKA  634 (691)
Q Consensus       595 ~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~  634 (691)
                      +.+|+  ...|...+.--...|+.+.+..+.+++.+..|+..
T Consensus       234 ~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~~~~~~  275 (308)
T d2onda1         234 SLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAFREEY  275 (308)
T ss_dssp             SSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTT
T ss_pred             CCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcccc
Confidence            23433  34788777777788999999999999988888754

>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=98.90  E-value=1.2e-07  Score=90.17  Aligned_cols=211  Identities=8%  Similarity=-0.033  Sum_probs=158.2

Q ss_pred             HHHHHHHHHHHcCCCCCchhHHHHHHHHHH--------------hcCCHHHHHHHHHhccc----CCHhHHHHHHHHHhc
Q 040394          448 VGSSLHAYSTKQGLLSSNVYVGTALLNFYA--------------KCGDAQSARMVFDAMRE----KNTVTWSAMIGGYGM  509 (691)
Q Consensus       448 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~--------------~~g~~~~A~~~~~~~~~----~~~~~~~~li~~~~~  509 (691)
                      .+..+|+++....  +.++..+...+..+.              ..+..++|..+|++..+    .+...|...+..+.+
T Consensus        34 Rv~~vyerAl~~~--~~~~~lW~~y~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~  111 (308)
T d2onda1          34 RVMFAYEQCLLVL--GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEES  111 (308)
T ss_dssp             HHHHHHHHHHHHH--TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCchHHHHHHHhhcccchHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHh
Confidence            3445566666554  555565555444332              22345788889988653    356678888999999


Q ss_pred             CCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHH-HHhcCChHHH
Q 040394          510 QGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDL-LARAGRLEEA  587 (691)
Q Consensus       510 ~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~-~~~~g~~~~A  587 (691)
                      .|+.+.|..+|+++.+.........|..++..+.+.|+.+.|.++|+...+   ..|+ ...|...... +...|+.+.|
T Consensus       112 ~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~---~~~~~~~~~~~~a~~e~~~~~~~~~a  188 (308)
T d2onda1         112 RMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARE---DARTRHHVYVTAALMEYYCSKDKSVA  188 (308)
T ss_dssp             TTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHT---STTCCTHHHHHHHHHHHHTSCCHHHH
T ss_pred             cccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHH---hCCCcHHHHHHHHHHHHHhccCHHHH
Confidence            999999999999999853333345788889999999999999999998753   3443 4444444443 3346899999


Q ss_pred             HHHHHhC--CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc----hhHHHHHHHHHhCCCcHHHHHHHHHHH
Q 040394          588 LEFMENM--PIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKA----CYYVLVSNLYASDGRWIRVNQVRELMK  661 (691)
Q Consensus       588 ~~~~~~~--~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~  661 (691)
                      ..+|+.+  ..+.+...|...+..+...|+++.|+.+|++++...|.++    ..|......-...|+.+.+..+.+++.
T Consensus       189 ~~i~e~~l~~~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~  268 (308)
T d2onda1         189 FKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRF  268 (308)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            9999998  3445677899999999999999999999999999776544    367777787788899999999999987


Q ss_pred             hC
Q 040394          662 QR  663 (691)
Q Consensus       662 ~~  663 (691)
                      +.
T Consensus       269 ~~  270 (308)
T d2onda1         269 TA  270 (308)
T ss_dssp             HH
T ss_pred             HH
Confidence            64

>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=98.86  E-value=6.2e-08  Score=92.22  Aligned_cols=121  Identities=9%  Similarity=-0.081  Sum_probs=50.9

Q ss_pred             HHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcC-ChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHH
Q 040394          356 ASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCH-VIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLV  434 (691)
Q Consensus       356 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~  434 (691)
                      .+.+.+..++|...++.+++..|.+..+|+....++...| ++++|+..++...+.+               +-+..+|.
T Consensus        52 ~~~~~e~~~~Al~~~~~ai~lnP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~---------------p~~~~a~~  116 (315)
T d2h6fa1          52 VLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ---------------PKNYQVWH  116 (315)
T ss_dssp             HHHHTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC---------------TTCHHHHH
T ss_pred             HHHhCCchHHHHHHHHHHHHHCCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH---------------HhhhhHHH
Confidence            3344444444444444444444444444444444444433 2444444444433211               11223333


Q ss_pred             HHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040394          435 SVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMR  493 (691)
Q Consensus       435 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  493 (691)
                      .+...+...|+.++|...++.+.+..  |.+...|..+...+.+.|++++|+..++.+.
T Consensus       117 ~~~~~~~~l~~~~eAl~~~~kal~~d--p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al  173 (315)
T d2h6fa1         117 HRRVLVEWLRDPSQELEFIADILNQD--AKNYHAWQHRQWVIQEFKLWDNELQYVDQLL  173 (315)
T ss_dssp             HHHHHHHHHTCCTTHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHH
T ss_pred             HHhHHHHhhccHHHHHHHHhhhhhhh--hcchHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            33333344444444444444444433  3444444444444444444444444444433

>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=98.86  E-value=3.8e-08  Score=95.10  Aligned_cols=273  Identities=7%  Similarity=-0.114  Sum_probs=183.0

Q ss_pred             CChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHh
Q 040394          160 RDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMRE  239 (691)
Q Consensus       160 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  239 (691)
                      +..++|..+++..++..|.+...|+..-..+...+..                     ...+...|++++|+.+++...+
T Consensus        43 ~~~~~al~~~~~~l~~~P~~~~a~~~r~~~l~~l~~~---------------------~~~~~~~~~~~~al~~~~~~l~  101 (334)
T d1dcea1          43 ELDESVLELTSQILGANPDFATLWNCRREVLQHLETE---------------------KSPEESAALVKAELGFLESCLR  101 (334)
T ss_dssp             CCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTT---------------------SCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhhh---------------------cchHHHHHHHHHHHHHHHHHHH
Confidence            3446777777777777766666665544333221111                     0122344556677777777765


Q ss_pred             CCCCCChhhHHHHHHHHHccC--ChhhHHHHHHHHHHHCCCCchHHH-HHHHHHHHhcCCHHHHHHHHHhcCC---CChh
Q 040394          240 GFVEGNQITLGSLVTACAKLR--ALHQGKWLHGYILKIGIEINSHLV-TALLDMYVKCGNIRDARSVFDELCS---IDLV  313 (691)
Q Consensus       240 ~~~~p~~~t~~~li~~~~~~~--~~~~a~~~~~~~~~~g~~~~~~~~-~~li~~~~~~g~~~~A~~~~~~~~~---~~~~  313 (691)
                      ... -+...+..+..++...+  +++++...+..+.+... ++...+ ......+...+..++|+..++....   .+..
T Consensus       102 ~~p-k~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~-~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p~~~~  179 (334)
T d1dcea1         102 VNP-KSYGTWHHRCWLLSRLPEPNWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYS  179 (334)
T ss_dssp             HCT-TCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHH
T ss_pred             hCC-CcHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhCc-hhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCCCCHH
Confidence            432 14444555555555444  46777777777777643 234443 3445667778999999999998844   3566


Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHh
Q 040394          314 SWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAK  393 (691)
Q Consensus       314 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~  393 (691)
                      +|+.+...+.+.|++++|...+......  .|+.   ......+...+..+++...+.......+.....+..+...+..
T Consensus       180 a~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~---~~~~~~~~~l~~~~~a~~~~~~~l~~~~~~~~~~~~l~~~~~~  254 (334)
T d1dcea1         180 SWHYRSCLLPQLHPQPDSGPQGRLPENV--LLKE---LELVQNAFFTDPNDQSAWFYHRWLLGRAEPLFRCELSVEKSTV  254 (334)
T ss_dssp             HHHHHHHHHHHHSCCCCSSSCCSSCHHH--HHHH---HHHHHHHHHHCSSCSHHHHHHHHHHSCCCCSSSCCCCHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHhHHh--HHHH---HHHHHHHHHhcchhHHHHHHHHHHHhCcchhhHHHHHHHHHHH
Confidence            8888889999999998887665544332  2222   2233445556777888888888888887766667777888888


Q ss_pred             cCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHH
Q 040394          394 CHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALL  473 (691)
Q Consensus       394 ~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~  473 (691)
                      .|+.++|...+.+..+.+               +.+..++..+...+...|+.++|...++...+..  |.....|..+.
T Consensus       255 ~~~~~~a~~~~~~~~~~~---------------p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~ld--P~~~~y~~~L~  317 (334)
T d1dcea1         255 LQSELESCKELQELEPEN---------------KWCLLTIILLMRALDPLLYEKETLQYFSTLKAVD--PMRAAYLDDLR  317 (334)
T ss_dssp             HHHHHHHHHHHHHHCTTC---------------HHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHHC--GGGHHHHHHHH
T ss_pred             HhhHHHHHHHHHHHHhhC---------------chHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC--cccHHHHHHHH
Confidence            899999999998877652               2244567778888889999999999999998887  66677777776


Q ss_pred             HHHH
Q 040394          474 NFYA  477 (691)
Q Consensus       474 ~~~~  477 (691)
                      ..+.
T Consensus       318 ~~~~  321 (334)
T d1dcea1         318 SKFL  321 (334)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            5555

>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=98.58  E-value=1.6e-07  Score=82.96  Aligned_cols=92  Identities=7%  Similarity=-0.126  Sum_probs=43.7

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhC-CCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCC
Q 040394          571 YVCMVDLLARAGRLEEALEFMENM-PIE-PDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDG  648 (691)
Q Consensus       571 ~~~li~~~~~~g~~~~A~~~~~~~-~~~-p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g  648 (691)
                      +...+..|.+.|++++|++.|++. ... .+...|..+..+|.+.|++++|+..++++++++|+++..|..++.+|...|
T Consensus         7 l~~~Gn~~~~~g~~~~Ai~~~~kal~~~p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~~~~a~~~lg~~~~~l~   86 (201)
T d2c2la1           7 LKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQLEME   86 (201)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCCcHHHHHHHHHHHHHCC
Confidence            333444444444444444444443 212 233344444444555555555555555555555555555555555555555


Q ss_pred             CcHHHHHHHHHHHh
Q 040394          649 RWIRVNQVRELMKQ  662 (691)
Q Consensus       649 ~~~~A~~~~~~~~~  662 (691)
                      ++++|...+++..+
T Consensus        87 ~~~~A~~~~~~al~  100 (201)
T d2c2la1          87 SYDEAIANLQRAYS  100 (201)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH
Confidence            55555555544443

>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=98.57  E-value=2.6e-07  Score=72.88  Aligned_cols=89  Identities=12%  Similarity=0.052  Sum_probs=58.3

Q ss_pred             HHHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHH
Q 040394          575 VDLLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIR  652 (691)
Q Consensus       575 i~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  652 (691)
                      ...+.+.|++++|+..|++. . .+.+...|..+..++...|++++|+..++++++++|+++..|..++.++...|++++
T Consensus        10 g~~~~~~g~~~eAi~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~g~~~~~~~~~~~   89 (117)
T d1elwa_          10 GNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRFEE   89 (117)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhcCCcchhhhhcccccccccccccccchhhhhHHHhccchhhHHHHHHHHHHHccCHHH
Confidence            44556666666666666665 2 233445666666666667777777777777777777777777777777777777777


Q ss_pred             HHHHHHHHHhC
Q 040394          653 VNQVRELMKQR  663 (691)
Q Consensus       653 A~~~~~~~~~~  663 (691)
                      |+..+++.++.
T Consensus        90 A~~~~~~a~~~  100 (117)
T d1elwa_          90 AKRTYEEGLKH  100 (117)
T ss_dssp             HHHHHHHHHTT
T ss_pred             HHHHHHHHHHh
Confidence            77777666654

>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=98.53  E-value=1.4e-07  Score=73.80  Aligned_cols=89  Identities=10%  Similarity=-0.034  Sum_probs=81.0

Q ss_pred             HHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCc
Q 040394          573 CMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRW  650 (691)
Q Consensus       573 ~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~  650 (691)
                      .+...+.+.|++++|+..+++. ...| +..+|..+..++.+.|++++|+..++++++++|+++.++..++.+|...|++
T Consensus        21 ~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~la~~y~~~g~~  100 (112)
T d1hxia_          21 EEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNA  100 (112)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHHHhhhcccccccchhhhhhhhhhhhhhhHHHhhcccccccccccccccchHHHHHHHHHCCCH
Confidence            4567788999999999999998 4445 5779999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 040394          651 IRVNQVRELMK  661 (691)
Q Consensus       651 ~~A~~~~~~~~  661 (691)
                      ++|.+.+++.+
T Consensus       101 ~~A~~~l~~~l  111 (112)
T d1hxia_         101 NAALASLRAWL  111 (112)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            99999998864

>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=98.48  E-value=8.1e-07  Score=69.97  Aligned_cols=103  Identities=13%  Similarity=0.097  Sum_probs=85.5

Q ss_pred             HHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCH
Q 040394          540 SACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRF  616 (691)
Q Consensus       540 ~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~  616 (691)
                      ..+...|++++|+..|++.++.   .|+ ...|..+..+|...|++++|++.+++. . .+.+...|..+..++...|++
T Consensus        11 ~~~~~~g~~~eAi~~~~~al~~---~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~g~~~~~~~~~   87 (117)
T d1elwa_          11 NKALSVGNIDDALQCYSEAIKL---DPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRF   87 (117)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhc---CCcchhhhhcccccccccccccccchhhhhHHHhccchhhHHHHHHHHHHHccCH
Confidence            4566778888888888877543   555 677888888999999999999998887 3 344677899999999999999


Q ss_pred             HHHHHHHHHHHhcCCCCchhHHHHHHHHH
Q 040394          617 DLGEVMIKKMLELHPDKACYYVLVSNLYA  645 (691)
Q Consensus       617 ~~A~~~~~~~~~~~p~~~~~~~~l~~~~~  645 (691)
                      ++|+..++++++..|+++.++..+..+-.
T Consensus        88 ~~A~~~~~~a~~~~p~~~~~~~~l~~l~~  116 (117)
T d1elwa_          88 EEAKRTYEEGLKHEANNPQLKEGLQNMEA  116 (117)
T ss_dssp             HHHHHHHHHHHTTCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHhC
Confidence            99999999999999999998888876643

>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=98.47  E-value=1.8e-06  Score=74.94  Aligned_cols=123  Identities=12%  Similarity=0.023  Sum_probs=89.3

Q ss_pred             HHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcC
Q 040394          504 IGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAG  582 (691)
Q Consensus       504 i~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g  582 (691)
                      ...+...|+++.|++.|+++    .+|+..++..+-.++...|++++|++.|++.++   +.|+ ...|..+..+|.+.|
T Consensus        12 g~~~~~~~d~~~Al~~~~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~---ldp~~~~a~~~~g~~~~~~g   84 (192)
T d1hh8a_          12 GVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSIN---RDKHLAVAYFQRGMLYYQTE   84 (192)
T ss_dssp             HHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHCCCHHHHHHHHHhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHH---HhhhhhhhHHHHHHHHHhhc
Confidence            55667788888888888754    356777777777788888888888888886643   4565 667778888888888


Q ss_pred             ChHHHHHHHHhC--CCCC---------------C-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC
Q 040394          583 RLEEALEFMENM--PIEP---------------D-VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK  633 (691)
Q Consensus       583 ~~~~A~~~~~~~--~~~p---------------~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~  633 (691)
                      ++++|++.|++.  -.++               + ..++..+..++...|++++|.+.++++.+..|+.
T Consensus        85 ~~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~~  153 (192)
T d1hh8a_          85 KYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEP  153 (192)
T ss_dssp             CHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSG
T ss_pred             cHHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCc
Confidence            888888777775  1111               1 1345566677778888888888888888888873

>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=98.45  E-value=2.9e-06  Score=79.43  Aligned_cols=194  Identities=9%  Similarity=-0.011  Sum_probs=126.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhccc-----CC----HhHHHHHHHHHhcCCChHHHHHHHHHHHHC----CCC-CCHH
Q 040394          468 VGTALLNFYAKCGDAQSARMVFDAMRE-----KN----TVTWSAMIGGYGMQGDGGGSLALFSDMLNE----EVQ-PNEV  533 (691)
Q Consensus       468 ~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~----~~~~~~li~~~~~~~~~~~A~~~~~~m~~~----g~~-p~~~  533 (691)
                      .|......|...|++++|...|.+..+     .+    ..+|..+..+|.+.|++++|++.+++..+.    |-. ....
T Consensus        39 ~y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~  118 (290)
T d1qqea_          39 LCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGAN  118 (290)
T ss_dssp             HHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHH
Confidence            355566778888889998888887653     12    347888888999999999999988876652    111 1123


Q ss_pred             HHHHHHHHhc-ccCCHHHHHHHHHHchhhc---CCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-------CH
Q 040394          534 IFTTILSACS-HTGMVGEGWKCFYSMCRDF---KFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-------DV  600 (691)
Q Consensus       534 ~~~~ll~~~~-~~g~~~~A~~~~~~m~~~~---~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-------~~  600 (691)
                      ++..+...|. ..|++++|.+.+++...-.   +..+. ..++..+...+...|++++|++.+++. ...|       ..
T Consensus       119 ~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~  198 (290)
T d1qqea_         119 FKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSL  198 (290)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGH
T ss_pred             HHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhH
Confidence            4555555563 4699999999988764321   22222 446778889999999999999999887 1111       11


Q ss_pred             -HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchh-----HHHHHHHHHh--CCCcHHHHHHHHHHH
Q 040394          601 -SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACY-----YVLVSNLYAS--DGRWIRVNQVRELMK  661 (691)
Q Consensus       601 -~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~-----~~~l~~~~~~--~g~~~~A~~~~~~~~  661 (691)
                       ..+...+..+...|+++.|...++++.+.+|..+..     ...++.++..  .+.+++|+..|+++.
T Consensus       199 ~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~~~  267 (290)
T d1qqea_         199 KDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFM  267 (290)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSS
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHh
Confidence             123445556678899999999999999988764432     3344455444  345788888775443

>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=98.44  E-value=5e-06  Score=77.79  Aligned_cols=98  Identities=8%  Similarity=-0.039  Sum_probs=50.1

Q ss_pred             HHHHHHHHHHhcCCchhHHHHHHHhhHCCCC-----CcH-HHHHHHHHHHhcCCChhhHHHHHHHHHHhCCC--c---hh
Q 040394          314 SWTAMIVGYTQSGYPDKALKLFTDKKWADFF-----PNH-VTIASVLSASAQLGNLNMGRMVHSLGIRLGLE--D---YT  382 (691)
Q Consensus       314 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~-----p~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~--~---~~  382 (691)
                      ++..+...+...|++++|++.|++.......     ... ..+...+..+...|+++.|...++...+..+.  +   ..
T Consensus       160 ~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~  239 (290)
T d1qqea_         160 CFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESN  239 (290)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HH
T ss_pred             HHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHH
Confidence            3455555566666666666666655443111     111 11222333444556666666666666555443  1   22


Q ss_pred             HHHHHHHHhHh--cCChHHHHHHHHhCCCCC
Q 040394          383 VINALVDMYAK--CHVIADARYIFETTSEKD  411 (691)
Q Consensus       383 ~~~~l~~~~~~--~g~~~~a~~~~~~~~~~~  411 (691)
                      ....++.++..  .+.+++|+..|+++.+.|
T Consensus       240 ~l~~l~~a~~~~d~e~~~eai~~y~~~~~lD  270 (290)
T d1qqea_         240 FLKSLIDAVNEGDSEQLSEHCKEFDNFMRLD  270 (290)
T ss_dssp             HHHHHHHHHHTTCTTTHHHHHHHHTTSSCCC
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHHhhcC
Confidence            33455555554  345788888888776543

>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=98.42  E-value=4.1e-06  Score=72.59  Aligned_cols=148  Identities=12%  Similarity=0.016  Sum_probs=106.5

Q ss_pred             HHHHHhcCCHHHHHHHHHhcccCCHhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHH
Q 040394          473 LNFYAKCGDAQSARMVFDAMREKNTVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGW  552 (691)
Q Consensus       473 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~  552 (691)
                      ...+...|+++.|++.|+++..++..+|..+..+|...|++++|++.|++.++.. +-+...|..+-.++.+.|++++|.
T Consensus        12 g~~~~~~~d~~~Al~~~~~i~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~~g~~~~A~   90 (192)
T d1hh8a_          12 GVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYDLAI   90 (192)
T ss_dssp             HHHHHHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHhhccHHHHH
Confidence            3456778888999988888888888888888888888999999999998888853 334567777777888889999998


Q ss_pred             HHHHHchhhcC-----------CC--CC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCCHH
Q 040394          553 KCFYSMCRDFK-----------FV--PS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEPDVSLFGAFLHGCGLYSRFD  617 (691)
Q Consensus       553 ~~~~~m~~~~~-----------~~--p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~~~~~~l~~~~~~~g~~~  617 (691)
                      +.|++......           ..  ++ ..++..+..++.+.|++++|.+.++.. ...|+.           ..+..+
T Consensus        91 ~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~~-----------~~~~~~  159 (192)
T d1hh8a_          91 KDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEP-----------RHSKID  159 (192)
T ss_dssp             HHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSG-----------GGGHHH
T ss_pred             HHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCc-----------chHHHH
Confidence            88887643211           11  11 245567788899999999999999887 556653           333455


Q ss_pred             HHHHHHHHHHhcCCC
Q 040394          618 LGEVMIKKMLELHPD  632 (691)
Q Consensus       618 ~A~~~~~~~~~~~p~  632 (691)
                      .|+..+.+.....|.
T Consensus       160 ~Al~~~~~~~~~~~~  174 (192)
T d1hh8a_         160 KAMECVWKQKLYEPV  174 (192)
T ss_dssp             HHHHHHHTTCCCCCC
T ss_pred             HHHHHHHhhhhCCcc
Confidence            666655554444443

>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=98.37  E-value=1.5e-06  Score=72.93  Aligned_cols=115  Identities=9%  Similarity=-0.036  Sum_probs=92.2

Q ss_pred             HHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCC
Q 040394          539 LSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSR  615 (691)
Q Consensus       539 l~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~  615 (691)
                      -..|.+.|++++|+..|++..+   +.|+ ...|..+..+|...|++++|++.|++. ...| +..+|..++.++...|+
T Consensus        17 gn~~~~~~~y~~A~~~~~~al~---~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~~~~a~~~~g~~~~~~g~   93 (159)
T d1a17a_          17 ANDYFKAKDYENAIKFYSQAIE---LNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALGK   93 (159)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH---HSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHcCCHHHHHHHhhhccc---cchhhhhhhhhhHHHHHhccccchHHHHHHHHHHHcccchHHHHHHHHHHHHcCC
Confidence            3456788899999999987754   3565 778888899999999999999999988 4444 55789999999999999


Q ss_pred             HHHHHHHHHHHHhcCCCCchhHHHHHHHH--HhCCCcHHHHHH
Q 040394          616 FDLGEVMIKKMLELHPDKACYYVLVSNLY--ASDGRWIRVNQV  656 (691)
Q Consensus       616 ~~~A~~~~~~~~~~~p~~~~~~~~l~~~~--~~~g~~~~A~~~  656 (691)
                      +++|...+++++.+.|+++..+..+..+.  ...+.+++|...
T Consensus        94 ~~eA~~~~~~a~~~~p~~~~~~~~l~~~~~~~~~~~~~~a~~~  136 (159)
T d1a17a_          94 FRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAG  136 (159)
T ss_dssp             HHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            99999999999999999998887776653  344556666544

>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=98.37  E-value=1.3e-06  Score=73.36  Aligned_cols=92  Identities=12%  Similarity=0.077  Sum_probs=83.2

Q ss_pred             HHHHHHHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCc
Q 040394          573 CMVDLLARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRW  650 (691)
Q Consensus       573 ~li~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~  650 (691)
                      .....|.+.|++++|++.|++. ...| +...|..+..+|...|++++|...++++++++|++..++..++.+|...|++
T Consensus        15 ~~gn~~~~~~~y~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~~~~a~~~~g~~~~~~g~~   94 (159)
T d1a17a_          15 TQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALGKF   94 (159)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHcCCHHHHHHHhhhccccchhhhhhhhhhHHHHHhccccchHHHHHHHHHHHcccchHHHHHHHHHHHHcCCH
Confidence            3456788999999999999998 4444 5678999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhCC
Q 040394          651 IRVNQVRELMKQRG  664 (691)
Q Consensus       651 ~~A~~~~~~~~~~g  664 (691)
                      ++|.+.+++..+..
T Consensus        95 ~eA~~~~~~a~~~~  108 (159)
T d1a17a_          95 RAALRDYETVVKVK  108 (159)
T ss_dssp             HHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHcC
Confidence            99999999998754

>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=98.25  E-value=1.5e-06  Score=76.45  Aligned_cols=94  Identities=6%  Similarity=-0.052  Sum_probs=52.3

Q ss_pred             HhHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHH
Q 040394          497 TVTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMV  575 (691)
Q Consensus       497 ~~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li  575 (691)
                      ...+......|.+.|++++|+..|++.++.. +-+...|..+..+|.+.|++++|+..|+..+   .+.|+ ...|..+.
T Consensus         4 a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al---~l~p~~~~a~~~lg   79 (201)
T d2c2la1           4 AQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRAL---ELDGQSVKAHFFLG   79 (201)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHT---TSCTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHH---HhCCCcHHHHHHHH
Confidence            3344445555666666666666666665532 2334445555556666666666666666442   34554 44555566


Q ss_pred             HHHHhcCChHHHHHHHHhC
Q 040394          576 DLLARAGRLEEALEFMENM  594 (691)
Q Consensus       576 ~~~~~~g~~~~A~~~~~~~  594 (691)
                      .+|.+.|++++|+..|++.
T Consensus        80 ~~~~~l~~~~~A~~~~~~a   98 (201)
T d2c2la1          80 QCQLEMESYDEAIANLQRA   98 (201)
T ss_dssp             HHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHH
Confidence            6666666666666655554

>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=98.24  E-value=2.6e-06  Score=67.18  Aligned_cols=105  Identities=11%  Similarity=0.006  Sum_probs=78.2

Q ss_pred             HHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCCh---HHHHHHHHhC-CCCCCH---HHHHHHHH
Q 040394          537 TILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRL---EEALEFMENM-PIEPDV---SLFGAFLH  608 (691)
Q Consensus       537 ~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~---~~A~~~~~~~-~~~p~~---~~~~~l~~  608 (691)
                      .++..+...+++++|.+.|++...   ..|+ ..++..+..++.+.++.   ++|++++++. ...|+.   .+|..+..
T Consensus         4 ~l~n~~~~~~~l~~Ae~~Y~~aL~---~~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~   80 (122)
T d1nzna_           4 AVLNELVSVEDLLKFEKKFQSEKA---AGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAV   80 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH---HSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHHh---hCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHH
Confidence            456666777888888888886643   3454 67777788888765544   4688888886 444433   36778888


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHH
Q 040394          609 GCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLY  644 (691)
Q Consensus       609 ~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~  644 (691)
                      +|.+.|++++|+..|+++++++|++......+..+.
T Consensus        81 ~y~~~g~~~~A~~~~~~aL~~~P~~~~A~~l~~~I~  116 (122)
T d1nzna_          81 GNYRLKEYEKALKYVRGLLQTEPQNNQAKELERLID  116 (122)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHhhhHHHHHHHHHHHHhCcCCHHHHHHHHHHH
Confidence            999999999999999999999999887776665443

>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=98.22  E-value=1e-05  Score=68.38  Aligned_cols=133  Identities=11%  Similarity=0.041  Sum_probs=94.1

Q ss_pred             HHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHH
Q 040394          499 TWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLL  578 (691)
Q Consensus       499 ~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~  578 (691)
                      .+......+.+.|++++|+..|++.++.  .|...            +..+.-......+        ...+|+.+..+|
T Consensus        15 ~l~~~G~~~~~~~~~~~Ai~~y~~al~~--~~~~~------------~~~~~~~~~~~~~--------~~~~~~nla~~y   72 (170)
T d1p5qa1          15 IVKERGTVYFKEGKYKQALLQYKKIVSW--LEYES------------SFSNEEAQKAQAL--------RLASHLNLAMCH   72 (170)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHH--TTTCC------------CCCSHHHHHHHHH--------HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH--hhhcc------------ccchHHHhhhchh--------HHHHHHHHHHHH
Confidence            4445566777778888888887777652  11100            0000000111111        023567788889


Q ss_pred             HhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHH
Q 040394          579 ARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRV  653 (691)
Q Consensus       579 ~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A  653 (691)
                      .+.|++++|+..+++. ...| +..+|..+..++...|++++|...|+++++++|+++.+...+..+..+.+...+.
T Consensus        73 ~k~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~P~n~~~~~~l~~~~~~~~~~~~~  149 (170)
T d1p5qa1          73 LKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIRRQLAR  149 (170)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhhhcccccchhhhhhhccccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999887 4445 6778999999999999999999999999999999999999998887766655544

>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=98.19  E-value=0.00037  Score=63.52  Aligned_cols=229  Identities=10%  Similarity=-0.045  Sum_probs=161.3

Q ss_pred             CHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHh----cCCHHHHHHHHHhcccC-CHhHHHHH
Q 040394          429 DAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAK----CGDAQSARMVFDAMREK-NTVTWSAM  503 (691)
Q Consensus       429 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~-~~~~~~~l  503 (691)
                      |+..+..|...+...++.++|.+.|++..+.|.    ...+..|...|..    ..+...|...+....++ +......+
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g~----~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~~~~a~~~l   76 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLKE----NSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYSNGCHLL   76 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC----HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCC----HHHHHHHHHHHHcCCCcchhHHHHHHhhcccccccccchhhcc
Confidence            345666777777889999999999999988763    4455556677766    66899999999887765 44555555


Q ss_pred             HHHHh----cCCChHHHHHHHHHHHHCCCCCCHHHHH-HHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHH
Q 040394          504 IGGYG----MQGDGGGSLALFSDMLNEEVQPNEVIFT-TILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLL  578 (691)
Q Consensus       504 i~~~~----~~~~~~~A~~~~~~m~~~g~~p~~~~~~-~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~  578 (691)
                      ...+.    ..++.+.|...++...+.|..+...... ..............+...+.... .   ..+...+..|...|
T Consensus        77 ~~~~~~~~~~~~~~~~a~~~~~~a~~~g~~~a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~-~---~~~~~~~~~L~~~~  152 (265)
T d1ouva_          77 GNLYYSGQGVSQNTNKALQYYSKACDLKYAEGCASLGGIYHDGKVVTRDFKKAVEYFTKAC-D---LNDGDGCTILGSLY  152 (265)
T ss_dssp             HHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHH-H---TTCHHHHHHHHHHH
T ss_pred             ccccccccccchhhHHHHHHHhhhhhhhhhhHHHhhcccccCCCcccchhHHHHHHhhhhh-c---ccccchhhhhhhhh
Confidence            44443    3567888999999998876433222211 11112234556777777777552 2   24456677777777


Q ss_pred             Hh----cCChHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHh----
Q 040394          579 AR----AGRLEEALEFMENMPIEPDVSLFGAFLHGCGL----YSRFDLGEVMIKKMLELHPDKACYYVLVSNLYAS----  646 (691)
Q Consensus       579 ~~----~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~----  646 (691)
                      ..    ..+...+..+++...-..+..+...+...+..    ..++++|...|+++.+..  ++..+..|+.+|.+    
T Consensus       153 ~~~~~~~~~~~~~~~~~~~a~~~g~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g--~~~a~~~LG~~y~~G~g~  230 (265)
T d1ouva_         153 DAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE--NGGGCFNLGAMQYNGEGV  230 (265)
T ss_dssp             HHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT--CHHHHHHHHHHHHTTSSS
T ss_pred             ccCCCcccccccchhhhhccccccccccccchhhhcccCcccccchhhhhhhHhhhhccc--CHHHHHHHHHHHHcCCCC
Confidence            75    45677788887776334466777777766665    579999999999998874  56788889999886    


Q ss_pred             CCCcHHHHHHHHHHHhCCCcc
Q 040394          647 DGRWIRVNQVRELMKQRGLSK  667 (691)
Q Consensus       647 ~g~~~~A~~~~~~~~~~g~~~  667 (691)
                      ..++++|.+++++..+.|..+
T Consensus       231 ~~n~~~A~~~~~kAa~~g~~~  251 (265)
T d1ouva_         231 TRNEKQAIENFKKGCKLGAKG  251 (265)
T ss_dssp             SCCSTTHHHHHHHHHHHTCHH
T ss_pred             ccCHHHHHHHHHHHHHCcCHH
Confidence            458999999999998888643

>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=98.16  E-value=9.4e-06  Score=68.62  Aligned_cols=64  Identities=9%  Similarity=-0.136  Sum_probs=59.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          601 SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       601 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      .+|+.+..+|.+.|++++|+..++++++++|+++.++..++.+|...|++++|...|++.++..
T Consensus        63 ~~~~nla~~y~k~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~  126 (170)
T d1p5qa1          63 ASHLNLAMCHLKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLY  126 (170)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhhhhcccccchhhhhhhccccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHhC
Confidence            3567788889999999999999999999999999999999999999999999999999998854

>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=98.12  E-value=3.6e-07  Score=92.97  Aligned_cols=209  Identities=7%  Similarity=-0.060  Sum_probs=110.4

Q ss_pred             HHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccCCHhHHH-HHHHHHhcCCChHHHHHHHHHHHHC
Q 040394          448 VGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMREKNTVTWS-AMIGGYGMQGDGGGSLALFSDMLNE  526 (691)
Q Consensus       448 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~-~li~~~~~~~~~~~A~~~~~~m~~~  526 (691)
                      +|.+.+++..+..  |.....+..+..+|...|++++|   |+++...|..... .-+....-...+..+.+.++...+.
T Consensus         4 eA~q~~~qA~~l~--p~~a~a~~~la~~~~~~~~l~ea---ye~~i~~dp~~a~~~~~e~~Lw~~~y~~~ie~~r~~~k~   78 (497)
T d1ya0a1           4 QSAQYLRQAEVLK--ADMTDSKLGPAEVWTSRQALQDL---YQKMLVTDLEYALDKKVEQDLWNHAFKNQITTLQGQAKN   78 (497)
T ss_dssp             HHHHHHHHHHHHH--GGGTCSSSCSSSSHHHHHHHHHH---HHHHHHHCHHHHHHHTHHHHHHHHHTHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHcC--CCCHHHHhhHHHHHHHHchHHHH---HHHHHHcChhhHHHHhHHHHHHHHHHHHHHHHHHHhccc
Confidence            4667777776654  44444555566667777777765   5554432221100 0011111111244566667766654


Q ss_pred             CCCCCHHHHHHHHHH--hcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC-CCCCCHHH
Q 040394          527 EVQPNEVIFTTILSA--CSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM-PIEPDVSL  602 (691)
Q Consensus       527 g~~p~~~~~~~ll~~--~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~-~~~p~~~~  602 (691)
                      ...++..-....+..  ....+.++.++..++   +.+++.|+ ...+..+...+.+.|+.++|...+++. ...| ..+
T Consensus        79 ~~~~~~~~~~~~~~~~l~~a~~~Y~~ai~~l~---~~~~l~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~-~~~  154 (497)
T d1ya0a1          79 RANPNRSEVQANLSLFLEAASGFYTQLLQELC---TVFNVDLPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSYIC-QHC  154 (497)
T ss_dssp             SSCTTTTHHHHHHHHHHHHHHHHHHHHHHHHT---C-------------------------------CCHHHHHHH-HHH
T ss_pred             ccCccHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHCCChhhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCCH-HHH
Confidence            434443322222221  223455666665555   34456665 556777888888888888887766554 1111 246


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Q 040394          603 FGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGL  665 (691)
Q Consensus       603 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~  665 (691)
                      +..++..+...|++++|+..|+++.++.|++...|..|+.++...|+..+|...|.+.+....
T Consensus       155 ~~~LG~l~~~~~~~~~A~~~y~~A~~l~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~~  217 (497)
T d1ya0a1         155 LVHLGDIARYRNQTSQAESYYRHAAQLVPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVKF  217 (497)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSSB
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCC
Confidence            777888889999999999999999999999999999999999999999999999988887543

>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=98.08  E-value=4.1e-06  Score=65.95  Aligned_cols=93  Identities=9%  Similarity=-0.028  Sum_probs=78.4

Q ss_pred             HHHHHHHHhcCChHHHHHHHHhC-CC-CCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhcCCCCc--hhHHHHHHHH
Q 040394          572 VCMVDLLARAGRLEEALEFMENM-PI-EPDVSLFGAFLHGCGLYS---RFDLGEVMIKKMLELHPDKA--CYYVLVSNLY  644 (691)
Q Consensus       572 ~~li~~~~~~g~~~~A~~~~~~~-~~-~p~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~~~~p~~~--~~~~~l~~~~  644 (691)
                      ..+++.+...+++++|.+.|++. .. +.+..++..+..++.+.+   ++++|+.+++++++.+|++.  .+++.++.+|
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y   82 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGN   82 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHH
Confidence            45778889999999999999998 33 446678888998887654   55679999999999887653  4789999999


Q ss_pred             HhCCCcHHHHHHHHHHHhCC
Q 040394          645 ASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       645 ~~~g~~~~A~~~~~~~~~~g  664 (691)
                      .+.|++++|++.++++++..
T Consensus        83 ~~~g~~~~A~~~~~~aL~~~  102 (122)
T d1nzna_          83 YRLKEYEKALKYVRGLLQTE  102 (122)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHhhhHHHHHHHHHHHHhC
Confidence            99999999999999999854

>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=98.03  E-value=1e-05  Score=64.62  Aligned_cols=93  Identities=8%  Similarity=0.074  Sum_probs=76.4

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhC-CCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCch-------hHHHHH
Q 040394          571 YVCMVDLLARAGRLEEALEFMENM-PIE-PDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKAC-------YYVLVS  641 (691)
Q Consensus       571 ~~~li~~~~~~g~~~~A~~~~~~~-~~~-p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~-------~~~~l~  641 (691)
                      +..+...+.+.|++++|++.|.+. ... .+...+..+..+|.+.|++++|+..++++++++|+++.       +|..++
T Consensus         7 ~k~~G~~~~~~~~y~~Ai~~y~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg   86 (128)
T d1elra_           7 EKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIG   86 (128)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHH
Confidence            345677888999999999999887 333 45678888999999999999999999999998888765       455667


Q ss_pred             HHHHhCCCcHHHHHHHHHHHhC
Q 040394          642 NLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       642 ~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                      .++...+++++|++.+++....
T Consensus        87 ~~~~~~~~~~~A~~~~~kal~~  108 (128)
T d1elra_          87 NSYFKEEKYKDAIHFYNKSLAE  108 (128)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCHHHHHHHHHHHHhc
Confidence            7788889999999999887653

>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=98.02  E-value=4.6e-05  Score=64.07  Aligned_cols=142  Identities=10%  Similarity=-0.027  Sum_probs=96.3

Q ss_pred             hHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHH
Q 040394          498 VTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDL  577 (691)
Q Consensus       498 ~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~  577 (691)
                      ..+......+.+.|++.+|+..|++.+..  .|.           ......+.. .....+        ...+|..+..+
T Consensus        16 ~~~~e~G~~~~~~~~~~~A~~~Y~~al~~--~~~-----------~~~~~~~~~-~~~~~~--------~~~~~~Nla~~   73 (168)
T d1kt1a1          16 AIVKEKGTVYFKGGKYVQAVIQYGKIVSW--LEM-----------EYGLSEKES-KASESF--------LLAAFLNLAMC   73 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--HTT-----------CCSCCHHHH-HHHHHH--------HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHH--HHH-----------hhccchhhh-hhcchh--------HHHHHHhHHHH
Confidence            34555666777777777777777765541  000           000000000 011111        02356677888


Q ss_pred             HHhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHH-HH
Q 040394          578 LARAGRLEEALEFMENM-P-IEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIR-VN  654 (691)
Q Consensus       578 ~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~-A~  654 (691)
                      |.+.|++++|++.+++. . .+.+..+|..+..++...|++++|...|+++++++|+++.+...+..+....+...+ ..
T Consensus        74 ~~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~P~n~~~~~~l~~~~~~~~~~~e~~k  153 (168)
T d1kt1a1          74 YLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQIFMCQKKAKEHNERDR  153 (168)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhhhcccchhhhhhhhhcccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhHHHHHH
Confidence            99999999999999987 3 345677899999999999999999999999999999999999888888766665543 44


Q ss_pred             HHHHHHH
Q 040394          655 QVRELMK  661 (691)
Q Consensus       655 ~~~~~~~  661 (691)
                      +.+..|-
T Consensus       154 k~~~~~f  160 (168)
T d1kt1a1         154 RTYANMF  160 (168)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5555554

>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=97.96  E-value=3.6e-05  Score=63.53  Aligned_cols=60  Identities=5%  Similarity=-0.148  Sum_probs=32.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHh
Q 040394          603 FGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQ  662 (691)
Q Consensus       603 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  662 (691)
                      |..+..+|.+.|++++|+..++++++.+|++...|..++.++...|++++|...|++.++
T Consensus        70 ~~Nla~~~~~l~~~~~Al~~~~~al~~~p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~  129 (153)
T d2fbna1          70 NLNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAAS  129 (153)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HhhHHHHHHHhcccchhhhhhhccccccchhhhhhHHhHHHHHHcCCHHHHHHHHHHHHH
Confidence            344444555555555555555555555555555555555555555555555555555544

>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=97.95  E-value=7.1e-05  Score=61.66  Aligned_cols=127  Identities=6%  Similarity=-0.045  Sum_probs=91.1

Q ss_pred             hHHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHH
Q 040394          498 VTWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDL  577 (691)
Q Consensus       498 ~~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~  577 (691)
                      ..+..-...+.+.|++.+|+..|++....  .|..           ..............        ....+|..+..+
T Consensus        18 ~~~~~~G~~~f~~~~y~~A~~~Y~~al~~--~~~~-----------~~~~~~~~~~~~~~--------~~~~~~~Nla~~   76 (153)
T d2fbna1          18 FDIKEEGNEFFKKNEINEAIVKYKEALDF--FIHT-----------EEWDDQILLDKKKN--------IEISCNLNLATC   76 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TTTC-----------TTCCCHHHHHHHHH--------HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhh--Ccch-----------hhhhhHHHHHhhhh--------HHHHHHhhHHHH
Confidence            35556677788888888888888887763  1110           00000000000010        112467778899


Q ss_pred             HHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHH
Q 040394          578 LARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYA  645 (691)
Q Consensus       578 ~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~  645 (691)
                      |.+.|++++|++.+++. ...| +..+|..+..++...|++++|...|+++++++|+++.+...+..+..
T Consensus        77 ~~~l~~~~~Al~~~~~al~~~p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~P~n~~~~~~l~~~~~  146 (153)
T d2fbna1          77 YNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSYELCVN  146 (153)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH
T ss_pred             HHHhcccchhhhhhhccccccchhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            99999999999999997 4444 66899999999999999999999999999999999988887766543

>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=97.92  E-value=2.3e-05  Score=60.70  Aligned_cols=90  Identities=4%  Similarity=-0.119  Sum_probs=60.3

Q ss_pred             HHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcC
Q 040394          115 QVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCR  194 (691)
Q Consensus       115 ~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  194 (691)
                      ..+...+.+.|++++|+..|++.++.. +-+..+|..+..++.+.|++++|+..++..++..|.+..++..+...|...|
T Consensus        20 ~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~la~~y~~~g   98 (112)
T d1hxia_          20 MEEGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEH   98 (112)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHhhhcccc-cccchhhhhhhhhhhhhhhHHHhhcccccccccccccccchHHHHHHHHHCC
Confidence            344555666777777777777776653 2245666666677777777777777777777776666677777777777777


Q ss_pred             ChHHHHHHHhc
Q 040394          195 DIGSSRQVFDE  205 (691)
Q Consensus       195 ~~~~A~~~~~~  205 (691)
                      ++++|.+.+++
T Consensus        99 ~~~~A~~~l~~  109 (112)
T d1hxia_          99 NANAALASLRA  109 (112)
T ss_dssp             HHHHHHHHHHH
T ss_pred             CHHHHHHHHHH
Confidence            77777666654

>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=97.90  E-value=4.4e-05  Score=64.34  Aligned_cols=130  Identities=9%  Similarity=0.060  Sum_probs=89.2

Q ss_pred             HHHHHHHHHhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHH
Q 040394          499 TWSAMIGGYGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDL  577 (691)
Q Consensus       499 ~~~~li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~  577 (691)
                      .+......+...|++++|+..|++.++.  .+..          .......          ....+.|. ...+..+..+
T Consensus        29 ~~~~~~~~~~~~~~y~~Ai~~y~~al~~--~~~~----------~~~~~~~----------~~~~~~~~~~~~~~nla~~   86 (169)
T d1ihga1          29 DLKNIGNTFFKSQNWEMAIKKYTKVLRY--VEGS----------RAAAEDA----------DGAKLQPVALSCVLNIGAC   86 (169)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--HHHH----------HHHSCHH----------HHGGGHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHh--hhhh----------hhhhhhH----------HHHHhChhhHHHHHHHHHH
Confidence            3445566677788888888888776541  0000          0000000          00112233 4567778888


Q ss_pred             HHhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCc
Q 040394          578 LARAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRW  650 (691)
Q Consensus       578 ~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~  650 (691)
                      +.+.|++++|+..+++. ...| +...|..+..++...|++++|+..|+++++++|+++.+...+..+..+....
T Consensus        87 ~~~~~~~~~Ai~~~~~al~~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~p~n~~~~~~l~~~~~~l~~~  161 (169)
T d1ihga1          87 KLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLKVKQKIKAQ  161 (169)
T ss_dssp             HHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHhhcccchhhhhhhhhhhhhhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHH
Confidence            89999999999988887 5555 4568888999999999999999999999999999988888887776544433

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.89  E-value=0.0039  Score=57.78  Aligned_cols=207  Identities=9%  Similarity=0.030  Sum_probs=112.8

Q ss_pred             CCchhHHHHHhhc---cCchhHHHHHHHHHHhCCCCchhhhHHHHHHhcCCChHHHHHHhccCCCCCcchHHHHHHHHHh
Q 040394           47 LPSIPCLNLLGLC---KSTGSLKAFHALLIVDGLTNDKCNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFL  123 (691)
Q Consensus        47 ~~~~~~~~ll~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~ll~~~~~  123 (691)
                      |+......+...|   |..+.|..++..+.        -+..++..|.+.+++..|.+.+.+..  +..+|..+...+.+
T Consensus        12 ~n~~d~~~i~~~c~~~~lye~A~~lY~~~~--------d~~rl~~~~v~l~~~~~avd~~~k~~--~~~~~k~~~~~l~~   81 (336)
T d1b89a_          12 PNNAHIQQVGDRCYDEKMYDAAKLLYNNVS--------NFGRLASTLVHLGEYQAAVDGARKAN--STRTWKEVCFACVD   81 (336)
T ss_dssp             C----------------CTTTHHHHHHHTT--------CHHHHHHHHHTTTCHHHHHHHHHHHT--CHHHHHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHCCCHHHHHHHHHhCC--------CHHHHHHHHHhhccHHHHHHHHHHcC--CHHHHHHHHHHHHh
Confidence            3333334444555   45555655554221        34567777788888888887776443  45577777777777


Q ss_pred             CCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHH
Q 040394          124 NDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVF  203 (691)
Q Consensus       124 ~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  203 (691)
                      .....-+     .+...+...++.....++..|-..|..++...+++........+...++.++..|++.+. ++..+.+
T Consensus        82 ~~e~~la-----~i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~~~~~~~~~~~L~~lyak~~~-~kl~e~l  155 (336)
T d1b89a_          82 GKEFRLA-----QMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFKP-QKMREHL  155 (336)
T ss_dssp             TTCHHHH-----HHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSTTCCHHHHHHHHHHHHTTCH-HHHHHHH
T ss_pred             CcHHHHH-----HHHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcCCccchHHHHHHHHHHHHhCh-HHHHHHH
Confidence            6655433     222333444556667788888888888888888887765444577788888888888653 3444444


Q ss_pred             hccCCC-----------ChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHH
Q 040394          204 DETLDK-----------NVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYI  272 (691)
Q Consensus       204 ~~~~~~-----------~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~  272 (691)
                      ......           ...-|.-++-.|.+.|+++.|..+.-.     -.++.......+..+.+..+.+...+.....
T Consensus       156 ~~~s~~y~~~k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~i~-----~~~~~~~~~~f~e~~~k~~N~e~~~~~i~~y  230 (336)
T d1b89a_         156 ELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMN-----HPTDAWKEGQFKDIITKVANVELYYRAIQFY  230 (336)
T ss_dssp             HHHSTTSCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHH-----STTTTCCHHHHHHHHHHCSSTHHHHHHHHHH
T ss_pred             HhccccCCHHHHHHHHHHcCChHHHHHHHHhcCCHHHHHHHHHH-----cchhhhhHHHHHHHHHccCChHHHHHHHHHH
Confidence            332111           112244444445555555544443222     1233334444555566666666555555555


Q ss_pred             HH
Q 040394          273 LK  274 (691)
Q Consensus       273 ~~  274 (691)
                      .+
T Consensus       231 L~  232 (336)
T d1b89a_         231 LE  232 (336)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.88  E-value=0.008  Score=55.60  Aligned_cols=295  Identities=11%  Similarity=0.098  Sum_probs=147.2

Q ss_pred             CCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHH
Q 040394          109 PDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVD  188 (691)
Q Consensus       109 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  188 (691)
                      ||..--..+...|.+.|.++.|..+|..+.         -|..++..+.+.++++.|.......     .+..+|..+..
T Consensus        12 ~n~~d~~~i~~~c~~~~lye~A~~lY~~~~---------d~~rl~~~~v~l~~~~~avd~~~k~-----~~~~~~k~~~~   77 (336)
T d1b89a_          12 PNNAHIQQVGDRCYDEKMYDAAKLLYNNVS---------NFGRLASTLVHLGEYQAAVDGARKA-----NSTRTWKEVCF   77 (336)
T ss_dssp             C----------------CTTTHHHHHHHTT---------CHHHHHHHHHTTTCHHHHHHHHHHH-----TCHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHCCCHHHHHHHHHhCC---------CHHHHHHHHHhhccHHHHHHHHHHc-----CCHHHHHHHHH
Confidence            555555566667778888888888887553         2667777777777777776665422     25667777777


Q ss_pred             HhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHH
Q 040394          189 MYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWL  268 (691)
Q Consensus       189 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~  268 (691)
                      .+.+.....-|.- .......+......++..|-..|.+++...+++..... -.++...++.++..+++.+.    .++
T Consensus        78 ~l~~~~e~~la~i-~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~~lyak~~~----~kl  151 (336)
T d1b89a_          78 ACVDGKEFRLAQM-CGLHIVVHADELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKFKP----QKM  151 (336)
T ss_dssp             HHHHTTCHHHHHH-TTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS-TTCCHHHHHHHHHHHHTTCH----HHH
T ss_pred             HHHhCcHHHHHHH-HHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcC-CccchHHHHHHHHHHHHhCh----HHH
Confidence            7777665554422 22212234444556777777778888777777766432 23455566677777766532    223


Q ss_pred             HHHHHHHCCCCchHHHHHHHHHHHhcCCHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHH
Q 040394          269 HGYILKIGIEINSHLVTALLDMYVKCGNIRDARSVFDELCSIDLVSWTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHV  348 (691)
Q Consensus       269 ~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  348 (691)
                      .+.+...+...|.   ..++..|-+.+-                  |.-++..|.+.|++++|..++-.   .  .++..
T Consensus       152 ~e~l~~~s~~y~~---~k~~~~c~~~~l------------------~~elv~Ly~~~~~~~~A~~~~i~---~--~~~~~  205 (336)
T d1b89a_         152 REHLELFWSRVNI---PKVLRAAEQAHL------------------WAELVFLYDKYEEYDNAIITMMN---H--PTDAW  205 (336)
T ss_dssp             HHHHHHHSTTSCH---HHHHHHHHTTTC------------------HHHHHHHHHHTTCHHHHHHHHHH---S--TTTTC
T ss_pred             HHHHHhccccCCH---HHHHHHHHHcCC------------------hHHHHHHHHhcCCHHHHHHHHHH---c--chhhh
Confidence            3333322111111   112233333333                  34445556666777666655322   1  12222


Q ss_pred             HHHHHHHHHhcCCChhhHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCC
Q 040394          349 TIASVLSASAQLGNLNMGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSP  428 (691)
Q Consensus       349 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p  428 (691)
                      -....+..+.+.++.+...++.....+.   .+...+.++......-+..+..+.+                        
T Consensus       206 ~~~~f~e~~~k~~N~e~~~~~i~~yL~~---~p~~i~~lL~~v~~~~d~~r~V~~~------------------------  258 (336)
T d1b89a_         206 KEGQFKDIITKVANVELYYRAIQFYLEF---KPLLLNDLLMVLSPRLDHTRAVNYF------------------------  258 (336)
T ss_dssp             CHHHHHHHHHHCSSTHHHHHHHHHHHHH---CGGGHHHHHHHHGGGCCHHHHHHHH------------------------
T ss_pred             hHHHHHHHHHccCChHHHHHHHHHHHHc---CHHHHHHHHHHhccCCCHHHHHHHH------------------------
Confidence            2223344445555555444444333332   2223344444444444444444433                        


Q ss_pred             CHHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhc
Q 040394          429 DAVTLVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAM  492 (691)
Q Consensus       429 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  492 (691)
                                  .+.+++.....+++.....+    +..+.+++...|...++++.-.+..+.-
T Consensus       259 ------------~k~~~l~li~p~Le~v~~~n----~~~vn~al~~lyie~~d~~~l~~~i~~~  306 (336)
T d1b89a_         259 ------------SKVKQLPLVKPYLRSVQNHN----NKSVNESLNNLFITEEDYQALRTSIDAY  306 (336)
T ss_dssp             ------------HHTTCTTTTHHHHHHHHTTC----CHHHHHHHHHHHHHTTCHHHHHHHHHHC
T ss_pred             ------------HhcCCcHHHHHHHHHHHHcC----hHHHHHHHHHHHhCcchhHHHHHHHHHh
Confidence                        33444555555565544433    3467888888888888876655555443

>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=97.87  E-value=4.8e-05  Score=64.37  Aligned_cols=69  Identities=13%  Similarity=0.033  Sum_probs=62.0

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHh-----CCCccCC
Q 040394          601 SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQ-----RGLSKSP  669 (691)
Q Consensus       601 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~g~~~~~  669 (691)
                      ..+..+...+...|++++|...++++++.+|.+...|..++.+|.+.|++++|.+.|+++.+     -|+.|.|
T Consensus        68 ~a~~~la~~~~~~g~~~~Al~~~~~al~~~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~  141 (179)
T d2ff4a2          68 LAHTAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGP  141 (179)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCH
T ss_pred             HHHHHHHHHHHHCCCchHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCH
Confidence            46777888899999999999999999999999999999999999999999999999999744     5776655

>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=97.84  E-value=8.2e-05  Score=62.46  Aligned_cols=63  Identities=8%  Similarity=-0.117  Sum_probs=58.3

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          602 LFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       602 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      +|..+..+|.+.|++++|+..++++++++|++...+..++.+|...|++++|++.++++++..
T Consensus        66 ~~~Nla~~~~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~  128 (168)
T d1kt1a1          66 AFLNLAMCYLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN  128 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC
T ss_pred             HHHhHHHHHHHhhhcccchhhhhhhhhcccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            455677788999999999999999999999999999999999999999999999999998754

>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=97.83  E-value=3e-05  Score=65.43  Aligned_cols=65  Identities=8%  Similarity=-0.120  Sum_probs=60.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          600 VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       600 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      ...|..+..++.+.|++++|+..++++++++|+++..|..++.+|...|++++|++.+++.++..
T Consensus        77 ~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~  141 (169)
T d1ihga1          77 LSCVLNIGACKLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIA  141 (169)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHhhcccchhhhhhhhhhhhhhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhC
Confidence            34677788889999999999999999999999999999999999999999999999999998853

>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=97.79  E-value=0.0017  Score=58.82  Aligned_cols=79  Identities=8%  Similarity=-0.115  Sum_probs=43.3

Q ss_pred             cHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHh----cCCHHHHHHHHHhcccC-CHhHHHHHHHHHhc----CCChHH
Q 040394          445 AVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAK----CGDAQSARMVFDAMREK-NTVTWSAMIGGYGM----QGDGGG  515 (691)
Q Consensus       445 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~-~~~~~~~li~~~~~----~~~~~~  515 (691)
                      +...+...++...+.|    ++.....+...|..    ..+.++|...|....+. ++..+..|...|..    .++.++
T Consensus       161 ~~~~~~~~~~~a~~~g----~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g~~~a~~~LG~~y~~G~g~~~n~~~  236 (265)
T d1ouva_         161 DLKKALASYDKACDLK----DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELENGGGCFNLGAMQYNGEGVTRNEKQ  236 (265)
T ss_dssp             CHHHHHHHHHHHHHTT----CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSSCCSTT
T ss_pred             ccccchhhhhcccccc----ccccccchhhhcccCcccccchhhhhhhHhhhhcccCHHHHHHHHHHHHcCCCCccCHHH
Confidence            4445555555555443    23333334444443    45677777777665543 55555556555554    336666


Q ss_pred             HHHHHHHHHHCC
Q 040394          516 SLALFSDMLNEE  527 (691)
Q Consensus       516 A~~~~~~m~~~g  527 (691)
                      |.+.|++..+.|
T Consensus       237 A~~~~~kAa~~g  248 (265)
T d1ouva_         237 AIENFKKGCKLG  248 (265)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHHHCc
Confidence            777777766655

>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=97.59  E-value=0.00015  Score=53.85  Aligned_cols=73  Identities=16%  Similarity=0.104  Sum_probs=57.9

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhC--------CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHH
Q 040394          571 YVCMVDLLARAGRLEEALEFMENM--------PIEPD-VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVS  641 (691)
Q Consensus       571 ~~~li~~~~~~g~~~~A~~~~~~~--------~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~  641 (691)
                      +-.+...+.+.|++++|++.|++.        ...++ ..++..|..++.+.|++++|+..++++++++|+++.++..+.
T Consensus         8 c~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~P~~~~a~~Nl~   87 (95)
T d1tjca_           8 SFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRANGNLK   87 (95)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhCcCCHHHHHHHH
Confidence            345677788888888888877776        11223 457888999999999999999999999999999998888775


Q ss_pred             HH
Q 040394          642 NL  643 (691)
Q Consensus       642 ~~  643 (691)
                      .+
T Consensus        88 ~~   89 (95)
T d1tjca_          88 YF   89 (95)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=97.57  E-value=0.00015  Score=59.96  Aligned_cols=89  Identities=12%  Similarity=-0.035  Sum_probs=65.5

Q ss_pred             HHHHHhcCChHHHHHHHHhC----CCCCC----------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC--------
Q 040394          575 VDLLARAGRLEEALEFMENM----PIEPD----------VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPD--------  632 (691)
Q Consensus       575 i~~~~~~g~~~~A~~~~~~~----~~~p~----------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~--------  632 (691)
                      ...+.+.|++++|++.|++.    +..|+          ...|+.+..+|...|++++|...+++++++.|.        
T Consensus        16 g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~   95 (156)
T d2hr2a1          16 AQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDE   95 (156)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccc
Confidence            34455667777777666665    21121          356788888899999999999999998875332        


Q ss_pred             ---CchhHHHHHHHHHhCCCcHHHHHHHHHHHhC
Q 040394          633 ---KACYYVLVSNLYASDGRWIRVNQVRELMKQR  663 (691)
Q Consensus       633 ---~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  663 (691)
                         ....+..++.+|...|++++|++.|++.++.
T Consensus        96 ~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~l  129 (156)
T d2hr2a1          96 GKLWISAVYSRALALDGLGRGAEAMPEFKKVVEM  129 (156)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cchhHHHHhhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence               1235778899999999999999999998763

>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=97.57  E-value=6.8e-05  Score=61.04  Aligned_cols=74  Identities=19%  Similarity=0.318  Sum_probs=49.0

Q ss_pred             HHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcC-----------CHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcH
Q 040394          585 EEALEFMENM-PIEP-DVSLFGAFLHGCGLYS-----------RFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWI  651 (691)
Q Consensus       585 ~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~g-----------~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~  651 (691)
                      ++|++.|++. .+.| +..+|..+..+|...|           ++++|...|+++++++|++..++..|...       .
T Consensus        58 ~~Ai~~~~kAl~l~P~~~~a~~~lG~~y~~~g~~~~~~~~~~~~~~~A~~~~~kal~l~P~~~~~~~~L~~~-------~  130 (145)
T d1zu2a1          58 QEAITKFEEALLIDPKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDEQPDNTHYLKSLEMT-------A  130 (145)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHH-------H
T ss_pred             HHHHHHHHHHHHhcchhhHHHhhHHHHHHHcccchhhHHHHHHhHHHhhhhhhcccccCCCHHHHHHHHHHH-------H
Confidence            4455555554 2333 3345555555554332           46889999999999999999888888665       3


Q ss_pred             HHHHHHHHHHhCCC
Q 040394          652 RVNQVRELMKQRGL  665 (691)
Q Consensus       652 ~A~~~~~~~~~~g~  665 (691)
                      +|.+++.++.+.|+
T Consensus       131 ka~~~~~e~~k~~~  144 (145)
T d1zu2a1         131 KAPQLHAEAYKQGL  144 (145)
T ss_dssp             THHHHHHHHHHSSS
T ss_pred             HHHHHHHHHHHHhc
Confidence            56677777777665

>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=97.47  E-value=0.001  Score=52.36  Aligned_cols=98  Identities=11%  Similarity=0.095  Sum_probs=76.6

Q ss_pred             HHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccc--C-C-------HhHHHH
Q 040394          433 LVSVISACASLGAVQVGSSLHAYSTKQGLLSSNVYVGTALLNFYAKCGDAQSARMVFDAMRE--K-N-------TVTWSA  502 (691)
Q Consensus       433 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~-------~~~~~~  502 (691)
                      +..+...+...|++++|...|.+..+.+  |.+...+..+..+|.+.|++++|...++++.+  | +       ..+|..
T Consensus         7 ~k~~G~~~~~~~~y~~Ai~~y~~al~~~--p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~   84 (128)
T d1elra_           7 EKELGNDAYKKKDFDTALKHYDKAKELD--PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYAR   84 (128)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC--cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHH
Confidence            4456677888999999999999999887  78888899999999999999999999988764  1 1       135666


Q ss_pred             HHHHHhcCCChHHHHHHHHHHHHCCCCCCHHH
Q 040394          503 MIGGYGMQGDGGGSLALFSDMLNEEVQPNEVI  534 (691)
Q Consensus       503 li~~~~~~~~~~~A~~~~~~m~~~g~~p~~~~  534 (691)
                      +...+...+++++|+..|++....  .|+...
T Consensus        85 lg~~~~~~~~~~~A~~~~~kal~~--~~~~~~  114 (128)
T d1elra_          85 IGNSYFKEEKYKDAIHFYNKSLAE--HRTPDV  114 (128)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--CCCHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHhc--CCCHHH
Confidence            777778888888888888877763  344433

>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=97.36  E-value=0.00024  Score=64.16  Aligned_cols=127  Identities=9%  Similarity=0.035  Sum_probs=82.4

Q ss_pred             HhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChH
Q 040394          507 YGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLE  585 (691)
Q Consensus       507 ~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~  585 (691)
                      ..+.|++++|+..+++.++.. +-|...+..+...++..|++++|.+.++...+   +.|+ ...+..+...+...+..+
T Consensus         6 aL~~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~---l~P~~~~~~~~l~~ll~a~~~~~   81 (264)
T d1zbpa1           6 ALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIK---LFPEYLPGASQLRHLVKAAQARK   81 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH---HCGGGHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---hCCCcHHHHHHHHHHHHhccccH
Confidence            456788888888888888752 44557777788888888888888888887643   4566 444444555554444444


Q ss_pred             HHHHHHHhC--CCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhH
Q 040394          586 EALEFMENM--PIEPDV-SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYY  637 (691)
Q Consensus       586 ~A~~~~~~~--~~~p~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~  637 (691)
                      ++..-....  ...|+. ..+......+...|+.++|...++++.+..|+.+..+
T Consensus        82 ~a~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~~p~~~~~~  136 (264)
T d1zbpa1          82 DFAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELRQEKGFLA  136 (264)
T ss_dssp             HHTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCCEEE
T ss_pred             HHHHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCCccc
Confidence            443332222  122322 3334445556778999999999999988888866543

>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=97.35  E-value=8.7e-05  Score=60.36  Aligned_cols=85  Identities=15%  Similarity=0.026  Sum_probs=58.7

Q ss_pred             hcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHH----------hcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhC
Q 040394          580 RAGRLEEALEFMENM-PIEP-DVSLFGAFLHGCG----------LYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASD  647 (691)
Q Consensus       580 ~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~----------~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~  647 (691)
                      +.+.+++|++.+++. ...| +..++..+..++.          ..+++++|+..++++++++|+++.+|..++.+|...
T Consensus         9 r~~~fe~A~~~~e~al~~~P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~P~~~~a~~~lG~~y~~~   88 (145)
T d1zu2a1           9 RILLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYTSF   88 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH
T ss_pred             HHccHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhcchhhHHHhhHHHHHHHc
Confidence            334455555555554 2222 3334444444443          234568999999999999999999999999999877


Q ss_pred             CC-----------cHHHHHHHHHHHhCC
Q 040394          648 GR-----------WIRVNQVRELMKQRG  664 (691)
Q Consensus       648 g~-----------~~~A~~~~~~~~~~g  664 (691)
                      |+           +++|.+.|++.++..
T Consensus        89 g~~~~~~~~~~~~~~~A~~~~~kal~l~  116 (145)
T d1zu2a1          89 AFLTPDETEAKHNFDLATQFFQQAVDEQ  116 (145)
T ss_dssp             HHHCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             ccchhhHHHHHHhHHHhhhhhhcccccC
Confidence            64           688888888887643

>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=97.25  E-value=8.1e-05  Score=75.11  Aligned_cols=221  Identities=10%  Similarity=-0.072  Sum_probs=99.8

Q ss_pred             hHHHHHHHHHHhCCCchhHHHHHHHHhHhcCChHHHHHHHHhCCCCCchhHHHHHHhhhCCCCCCHHHHHHHHHHHhccC
Q 040394          365 MGRMVHSLGIRLGLEDYTVINALVDMYAKCHVIADARYIFETTSEKDVIAWNSIISGLDDNVSPDAVTLVSVISACASLG  444 (691)
Q Consensus       365 ~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~p~~~~~~~ll~~~~~~~  444 (691)
                      +|.+.++++.+..+.....+..+..+|...|++++|   |+++...|                |+...-......+- ..
T Consensus         4 eA~q~~~qA~~l~p~~a~a~~~la~~~~~~~~l~ea---ye~~i~~d----------------p~~a~~~~~e~~Lw-~~   63 (497)
T d1ya0a1           4 QSAQYLRQAEVLKADMTDSKLGPAEVWTSRQALQDL---YQKMLVTD----------------LEYALDKKVEQDLW-NH   63 (497)
T ss_dssp             HHHHHHHHHHHHHGGGTCSSSCSSSSHHHHHHHHHH---HHHHHHHC----------------HHHHHHHTHHHHHH-HH
T ss_pred             HHHHHHHHHHHcCCCCHHHHhhHHHHHHHHchHHHH---HHHHHHcC----------------hhhHHHHhHHHHHH-HH
Confidence            456666777666666555556666667777776665   33332211                11100000000000 01


Q ss_pred             cHHHHHHHHHHHHHcCCCCCchhHHHHHH--HHHHhcCCHHHHHHHHHhccc---CCHhHHHHHHHHHhcCCChHHHHHH
Q 040394          445 AVQVGSSLHAYSTKQGLLSSNVYVGTALL--NFYAKCGDAQSARMVFDAMRE---KNTVTWSAMIGGYGMQGDGGGSLAL  519 (691)
Q Consensus       445 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~--~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~A~~~  519 (691)
                      .+..+.+.++...+... .++........  ..+...+.++.|+..+....+   ++...+..+...+.+.|+.+.|...
T Consensus        64 ~y~~~ie~~r~~~k~~~-~~~~~~~~~~~~~~l~~a~~~Y~~ai~~l~~~~~l~~~~~~~~~~lg~~~~~~~~~~~A~~~  142 (497)
T d1ya0a1          64 AFKNQITTLQGQAKNRA-NPNRSEVQANLSLFLEAASGFYTQLLQELCTVFNVDLPCRVKSSQLGIISNKQTHTSAIVKP  142 (497)
T ss_dssp             HTHHHHHHHHHHHSCSS-CTTTTHHHHHHHHHHHHHHHHHHHHHHHHTC-------------------------------
T ss_pred             HHHHHHHHHHHhccccc-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCChhhHHHHHHhHHHHHhCCCHHHHHHH
Confidence            12334444554444332 22222211111  112233445555555444332   2445566666777777777777776


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCC-hhHHHHHHHHHHhcCChHHHHHHHHhC--CC
Q 040394          520 FSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPS-MKHYVCMVDLLARAGRLEEALEFMENM--PI  596 (691)
Q Consensus       520 ~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~~--~~  596 (691)
                      +++....  .| ..++..+-..+...|++++|...|++..   .+.|+ ...|+.|...+...|+..+|+..|.+.  -.
T Consensus       143 ~~~al~~--~~-~~~~~~LG~l~~~~~~~~~A~~~y~~A~---~l~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~  216 (497)
T d1ya0a1         143 QSSSCSY--IC-QHCLVHLGDIARYRNQTSQAESYYRHAA---QLVPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVK  216 (497)
T ss_dssp             CCHHHHH--HH-HHHHHHHHHHHHHTTCHHHHHHHHHHHH---HHCTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSS
T ss_pred             HHHHhCC--CH-HHHHHHHHHHHHHcccHHHHHHHHHHHH---HHCCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC
Confidence            6655431  11 2345556667777778888888877654   34566 567777888888888888887777776  23


Q ss_pred             CCCHHHHHHHHHHHHh
Q 040394          597 EPDVSLFGAFLHGCGL  612 (691)
Q Consensus       597 ~p~~~~~~~l~~~~~~  612 (691)
                      +|-..++..|...+.+
T Consensus       217 ~~~~~a~~nL~~~~~~  232 (497)
T d1ya0a1         217 FPFPAASTNLQKALSK  232 (497)
T ss_dssp             BCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            4555667777666543

>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=97.16  E-value=0.00052  Score=50.72  Aligned_cols=65  Identities=6%  Similarity=-0.085  Sum_probs=55.0

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC-------chhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          600 VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK-------ACYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       600 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~-------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      ...+-.+...+.+.|++++|+..++++++..|.+       ..++..++.+|.+.|++++|++.++++++..
T Consensus         5 addc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~   76 (95)
T d1tjca_           5 AEDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELD   76 (95)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhC
Confidence            3345567888999999999999999999865443       4578899999999999999999999998854

>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=97.08  E-value=0.0037  Score=52.28  Aligned_cols=71  Identities=11%  Similarity=0.010  Sum_probs=41.3

Q ss_pred             hhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHH-----HHCCCCchHH
Q 040394          212 VSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYIL-----KIGIEINSHL  283 (691)
Q Consensus       212 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~-----~~g~~~~~~~  283 (691)
                      ..+..+...+...|++++|+..++++..... -+...|..++.++...|+.++|.+.|+.+.     +.|+.|...+
T Consensus        68 ~a~~~la~~~~~~g~~~~Al~~~~~al~~~P-~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          68 LAHTAKAEAEIACGRASAVIAELEALTFEHP-YREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHHHCCCchHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            3455556666666666666666666655322 245556666666666666666666666552     2466666544

>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=96.99  E-value=0.0022  Score=52.50  Aligned_cols=65  Identities=17%  Similarity=0.114  Sum_probs=45.9

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhC--------CCCCC-----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC
Q 040394          569 KHYVCMVDLLARAGRLEEALEFMENM--------PIEPD-----VSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDK  633 (691)
Q Consensus       569 ~~~~~li~~~~~~g~~~~A~~~~~~~--------~~~p~-----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~  633 (691)
                      ..|+.+..+|...|++++|++.+++.        ...++     ...+..+..+|...|++++|...|++++++.|..
T Consensus        56 ~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~l~~~~  133 (156)
T d2hr2a1          56 FCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEER  133 (156)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhHHh
Confidence            34666667777777777776666554        12222     1256778889999999999999999999876543

>d1qsaa1 a.118.5.1 (A:1-450) 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Bacterial muramidases
family: Bacterial muramidases
domain: 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain
species: Escherichia coli [TaxId: 562]

Probab=96.88  E-value=0.23  Score=48.23  Aligned_cols=115  Identities=8%  Similarity=-0.010  Sum_probs=62.6

Q ss_pred             CChHHHHHHHHHHHHCCCC-CCHH-HHH-HHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHHH
Q 040394          511 GDGGGSLALFSDMLNEEVQ-PNEV-IFT-TILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEEA  587 (691)
Q Consensus       511 ~~~~~A~~~~~~m~~~g~~-p~~~-~~~-~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A  587 (691)
                      .+.+.|...+......... ++.. ... .+.......+..+.+...+.....   ...+......++....+.+++..+
T Consensus       228 ~d~~~a~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~~w~~~~al~~~~~~~~  304 (450)
T d1qsaa1         228 QDAENARLMIPSLAQAQQLNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIM---RSQSTSLIERRVRMALGTGDRRGL  304 (450)
T ss_dssp             HCHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHH---TCCCHHHHHHHHHHHHHHTCHHHH
T ss_pred             cChhHHHHHHHhhhhcccccHHHHHHHHHHHHHHHHHcCchHHHHHHHHhhcc---cccchHHHHHHHHHHHHcCChHHH
Confidence            4667777777776654222 2111 111 122233445556666666654422   123333334444555566777778


Q ss_pred             HHHHHhCCCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040394          588 LEFMENMPIEPD--VSLFGAFLHGCGLYSRFDLGEVMIKKMLE  628 (691)
Q Consensus       588 ~~~~~~~~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  628 (691)
                      ...+..+...|.  ..-.--+..++...|+.+.|...+..+..
T Consensus       305 ~~~~~~l~~~~~~~~r~~YW~gRa~~~~G~~~~A~~~~~~~a~  347 (450)
T d1qsaa1         305 NTWLARLPMEAKEKDEWRYWQADLLLERGREAEAKEILHQLMQ  347 (450)
T ss_dssp             HHHHHHSCTTGGGSHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHhcCcccccHHHHHHHHHHHHHHcCChhhHHHHHHHHhc
Confidence            888877743332  22223456667777888888877777654

>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=96.87  E-value=0.0011  Score=59.63  Aligned_cols=117  Identities=10%  Similarity=-0.019  Sum_probs=71.4

Q ss_pred             HhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHH
Q 040394          122 FLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQ  201 (691)
Q Consensus       122 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  201 (691)
                      .+.|++++|+..+++.++.. +-+...+..+...++..|++++|...++...+..+.+...+..+...+...+..+++..
T Consensus         7 L~~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~P~~~~~~~~l~~ll~a~~~~~~a~~   85 (264)
T d1zbpa1           7 LSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYLPGASQLRHLVKAAQARKDFAQ   85 (264)
T ss_dssp             TTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhccccHHHHH
Confidence            45677777777777777762 44556777777777777777777777777777766666666666655555444444333


Q ss_pred             HHhcc--C-CC-ChhhHHHHHHHHHhCCChhHHHHHHHHHHh
Q 040394          202 VFDET--L-DK-NVVSWTSMIAGYVQNDCAQEGLVLFNRMRE  239 (691)
Q Consensus       202 ~~~~~--~-~~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  239 (691)
                      -...-  . +| +...+......+...|+.++|.+++++..+
T Consensus        86 ~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e  127 (264)
T d1zbpa1          86 GAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEE  127 (264)
T ss_dssp             SCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence            22211  1 11 122333344556667777777777777655

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=96.32  E-value=0.12  Score=38.27  Aligned_cols=141  Identities=9%  Similarity=0.019  Sum_probs=98.9

Q ss_pred             HhcCCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHHHHHhcCChHH
Q 040394          507 YGMQGDGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVDLLARAGRLEE  586 (691)
Q Consensus       507 ~~~~~~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~  586 (691)
                      +.-.|..++..+++.+...   +.+..-||.+|--....-+-+-..++++.+-+-+.+              ..+++...
T Consensus        12 ~ildG~ve~Gveii~k~~~---ss~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~FDl--------------s~C~Nlk~   74 (161)
T d1wy6a1          12 FLLDGYIDEGVKIVLEITK---SSTKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDL--------------DKCQNLKS   74 (161)
T ss_dssp             HHHTTCHHHHHHHHHHHHH---HSCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCG--------------GGCSCTHH
T ss_pred             HHHhhhHHhHHHHHHHHcc---cCCccccceeeeecccccchHHHHHHHHHHhhhcCc--------------hhhhcHHH
Confidence            3456778888888888776   335555666665444555556666666665222222              23555555


Q ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhCCCcHHHHHHHHHHHhCCCc
Q 040394          587 ALEFMENMPIEPDVSLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVLVSNLYASDGRWIRVNQVRELMKQRGLS  666 (691)
Q Consensus       587 A~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g~~  666 (691)
                      ....+-.++  .+...++..+..+.++|+-++-.++++.+++.+.-++.....++.+|.+.|...++.+++.+.-+.|++
T Consensus        75 vv~C~~~~n--~~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn~~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          75 VVECGVINN--TLNEHVNKALDILVIQGKRDKLEEIGREILKNNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             HHHHHHHTT--CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHhc--chHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            555555554  234456667788889999999999999988865555899999999999999999999999999999985

>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=95.16  E-value=0.035  Score=41.94  Aligned_cols=74  Identities=7%  Similarity=0.098  Sum_probs=46.8

Q ss_pred             CChhHHHHHHHHHHhcC---ChHHHHHHHHhC-CCCC-CH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCchhHHH
Q 040394          566 PSMKHYVCMVDLLARAG---RLEEALEFMENM-PIEP-DV-SLFGAFLHGCGLYSRFDLGEVMIKKMLELHPDKACYYVL  639 (691)
Q Consensus       566 p~~~~~~~li~~~~~~g---~~~~A~~~~~~~-~~~p-~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~  639 (691)
                      |...+--....++.+..   +.++++.++++. ...| +. ..+-.|.-+|.+.|++++|...++++++.+|++......
T Consensus        33 ~s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~ieP~n~qA~~L  112 (124)
T d2pqrb1          33 ATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERNNKQVGAL  112 (124)
T ss_dssp             SCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             CCcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHccCCCcHHHHHH
Confidence            34444445556666554   345677777776 2233 32 355566677778888888888888888888887655443

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=94.90  E-value=0.15  Score=39.48  Aligned_cols=83  Identities=5%  Similarity=-0.160  Sum_probs=49.8

Q ss_pred             CChHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhcCCCCchhHHHHHHHHHh----CCCcHHH
Q 040394          582 GRLEEALEFMENMPIEPDVSLFGAFLHGCGL----YSRFDLGEVMIKKMLELHPDKACYYVLVSNLYAS----DGRWIRV  653 (691)
Q Consensus       582 g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~----~g~~~~A  653 (691)
                      .+.++|++++++.-..-+......|...|..    ..|.++|..+|+++.+..  ++.....|+.+|..    ..+.++|
T Consensus        37 ~~~~~a~~~~~~aa~~g~~~a~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa~~g--~~~a~~~Lg~~y~~G~gv~~d~~~A  114 (133)
T d1klxa_          37 INKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQYYSKACGLN--DQDGCLILGYKQYAGKGVVKNEKQA  114 (133)
T ss_dssp             SCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT--CHHHHHHHHHHHHHTSSSCCCHHHH
T ss_pred             cCHHHHHHHHhhhhcccchhhhhhHHHhhhhccccchhhHHHHHHHhhhhccC--cchHHHHHHHHHHcCCccCCCHHHH
Confidence            3445555555554112233444444444432    356778888888876643  35566667777765    4578888


Q ss_pred             HHHHHHHHhCCCc
Q 040394          654 NQVRELMKQRGLS  666 (691)
Q Consensus       654 ~~~~~~~~~~g~~  666 (691)
                      .+++++..+.|..
T Consensus       115 ~~~~~~Aa~~G~~  127 (133)
T d1klxa_         115 VKTFEKACRLGSE  127 (133)
T ss_dssp             HHHHHHHHHTTCH
T ss_pred             HHHHHHHHHCCCH
Confidence            8888888777753

>d1qsaa1 a.118.5.1 (A:1-450) 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Bacterial muramidases
family: Bacterial muramidases
domain: 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain
species: Escherichia coli [TaxId: 562]

Probab=93.58  E-value=3.3  Score=39.52  Aligned_cols=266  Identities=6%  Similarity=-0.104  Sum_probs=137.6

Q ss_pred             hhhHHHHHHhcCCChHHHHHHhccCCCCCcchHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCC
Q 040394           82 CNTKLVSMYGSFGHVKYARSVFDSMPNPDFYSFQVMIRWYFLNDLYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRD  161 (691)
Q Consensus        82 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~  161 (691)
                      +....+..+++.+++......+..-+ .+...-.....+....|+..+|......+-..| ...                
T Consensus        74 lr~~~l~~L~~~~~w~~~~~~~~~~p-~~~~~~c~~~~A~~~~g~~~~a~~~~~~lW~~~-~~~----------------  135 (450)
T d1qsaa1          74 LQSRFVNELARREDWRGLLAFSPEKP-GTTEAQCNYYYAKWNTGQSEEAWQGAKELWLTG-KSQ----------------  135 (450)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHCCSCC-SSHHHHHHHHHHHHHTTCHHHHHHHHHHHHSCS-SCC----------------
T ss_pred             HHHHHHHHHHhccCHHHHHHhccCCC-CCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CCC----------------
Confidence            44555677888888888777664322 233334456677778888888888777766554 122                


Q ss_pred             hhHHHHHHHHHHHhCCCChhHHHHHHHHhHhcCChHHHHHHHhccCCCChhhHHHHHHHHHhCCChhHHHHHHHHHHhCC
Q 040394          162 IDEGMKVHCEIVKVGGPDSFVLTGLVDMYAKCRDIGSSRQVFDETLDKNVVSWTSMIAGYVQNDCAQEGLVLFNRMREGF  241 (691)
Q Consensus       162 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~  241 (691)
                      .+....++..+.+.|..+...+-.-+..+...|++..|..+...+...........+....   +...+......     
T Consensus       136 p~~c~~l~~~~~~~~~lt~~~~~~R~~~~l~~~~~~~a~~l~~~l~~~~~~~~~a~~~l~~---~p~~~~~~~~~-----  207 (450)
T d1qsaa1         136 PNACDKLFSVWRASGKQDPLAYLERIRLAMKAGNTGLVTVLAGQMPADYQTIASAIISLAN---NPNTVLTFART-----  207 (450)
T ss_dssp             CTHHHHHHHHHHHTTCSCHHHHHHHHHHHHHTTCHHHHHHHHHTCCGGGHHHHHHHHHHHH---CGGGHHHHHHH-----
T ss_pred             chHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCChhhHHHHHhhCChhHHHHHHHHHHHHh---ChHhHHHHHhc-----
Confidence            2233334444445554444444455566667788888888888776555445555554432   22333222221     


Q ss_pred             CCCChhhHHHHHHHHHc--cCChhhHHHHHHHHHHHCCCCchHH---HHHHHHHHHhcCCHHHHHHHHHhc--CCCChhH
Q 040394          242 VEGNQITLGSLVTACAK--LRALHQGKWLHGYILKIGIEINSHL---VTALLDMYVKCGNIRDARSVFDEL--CSIDLVS  314 (691)
Q Consensus       242 ~~p~~~t~~~li~~~~~--~~~~~~a~~~~~~~~~~g~~~~~~~---~~~li~~~~~~g~~~~A~~~~~~~--~~~~~~~  314 (691)
                      ..++......+..++.+  ..+.+.+..++..............   ...+...+...+..+.+...+...  ...+...
T Consensus       208 ~~~~~~~~~~~~~~l~rla~~d~~~a~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~~~~~~~~~~~~~~  287 (450)
T d1qsaa1         208 TGATDFTRQMAAVAFASVARQDAENARLMIPSLAQAQQLNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRSQSTSL  287 (450)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHTCCCHHH
T ss_pred             CCCChhhhHHHHHHHHHHhccChhHHHHHHHhhhhcccccHHHHHHHHHHHHHHHHHcCchHHHHHHHHhhcccccchHH
Confidence            11233333333333333  2356667776666655432222111   111222223344555565555444  2223333


Q ss_pred             HHHHHHHHHhcCCchhHHHHHHHhhHCCCCCcHHHHHHHHHHHhcCCChhhHHHHHHHHH
Q 040394          315 WTAMIVGYTQSGYPDKALKLFTDKKWADFFPNHVTIASVLSASAQLGNLNMGRMVHSLGI  374 (691)
Q Consensus       315 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~  374 (691)
                      ..-.+......+++..+...++.|... ........--+..++...|+.+.|...+..+.
T Consensus       288 ~~w~~~~al~~~~~~~~~~~~~~l~~~-~~~~~r~~YW~gRa~~~~G~~~~A~~~~~~~a  346 (450)
T d1qsaa1         288 IERRVRMALGTGDRRGLNTWLARLPME-AKEKDEWRYWQADLLLERGREAEAKEILHQLM  346 (450)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHSCTT-GGGSHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCChHHHHHHHHhcCcc-cccHHHHHHHHHHHHHHcCChhhHHHHHHHHh
Confidence            333444455566777777777666432 11222333344455556666666666655554

>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=93.54  E-value=0.39  Score=35.96  Aligned_cols=68  Identities=6%  Similarity=-0.007  Sum_probs=53.5

Q ss_pred             CCCHHHHHHHHHHHHhc---CCHHHHHHHHHHHHhcCCCCc-hhHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Q 040394          597 EPDVSLFGAFLHGCGLY---SRFDLGEVMIKKMLELHPDKA-CYYVLVSNLYASDGRWIRVNQVRELMKQRG  664 (691)
Q Consensus       597 ~p~~~~~~~l~~~~~~~---g~~~~A~~~~~~~~~~~p~~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~~g  664 (691)
                      .|...+--...+++.++   .+.++|+.+++++.+.+|.+. ..++.|+.+|.+.|++++|.+.++++++..
T Consensus        32 ~~s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~ie  103 (124)
T d2pqrb1          32 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHE  103 (124)
T ss_dssp             GSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             CCCcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHccC
Confidence            35555666667777765   456789999999998888765 688889999999999999999999988753

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=93.11  E-value=0.63  Score=35.74  Aligned_cols=58  Identities=10%  Similarity=0.054  Sum_probs=30.3

Q ss_pred             ChhHHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHHHHh
Q 040394          126 LYKDIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLVDMY  190 (691)
Q Consensus       126 ~~~~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~  190 (691)
                      ++++|+++|++..+.|   +......+.  .....+.++|.+.++...+.|  ++.....|...|
T Consensus         8 d~~~A~~~~~kaa~~g---~~~a~~~l~--~~~~~~~~~a~~~~~~aa~~g--~~~a~~~Lg~~y   65 (133)
T d1klxa_           8 DLKKAIQYYVKACELN---EMFGCLSLV--SNSQINKQKLFQYLSKACELN--SGNGCRFLGDFY   65 (133)
T ss_dssp             HHHHHHHHHHHHHHTT---CTTHHHHHH--TCTTSCHHHHHHHHHHHHHTT--CHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCC---Chhhhhhhc--cccccCHHHHHHHHhhhhccc--chhhhhhHHHhh
Confidence            5667777777776665   222222222  233456666777766666554  333344444443

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=91.27  E-value=2  Score=31.69  Aligned_cols=67  Identities=10%  Similarity=-0.083  Sum_probs=46.7

Q ss_pred             hhhHHHHHHHHHhCCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHccCChhhHHHHHHHHHHHCCC
Q 040394          211 VVSWTSMIAGYVQNDCAQEGLVLFNRMREGFVEGNQITLGSLVTACAKLRALHQGKWLHGYILKIGIE  278 (691)
Q Consensus       211 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~~~~a~~~~~~~~~~g~~  278 (691)
                      ..-.+..++.+.++|+-+.-.++++.+.++ -+|++...--+..+|.+.|+..++.+++.+..+.|+.
T Consensus        86 se~vdlALd~lv~~~kkd~Ld~i~~~l~kn-~~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          86 NEHVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             CHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            344566677777888887777787776553 4566666777777788888888877777777777653

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=84.32  E-value=4.7  Score=28.12  Aligned_cols=63  Identities=13%  Similarity=0.174  Sum_probs=48.5

Q ss_pred             ChHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHchhhcCCCCChhHHHHHHH
Q 040394          512 DGGGSLALFSDMLNEEVQPNEVIFTTILSACSHTGMVGEGWKCFYSMCRDFKFVPSMKHYVCMVD  576 (691)
Q Consensus       512 ~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~g~~~~A~~~~~~m~~~~~~~p~~~~~~~li~  576 (691)
                      |.=++.+-+..+....+.|++....+.+++|-+..++..|.++++.+..+  +.++...|..++.
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K--~~~~k~~y~yilq   83 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK--AGPHKEIYPYVIQ   83 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--TTTCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH--hcCcHHHHHHHHH
Confidence            34456667777777888999999999999999999999999999988444  4445566766654

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=83.11  E-value=2  Score=30.05  Aligned_cols=59  Identities=12%  Similarity=0.209  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHHcCCCCCcchHHHHHHHHcccCChhHHHHHHHHHHHhCCCChhHHHHHH
Q 040394          129 DIVEFYKCMRKRLKEHDNFVFSKVLKACCELRDIDEGMKVHCEIVKVGGPDSFVLTGLV  187 (691)
Q Consensus       129 ~a~~~~~~m~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~  187 (691)
                      ++.+-++.+......|++......+++|.+.+++..|..+++-++...-++...|..++
T Consensus        24 e~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~~~~k~~y~yil   82 (105)
T d1v54e_          24 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVI   82 (105)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCcHHHHHHHH
Confidence            44555566666678888888888888888888888888888888765533444555544